@article {pmid39055759,
year = {2024},
author = {Paico-Ruiz, AA and Chávez, CAV and Chaupe, NNS and Cortegano, CAA},
title = {Effects of peptides and probiotics supplementation via diet on blood parameters and growth performance of Piaractus brachypomus during the growth-out phase.},
journal = {Open veterinary journal},
volume = {14},
number = {6},
pages = {1384-1393},
doi = {10.5455/OVJ.2024.v14.i6.6},
pmid = {39055759},
issn = {2218-6050},
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Animal Feed/analysis ; *Dietary Supplements ; *Diet/veterinary ; *Peptides/administration & dosage ; Random Allocation ; },
abstract = {BACKGROUND: There is no evidence of peptides-probiotics symbiosis as supplements in aquafeeds.

AIM: To evaluate the effect of peptides and probiotics supplementation via diet on blood parameters and growth performance of juvenile Piaractus brachypomus, an Amazonian fish, during the growth-out phase.

METHODS: 120 juvenile P. brachypomus (242.77 g) were placed into twelve 200-l tanks (10 fish/tank), housed in an indoor open system with constant water renovation (flow rate:1.50 l/minute). The experiment used a completely randomized design with a 4 × 5 factorial arrangement [4 doses of supplementation (CD: commercial diet; PepD: CD+1.50% of peptides per CD weight; ProD: CD+40.00 ml of activated probiotics per kg of diet (Lactobacillus spp., Rhodopseudomonas spp., Saccharomycetes spp.); PepProD: CD+Pep+Pro); 5 sampling times (zero, second, fourth, sixth, and eighth week); n = 3]. Fish were fed twice a day at a feeding rate of 1% of body weight. At each sampling time, blood was collected and fish were measured for growth performance analysis. Data were analyzed by using two-way ANOVA and Tukey's test (p < 0.05).

RESULTS: The values of hematocrit (18.31%), leukocytes (1,216.67 mm[3]), neutrophils (81.27%), lymphocytes (18.73%), albumin (1.08 g/dl), relative growth rate (1.002%/day), and the Fulton allometric condition factor (2.03) remained constant throughout the experiment (p > 0.05). Plasma glucose decreased for all fish in the second week (59.56 mg/dl); then, that level increased in fish fed with the CD (89.00 mg/dl), while fish fed with PepD, ProD, and PepProD showed constant values (57.22 mg/dl). The plasma protein levels were constant in fish fed with the PepD and PepProD, (p > 0.05), while fish fed with the CD and ProD showed non-constant and higher values. At the end of the trial, fish fed with the PepProD showed the highest weight gain and the lowest feed conversion rate (39.66 g; 0.97).

CONCLUSION: It is possible to maintain the stability of plasma glucose and plasma protein by supplementing diets with peptides, but the peptides-probiotics symbiosis administrated via diet contributes to maintaining the stability of plasma glucose and plasma protein and to improve the growth performance of juvenile P. brachypomus during the growth-out phase.},
}

Animals
*Probiotics/administration & dosage/pharmacology
*Animal Feed/analysis
*Dietary Supplements
*Diet/veterinary
*Peptides/administration & dosage
Random Allocation

@article {pmid39054882,
year = {2024},
author = {Tang, B and Man, J and Romero, F and Bergmann, J and Lehmann, A and Rillig, MC},
title = {Mycorrhization enhances plant growth and stabilizes biomass allocation under drought.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17438},
doi = {10.1111/gcb.17438},
pmid = {39054882},
issn = {1365-2486},
support = {031B1266//European Joint Programme-Soils project 'Symbiotic Solutions for Healthy Agricultural Landscapes (SOIL-HEAL)', national support for which came from the German Federal Ministry of Education and Research/ ; },
mesh = {*Droughts ; *Mycorrhizae/physiology ; *Biomass ; *Symbiosis ; *Plant Development ; Plant Roots/growth & development/microbiology/metabolism ; Climate Change ; Photosynthesis ; Water/metabolism ; },
abstract = {Plants and their symbionts, such as arbuscular mycorrhizal (AM) fungi, are increasingly subjected to various environmental stressors due to climate change, including drought. As a response to drought, plants generally allocate more biomass to roots over shoots, thereby facilitating water uptake. However, whether this biomass allocation shift is modulated by AM fungi remains unknown. Based on 5691 paired observations from 154 plant species, we conducted a meta-analysis to evaluate how AM fungi modulate the responses of plant growth and biomass allocation (e.g., root-to-shoot ratio, R/S) to drought. We found that AM fungi attenuate the negative impact of drought on plant growth, including biomass production, photosynthetic performance and resource (e.g. nutrient and water) uptake. Accordingly, drought significantly increased R/S in non-inoculated plants, but not in plants symbiotic with established AM fungal symbioses. These results suggest that AM fungi promote plant growth and stabilize their R/S through facilitating nutrient and water uptake in plants under drought. Our findings highlight the crucial role of AM fungi in enhancing plant resilience to drought by optimizing resource allocation. This knowledge opens avenues for sustainable agricultural practices that leverage symbiotic relationships for climate adaptation.},
}

*Droughts
*Mycorrhizae/physiology
*Biomass
*Symbiosis
*Plant Development
Plant Roots/growth & development/microbiology/metabolism
Climate Change
Photosynthesis
Water/metabolism

@article {pmid39054868,
year = {2024},
author = {Sorwar, E and Oliveira, JIN and Malar C, M and Krüger, M and Corradi, N},
title = {Assembly and comparative analyses of the Geosiphon pyriformis metagenome.},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16681},
doi = {10.1111/1462-2920.16681},
pmid = {39054868},
issn = {1462-2920},
support = {RGPIN2020-05643//Natural Sciences and Engineering Research Council/ ; RGPAS-2020-00033//Discovery Accelerator Supplements Program/ ; IT16902//Mitacs Accelerate Program/ ; },
mesh = {*Symbiosis ; *Metagenome ; Phylogeny ; Cyanobacteria/genetics/classification/metabolism ; Nostoc/genetics/metabolism ; Metagenomics ; Genome, Fungal ; Genome, Bacterial ; },
abstract = {Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.},
}

*Symbiosis
*Metagenome
Phylogeny
Cyanobacteria/genetics/classification/metabolism
Nostoc/genetics/metabolism
Metagenomics
Genome, Fungal
Genome, Bacterial

@article {pmid39054168,
year = {2024},
author = {Duron, O},
title = {Nutritional symbiosis in ticks: singularities of the genus Ixodes: (Trends in Parasitology, Published online June 27, 2024).},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2024.07.001},
pmid = {39054168},
issn = {1471-5007},
}

@article {pmid39053599,
year = {2024},
author = {Li, P and Luo, Y and Tian, J and Cheng, Y and Wang, S and An, X and Zheng, J and Yan, H and Duan, H and Zhang, J and Pan, Z and Chen, Y and Wang, R and Zhou, H and Wang, Z and Tan, Z and Li, X},
title = {Outdoor tubular photobioreactor microalgae-microorganisms biofilm treatment of municipal wastewater: Enhanced heterotrophic assimilation and synergistic aerobic denitrogenation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131151},
doi = {10.1016/j.biortech.2024.131151},
pmid = {39053599},
issn = {1873-2976},
abstract = {This research evaluated a microalgae consortium (MC) in a pilot-scale tubular photobioreactor for municipal wastewater (MWW) treatment, compared with an aeration column photobioreactor. Transitioning from suspended MC to a microalgae-microbial biofilm (MMBF) maintained treatment performance despite increasing influent from 50 L to 150 L in a 260 L system. Carbon and nitrogen removal were effective, but phosphorus removal varied due to biofilm shading and the absence of phosphorus-accumulating organisms. High influent flow caused MMBF detachment due to shear stress. Stabilizing and re-establishing the MMBF showed that a stable phycosphere influenced microbial diversity and interactions, potentially destabilizing the MMBF. Heterotrophic nitrification-aerobic denitrification bacteria were crucial for MC equilibrium. Elevated gene expression related to nitrogen fixation, organic nitrogen metabolism, and nitrate reduction confirmed strong microalgal symbiosis, highlighting MMBF's treatment potential. This study supports the practical application of microalgae in wastewater treatment.},
}

@article {pmid39053471,
year = {2024},
author = {Tu, T and Gao, Z and Li, L and Chen, J and Ye, K and Xu, T and Mai, S and Han, Q and Chen, C and Wu, S and Dong, Y and Chen, J and Huang, L and Guan, Y and Xie, F and Chen, X},
title = {Soybean symbiotic-nodule zonation and cell differentiation are defined by NIN2 signaling and GH3-dependent auxin homeostasis.},
journal = {Developmental cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.devcel.2024.07.001},
pmid = {39053471},
issn = {1878-1551},
abstract = {Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.},
}

@article {pmid39051869,
year = {2024},
author = {Agrawal, A and Barik, TK and Patel, AK},
title = {Characterization of Leclercia adecarboxylata isolated from field collected Anopheles subpictus, Berhampur, Odisha.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/JVBD.JVBD_22_24},
pmid = {39051869},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: Malaria, a vector-borne diseases caused by Plasmodium species and transmitted by Anopheles species. Among them, Anopheles subpictus has emerged as a potent malarial vector in coastal areas of India. Numerous studies highlighted that bacterial communities within mosquito influence vector competence. The present study was designed to isolate and characterize bacterial microbiota from A. subpictus larvae.

METHODS: Isolation and purification of the predominant bacterial strain (AL1). Morphological, biochemical, antibiotic susceptibility and molecular characterization of the isolated bacteria.

RESULTS: Bacterial isolate (AL1) was found to be rod, gram negative, catalase positive and oxidase negative. AL1 was identified as Leclercia adecarboxylata (Accession number: OR649235) through 16S rRNA ribotyping. Further, leaf extract of Nyctanthes arbortristis showed inhibitory effect against AL1.

INTERPRETATION CONCLUSION: This is the first report on isolation of symbiotic bacteria (L. adecarboxylata) from A. subpictus and its control by leaf extract of Nyctanthes arbortristis. Isolated gram-negative bacterial strain might inhibit the development of mosquito vector and might use for various biological control strategies to combat malaria transmission.},
}

@article {pmid39051586,
year = {2024},
author = {Tursi, A and Mocci, G and Usai Satta, P and Elisei, W},
title = {Impact of a Symbiotic Mixture on Moderate-to-severe Diverticular Disease of the Colon.},
journal = {Reviews on recent clinical trials},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115748871308652240712101604},
pmid = {39051586},
issn = {1876-1038},
abstract = {BACKGROUND: Microbial imbalance is thought to play a role in the pathogenesis of Diverticular Disease (DD).

OBJECTIVE: We aimed to assess the efficacy of a symbiotic mixture (Prolactis GG Plus®) in the treatment of moderate to severe DD, scored according to the Diverticular Inflammation and Complication Assessment (DICA) classification.

METHODS: A retrospective study was conducted enrolling the following patients: at the first diagnosis of DD; in whom DD was diagnosed with colonoscopy and scored according to DICA classification; treated with Prolactis GG Plus® two times/daily for 2 consecutive months; in whom the severity of the abdominal pain was scored with a 10-points visual-analogue scale (VAS) at baseline and the end of follow-up; in whom fecal calprotectin (FC) was assessed at baseline and the end of follow-up as μg/g.

RESULTS: Twenty-four patients were identified (10 males, 14 females; 16 as DICA 2, and 8 as DICA 3). Prolactis GG Plus® decreased the severity of abdominal pain both in DICA 2 (p =0.02) and DICA 3 patients (p =0.01), while FC decreased significantly in DICA 2 (p <0.02) but not in DICA 3 (p =0.123) patients. Acute diverticulitis occurred during the follow-up in two DICA 3 patients but none DICA 2 patients. Add-on therapy was required by eight DICA 2 (50%) and six DICA 3 patients (75%).

CONCLUSION: In newly diagnosed patients with DD, the symbiotic mixture Prolactis GG Plus® can be a potential treatment for moderate (DICA 2) DD as a single treatment.},
}

@article {pmid39051391,
year = {2024},
author = {Bulaj, G and Coleman, M and Johansen, B and Kraft, S and Lam, W and Phillips, K and Rohaj, A},
title = {Redesigning Pharmacy to Improve Public Health Outcomes: Expanding Retail Spaces for Digital Therapeutics to Replace Consumer Products That Increase Mortality and Morbidity Risks.},
journal = {Pharmacy (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/pharmacy12040107},
pmid = {39051391},
issn = {2226-4787},
support = {35166//ALSAM Foundation/ ; },
abstract = {United States healthcare outcomes, including avoidable mortality rates, are among the worst of high-income countries despite the highest healthcare spending per capita. While community pharmacies contribute to chronic disease management and preventive medicine, they also offer consumer products that increase mortality risks and the prevalence of cardiovascular diseases, diabetes, cancer, and depression. To resolve these contradictions, our perspective article describes opportunities for major pharmacy chains (e.g., CVS Pharmacy and Walgreens) to introduce digital health aisles dedicated to prescription and over-the-counter digital therapeutics (DTx), together with mobile apps and wearables that support disease self-management, wellness, and well-being. We provide an evidence-based rationale for digital health aisles to replace spaces devoted to sugar-sweetened beverages and other unhealthy commodities (alcohol, tobacco) that may increase risks for premature death. We discuss how digital health aisles can serve as marketing and patient education resources, informing customers about commercially available DTx and other technologies that support healthy lifestyles. Since pharmacy practice requires symbiotic balancing between profit margins and patient-centered, value-based care, replacing health-harming products with health-promoting technologies could positively impact prevention of chronic diseases, as well as the physical and mental health of patients and caregivers who visit neighborhood pharmacies in order to pick up medicines.},
}

@article {pmid39049923,
year = {2024},
author = {Treviso, RL and Sant'Anna, V and Fabricio, MF and Ayub, MAZ and Brandelli, A and Hickert, LR},
title = {Time and temperature influence on physicochemical, microbiological, and sensory profiles of yerba mate kombucha.},
journal = {Journal of food science and technology},
volume = {61},
number = {9},
pages = {1733-1742},
pmid = {39049923},
issn = {0022-1155},
abstract = {UNLABELLED: The present work aimed to evaluate the features of yerba mate kombucha during 7 days of fermentation at either 25 ºC or 30 ºC, monitoring physicochemical changes, sensory profile, and sensorial acceptance. The symbiotic microbial culture of active bacteria and yeasts (SCOBY) at the beginning and the end of the bioprocess was also identified. The yerba mate kombuchas fermented at 25 ºC for 5 days or 30 ºC for 4 days were suitable for consumption according to Brazilian standards. Acetic acid, ethanol, and chlorophyll contents were dependent on fermentation time and temperature, unlike the total phenolic content. The main yeast and bacterium in SCOBY were Brettanomyces bruxellensis and Komagataeibacter rhaeticus, respectively, which remained dominant when fermentation was conducted for up to 7 days at both temperatures. Fermentation of yerba mate infusion led to products characterized by sourness, vinegar bitter, and fermented flavors and aromas, making the acceptance of non-fermented Yerba mate preferable to fermented infusions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-024-05951-z.},
}

@article {pmid39049854,
year = {2024},
author = {Jiang, Y and Wang, M and Yan, X and Liu, M and Guo, X},
title = {Exotic plants introduction changed soil nutrient cycle and symbiotic relationship with arbuscular mycorrhizal fungi in wetland ecological projects.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1410009},
pmid = {39049854},
issn = {1664-462X},
abstract = {In the process of applying exotic plants to wetland ecological restoration, insufficiently evaluated alien species may exhibit strong competitiveness and fecundity. Once introduced, they can displace native flora, disrupt the original ecological balance, diminish biodiversity, and even induce ecosystem dysfunction. Furthermore, exotic plants have the potential to alter soil microbial community structure, including the composition and activity of beneficial symbiotic microorganisms such as arbuscular mycorrhizal fungi (AMF), thereby impacting soil nutrient cycling and interplant nutrient competition. Here, we conducted three consecutive years of sampling experiments to investigate the succession of AMF communities associated with the invasive plant Spartina alterniflora along an initial introduction chronosequence, and to identify the key environmental factors influencing its response to S. alterniflora invasion. Our findings reveal that early-stage invasion by S. alterniflora alters the composition of soil AMF communities with unclassified_c__Glomeromycetes and Glomus-viscosum-VTX00063 consistently dominating. Additionally, as the duration of introduction increases, the diversity of rhizosphere soil AMF significantly decreases, while its evenness remains relatively stable. It's indicated that soil ω, AN, AK and N/P ratio were the main influencing factors of the integral AMF community. Notably, soil available phosphorus (AP) emerges as a positive influence on the important AMF taxa. The results confirm the mutual feedback effect between the invasion of the perennial herb S. alterniflora and AMF, in which specific AMF assist in nutrient absorption to promote S. alterniflora growth, potentially facilitating its rapid and successful invasion of new habitats. Given the likely differential effects of AMF communities on various plant species, our findings could contribute to anticipating future AMF-mediated effects during the introduction of alien plants.},
}

@article {pmid39048698,
year = {2024},
author = {Shikina, S and Yoshioka, Y and Chiu, YL and Uchida, T and Chen, E and Cheng, YC and Lin, TC and Chu, YL and Kanda, M and Kawamitsu, M and Fujie, M and Takeuchi, T and Zayasu, Y and Satoh, N and Shinzato, C},
title = {Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {899},
pmid = {39048698},
issn = {2399-3642},
support = {20H03235, 20K21860, and 24K01847//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20J21301//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Anthozoa/genetics/metabolism ; Animals ; *Transcriptome ; *Genome ; Symbiosis/genetics ; Polyps/genetics/pathology ; Gene Expression Profiling ; Organ Specificity ; },
abstract = {Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.},
}

*Anthozoa/genetics/metabolism
Animals
*Transcriptome
*Genome
Symbiosis/genetics
Polyps/genetics/pathology
Gene Expression Profiling
Organ Specificity

@article {pmid39048602,
year = {2024},
author = {Hainan, L and Peng, L and Qingqing, L and Fang, L and Dong, Z and Shenfa, H and Jie, Y and Zhiheng, L},
title = {Responses of nitrobenzene removal performance and microbial community by modified biochar supported zerovalent iron in anaerobic soil.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17078},
pmid = {39048602},
issn = {2045-2322},
support = {2023YFC3709600//National Key Research and Development Program of China/ ; 16th//2022 Shanghai Oriental Talent Plan Leading Project/ ; },
mesh = {*Charcoal/chemistry ; *Nitrobenzenes/chemistry ; *Iron/chemistry ; *Soil Microbiology ; Anaerobiosis ; Soil/chemistry ; Biodegradation, Environmental ; Microbiota ; Groundwater/chemistry/microbiology ; Soil Pollutants/chemistry ; },
abstract = {Biochar-supported ZVI have received increasing attention for their potential to remove nitrobenzene in groundwater and soil. However, the capacity of this material to enhance the biological reduction of nitrobenzene and alter microbial communities in anaerobic groundwater have not been explored. In this study, the nitrobenzene removal performance and mechanism of modified biochar-supported zerovalent iron (ZVI) composites were explored in anaerobic soil. The results showed that the 700 °C biochar composite enhanced the removal of nitrobenzene and inhibited its release from soil to the aqueous phase. NaOH-700-Fe50 had the highest removal rate of nitrobenzene, reaching 64.4%. However, the 300 °C biochar composite inhibited the removal of nitrobenzene. Microbial degradation rather than ZVI-mediated reduction was the main nitrobenzene removal pathway. The biochar composites changed the richness and diversity of microbial communities. ZVI enhanced the symbiotic relationship between microbial genera and weakened competition between soil microbial genera. In summary, the 700 °C modified biochar composite enhanced the removal of nitrobenzene by increasing microbial community richness and diversity, by upregulating functional genes, and by promoting electron transfer. Overall, the modified biochar-supported ZVI composites could be used for soil remediation, and NaOH-700-Fe50 is a promising composite material for the on-site remediation of nitrobenzene-contaminated groundwater.},
}

*Charcoal/chemistry
*Nitrobenzenes/chemistry
*Iron/chemistry
*Soil Microbiology
Anaerobiosis
Soil/chemistry
Biodegradation, Environmental
Microbiota
Groundwater/chemistry/microbiology
Soil Pollutants/chemistry

@article {pmid39047569,
year = {2024},
author = {Zhou, J and Lin, WH and Yu, YL and Dong, CD and Zhang, H and Hu, Z and Kao, CM},
title = {Transitioning weathered oil fields towards new energy: A review on utilizing hydrogenotrophic methanogens for petroleum hydrocarbons remediation.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135279},
doi = {10.1016/j.jhazmat.2024.135279},
pmid = {39047569},
issn = {1873-3336},
abstract = {The weathering process can cause the volatilization of light components in crude oil, leading to the accumulation of total petroleum hydrocarbons (TPH) in weathered oil field soils. These TPH compounds are relatively resistant to biodegradation, posing a significant environmental hazard by contributing to soil degradation. TPH represents a complex mixture of petroleum-based hydrocarbons classified as persistent organic pollutants in soil and groundwater. The release of TPH pollutants into the environment poses serious threats to ecosystems and human health. Currently, various methods are available for TPH-contaminated soil remediation, with bioremediation technology recognized as an environmentally friendly and cost-effective approach. While converting TPH to CO2 is a common remediation method, the complex structures and diverse types of petroleum hydrocarbons (PHs) involved can result in excessive CO2 generation, potentially exacerbating the greenhouse effect. Alternatively, transforming TPH into energy forms like methane through bioremediation, followed by collection and reuse, can reduce greenhouse gas emissions and energy consumption. This process relies on the synergistic interaction between Methanogens archaea and syntrophic bacteria, forming a consortium known as the oil-degrading bacterial consortium. Methanogens produce methane through anaerobic digestion (AD), with hydrogenotrophic methanogens (HTMs) utilizing H2 as an electron donor, playing a crucial role in biomethane production. Candidatus Methanoliparia (Ca. Methanoliparia) was found in the petroleum archaeal community of weathered Oil field in northeast China. Ca. Methanoliparia has demonstrated its independent ability to decompose and produce new energy (biomethane) without symbiosis, contribute to transitioning weathered oil fields towards new energy. Therefore, this review focuses on the principles, mechanisms, and developmental pathways of HTMs during new energy production in the degradation of PHs. It also discusses strategies to enhance TPH degradation and recovery methods.},
}

@article {pmid39047091,
year = {2024},
author = {Wang, H and Xiao, H and Feng, B and Lan, Y and Fung, CW and Zhang, H and Yan, G and Lian, C and Zhong, Z and Li, J and Wang, M and Wu, AR and Li, C and Qian, PY},
title = {Single-cell RNA-seq reveals distinct metabolic "microniches" and close host-symbiont interactions in deep-sea chemosynthetic tubeworm.},
journal = {Science advances},
volume = {10},
number = {30},
pages = {eadn3053},
doi = {10.1126/sciadv.adn3053},
pmid = {39047091},
issn = {2375-2548},
mesh = {Animals ; *Symbiosis ; *Single-Cell Analysis/methods ; *Polychaeta/metabolism/microbiology/genetics ; *RNA-Seq/methods ; Gammaproteobacteria/metabolism/genetics ; Single-Cell Gene Expression Analysis ; },
abstract = {Vestimentiferan tubeworms that thrive in deep-sea chemosynthetic ecosystems rely on a single species of sulfide-oxidizing gammaproteobacterial endosymbionts housed in a specialized symbiotic organ called trophosome as their primary carbon source. While this simple symbiosis is remarkably productive, the host-symbiont molecular interactions remain unelucidated. Here, we applied an approach for deep-sea in situ single-cell fixation in a cold-seep tubeworm, Paraescarpia echinospica. Single-cell RNA sequencing analysis and further molecular characterizations of both the trophosome and endosymbiont indicate that the tubeworm maintains two distinct metabolic "microniches" in the trophosome by controlling the availability of chemosynthetic gases and metabolites, resulting in oxygenated and hypoxic conditions. The endosymbionts in the oxygenated niche actively conduct autotrophic carbon fixation and are digested for nutrients, while those in the hypoxic niche conduct anaerobic denitrification, which helps the host remove ammonia waste. Our study provides insights into the molecular interactions between animals and their symbiotic microbes.},
}

Animals
*Symbiosis
*Single-Cell Analysis/methods
*Polychaeta/metabolism/microbiology/genetics
*RNA-Seq/methods
Gammaproteobacteria/metabolism/genetics
Single-Cell Gene Expression Analysis

@article {pmid39046305,
year = {2024},
author = {Boccato, E and Petruzzellis, F and Bordenave, CD and Nardini, A and Tretiach, M and Mayr, S and Candotto Carniel, F},
title = {The sound of lichens: ultrasonic acoustic emissions during desiccation question cavitation events in the hyphae.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erae318},
pmid = {39046305},
issn = {1460-2431},
abstract = {Lichens are a mutualistic symbiosis between a fungus and one or more photosynthetic partners. They are photosynthetically active during desiccation until relative water contents (RWC) as low as 30% (on dry mass). Experimental evidence suggests that during desiccation, the photobionts have a higher hydration level than the surrounding fungal pseudo-tissues. Explosive cavitation events in the hyphae might cause water movements towards the photobionts. This hypothesis was tested in two foliose lichens by measurements of ultrasonic acoustic emissions (UAE), a method commonly used in vascular plants but never in lichens, and by measurements of photosystem II efficiency, water potential and RWC. Thallus structural changes were characterised by low-temperature scanning electron microscopy. The thalli were silent between 380% and 30% RWCs, i.e. when explosive cavitation events should cause movements of liquid water. Nevertheless, the thalli emitted UAE at approximately 5% RWC. Accordingly, the medullary hyphae were partially shrunk at about 15% RWC, whereas they were completely shrunk below 5% RWC. These results do not support the hypothesis of hyphal cavitation and suggest that the UAE originate from structural changes at hyphal level. The shrinking of hyphae is proposed as an adaptation to avoid cell damage at very low RWCs.},
}

@article {pmid39046282,
year = {2024},
author = {Dupuis, S and Lingappa, UF and Mayali, X and Sindermann, ES and Chastain, JL and Weber, PK and Stuart, R and Merchant, SS},
title = {Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae140},
pmid = {39046282},
issn = {1751-7370},
abstract = {Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B12-producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15NH4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B12 and supported the growth of a B12-dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.},
}

@article {pmid39045293,
year = {2024},
author = {Rosenberg, J and Flynn, T and Merollini, K and Linn, J and Nabukalu, D and Davis, C},
title = {Exploring the 'citizen organization': an evaluation of a regional Australian community-based palliative care service model.},
journal = {Palliative care and social practice},
volume = {18},
number = {},
pages = {26323524241260427},
pmid = {39045293},
issn = {2632-3524},
abstract = {BACKGROUND: Little Haven is a rural, community-based specialist palliative care service in Gympie, Australia. Its goals are to provide highest quality of care, support and education for those experiencing or anticipating serious illness and loss. Families and communities work alongside clinical services, with community engagement influencing compassionate care and support of dying people, their families and communities. Public Health Palliative Care promotes community engagement by community-based palliative care services and is grounded in equal partnerships between civic life, community members, patients and carers, and service providers. This takes many forms, including what we have termed the 'citizen organization'.

OBJECTIVES: This paper reports on an evaluation of Little Haven's model of care and explores the organization's place as a 'citizen' of the community it services.

DESIGN: A co-designed evaluation approach utilizing mixed-method design is used.

METHODS: Multiple data sources obtained a broad perspective of the model of care including primary qualitative data from current patients, current carers, staff, volunteers and organizational stakeholders (interviews and focus groups); and secondary quantitative survey data from bereaved carers. Thematic analysis and descriptive statistics were generated.

RESULTS: This model of care demonstrates common service elements including early access to holistic, patient/family-centred, specialized palliative care at little or no cost to users, with strong community engagement. These elements enable high-quality care for patients and carers who describe the support as 'over and above', enabling good quality of life and care at home. Staff and volunteers perceive the built-in flexibility of the model as critical to its outcomes; the interface between the service and the community is similarly stressed as a key service element. Organizational stakeholders observed the model as a product of local activism and accountability to the community.

CONCLUSION: All participant groups agree the service model enables the delivery of excellent care. The construction of a community palliative care service as a citizen organization emerged as a new concept.},
}

@article {pmid39044145,
year = {2024},
author = {Xia, X and Liu, BQ and Yu, PH and Yu, ZP and Zhang, R and Luo, GH and Fang, JC},
title = {Antibiotic feeding changes the bacterial community of Chilo suppressalis and thereby affects its pesticide tolerance.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {273},
pmid = {39044145},
issn = {1471-2180},
support = {2022ZB773//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 2022YFD1400400//National Key R&D Plan/ ; 2022YFD1400400//National Key R&D Plan/ ; CARS-01-39//the Earmarked Fund for CARS/ ; CARS-01-39//the Earmarked Fund for CARS/ ; BE2022424//Carbon Peak Carbon Neutral Science and Technology Innovation Special Fund of Jiangsu Province/ ; BE2022424//Carbon Peak Carbon Neutral Science and Technology Innovation Special Fund of Jiangsu Province/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria/drug effects/genetics/classification/isolation & purification ; Pesticides/pharmacology ; Moths/microbiology/drug effects ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Tetracycline/pharmacology ; },
abstract = {BACKGROUND: Owing to the widespread use of chemical pesticides to control agricultural pests, pesticide tolerance has become a serious problem. In recent years, it has been found that symbiotic bacteria are related to pesticides tolerance. To investigate the potential role of microorganisms in the pesticide tolerance of Chilo suppressalis, this study was conducted.

RESULTS: The insect was fed with tetracycline and cefixime as the treatment group (TET and CFM, respectively), and did not add antibiotics in the control groups (CK). The 16S rDNA sequencing results showed that antibiotics reduced the diversity of C. suppressalis symbiotic microorganisms but did not affect their growth and development. In bioassays of the three C. suppressalis groups (TET, CFM, and CK), a 72 h LC50 fitting curve was calculated to determine whether long-term antibiotic feeding leads to a decrease in pesticide resistance. The CK group of C. suppressalis was used to determine the direct effect of antibiotics on pesticide tolerance using a mixture of antibiotics and pesticides. Indirect evidence suggests that antibiotics themselves did not affect the pesticide tolerance of C. suppressalis. The results confirmed that feeding C. suppressalis cefixime led to a decrease in the expression of potential tolerance genes to chlorantraniliprole.

CONCLUSIONS: This study reveals the impact of antibiotic induced changes in symbiotic microorganisms on the pesticide tolerance of C. suppressalis, laying the foundation for studying the interaction between C. suppressalis and microorganisms, and also providing new ideas for the prevention and control of C. suppressalis and the creation of new pesticides.},
}

*Anti-Bacterial Agents/pharmacology
Animals
*Bacteria/drug effects/genetics/classification/isolation & purification
Pesticides/pharmacology
Moths/microbiology/drug effects
Symbiosis
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Tetracycline/pharmacology

@article {pmid39043273,
year = {2024},
author = {Liu, J and Sun, P and Chen, Y and Guo, J and Liu, L and Zhao, X and Xin, J and Liu, X},
title = {The regulation pathways of biochar and microorganism in soil-plant system by multiple statistical methods: the forms of carbon participation in coastal wetlands.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {142918},
doi = {10.1016/j.chemosphere.2024.142918},
pmid = {39043273},
issn = {1879-1298},
abstract = {Coastal wetlands possess significant carbon storage capabilities. However, in coastal soil-plant systems augmented with biochar and microorganisms, the mechanisms of these amendments and carbon participation remain unclear. This study utilized pot experiments to explore how Enteromorpha prolifera biochar and Arbuscular mycorrhizal fungi (AMF) affect soil organic carbon (SOC), carbon-related microbes, photosynthetic and osmotic system of Suaeda salsa. The results showed biochar reduced exchangeable sodium percentage by 6.9% through adsorption and ion exchange, and increased SOC content by 34.4%. The abundance of carbon-related microorganisms (Bacteroidota and Chloroflexi) was increased and carbon metabolizing enzyme (cellulase and sucrase) activity in the soil was enhanced. AMF significantly improved plant growth compared with CK, as evidenced by the enhanced dry weight by 2.34 times. A partial least squares pathway model (PLS-PM) and correlation analysis suggested that the combined effect of biochar and AMF could be outlined as two pathways: soil and plant. Biochar increased SOC, improved the growth of soil carbon metabolizing microorganisms, and further promoted the activity of carbon-related enzymes. Additionally, AMF facilitated nutrient absorption by plants through root symbiosis, with biochar further enhancing this process by acting as a nutrient adsorber. These combined effects of biochar and AMF at soil and plant level enhanced the photosynthetic process of Suaeda salsa. The transport of photosynthetic products to the roots can increase the carbon storage in the soil. This study provides quantitative evidence supporting the increase of carbon storage in coastal wetland soil-plant systems through a combined application of biochar and AMF.},
}

@article {pmid39043241,
year = {2024},
author = {Taylor, BN and Komatsu, KJ},
title = {More diverse rhizobial communities can lead to higher symbiotic nitrogen fixation rates, even in nitrogen-rich soils.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2027},
pages = {20240765},
pmid = {39043241},
issn = {1471-2954},
support = {//Maryland Native Plant Society/ ; },
mesh = {*Nitrogen Fixation ; *Symbiosis ; *Soil/chemistry ; *Nitrogen/metabolism ; *Soil Microbiology ; *Rhizobium/physiology/metabolism ; Fabaceae/microbiology ; Biodiversity ; },
abstract = {Symbiotic nitrogen (N) fixation (SNF) by legumes and their rhizobial partners is one of the most important sources of bioavailable N to terrestrial ecosystems. While most work on the regulation of SNF has focussed on abiotic drivers such as light, water and soil nutrients, the diversity of rhizobia with which individual legume partners may play an important but under-recognized role in regulating N inputs from SNF. By experimentally manipulating the diversity of rhizobia available to legumes, we demonstrate that rhizobial diversity can increase average SNF rates by more than 90%, and that high rhizobial diversity can induce increased SNF even under conditions of high soil N fertilization. However, the effects of rhizobial diversity, the conditions under which diversity effects were the strongest, and the likely mechanisms driving these diversity effects differed between the two legume species we assessed. These results provide evidence that biodiversity-ecosystem function relationships can occur at the scales of an individual plant and that the effects of rhizobial diversity may be as important as long-established abiotic factors, such as N availability, in driving terrestrial N inputs via SNF.},
}

*Nitrogen Fixation
*Symbiosis
*Soil/chemistry
*Nitrogen/metabolism
*Soil Microbiology
*Rhizobium/physiology/metabolism
Fabaceae/microbiology
Biodiversity

@article {pmid39042424,
year = {2024},
author = {Coutry, N and Gasmi, I and Herbert, F and Jay, P},
title = {Mechanisms of intestinal dysbiosis: new insights into tuft cell functions.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2379624},
pmid = {39042424},
issn = {1949-0984},
mesh = {*Dysbiosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; *Paneth Cells/metabolism ; Symbiosis ; Bacteria/classification/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Tuft Cells ; },
abstract = {Symbiosis between the host and intestinal microbial communities is essential for human health. Disruption in this symbiosis is linked to gastrointestinal diseases, including inflammatory bowel diseases, as well as extra-gastrointestinal diseases. Unbalanced gut microbiome or gut dysbiosis contributes in multiple ways to disease frequency, severity and progression. Microbiome taxonomic profiling and metabolomics approaches greatly improved our understanding of gut dysbiosis features; however, the precise mechanisms involved in gut dysbiosis establishment still need to be clarified. The aim of this review is to present new actors and mechanisms underlying gut dysbiosis formation following parasitic infection or in a context of altered Paneth cells, revealing the existence of a critical crosstalk between Paneth and tuft cells to control microbiome composition.},
}

*Dysbiosis/microbiology
Humans
*Gastrointestinal Microbiome
Animals
*Paneth Cells/metabolism
Symbiosis
Bacteria/classification/metabolism/genetics
Inflammatory Bowel Diseases/microbiology/metabolism
Intestinal Mucosa/microbiology/metabolism
Tuft Cells

@article {pmid39042246,
year = {2024},
author = {Favoreto, AL and Domingues, MM and de Carvalho, VR and Ribeiro, MF and Zanuncio, JC and Wilcken, CF},
title = {Detection of Arsenophonus in Glycaspis brimblecombei (Hemiptera: Aphalaridae) populations in Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39042246},
issn = {1678-4405},
support = {Conselho Nacional de Desenvolvimento Científico e Tecnológico//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CAPES-Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)/ ; Programa Cooperativo sobre Proteção Florestal (PROTEF) do Instituto de Pesquisas e Estudos Florestais (IPEF)//Programa Cooperativo sobre Proteção Florestal (PROTEF) do Instituto de Pesquisas e Estudos Florestais (IPEF)/ ; },
abstract = {Eucalyptus is the most intensively managed tree genus in the world. Different factors, including damage by insect pests, affect its growth and productivity. Among these pests is Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae), an exotic insect of Australian origin. The evolutionary success of this insect depends on symbiotic associations with microorganisms. The influence of these microorganisms on insect pests and their natural enemies is important for integrated management tactics. Within this context, this work aimed to detect Arsenophonus in populations of G. brimblecombei in Brazil. Eucalyptus branches infested with G. brimblecombei nymphs were collected in commercial eucalyptus plantations in six Brazilian states. Specimens of this pest were sampled soon after emergence and frozen for molecular analysis. The genomic DNA of G. brimblecombei adults from each population was extracted and used to detect the endosymbiont Arsenophonus by polymerase chain reaction (PCR) employing specific primers that target its 23 S rRNA gene. This endosymbiont was identified in all of the studied G. brimblecombei populations. This is the first report on the association between Arsenophonus and G. brimblecombei in Brazil.},
}

@article {pmid39041709,
year = {2024},
author = {Kastner, K and Bitter, J and Pfeiffer, M and Grininger, C and Oberdorfer, G and Pavkov-Keller, T and Weber, H and Nidetzky, B},
title = {Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202410681},
doi = {10.1002/anie.202410681},
pmid = {39041709},
issn = {1521-3773},
abstract = {Flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free-living and symbiotic bacteria have developed, alongside hydrolysis, a non-hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase-catalyzed reactions. Here, based on study of enzymes from the phytopathogen Agrobacterium tumefaciens, we reveal a conserved Mn2+ metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3-keto-glucosides and water addition to the resulting 2-hydroxy-3-keto-glycal product, yielding 3-keto-glucose. Extending our search of GUL-encoded putative lyases to the human gut commensal Bacteroides thetaiotaomicron, we discover a Ca2+ metallocenter active site in a putative glycoside hydrolase-like protein and demonstrate its catalytic function in the eliminative cleavage of 3-keto-glucosides of opposite (alpha) anomeric configuration as preferred by the A. tumefaciens enzyme (beta). Findings identify a basic set of GUL-encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in bacteria.},
}

@article {pmid39041078,
year = {2024},
author = {Wang, L and Zhang, JY and Yuan, Y and Liu, TR},
title = {[Effects of soil relative water content on growth characteristics of Armillaria spp. and seedling production of Gastrodia elata f. glauca].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {12},
pages = {3178-3184},
doi = {10.19540/j.cnki.cjcmm.20240215.101},
pmid = {39041078},
issn = {1001-5302},
mesh = {*Seedlings/growth & development/metabolism ; *Gastrodia/growth & development/chemistry/metabolism/microbiology ; *Soil/chemistry ; *Water/metabolism ; *Armillaria/growth & development/metabolism ; },
abstract = {The seedling survival rate, yield, and individual weight of Gastrodia elata is closely related to the soil relative water content(RWC) and the growth characteristics of the associated fungi Armillaria spp. This study explored the effects of the soil RWC on the growth characteristics of Armillaria spp. and the seedling production of G. elata f. glauca, aiming to provide guidance for breeding G. elata f. glauca and selecting elite strains of Armillaria. According to the growth characteristics on the medium for activation, thirty strains of Armillaria were classified into 4 clusters. Two strains with good growth indicators were selected from each cluster and cultiva-ted with immature tuber(Mima) and the branches of the broad-leaved trees in a water-controlled box. The results showed that the Armillaria clusters with uniaxial branches of rhizoid cords, such as clusters Ⅲ and Ⅳ, were excellent clusters in symbiosis with G. elata f. glauca. The soil RWC had significant effects on the growth characteristics of Armillaria strains and the seedling survival rate, yield, and individual weight of G. elata f. glauca. The growth characteristics of Armillaria strains and the seedling survival rate, yield, and individual weight of G. elata f. glauca in the case of the soil RWC being 75% were significantly better than those in the case of other soil RWC. Cultivating Mima with elite strains of Armillaria, together with branches of broad-leaved trees, in the greenhouses with the artificial control of the soil RWC, can achieve efficient seedling production and Mima utilization of G. elata f. glauca.},
}

*Seedlings/growth & development/metabolism
*Gastrodia/growth & development/chemistry/metabolism/microbiology
*Soil/chemistry
*Water/metabolism
*Armillaria/growth & development/metabolism

@article {pmid39041011,
year = {2024},
author = {Holt, JR and Cavichiolli de Oliveira, N and Medina, RF and Malacrinò, A and Lindsey, ARI},
title = {Insect-microbe interactions and their influence on organisms and ecosystems.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11699},
pmid = {39041011},
issn = {2045-7758},
abstract = {Microorganisms are important associates of insect and arthropod species. Insect-associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect-associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect-microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect-microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities.},
}

@article {pmid39040687,
year = {2024},
author = {Liu, Z and Guo, Z and Zhou, J and Guo, X and Chen, Y},
title = {Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {2717-2726},
pmid = {39040687},
issn = {2001-0370},
abstract = {Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.},
}

@article {pmid39038530,
year = {2024},
author = {Makiura, T and Matsutani, M and Tseng, HC and Fujimoto, N and Ohnishi, A},
title = {Succinate-mediated symbiosis between Dialister hominis and an uncharacterized Segatella-like pectinophile.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {102883},
doi = {10.1016/j.anaerobe.2024.102883},
pmid = {39038530},
issn = {1095-8274},
abstract = {OBJECTIVES: Syntrophy has been documented between pectinophiles and methanol-utilizing bacteria, along with instances of cross-feeding between pectinophiles and methanogens. However, studies on the ecology of pectinophiles in anaerobic digestion (AD) are lacking. Therefore, in this study, we aimed to elucidate the ecology of pectinophiles by isolating novel pectinophile forms and conducting a comprehensive analysis of their physiology and ecology.

METHODS: Complex microbial communities from AD systems were enriched in a pectin-containing medium; subsequently, specific strains were isolated using a pectinophile isolation method. The carbon source assimilation and growth ability of the isolates, along with their symbiotic relationships, were evaluated using batch tests.

RESULTS: Strain LPYR103-Pre exhibited 16S rRNA gene sequence similarity and average nucleotide identity values of 94.3% and 77.9%, respectively, compared to its closest related species, Segatella cerevisiae. Strain LPYR103-Pre demonstrated attenuated growth in the presence of eight common sugars but exhibited remarkably high growth in the presence of pectin, D-galacturonate, and D-glucuronate, with succinate being identified as a primary metabolite. Accumulation of succinate inhibited the growth of strain LPYR103-Pre. However, this growth impediment was alleviated by Dialister hominis LPYG114-Dih, whose growth required succinate.

CONCLUSIONS: Our results elucidate the specific carbon source requirements of the Segatella-like strain LPYR103-Pre and succinate-mediated symbiosis involving D. hominis. These findings provide new insights into the degradation of pectin and its degradation products during AD, contributing to the identification of unknown pectinophiles.},
}

@article {pmid39037262,
year = {2024},
author = {Jung, JM and Rahman, A and Schiffer, AM and Weisberg, AJ},
title = {Beav: a bacterial genome and mobile element annotation pipeline.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0020924},
doi = {10.1128/msphere.00209-24},
pmid = {39037262},
issn = {2379-5042},
abstract = {UNLABELLED: Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav.

IMPORTANCE: Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.},
}

@article {pmid39036777,
year = {2024},
author = {Chen, Y and Chen, B and Liang, R and Wang, S and An, M and Zhang, J and Liang, J and Wang, Y and Gao, X and Liang, J},
title = {Four new species of Russulasubsect.Cyanoxanthinae from China (Russulales, Russulaceae).},
journal = {MycoKeys},
volume = {107},
number = {},
pages = {21-50},
pmid = {39036777},
issn = {1314-4049},
abstract = {Four new species of Russulasubsect.Cyanoxanthinae, viz. Russulaatrochermesina Y.L. Chen & J.F. Liang, R.lavandula Y.L. Chen, B. Chen & J.F. Liang, R.lilaceofusca Y.L. Chen & J.F. Liang and R.perviridis Y.L. Chen, B. Chen & J.F. Liang, from China are proposed, based on morphological and molecular evidence. Russulaatrochermesina can be distinguished by its violet pileus with tuberculate-striate margin, distant lamellae that stain greyish-yellow when bruised, basidiospores ornamented by isolated warts, wide hymenial cystidia on lamellae edges, cystidia content negative reaction in sulphovanillin and branched subterminal cells in pileipellis. Russulalavandula has a purplish-white to violet red pileus with a yellow centre, frequently present lamellulae and furcations, stipe often with pale yellow near the base, isolated basidiospores ornamentation and unbranched cuticular hyphal terminations, while R.lilaceofusca is characterised by its lilac brown to dark brown pileus, crowded lamellae with lamellulae and furcations, stipe often turning reddish-yellow when bruised, subreticulate basidiospores ornamentation and clavate hymenial cystidia often with capitate appendage whose contents that change to reddish-black in sulphovanillin. Russulaperviridis is characterised by its large basidiomata, smooth pileus surface, frequently present lamellulae and furcations, stipe with yellow-brown tinge, globose to broadly ellipsoid basidiospores with subreticulate ornamentation, long hymenial cystidia that turn greyish-black in sulphovanillin and symbiotic with Quercussemecarpifolia. Phylogenetic analyses, based on multi-gene ITS+LSU+mtSSU+rpb2, indicate that R.atrochermesina, R.lavandula, R.lilaceofusca and R.perviridis are closely related to R.pallidirosea and R.purpureorosea, R.banwatchanensis, R.lakhanpalii and R.nigrovirens, respectively.},
}

@article {pmid39035357,
year = {2024},
author = {Qadri, H and Shah, AH and Almilaibary, A and Mir, MA},
title = {Microbiota, natural products, and human health: exploring interactions for therapeutic insights.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1371312},
pmid = {39035357},
issn = {2235-2988},
mesh = {Humans ; *Biological Products/pharmacology/metabolism ; *Gastrointestinal Microbiome/physiology ; Bacteria/metabolism/classification ; Animals ; Host Microbial Interactions ; Symbiosis ; },
abstract = {The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.},
}

Humans
*Biological Products/pharmacology/metabolism
*Gastrointestinal Microbiome/physiology
Bacteria/metabolism/classification
Animals
Host Microbial Interactions
Symbiosis

@article {pmid39034969,
year = {2024},
author = {Kotakadi, SM and Bangarupeta, MJ and Kandati, K and Borelli, DPR and Sayyed, JA and Shaik, MI and Nannepaga, JS},
title = {Biosynthesized MgONPs using Syzygium cumini seed extract: Characterization, In vitro anti-oxidant and anti-microbial activity.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {43},
number = {},
pages = {e00846},
pmid = {39034969},
issn = {2215-017X},
abstract = {The present study investigates S. cumini seed extracts which are considered as a promising and valuable source of bioactive compounds were prepared using different solvents such as methanol, ethanol, petroleum ether, acetone, chloroform, and diethyl ether. Among these solvents, methanol exhibited the highest extraction with a yield of 42 %. HPLC analysis revealed the highest concentration of quercetin flavonoids (49.62 mg/gm) in the methanolic S. cumini seed extract. Thus, the current work deals with the MgONPs synthesis through a biological approach using different S. cumini seed extracts. In vitro anti-oxidant properties were evaluated, which showed an IC50 value of 22.46 μg/mL for MgONPs synthesized from methanolic extract, surpassing the anti-oxidant potency of ascorbic acid by threefold. By leveraging the rich repository of bioactive compounds found within S. cumini seed extract, this study presents a novel approach to MgONPs synthesis. Exploring the symbiotic relationship between S. cumini seed extract and MgONPs, this research elucidates the pivotal role of bioactive compounds in guiding the formation and properties of nanostructures. Further anti-microbial studies on MgONPs from methanolic S. cumini seed extract were conducted against four different bacterial strains (Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and S. typhimurium), revealing potent anti-microbial activity with 5.3 mm of inhibition for 100 µl against S. typhimurium. These findings suggest that S. cumini is a source of bioactive compounds responsible for the successful synthesis of MgONPs. Characterization studies of MgONPs were also carried out using UV-vis spectroscopy, FTIR, SEM, XRD, DSC and HPLC.},
}

@article {pmid39034691,
year = {2024},
author = {Nef, C and Pierella Karlusich, JJ and Bowler, C},
title = {From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1909},
pages = {20230172},
doi = {10.1098/rstb.2023.0172},
pmid = {39034691},
issn = {1471-2970},
support = {//Université de Recherche Paris Sciences et Lettres/ ; //Horizon 2020 Framework Programme/ ; //Fonds Français pour l'Environnement Mondial/ ; //Simons Foundation/ ; //Agence Nationale de la Recherche/ ; //HORIZON EUROPE European Research Council/ ; },
mesh = {*Phytoplankton/metabolism/physiology ; *Food Chain ; Ecosystem ; },
abstract = {Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.},
}

*Phytoplankton/metabolism/physiology
*Food Chain
Ecosystem

@article {pmid39032279,
year = {2024},
author = {Zhang, H and Hao, Z and Zhang, R and Tong, J and Wang, X and Liu, J and Gao, Y and Wang, X and Su, Q and Wen, H and Fan, Y and Liu, F and Li, X and Tong, C and Wang, X},
title = {Artemisia argyi polyphenols Attenuates DSS-induced colitis in mice by regulating the structural composition of gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {132},
number = {},
pages = {155897},
doi = {10.1016/j.phymed.2024.155897},
pmid = {39032279},
issn = {1618-095X},
abstract = {BACKGROUND: Intestinal health is affected by heredity, lifestyle, and structure of gut microbiota. The imbalance of symbiotic and harmful bacteria in gut microbiota may increase the occurrence of colonic inflammation. Supplementary A. muciniphila can improve the survival rate of colitis mice, reduce colon tissue injury, and the expression of anti-inflammatory factors was upregulated. Artemisia argyi has been reported to have anti-inflammatory, antioxidant, bactericidal, and immunomodulatory effects. However, its anti-inflammatory effect and mechanism, and its influence on gut microbiota and metabolites are still unclear yet.

PURPOSE: To explore whether Artemisia argyi Polyphenols(AAPs) can alleviate ulcerative colitis (UC) by changing gut microbiota.

METHODS: The therapeutic effect of AAPs on colitis was investigated by inducing ulcerative colitis in mice using dextran sodium sulfate (DSS) and administering different doses of AAPs orally to mice. Exploring the levels of inflammatory proteins, oxidative stress proteins, and barrier proteins using western blotting and immunofluorescence, and explored the structural changes of gut microbiota and its metabolites. Meanwhile, in order to explore whether the role of AAPs in alleviating colitis is based on the regulation of gut microbiota structure, we conducted fecal microbiota transplantation (FMT).

RESULTS: It showed that AAPs and FMT trial alleviated DSS-induced colonic injury, including clinical parameters and pathological injury of colon tissue, reduction in the expression of inflammatory proteins: IL-6, TNF-α, p-p65, p-IκBα, and increase in the expression of antioxidant proteins: Nrf2, NQO-1 and HO-1 and barrier proteins: Claudin-1, Occludin, ZO-1 and MUC2. AAPs and FMT promoted the content of beneficial bacteria, such as Butyricimonas and Lactobacillus, and the content of beneficial metabolites for instance acetic acid, butyric acid, and valeric acid has also increased.

CONCLUSION: These results suggested that AAPs might improve DSS-induced colonic injury by changing the structural of gut microbiota while promoting the synthesis of fatty acids in the intestine, thereby providing a theoretical basis for using AAPs to treat ulcerative colitis.},
}

@article {pmid39031969,
year = {2024},
author = {Peterson, BW and Tjakkes, GH and Renkema, AM and Manton, DJ and Ren, Y},
title = {The oral microbiota and periodontal health in orthodontic patients.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12594},
pmid = {39031969},
issn = {1600-0757},
abstract = {The oral microbiota develops within the first 2 years of childhood and becomes distinct from the parents by 4 years-of-age. The oral microbiota plays an important role in the overall health/symbiosis of the individual. Deviations from the state of symbiosis leads to dysbiosis and an increased risk of pathogenicity. Deviations can occur not only from daily life activities but also from orthodontic interventions. Orthodontic appliances are formed from a variety of biomaterials. Once inserted, they serve as a breeding ground for microbial attachment, not only from new surface areas and crevices but also from material physicochemical interactions different than in the symbiotic state. Individuals undergoing orthodontic treatment show, compared with untreated people, qualitative and quantitative differences in activity within the oral microbiota, induced by increased retention of supra- and subgingival microbial plaque throughout the treatment period. These changes are at the root of the main undesirable effects, such as gingivitis, white spot lesions (WSL), and more severe caries lesions. Notably, the oral microbiota profile in the first weeks of orthodontic intervention might be a valuable indicator to predict and identify higher-risk individuals with respect to periodontal health and caries risk within an otherwise healthy population. Antimicrobial coatings have been used to dissuade microbes from adhering to the biomaterial; however, they disrupt the host microbiota, and several bacterial strains have become resistant. Smart biomaterials that can reduce the antimicrobial load preventing microbial adhesion to orthodontic appliances have shown promising results, but their complexity has kept many solutions from reaching the clinic. 3D printing technology provides opportunities for complex chemical syntheses to be performed uniformly, reducing the cost of producing smart biomaterials giving hope that they may reach the clinic in the near future. The purpose of this review is to emphasize the importance of the oral microbiota during orthodontic therapy and to use innovative technologies to better maintain its healthy balance during surgical procedures.},
}

@article {pmid39031570,
year = {2024},
author = {Majid, M and Wani, AH and Ganai, BA},
title = {Evaluating the Biocontrol Efficacy and Antioxidant Potential of Phellinus caribaeo-quercicola-A First Report Dual-Action Endophyte From Inula racemosa Hook. F.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400080},
doi = {10.1002/jobm.202400080},
pmid = {39031570},
issn = {1521-4028},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Phellinus caribaeo-quercicola is a basidiomycetous fungus, isolated as an endophyte in this study from the healthy and symptomless leaves of Inula racemosa Hook. f., an important medicinal herb growing in Kashmir Himalaya. This study combines morphological, molecular and phylogenetic techniques to identify the fungal endophyte, using the ITS sequence of nrDNA. A detached leaf assay was conducted to assess the pathogenicity of the fungal endophyte suggesting its mutually symbiotic relationship with the host. The authors also investigated the antifungal potential of the isolated endophytic strain to ascertain its use as a biocontrol agent. The study shows that P. caribaeo-quercicola INL3-2 strain exhibits biocontrol activity against four key fungal phytopathogens that cause significant agronomic and economic losses: Aspergillus flavus, Aspergillus niger, Fusarium solani, and Fusarium oxysporum. Notably, P. caribaeo-quercicola INL3-2 strain is highly effective against A. flavus, with an inhibition percentage of 57.63%. In addition, this study investigates the antioxidant activity of P. caribaeo-quercicola INL3-2 strain crude extracts using ethyl acetate and methanol as solvents. The results showed that the methanolic fraction of P. caribaeo-quercicola exhibits potential as an antioxidant agent, with an IC50 value of 171.90 ± 1.15 µg/mL. This investigation is first of its kind and marks the initial report of this fungal basidiomycete, P. caribaeo-quercicola, as an endophyte associated with a medicinal plant. The findings of this study highlight the potential of P. caribaeo-quercicola INL3-2 strain as a dual-action agent with both biocontrol and antioxidant properties consistent with the medicinal properties of Inula racemosa. This endophytic fungus could be a promising source of natural compounds for use in agriculture, medicine, and beyond.},
}

@article {pmid39030686,
year = {2024},
author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB},
title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae132},
pmid = {39030686},
issn = {1751-7370},
abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacteria-host interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20 000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.},
}

@article {pmid39030411,
year = {2024},
author = {Yang, Q and Yang, B and Yang, B and Zhang, W and Tang, X and Sun, H and Zhang, Y and Li, J and Ling, J and Dong, J},
title = {Alleviating Coral Thermal Stress via Inoculation with Quorum Quenching Bacteria.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {},
number = {},
pages = {},
pmid = {39030411},
issn = {1436-2236},
support = {2021YFC3100500//National Key Research and Development Program of China/ ; 2022YFC3102003//National Key Research and Development Program of China/ ; 2022YFC3102004//National Key Research and Development Program of China/ ; 42106197//National Natural Science Foundation of China/ ; 42276160//National Natural Science Foundation of China/ ; 422QN440//Hainan Provincial Natural Science Foundation of China, China/ ; ISEE2021ZD03//Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences/ ; ISEE2021ZD03//Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences/ ; 2021B1212050023//Science and Technology Planning Project of Guangdong Province, China/ ; },
abstract = {In the background of global warming, coral bleaching induced by elevated seawater temperature is the primary cause of coral reef degradation. Coral microbiome engineering using the beneficial microorganisms for corals (BMCs) has become a hot spot in the field of coral reef conservation and restoration. Investigating the potential of alleviating thermal stress by quorum quenching (QQ) bacteria may provide more tools for coral microbial engineering remediation. In this study, QQ bacteria strain Pseudoalteromonas piscicida SCSIO 43740 was screened among 75 coral-derived bacterial strains, and its quorum sensing inhibitor (QSI) compound was isolated and identified as 2,4-di-tert-butylphenol (2,4-DTBP). Then, the thermal stress alleviating potential of QQ bacteria on coral Pocillopora damicornis was tested by a 30-day controlled experiment with three different treatments: control group (Con: 29 °C), high temperature group (HT: 31 °C), and the group of high temperature with QQ bacteria inoculation (HTQQ: 31 °C + QQ bacteria). The results showed that QQ bacteria SCSIO 43740 inoculation can significantly mitigate the loss of symbiotic algae and impairment of photosynthesis efficiency of coral P. damicornis under thermal stress. Significant difference in superoxide dismutase (SOD) and catalase (CAT) enzyme activities between HT and HTQQ was not observed. In addition, QQ bacteria inoculation suppressed the coral microbial community beta-dispersion and improved the stability of microbial co-occurrence network under thermal stress. It was suggested that QQ bacteria inoculation can alleviate coral thermal stress via reshaping microbial interaction and maintain community stability of coral microbiome. This study provided new evidence for the probiotic function of QQ bacteria in corals, which shedding light on the development of new microbiological tools for coral reef conservation.},
}

@article {pmid39030351,
year = {2024},
author = {Gong, S and Liang, J and Xu, L and Wang, Y and Li, J and Jin, X and Yu, K and Zhang, Y},
title = {Diel transcriptional responses of coral-Symbiodiniaceae holobiont to elevated temperature.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {882},
pmid = {39030351},
issn = {2399-3642},
mesh = {*Anthozoa/genetics/physiology ; Animals ; *Symbiosis ; Circadian Rhythm/genetics ; Transcription, Genetic ; Hot Temperature ; Dinoflagellida/genetics/physiology ; Temperature ; },
abstract = {Coral exhibits diel rhythms in behavior and gene transcription. However, the influence of elevated temperature, a key factor causing coral bleaching, on these rhythms remains poorly understood. To address this, we examined physiological, metabolic, and gene transcription oscillations in the Acropora tenuis-Cladocopium sp. holobiont under constant darkness (DD), light-dark cycle (LD), and LD with elevated temperature (HLD). Under LD, the values of photosystem II efficiency, reactive oxygen species leakage, and lipid peroxidation exhibited significant diel oscillations. These oscillations were further amplified during coral bleaching under HLD. Gene transcription analysis identified 24-hour rhythms for specific genes in both coral and Symbiodiniaceae under LD. Notably, these rhythms were disrupted in coral and shifted in Symbiodiniaceae under HLD. Importantly, we identified over 20 clock or clock-controlled genes in this holobiont. Specifically, we suggested CIPC (CLOCK-interacting pacemaker-like) gene as a core clock gene in coral. We observed that the transcription of two abundant rhythmic genes encoding glycoside hydrolases (CBM21) and heme-binding protein (SOUL) were dysregulated by elevated temperature. These findings indicate that elevated temperatures disrupt diel gene transcription rhythms in the coral-Symbiodiniaceae holobiont, affecting essential symbiosis processes, such as carbohydrate utilization and redox homeostasis. These disruptions may contribute to the thermal bleaching of coral.},
}

*Anthozoa/genetics/physiology
Animals
*Symbiosis
Circadian Rhythm/genetics
Transcription, Genetic
Hot Temperature
Dinoflagellida/genetics/physiology
Temperature

@article {pmid39029900,
year = {2024},
author = {Yue, T and Dong, Y and Huo, Q and Li, W and Wang, X and Zhang, S and Fan, H and Wu, X and He, X and Zhao, Y and Li, D},
title = {Nicotinamide riboside alleviates ionizing radiation-induced intestinal senescence by alleviating oxidative damage and regulating intestinal metabolism.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.07.010},
pmid = {39029900},
issn = {2090-1224},
abstract = {INTRODUCTION: The intestine, frequently subjected to pelvic or abdominal radiotherapy, is particularly vulnerable to delayed effects of acute radiation exposure (DEARE) owing to its high radiation sensitivity. Radiation-induced intestinal senescence, a result of DEARE, profoundly affects the well-being and quality of life of radiotherapy patients. However, targeted pharmaceutical interventions for radiation-induced senescence are currently scarce. Our findings showcase that nicotinamide riboside(NR) effectively alleviates radiation-induced intestinal senescence, offering crucial implications for utilizing NR as a pharmacological agent to combat intestinal DEARE.

OBJECTIVES: The aim of this study was to investigate the ability of NR to reduce radiation induced intestinal senescence and explore its related mechanisms.

METHODS: Male C57BL/6J mice were randomly divided into CON, IR, and IR + NR groups. The mice in the IR and IR + NR groups were subjected to a 6.0 Gy γ-ray total body exposure. After 8 weeks, the mice in the IR + NR group received NR via gavage at a dose of 400 mg/kg/d for 21 days. Then the mice were used for sample collection.

RESULTS: Our results demonstrate that NR can significantly mitigate radiation-induced intestinal senescence. Furthermore, our findings indicate that NR can mitigate oxidative damage, restore the normal function of intestinal stem cells, regulate the disruption of the intestinal symbiotic ecosystem and address metabolic abnormalities. In addition, the underlying mechanisms involve the activation of SIRT6, SIRT7 and the inhibition of the mTORC1 pathway by NR.

CONCLUSION: In conclusion, our results reveal the substantial inhibitory effects of NR on radiation-induced intestinal senescence. These findings offer valuable insights into the potential therapeutic use of NR as a pharmacological agent for alleviating intestinal DEARE.},
}

@article {pmid39029750,
year = {2024},
author = {Cao, X and Liu, J and Zhang, L and Mao, W and Li, M and Wang, H and Sun, W},
title = {Response of soil microbial ecological functions and biological characteristics to organic fertilizer combined with biochar in dry direct-seeded paddy fields.},
journal = {The Science of the total environment},
volume = {948},
number = {},
pages = {174844},
doi = {10.1016/j.scitotenv.2024.174844},
pmid = {39029750},
issn = {1879-1026},
abstract = {Biochar and organic fertilizer are commonly used to maintain soil health and sustainable agroecosystems, and the alternate wet-dry management of soil moisture in dry direct-seeded paddy fields can complicate the effects of biochar and organic fertilizer on soil microhabitats. Therefore, this study used chicken manure organic fertilizer to replace some of the inorganic fertilizer and applied biochar to explore the ability of biochar and organic fertilizer to regulate the functions of the soil microhabitat in dry direct-seeded paddy fields. The coupling effect of organic fertilizer and biochar increased the diversity and richness of soil bacteria but had no significant effect on soil fungi. Biochar and organic fertilizer affected the distribution and composition of soil bacteria and fungi, and the total number of soil bacteria and fungi increased by 1365 and -71 (5 t/hm[2] biochar and no organic fertilizer), 660 and 79 (10 t/hm[2] biochar and no organic fertilizer), 3121 and 7 (no biochar and 20 % organic fertilizer substitution), 1873 and -72 (5 t/hm[2] biochar and 20 % organic fertilizer substitution), and -544 and -65 (10 t/hm[2] biochar and 20 % organic fertilizer substitution), respectively, compared with that of the control treatment. Compared with the application of biochar alone, the coupling effect of biochar and organic fertilizer increased the average degree (0.95 and 0.16), links (190 and 32), and ratio of fungal positive links (1.651 %), and decreased the modularity (0.034 and 0.052) and ratio of bacterial positive links (6.482 %) of bacterial and fungal networks. In addition, the coupling effect resulted in a more complex association between soil microbial diversity and richness and microbial ecological functions. Random forest predictions indicated that, organic fertilizer as a random factor, changes in the abundance of bacterial Bacteroidetes and Nitrospirae and fungal Monoblepharomycota were the main factors driving the differences in soil microbial ecological functions.},
}

@article {pmid39029396,
year = {2024},
author = {Fan, X and Kong, L and Wang, J and Tan, Y and Xu, X and Li, M and Zhu, L},
title = {Surface-programmed microbiome assembly in phycosphere to microplastics contamination.},
journal = {Water research},
volume = {262},
number = {},
pages = {122064},
doi = {10.1016/j.watres.2024.122064},
pmid = {39029396},
issn = {1879-2448},
abstract = {Recalcitrance in microplastics accounts for ubiquitous white pollution. Of special interest are the capabilities of microorganisms to accelerate their degradation sustainably. Compared to the well-studied pure cultures in degrading natural polymers, the algal-bacterial symbiotic system is considered as a promising candidate for microplastics removal, cascading bottom-up impacts on ecosystem-scale processes. This study selected and enriched the algae-associated microbial communities hosted by the indigenous isolation Desmodesmus sp. in wastewater treatment plants with micro-polyvinyl chloride, polyethylene terephthalate, polyethylene, and polystyrene contamination. Results elaborated that multiple settled and specific affiliates were recruited by the uniform algae protagonist from the biosphere under manifold microplastic stress. Alteration of distinct chemical functionalities and deformation of polymers provide direct evidence of degradation in phycosphere under illumination. Microplastic-induced phycosphere-derived DOM created spatial gradients of aromatic protein, fulvic and humic acid-like and tryptophan components to expanded niche-width. Surface thermodynamic analysis was conducted to simulate the reciprocal and reversible interaction on algal-bacterial and phycosphere-microplastic interface, revealing the enhancement of transition to stable and irreversible aggregation for functional microbiota colonization and microplastics capture. Furthermore, pangenomic analysis disclosed the genes related to the chemotaxis and the proposed microplastics biodegradation pathway in enriched algal-bacterial microbiome, orchestrating the evidence for common synthetic polymer particles and ultimately to confirm the effectiveness and potential. The present study emphasizes the necessity for future endeavors aimed at fully leveraging the potential of algal-bacterial mutualistic systems within sustainable bioremediation strategies targeting the eradication of microplastic waste.},
}

@article {pmid39028839,
year = {2024},
author = {Chien, H and Kuo, TY and Yao, CH and Su, YR and Chang, YT and Guo, ZL and Chang, KC and Hsieh, YH and Yang, SY},
title = {Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiae381},
pmid = {39028839},
issn = {1532-2548},
abstract = {The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, the NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive calcium and calmodulin-dependent kinase (CCaMK) via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscule size. BCP1, SbtM1, and WRI5a, whose expression associated with NF-YC3 levels, might be downstream of NF-YC3. NF-YC3 interacted with NF-YB3a, NF-YB5c, or NF-YB3b, in yeast (Saccharomyces cerevisiae) and in planta, and interacted with NF-YA3a in yeast. Spatial expression of three NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Simultaneous knockdown of three NF-YBs, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be an important downstream gene of the common symbiosis signaling pathway.},
}

@article {pmid39027904,
year = {2024},
author = {Li, Y and Zhang, B and Jiang, L and Cheng, T and Cheng, H and Qian, P},
title = {Gut microbiota plays pivotal roles in benign and malignant hematopoiesis.},
journal = {Blood science (Baltimore, Md.)},
volume = {6},
number = {4},
pages = {e00200},
pmid = {39027904},
issn = {2543-6368},
abstract = {Accumulated evidence emerges that dynamic changes in human gut microbiota and microbial metabolites can alter the ecological balance of symbiotic hosts. The gut microbiota plays a role in various diseases through different mechanisms. More and more attention has been paid to the effects that human microbiota extends beyond the gut. This review summarized the current understanding of the roles that gut microbiota plays in hematopoietic regulation and the occurrence and development of benign and malignant hematologic diseases. The progress of the application of microbiota in treatment was discussed in order to provide new insights into clinical diagnosis and treatment in the future.},
}

@article {pmid39027456,
year = {2024},
author = {Sorrentino, GP and Guimaraes, R and Cornelio, A and Zanoletti, A and Valentim, B and Bontempi, E},
title = {Mitigating CO2 emissions through an industrial symbiosis approach: Leveraging cork ash carbonation.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e32893},
pmid = {39027456},
issn = {2405-8440},
abstract = {This study explores for the first time the potential use of carbonation as a method for managing cork ash, a byproduct of biomass waste incineration. Additionally, the cork ash was combined with fly ash from municipal solid waste incineration to leverage the carbonation reaction's ability to stabilize heavy metals. The findings suggest that subjecting biomass ash to carbonation can lead to the formation of mineral carbonates, effectively capturing CO2 and reducing its release into the atmosphere. The combination of various alkaline wastes and the stabilization of leachable heavy metals through carbonation reactions also opens opportunities for synergies between different industrial sectors. Finally, the study proposes a route for the obtained materials valorisation via 'end of waste': the reuse of the resulting materials as substitutes for natural resources, particularly in applications like building materials and polymer composites, can further enhance carbon dioxide savings.},
}

@article {pmid39026795,
year = {2024},
author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC},
title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.23.576914},
pmid = {39026795},
issn = {2692-8205},
abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.},
}

@article {pmid39025984,
year = {2024},
author = {Sikorskaya, TV and Ermolenko, EV and Ginanova, TT and Boroda, AV and Efimova, KV and Bogdanov, M},
title = {Membrane vectorial lipidomic features of coral host cells' plasma membrane and lipid profiles of their endosymbionts Cladocopium.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {878},
pmid = {39025984},
issn = {2399-3642},
support = {R01GM121493-6//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {Animals ; *Anthozoa/metabolism/physiology/microbiology ; *Symbiosis ; *Cell Membrane/metabolism ; *Lipidomics ; *Dinoflagellida/metabolism/physiology ; Membrane Lipids/metabolism ; },
abstract = {The symbiotic relationships between coral animal host and autotrophic dinoflagellates are based on the mutual exchange and tight control of nutritional inputs supporting successful growth. The corals Sinularia heterospiculata and Acropora aspera were cultivated using a flow-through circulation system supplying seawater during cold and warm seasons of the year, then sorted into host cells and symbionts and subjected to phylogenetic, morphological, and advanced lipid analyses. Here we show, that the lipidomes of the dinoflagellates Cladocopium C1/C3 and acroporide-specific Cladocopium hosted by the corals, are determined by lipidomic features of different thermosensitivity and unique betaine- and phospholipid molecular species. Phosphatidylserines and ceramiaminoethylphosphonates are not detected in the symbionts and predominantly localized on the inner leaflet of the S. heterospiculata host plasma membrane. The transmembrane distribution of phosphatidylethanolamines of S. heterospiculata host changes during different seasons of the year, possibly contributing to mutualistic nutritional exchange across this membrane complex to provide the host with a secure adaptive mechanism and ecological benefits.},
}

Animals
*Anthozoa/metabolism/physiology/microbiology
*Symbiosis
*Cell Membrane/metabolism
*Lipidomics
*Dinoflagellida/metabolism/physiology
Membrane Lipids/metabolism

@article {pmid39025305,
year = {2024},
author = {Ahmad, A and Amin, KA and Ashraf, SS},
title = {Biological effects of culture medium on Tetraselmis chuii and Dunaliella tertiolecta: Implications for emerging pollutants degradation.},
journal = {Chemosphere},
volume = {363},
number = {},
pages = {142868},
doi = {10.1016/j.chemosphere.2024.142868},
pmid = {39025305},
issn = {1879-1298},
abstract = {In this study, laboratory-scale cultivation of T. chuii and D. tertiolecta was conducted using Conway, F/2, and TMRL media to evaluate their biochemical composition and economic costs. The highest cell density (30.36 × 10[6] cells/mL) and dry weight (0.65 g/L) for T. chuii were achieved with Conway medium. This medium also produced biomass with maximum lipid content (25.65%), proteins (27.84%), and total carbohydrates (8.45%) compared with F/2 and TMRL media. D. tertiolecta reached a maximum cell density of 17.50 × 10[6] cells/mL in F/2 medium, which was notably lower than that of T. chuii. Furthermore, the media cost varied from US$0.23 to US$0.74 for each 1 L of media, primarily due to the addition of Na3PO4, KNO3, and cyanocobalamin. Thus, biomass production rates varied between US$38.81 and US$128.80 per kg on a dry weight basis. These findings comprehensively compare laboratory conditions and the costs associated with biomass production in different media. Additionally, this study explored the potential of T. chuii and D. tertiolecta strains, as well as their consortia with bacteria, for the degradation of various emerging pollutants (EPs), including caffeine, salicylic acid, DEET, imidacloprid, MBT, cimetidine, venlafaxine, methylparaben, thiabendazole, and paracetamol. Both microalgal strains demonstrated effective degradation of EPs, with enhanced degradation observed in microalgae-bacterial consortia. These results suggest that the symbiotic relationship between microalgae and bacteria can be harnessed for the bioremediation of EPs, thereby offering valuable insights into the environmental applications of microalgal cultivation.},
}

@article {pmid39024451,
year = {2024},
author = {Wilde, J and Slack, E and Foster, KR},
title = {Host control of the microbiome: Mechanisms, evolution, and disease.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6706},
pages = {eadi3338},
doi = {10.1126/science.adi3338},
pmid = {39024451},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Biological Evolution ; Homeostasis ; *Host Microbial Interactions/genetics ; *Microbiota/genetics ; *Selection, Genetic ; *Symbiosis ; },
abstract = {Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.},
}

Animals
Humans
*Biological Evolution
Homeostasis
*Host Microbial Interactions/genetics
*Microbiota/genetics
*Selection, Genetic
*Symbiosis

@article {pmid39024445,
year = {2024},
author = {Soyano, T and Akamatsu, A and Takeda, N and Watahiki, MK and Goh, T and Okuma, N and Suganuma, N and Kojima, M and Takebayashi, Y and Sakakibara, H and Nakajima, K and Kawaguchi, M},
title = {Periodic cytokinin responses in Lotus japonicus rhizobium infection and nodule development.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6706},
pages = {288-294},
doi = {10.1126/science.adk5589},
pmid = {39024445},
issn = {1095-9203},
mesh = {*Cytokinins/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Lotus/genetics/growth & development/metabolism ; Mutation ; *Plant Root Nodulation ; *Root Nodules, Plant/growth & development/microbiology ; Signal Transduction ; *Symbiosis ; *Mesorhizobium/genetics/physiology ; *Host Microbial Interactions ; },
abstract = {Host plants benefit from legume root nodule symbiosis with nitrogen-fixing bacteria under nitrogen-limiting conditions. In this interaction, the hosts must regulate nodule numbers and distribution patterns to control the degree of symbiosis and maintain root growth functions. The host response to symbiotic bacteria occurs discontinuously but repeatedly at the region behind the tip of the growing roots. Here, live-imaging and transcriptome analyses revealed oscillating host gene expression with approximately 6-hour intervals upon bacterial inoculation. Cytokinin response also exhibited a similar oscillation pattern. Cytokinin signaling is crucial to maintaining the periodicity, as observed in cytokinin receptor mutants displaying altered infection foci distribution. This periodic regulation influences the size of the root region responsive to bacteria, as well as the nodulation process progression.},
}

*Cytokinins/metabolism
Gene Expression Profiling
*Gene Expression Regulation, Plant
*Lotus/genetics/growth & development/metabolism
Mutation
*Plant Root Nodulation
*Root Nodules, Plant/growth & development/microbiology
Signal Transduction
*Symbiosis
*Mesorhizobium/genetics/physiology
*Host Microbial Interactions

@article {pmid39023266,
year = {2024},
author = {Lyu, D and Duan, Q and Duan, R and Qin, S and Zheng, X and Lu, X and Bukai, A and Zhang, P and Han, H and He, Z and Sha, H and Wu, D and Xiao, M and Jing, H and Wang, X},
title = {Symbiosis of a lytic bacteriophage and Yersinia pestis and characteristics of plague in Marmota himalayana.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0099524},
doi = {10.1128/aem.00995-24},
pmid = {39023266},
issn = {1098-5336},
abstract = {Surveillance for animal plague was conducted in the Marmota himalayana plague focus of the Qinghai-Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of Yersinia pestis isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (P < 0.05). Twenty-one Y. pestis-specific phages were isolated, among which one Y. pestis lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with Y. pestis. Microscopy revealed the coexistence of lysed and non-lysed colonies of Y. pestis AKS2022HT87. Genome-wide analysis showed that certain strains of the Y. pestis AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and Y. pestis observed in vitro was highlighted in this study, laying the basis for further exploring the relationship between Y. pestis and its bacteriophages.IMPORTANCEBacteriophages and host bacteria commonly coexist in vivo or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging in vitro due to limited medium nutrients. In this work, the natural symbiosis between Yersinia pestis and specific phages has been discovered in a Marmota himalayana specimen. Epidemiological analysis presented the characteristics of the Y. pestis and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the Y. pestis and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.},
}

@article {pmid39023256,
year = {2024},
author = {Graebin, A and Amaral, KD and Lira, DC and Collares, LJ and Bernardes, RC and Turchen, LM and Della-Lucia, TMC and Guedes, RNC},
title = {Nasturtium leaf compounds, diphenyl disulfide and lyral, against Atta sexdens (Hymenoptera: Formicidae) and their symbiotic fungi.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toae154},
pmid = {39023256},
issn = {1938-291X},
abstract = {Social insect pests, particularly leaf-cutting ants, present a considerable challenge in terms of control. Leaf-cutting ants are significant agricultural, forestry, and pasture pests, and understanding their behavior and defense mechanisms is essential for managing their colonies effectively. While toxic ant baits are a primary control method, the limited availability of effective insecticides and concerns over their hazardous nature has spurred the search for alternative solutions, particularly natural compounds, which aligns with the goals of forest certification groups. In the light of previous evidence demonstrating the efficacy of nasturtium leaves (Tropaeolum majus L. (Brassicales: Tropaeolaceae)) in suppressing leaf-cutting ant colonies, this study investigates 2 active components of nasturtium leaf extracts: diphenyl disulfide and lyral. We tested their impact on Atta sexdens (L.) (Hymenoptera: Formicidae), the most prevalent leaf-cutter ant species in Brazil, and their symbiotic fungus, Leucoagaricus gongylophorus (Möller) Singer (Agaricales: Agaricaceae). We conducted experiments with increasing concentrations of diphenyl disulfide and lyral, assessing their effects on the symbiotic fungus and on forager workers and gardeners of A. sexdens colonies. Our findings revealed no fungicidal activity, and ant mortality was minimal in both topical and ingestion bioassays with the exception of gardeners topically exposed to diphenyl sulfide. Furthermore, the compounds did not affect leaf ingestion, but diphenyl disulfide did increase interactions among foragers. These results suggest that neither diphenyl disulfide nor lyral are the primary contributors to the suppression of leaf-cutting ant colonies by nasturtium leaves. However, they may enhance the formicidal activity of other compounds present in nasturtium leaves.},
}

@article {pmid39022956,
year = {2024},
author = {He, LL and Liu, YR and Liu, WR and Wang, JF and Yu, YH and Qian, FY},
title = {[Rapid Start-up of Continuous Autotrophic Nitrogen Removal Reactor by Hybrid-inoculating PN and PN/A Granular Sludges].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {7},
pages = {4082-4089},
doi = {10.13227/j.hjkx.202308176},
pmid = {39022956},
issn = {0250-3301},
mesh = {*Bioreactors/microbiology ; *Nitrogen/metabolism/isolation & purification ; *Waste Disposal, Fluid/methods ; *Sewage/microbiology ; *Autotrophic Processes ; Bacteria/metabolism/isolation & purification/genetics ; Wastewater/chemistry ; Ammonium Compounds/metabolism/isolation & purification ; },
abstract = {The rapid cultivation of partial nitritation/ANAMMOX （PN/A） granular sludge in a continuous-flow mode is one of the key technologies for efficient biological nitrogen removal in domestic wastewater treatment. Compared with that in PN/A granular sludge, PN granular sludge demonstrates a shorter incubation period and suitability for batch culture. It is also a good carrier for enriching ANAMMOX （AMX） bacteria. In this study, we established a continuous-flow autotrophic nitrogen removal process in three continuously stirred tank reactors （CSTR） （R1-R3） by hybrid-inoculating PN/A and PN granular sludge at the mass ratios of 3∶1, 1∶1, and 1∶3, respectively. By implementing high ammonium nitrogen loading and short hydraulic retention time, continuous autotrophic nitrogen removal processes were successfully started up in the three CSTRs. The results showed that compared with that of R1 and R2, R3 had a longer start-up time but a similar steady-state nitrogen removal performance. The total nitrogen removal load of R3 could be more than 2.6 kg·（m[3]·d）[-1]. Intriguingly, the inoculated PN granular sludge served as a precursor for PN/A granular sludge cultivation. This approach facilitated the enrichment of anaerobic ammonia-oxidizing bacteria （AMX） by introducing abundant ammonium-oxidizing bacteria （AOB） and nitrite nitrogen substrates into the CSTR. According to the results of high-throughput sequencing, the microbial abundance and diversity of the mature granules in R1-R3 were significantly higher than those of the inoculation sludge. AOB （genus Nitrosomonas）, AMX （genera Candidatus Kuenenia and Candidatus Brocadia）, and symbiotic heterotrophs, such as Chloroflexi, Bacteroidetes, and Chlorobi, drove the autotrophic nitrogen removal process and maintained the stability of the granular structure. In summary, a novel start-up strategy of hybrid-inoculating granular sludge was provided for a continuous-flow autotrophic nitrogen removal in engineering application.},
}

*Bioreactors/microbiology
*Nitrogen/metabolism/isolation & purification
*Waste Disposal, Fluid/methods
*Sewage/microbiology
*Autotrophic Processes
Bacteria/metabolism/isolation & purification/genetics
Wastewater/chemistry
Ammonium Compounds/metabolism/isolation & purification

@article {pmid39021943,
year = {2024},
author = {Idowu, AP and Yamamoto, K and Koizumi, T and Matsutani, M and Takada, K and Shiwa, Y and Asfaw, A and Matsumoto, R and Ouyabe, M and Pachakkil, B and Kikuno, H and Shiwachi, H},
title = {Changes in the rhizosphere and root-associated bacteria community of white Guinea yam (Dioscorea rotundata Poir.) impacted by genotype and nitrogen fertilization.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e33169},
pmid = {39021943},
issn = {2405-8440},
abstract = {The bacterial diversity and composition of water yam (Dioscorea alata L. cv. A-19), which can grow without chemical fertilization, have recently been characterized with no significant differences compared with the use of chemical fertilization. However, the diversity and community structure of bacteria associated with the white Guinea yam (Dioscorea rotundata), the most cultivated and economically important yam in West Africa, have not yet been investigated. This study characterized the bacterial diversity and composition associated with bulk soil, rhizosphere, and plant roots in six white Guinea yam genotypes (S004, S020, S032, S042, S058, and S074) in field experiments in Ibadan, Nigeria under N-based chemical fertilizer application. The largest diversity of bacteria was found in the bulk soil, followed by the rhizosphere and roots. Based on the alpha diversity analysis, the bacterial diversity in both S020 and S042 increased with fertilizer application among the bulk soil samples. S058 grown under no-fertilizer conditions had the highest bacterial diversity among the rhizosphere samples. Beta diversity analysis highlighted the significant difference in the composition of bacteria associated with the genotypes and fertilizer treatments, and S032 had a unique bacterial composition compared to the other genotypes. The dominant phylum across all sample types was Proteobacteria. Actinobacteriota was the dominant phylum among bulk soil samples. At the genus level, Bacillus was the most abundant bacterial genus across both the control and treated samples. Pseudomonas was predominant across all rhizosphere samples. Chryseobacterium, Sphingobium, Delftia and Klebsiella associated with the rhizosphere were shown the altered relative abundance between the control and treated samples depending on genotypes. A genus related to symbiotic nitrogen-fixing bacteria, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, showed higher relative abundance among all root samples, indicating that it is a core bacterial genus. Furthermore, the field application of chemical fertilizer had a significant impact on the relative abundances of two genera related to symbiotic nitrogen-fixers, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Bradyrhizobium in the rhizosphere and root. These results suggest that N-based chemical fertilizers and plant genotypes would influence the compositional arrangement of associated bacterial communities, including symbiotic nitrogen-fixing bacteria.},
}

@article {pmid39021621,
year = {2024},
author = {Aihetanmu, S and Liang, Z and Zhang, X and Luo, B and Zhang, H and Huang, J and Tian, F and Sun, H and Ni, Y},
title = {Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1399743},
pmid = {39021621},
issn = {1664-302X},
abstract = {Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.},
}

@article {pmid39021394,
year = {2024},
author = {Nakhforoosh, A and Hallin, E and Karunakaran, C and Korbas, M and Stobbs, J and Kochian, L},
title = {Visualization and Quantitative Evaluation of Functional Structures of Soybean Root Nodules via Synchrotron X-ray Imaging.},
journal = {Plant phenomics (Washington, D.C.)},
volume = {6},
number = {},
pages = {0203},
pmid = {39021394},
issn = {2643-6515},
abstract = {The efficiency of N2-fixation in legume-rhizobia symbiosis is a function of root nodule activity. Nodules consist of 2 functionally important tissues: (a) a central infected zone (CIZ), colonized by rhizobia bacteria, which serves as the site of N2-fixation, and (b) vascular bundles (VBs), serving as conduits for the transport of water, nutrients, and fixed nitrogen compounds between the nodules and plant. A quantitative evaluation of these tissues is essential to unravel their functional importance in N2-fixation. Employing synchrotron-based x-ray microcomputed tomography (SR-μCT) at submicron resolutions, we obtained high-quality tomograms of fresh soybean root nodules in a non-invasive manner. A semi-automated segmentation algorithm was employed to generate 3-dimensional (3D) models of the internal root nodule structure of the CIZ and VBs, and their volumes were quantified based on the reconstructed 3D structures. Furthermore, synchrotron x-ray fluorescence imaging revealed a distinctive localization of Fe within CIZ tissue and Zn within VBs, allowing for their visualization in 2 dimensions. This study represents a pioneer application of the SR-μCT technique for volumetric quantification of CIZ and VB tissues in fresh, intact soybean root nodules. The proposed methods enable the exploitation of root nodule's anatomical features as novel traits in breeding, aiming to enhance N2-fixation through improved root nodule activity.},
}

@article {pmid39021362,
year = {2024},
author = {Li, C and Han, Y and Zou, X and Zhang, X and Ran, Q and Dong, C},
title = {A systematic discussion and comparison of the construction methods of synthetic microbial community.},
journal = {Synthetic and systems biotechnology},
volume = {9},
number = {4},
pages = {775-783},
pmid = {39021362},
issn = {2405-805X},
abstract = {Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.},
}

@article {pmid39021277,
year = {2024},
author = {Shah, I and Sarim, KM and Sikka, VK and Dudeja, SS and Gahlot, DK},
title = {Developed Rhizobium Strains Enhance Soil Fertility and Yield of Legume Crops in Haryana, India.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400327},
doi = {10.1002/jobm.202400327},
pmid = {39021277},
issn = {1521-4028},
support = {//This research was funded by the Indian Council of Agricultural Research (ICAR) under the Emeritus Scientist Scheme (Agri.Edu/9/19/2016/ES/HRD-5298 C(b) MBBB-10-ICAR). Open Access funding was provided by Umeå University, Sweden./ ; },
abstract = {Three strains of Gram-negative bacterium, Rhizobium, were developed by gamma (γ)-irradiation random mutagenesis. The developed strains were evaluated for their augmented features for symbiotic association, nitrogen fixation, and crop yield of three leguminous plants-chickpea, field-pea, and lentil-in agricultural fields of the northern Indian state of Haryana. Crops treated with developed mutants exhibited significant improvement in plant features and the yield of crops when compared to the control-uninoculated crops and crops grown with indigenous or commercial crop-specific strains of Rhizobium. This improvement was attributed to generated mutants, MbPrRz1 (on chickpea), MbPrRz2 (on lentil), and MbPrRz3 (on field-pea). Additionally, the cocultured symbiotic response of MbPrRz1 and MbPrRz2 mutants was found to be more pronounced on all three crops. The statistical analysis using Pearson's correlation coefficients revealed that nodulation and plant biomass were the most related parameters of crop yield. Among the effectiveness of developed mutants, MbPrRz1 yielded the best results for all three tested crops. Moreover, the developed mutants enhanced macro- and micronutrients of the experimental fields when compared with fields harboring the indigenous rhizobial community. These developed mutants were further genetically characterized, predominantly expressing nitrogen fixation marker, nifH, and appeared to belong to Mesorhizobium ciceri (MbPrRz1) and Rhizobium leguminosarum (both MbPrRz2 and MbPrRz3). In summary, this study highlights the potential of developed Rhizobium mutants as effective biofertilizers for sustainable agriculture, showcasing their ability to enhance symbiotic relationships, crop yield, and soil fertility.},
}

@article {pmid39020961,
year = {2024},
author = {Adhikari, SK},
title = {Quasi-one- and quasi-two-dimensional symbiotic solitons bound by dipolar interaction.},
journal = {Physical review. E},
volume = {109},
number = {6-1},
pages = {064206},
doi = {10.1103/PhysRevE.109.064206},
pmid = {39020961},
issn = {2470-0053},
abstract = {We study the formation of quasi-one- (quasi-1D) and quasi-two-dimensional (quasi-2D) symbiotic solitons bound by an interspecies dipolar interaction in a binary dipolar Bose-Einstein condensate. These binary solitons have a repulsive intraspecies contact interaction stronger than the intraspecies dipolar interaction, so that they can not be bound in isolation in the absence of an interspecies dipolar interaction. These symbiotic solitons are bound in the presence of an interspecies dipolar interaction and zero interspecies contact interaction. The quasi-1D solitons are free to move along the polarization z direction of the dipolar atoms, whereas the quasi-2D solitons move in the x-z plane. To illustrate these, we consider a ^{164}E
r-^{166}E
r mixture with scattering lengths a(^{164}E
r)=81a_{0}
and a(^{166}E
r)=68a_{0}
and with dipolar lengths a_{dd}(
^{164}E
r)≈a_{dd}(
^{166}E
r)≈65a_{0},
where a_{0}
is the Bohr radius. In each of the two components a>a_{dd},
which stops the binding of solitons in each component in isolation, whereas a binary quasi-1D or a quasi-2D ^{164}E
r-^{166}E
r soliton is bound in the presence of an interspecies dipolar interaction. The stationary states were obtained by imaginary-time propagation of the underlying mean-field model; dynamical stability of the solitons was established by real-time propagation over a long period of time.},
}

@article {pmid39020319,
year = {2024},
author = {Fang, CC and Liu, YH and Huang, SH},
title = {The symbiotic experiences of residents with and without dementia co-living in Taiwan's long-term care facilities: a phenomenological study.},
journal = {BMC geriatrics},
volume = {24},
number = {1},
pages = {611},
pmid = {39020319},
issn = {1471-2318},
mesh = {Humans ; Taiwan/epidemiology ; *Dementia/psychology/epidemiology ; Male ; *Long-Term Care/psychology ; Female ; Aged ; Cross-Sectional Studies ; Aged, 80 and over ; Nursing Homes ; Middle Aged ; },
abstract = {BACKGROUND: In Taiwan, residents with and without dementia mostly co-live in long-term care facilities. The behavioral and psychiatric symptoms of dementia residents often pose challenges for others living together. This study explored the symbiotic experiences of residents without dementia co-living with those with dementia in long-term care facilities in Taiwan to present their experiences of living together.

METHODS: This was a cross-sectional descriptive study with a phenomenological design. Semi-structured face-to-face interviews were conducted with 30 residents without dementia from three long-term care institutions in Taiwan. Colaizzi's data processing steps were used for analysis.

RESULTS: The analysis of interview transcripts revealed that the experiences of residents who lived with those with dementia were that of a "symbiosis." Three core themes were found: "the impact of co-living," "facing difficulties and coping," and "companionship and reciprocity." This study showed that residents without dementia may be affected by the behavioral and psychiatric symptoms of residents with dementia when co-living in long-term care facilities. However, there are also positive and mutually beneficial interactions between them. By helping people with dementia in their daily lives, residents without dementia feel happy and accomplished and their self-worth is enhanced. Furthermore, residents with dementia have more opportunities for social engagement and co-living interactions.

CONCLUSION: These results can guide long-term care facilities without special care dementia units to support residents without dementia, reduce the interference of the behavioral and psychiatric symptoms of residents with dementia, and promote mutual benefits. However, these findings warrant further investigation.},
}

Humans
Taiwan/epidemiology
*Dementia/psychology/epidemiology
Male
*Long-Term Care/psychology
Female
Aged
Cross-Sectional Studies
Aged, 80 and over
Nursing Homes
Middle Aged

@article {pmid39018775,
year = {2024},
author = {Ren, J and Cui, Z and Wang, Y and Ning, Q and Gao, Y},
title = {Transcriptomic insights into the potential impacts of flavonoids and nodule-specific cysteine-rich peptides on nitrogen fixation in Vicia villosa and Vicia sativa.},
journal = {Plant physiology and biochemistry : PPB},
volume = {214},
number = {},
pages = {108936},
doi = {10.1016/j.plaphy.2024.108936},
pmid = {39018775},
issn = {1873-2690},
abstract = {Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes.},
}

@article {pmid39018459,
year = {2024},
author = {Kho, K and Cheng, T and Buddelmeijer, N and Boneca, IG},
title = {When the Host Encounters the Cell Wall and Vice Versa.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-094053},
pmid = {39018459},
issn = {1545-3251},
abstract = {Peptidoglycan (PGN) and associated surface structures such as secondary polymers and capsules have a central role in the physiology of bacteria. The exoskeletal PGN heteropolymer is the major determinant of cell shape and allows bacteria to withstand cytoplasmic turgor pressure. Thus, its assembly, expansion, and remodeling during cell growth and division need to be highly regulated to avoid compromising cell survival. Similarly, regulation of the assembly impacts bacterial cell shape; distinct shapes enhance fitness in different ecological niches, such as the host. Because bacterial cell wall components, in particular PGN, are exposed to the environment and unique to bacteria, these have been coopted during evolution by eukaryotes to detect bacteria. Furthermore, the essential role of the cell wall in bacterial survival has made PGN an important signaling molecule in the dialog between host and microbes and a target of many host responses. Millions of years of coevolution have resulted in a pivotal role for PGN fragments in shaping host physiology and in establishing a long-lasting symbiosis between microbes and the host. Thus, perturbations of this dialog can lead to pathologies such as chronic inflammatory diseases. Similarly, pathogens have devised sophisticated strategies to manipulate the system to enhance their survival and growth.},
}

@article {pmid39018411,
year = {2024},
author = {Shoham, S and Keren, R and Lavy, A and Polishchuk, I and Pokroy, B and Ilan, M},
title = {Out of the blue: Hyperaccumulation of molybdenum in the Indo-Pacific sponge Theonella conica.},
journal = {Science advances},
volume = {10},
number = {29},
pages = {eadn3923},
pmid = {39018411},
issn = {2375-2548},
mesh = {*Molybdenum/metabolism ; Animals ; *Porifera/metabolism ; Indian Ocean ; Pacific Ocean ; },
abstract = {Molybdenum is an essential micronutrient, but because of its toxicity at high concentrations, its accumulation in living organisms has not been widely demonstrated. In this study, we report that the marine sponge Theonella conica accumulates exceptionally high levels of molybdenum (46,793 micrograms per gram of dry weight) in a wide geographic distribution from the northern Red Sea to the reefs of Zanzibar, Indian Ocean. The element is found in various sponge body fractions and correlates to selenium. We further investigated the microbial composition of the sponge and compared it to its more studied congener, Theonella swinhoei. Our analysis illuminates the symbiotic bacterium Entotheonella sp. and its role in molybdenum accumulation. Through microscopic and analytical methods, we provide evidence of intracellular spheres within Entotheonella sp. that exhibit high molybdenum content, further unraveling the intricate mechanisms behind molybdenum accumulation in this sponge species and its significance in the broader context of molybdenum biogeochemical cycling.},
}

*Molybdenum/metabolism
Animals
*Porifera/metabolism
Indian Ocean
Pacific Ocean

@article {pmid39016123,
year = {2024},
author = {Scott, TJ and Queller, DC and Strassmann, JE},
title = {Complex third-party effects in the Dictyostelium-Paraburkholderia symbiosis: prey bacteria that are eaten, carried or left behind.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2027},
pages = {20241111},
pmid = {39016123},
issn = {1471-2954},
support = {DEB-1753743, IOS-1656756, DEB-2237266//National Science Foundation/ ; },
mesh = {*Dictyostelium/physiology/microbiology ; *Symbiosis ; Burkholderiaceae/physiology ; },
abstract = {Symbiotic interactions may change depending on third parties like predators or prey. Third-party interactions with prey bacteria are central to the symbiosis between Dictyostelium discoideum social amoeba hosts and Paraburkholderia bacterial symbionts. Symbiosis with inedible Paraburkholderia allows host D. discoideum to carry prey bacteria through the dispersal stage where hosts aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey are scarce but harms hosts when prey bacteria are plentiful, possibly because hosts leave some prey bacteria behind while carrying. Thus, understanding benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried and left behind by infected hosts. We found that Paraburkholderia infection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was too small to explain why infected hosts produced fewer spores than uninfected hosts. Turning to carried bacteria, we found that hosts carry prey bacteria more often after developing in prey-poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multi-faceted interactions with third parties shape the evolution of symbioses in complex ways.},
}

*Dictyostelium/physiology/microbiology
*Symbiosis
Burkholderiaceae/physiology

@article {pmid39014094,
year = {2024},
author = {Duan, S and Feng, G and Limpens, E and Bonfante, P and Xie, X and Zhang, L},
title = {Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39014094},
issn = {1740-1534},
abstract = {The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.},
}

@article {pmid39013300,
year = {2024},
author = {Tewari, N and Dey, P},
title = {Navigating commensal dysbiosis: Gastrointestinal host-pathogen interplay orchestrating opportunistic infections.},
journal = {Microbiological research},
volume = {286},
number = {},
pages = {127832},
doi = {10.1016/j.micres.2024.127832},
pmid = {39013300},
issn = {1618-0623},
abstract = {The gut commensals, which are usually symbiotic or non-harmful bacteria that live in the gastrointestinal tract, have a positive impact on the health of the host. This review, however, specifically discuss distinct conditions where commensals aid in the development of pathogenic opportunistic infections. We discuss that the categorization of gut bacteria as either pathogens or non-pathogens depends on certain circumstances, which are significantly affected by the tissue microenvironment and the dynamic host-microbe interaction. Under favorable circumstances, commensals have the ability to transform into opportunistic pathobionts by undergoing overgrowth. These conditions include changes in the host's physiology, simultaneous infection with other pathogens, effective utilization of nutrients, interactions between different species of bacteria, the formation of protective biofilms, genetic mutations that enhance pathogenicity, acquisition of genes associated with virulence, and the ability to avoid the host's immune response. These processes allow commensals to both initiate infections themselves and aid other pathogens in populating the host. This review highlights the need of having a detailed and sophisticated knowledge of the two-sided nature of gut commensals. Although commensals mostly promote health, they may also become harmful in certain changes in the environment or the body's functioning. This highlights the need of acknowledging the intricate equilibrium in interactions between hosts and microbes, which is crucial for preserving intestinal homeostasis and averting diseases. Finally, we also emphasize the further need of research to better understand and anticipate the behavior of gut commensals in different situations, since they play a crucial and varied role in human health and disease.},
}

@article {pmid39013023,
year = {2024},
author = {Ni, H and Hou, X and Tian, S and Liu, C and Zhang, G and Peng, Y and Chen, L and Wang, J and Chen, Q and Xin, D},
title = {Insights into the Early Steps of the Symbiotic Interaction between Soybean (Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c02312},
pmid = {39013023},
issn = {1520-5118},
abstract = {Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.},
}

@article {pmid39012965,
year = {2024},
author = {Drapek, C and Rizza, A and Mohd-Radzman, NA and Schiessl, K and Dos Santos Barbosa, F and Wen, J and Oldroyd, GED and Jones, AM},
title = {GA dynamics governing nodulation revealed using GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula lateral organs.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae201},
pmid = {39012965},
issn = {1532-298X},
abstract = {During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically-encoded second generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions and maintaining accumulation in the mature nodule meristem. We show, through mis-expression of GA catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.},
}

@article {pmid39012828,
year = {2024},
author = {Sgroi, M and Hoey, D and Medina Jimenez, K and Bowden, SL and Hope, M and Wallington, EJ and Schornack, S and Bravo, A and Paszkowski, U},
title = {The receptor-like kinase ARK controls symbiotic balance across land plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {30},
pages = {e2318982121},
doi = {10.1073/pnas.2318982121},
pmid = {39012828},
issn = {1091-6490},
support = {BB/M011194/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/P003176/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/P003419/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V002295/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Symbiosis/genetics ; *Mycorrhizae/physiology/genetics ; *Gene Expression Regulation, Plant ; *Embryophyta/genetics ; *Plant Proteins/genetics/metabolism ; Marchantia/genetics/microbiology ; Phylogeny ; },
abstract = {The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.},
}

*Symbiosis/genetics
*Mycorrhizae/physiology/genetics
*Gene Expression Regulation, Plant
*Embryophyta/genetics
*Plant Proteins/genetics/metabolism
Marchantia/genetics/microbiology
Phylogeny

@article {pmid39012539,
year = {2024},
author = {Zeb, A and Khan, Y and He, H and Zhang, D and Shen, S},
title = {Molecular identification of Halomonas AZ07 and its multifunctional enzymatic activities to degrade Pyropia yezoensis under high-temperature condition.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {816},
pmid = {39012539},
issn = {1573-4978},
mesh = {*Halomonas/genetics/metabolism/enzymology ; *RNA, Ribosomal, 16S/genetics ; Hot Temperature ; Rhodophyta/genetics ; Phylogeny ; Microbiota/genetics ; Seaweed/metabolism/microbiology ; Temperature ; Edible Seaweeds ; Porphyra ; },
abstract = {BACKGROUND: Pyropia yezoensis a commercially important red seaweed species, is susceptible to various microorganisms infections, among which bacterial infections are the most prominent ones. Pyropia yezoensis is often affected by harmful bacterial communities under high temperatures that can lead to its degradation and economic losses. The current study aimed to explore Pyropia yezoensis-associated microbiota and further identify potential isolates, which can degrade Pyropia yezoensis under high-temperature conditions.

METHODS AND RESULTS: The 16S rRNA gene sequencing was used to identify the agarolytic bacterial species. The results showed that Chromohalobacter sp. strain AZ6, Pseudoalteromonas sp. strain AZ, Psychrobacter sp. strain AZ3, Vibrio sp. strain AZ, and Halomonas sp. strain AZ07 exhibited algicidal properties as these strains were more abundant at high temperature (25 °C). Among the five isolated strains, the potential isolate Halomonas sp. strain AZ07 showed high production of agarolytic enzymes, including lipase, protease, cellulase, and amylase. This study confirmed that the isolated strain could produce these four different enzymes. The strain Halomonas AZ07 was co-treated with Pyropia yezoensis cells under two different temperature environments, including 13 °C and 25 °C. The degradation of Pyropia yezoensis occurred at the optimum temperature of 25 °C and effectively degraded their cell wall, proteins, lipids, and carbohydrates.

CONCLUSION: The successful cultivation of Pyropia yezoensis in coastal farm environments is dependent on specific temperature and environmental factors, and lower temperatures have been observed to be particularly beneficial for the survival and growth of Pyropia yezoensis. The temperature below 13 °C was confirmed to be the best niche for the symbiotic relationship of microbiota associated with Pyropia yezoensis for its growth, development, and production.},
}

*Halomonas/genetics/metabolism/enzymology
*RNA, Ribosomal, 16S/genetics
Hot Temperature
Rhodophyta/genetics
Phylogeny
Microbiota/genetics
Seaweed/metabolism/microbiology
Temperature
Edible Seaweeds
Porphyra

@article {pmid39012472,
year = {2024},
author = {Huang, J and Xu, J and Zhang, H and Liu, J and He, C},
title = {Combined Effects of Tetracycline and Copper Ion on Microorganisms During the Biological Phosphorus Removal.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {113},
number = {2},
pages = {13},
pmid = {39012472},
issn = {1432-0800},
support = {2023t07010002//The Anhui Provincial Key Research and Development Project/ ; 2022AH010019//The Natural Science Project for Colleges of Anhui Province/ ; (DTR2023029)//The project for cultivating academic (or disciplinary) leaders/ ; (52300022)//The national Natural Science Foundation of China/ ; },
mesh = {*Phosphorus ; *Tetracycline/pharmacology ; *Copper/toxicity ; *Water Pollutants, Chemical ; *Wastewater/chemistry/microbiology ; Waste Disposal, Fluid/methods ; Bacteria/drug effects/metabolism ; },
abstract = {Tetracycline and copper ion are common pollutants in wastewater, and the effects of mixed pollutants on microorganisms in wastewater biological treatment have been less studied. In order to reveal the effects of mixed pollutants of tetracycline and copper ion on the microorganisms during the biological phosphorus removal, three ratios of tetracycline and copper ions were designed by the direct equipartition ray method. The relative abundance and diversity of microbial community were investigated, and the microbial interactions were revealed through microbiological methods. The results demonstrated that, for three different ratios, the inhibitory effect of specific phosphorus uptake rate became more significant with the increase of the tetracycline-copper ions concentration and the reaction time. The microbial community decreased with the increase of the proportion of tetracycline in different ratios. The relative abundance of Acinetobacter decreased with the increase of the proportion of tetracycline, while the relative abundance of Ca.Competibacter was higher under the conditions of low mixtures concentrations. Positive interactions and symbiotic relationships among microorganisms were predominant for three different ratios. However, as the proportion of tetracycline increased, the community structure of microorganisms shifted from phosphate-accumulating organisms to glycogen accumulating organisms and denitrifying bacteria. This study can provide a reference for the effect of mixed pollutants on microorganisms and the mechanism of wastewater treatment.},
}

*Phosphorus
*Tetracycline/pharmacology
*Copper/toxicity
*Water Pollutants, Chemical
*Wastewater/chemistry/microbiology
Waste Disposal, Fluid/methods
Bacteria/drug effects/metabolism

@article {pmid39011306,
year = {2024},
author = {Del-Canto, A and Sanz-Saez, A and Heath, KD and Grillo, MA and Heras, J and Lacuesta, M},
title = {Conventional management has a greater negative impact on Phaseolus vulgaris L. rhizobia diversity and abundance than water scarcity.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1408125},
pmid = {39011306},
issn = {1664-462X},
abstract = {INTRODUCTION: Drought is one of the biggest problems for crop production and also affects the survival and persistence of soil rhizobia, which limits the establishment of efficient symbiosis and endangers the productivity of legumes, the main source of plant protein worldwide.

AIM: Since the biodiversity can be altered by several factors including abiotic stresses or cultural practices, the objective of this research was to evaluate the effect of water availability, plant genotype and agricultural management on the presence, nodulation capacity and genotypic diversity of rhizobia.

METHOD: A field experiment was conducted with twelve common bean genotypes under irrigation and rain-fed conditions, both in conventional and organic management. Estimation of the number of viable rhizobia present in soils was performed before the crop establishment, whereas the crop yield, nodule number and the strain diversity of bacteria present in nodules were determined at postharvest.

RESULTS: Rainfed conditions reduced the number of nodules and of isolated bacteria and their genetic diversity, although to a lesser extent than the agrochemical inputs related to conventional management. In addition, the effect of water scarcity on the conventional management soil was greater than observed under organic conditions.

CONCLUSIONS: The preservation of diversity will be a key factor to maintain crop production in the future, as problems caused by drought will be exacerbated by climate change and organic management can help to maintain the biodiversity of soil microbiota, a fundamental aspect for soil health and quality.},
}

@article {pmid39010998,
year = {2024},
author = {Dagar, J and Maurya, S and Antil, S and Abraham, JS and Somasundaram, S and Lal, R and Makhija, S and Toteja, R},
title = {Symbionts of Ciliates and Ciliates as Symbionts.},
journal = {Indian journal of microbiology},
volume = {64},
number = {2},
pages = {304-317},
pmid = {39010998},
issn = {0046-8991},
abstract = {Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.},
}

@article {pmid39010986,
year = {2024},
author = {Shinde, DB and Mahore, JG and Giram, PS and Singh, SL and Sharda, A and Choyan, D and Musale, S},
title = {Microbiota of Saliva: A Non-invasive Diagnostic Tool.},
journal = {Indian journal of microbiology},
volume = {64},
number = {2},
pages = {328-342},
pmid = {39010986},
issn = {0046-8991},
abstract = {Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.},
}

@article {pmid39010257,
year = {2024},
author = {Zhao, B and Li, C and Hu, T and Gao, Y and Fan, L and Zhang, X},
title = {Robust {Pb10}-
Cluster-Based Metal-Organic Framework for Capturing and Converting CO2 into Cyclic Carbonates under Mild Conditions.},
journal = {Inorganic chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.inorgchem.4c02093},
pmid = {39010257},
issn = {1520-510X},
abstract = {Developing a highly active catalyst that can efficiently capture and convert carbon dioxide (CO2) into high-value-added energy materials remains a severe challenge, which inspires us to explore effective metal-organic frameworks (MOFs) with high chemical stability and high-density active sites. Herein, we report a robust 3D lead(II)-organic framework of {(Me2NH2)2[Pb5(PTTPA)2(H2O)3]·2DMF·3H2O}n
(NUC-111) with unreported [Pb10(COO)22(H2O)6] clusters (abbreviated as {Pb10})
as nodes (H6PTTPA = 4,4',4″-(pyridine-2,4,6-triyl)triisophthalic acid). After thermal activation, NUC-111a is functionalized by the multifarious symbiotic acid-base active sites of open Pb[2+] sites and uncoordinated pyridine groups on the inner surface of the void volume. Gas adsorption tests confirm that NUC-111a displays a higher separation performance for mixed gases of f CO2 and CH4 with the selectivity of CO2/CH4 at 273 K and 101 kPa being 31 (1:99, v/v), 23 (15:85, v/v), and 8 (50:50, v/v), respectively. When the temperature rises to 298 K, the selectivity of CO2/CH4 at 101 kPa is 26 (1:99, v/v), 22 (15:85, v/v), and 11 (50:50, v/v). Moreover, activated NUC-111a exhibited excellent catalytic performance, stability, and recyclability for the cycloaddition of CO2 with epoxides under mild conditions. Hence, this work provides valuable insight into designing MOFs with multifunctionality for CO2 capture, separation, and conversion.},
}

@article {pmid39009513,
year = {2024},
author = {Shoji, F},
title = {[The Role of Gut Microbiota in Lung Carcinogenesis and Cancer Immunotherapy].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {51},
number = {6},
pages = {597-602},
pmid = {39009513},
issn = {0385-0684},
mesh = {Humans ; *Lung Neoplasms/immunology/therapy/microbiology ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; Animals ; Carcinogenesis/immunology ; Dysbiosis/immunology/therapy/microbiology ; },
abstract = {In recent years, the human microbiota, especially the gut microbiota, has been attracting attention in various fields, and it is one of the topics in the field of oncology. The human microbiota is known to act directly or indirectly on host immunity, and the gut and lung microbiota influence each other through the"gut-lung axis". It has been suggested that dysbiosis, a condition in which the symbiosis of the human microbiota is disrupted, induces lung inflammation and various respiratory diseases, and is also implicated in the immune microenvironment of lung cancer. It is also widely known that the gut microbiota modulates the efficacy of cancer immunotherapy, a major pillar of lung cancer treatment, and many clinical trials targeting the gut microbiota, such as fecal microbiome transplantation and biotics intervention, are currently being conducted. In the future, research on lung carcinogenesis mechanisms and lung cancer treatment focusing on the human microbiota will become increasingly active.},
}

Humans
*Lung Neoplasms/immunology/therapy/microbiology
*Gastrointestinal Microbiome/immunology
*Immunotherapy/methods
Animals
Carcinogenesis/immunology
Dysbiosis/immunology/therapy/microbiology

@article {pmid39008621,
year = {2024},
author = {Bonetto, M and Cofré, N and Calvo, F and Silvente, S},
title = {Effects of arbuscular mycorrhizal fungi in the rhizosphere of two olive (Olea europaea) varieties Arbequina and Barnea under water deficit conditions.},
journal = {Functional plant biology : FPB},
volume = {51},
number = {},
pages = {},
doi = {10.1071/FP24108},
pmid = {39008621},
issn = {1445-4416},
mesh = {*Olea/microbiology ; *Mycorrhizae/physiology ; *Rhizosphere ; *Water/metabolism ; Droughts ; Proline/metabolism ; Symbiosis ; Plant Stomata/physiology ; Plant Stems/microbiology ; Plant Roots/microbiology ; Malondialdehyde/metabolism ; },
abstract = {One strategy to improve olive (Olea europaea) tree drought tolerance is through the symbiosis of arbuscular mycorrhizal fungi (AMF), which helps alleviate water deficit through a combination of morphophysiological effects. Cuttings of olive varieties Arbequina (A) and Barnea (B) were grown with (+AMF) or without (-AMF) inoculum in the olive grove rhizosphere soil. One year after establishment, pots were exposed to four different water regimes: (1) control (100% of crop evapotranspiration); (2) short-period drought (20days); (3) long-period drought (25days); and (4) rewatering (R). To evaluate the influence of AMF on tolerance to water stress, stem water potential, stomatal conductance and the biomarkers for water deficit malondialdehyde, proline, soluble sugars, phenols, and flavonoids were evaluated at the end of the irrigation regimes. Stem water potential showed higher values in A(+) and B(+) in all water conditions, and the opposite was true for stomatal conductance. For proline and soluble sugars, the stem water potential trend is repeated with some exceptions. AMF inoculum spore communities from A(+ and -) and B(+ and -) were characterised at the morphospecies level in terms of richness and abundance. Certain morphospecies were identified as potential drought indicators. These results highlight that the benefits of symbiotic relationships between olive and native AMF can help to mitigate the effects of abiotic stress in soils affected by drought.},
}

*Olea/microbiology
*Mycorrhizae/physiology
*Rhizosphere
*Water/metabolism
Droughts
Proline/metabolism
Symbiosis
Plant Stomata/physiology
Plant Stems/microbiology
Plant Roots/microbiology
Malondialdehyde/metabolism

@article {pmid39007421,
year = {2024},
author = {Sin, WC and Liu, J and Zhong, JY and Lam, HM and Lim, BL},
title = {Comparative proteomics analysis of root and nodule mitochondria of soybean.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15026},
pmid = {39007421},
issn = {1365-3040},
support = {//Innovation and Technology Fund/ ; AoE/M-403/16//Hong Kong Research Grants Council/ ; },
abstract = {Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy-intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data-independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain-associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.},
}

@article {pmid39005400,
year = {2024},
author = {Zhang, X and Luo, Z and Marand, AP and Yan, H and Jang, H and Bang, S and Mendieta, JP and Minow, MAA and Schmitz, RJ},
title = {A spatially resolved multiomic single-cell atlas of soybean development.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.03.601616},
pmid = {39005400},
issn = {2692-8205},
abstract = {Cis -regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.},
}

@article {pmid39005142,
year = {2024},
author = {Cabuslay, C and Wertz, JT and Béchade, B and Hu, Y and Braganza, S and Freeman, D and Pradhan, S and Mukhanova, M and Powell, S and Moreau, C and Russell, JA},
title = {Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17454},
doi = {10.1111/mec.17454},
pmid = {39005142},
issn = {1365-294X},
support = {1442144//Division of Environmental Biology/ ; 1442156//Division of Environmental Biology/ ; 1442256//Division of Environmental Biology/ ; 1900357//Division of Environmental Biology/ ; 2041772//National Science Foundation Graduate Research Fellowship Program/ ; },
abstract = {The evolution of animals and their gut symbionts is a complex phenomenon, obscured by lability and diversity. In social organisms, transmission of symbionts among relatives may yield systems with more stable associations. Here, we study the history of a social insect symbiosis involving cephalotine ants and their extracellular gut bacteria, which come predominantly from host-specialized lineages. We perform multi-locus phylogenetics for symbionts from nine bacterial orders, and map prior amplicon sequence data to lineage-assigned symbiont genomes, studying distributions of rigorously defined symbionts across 20 host species. Based on monophyly and additional hypothesis testing, we estimate that these specialized gut bacteria belong to 18 distinct lineages, of which 15 have been successfully isolated and cultured. Several symbiont lineages showed evidence for domestication events that occurred later in cephalotine evolutionary history, and only one lineage was ubiquitously detected in all 20 host species and 48 colonies sampled with amplicon 16S rRNA sequencing. We found evidence for phylogenetically constrained distributions in four symbionts, suggesting historical or genetic impacts on community composition. Two lineages showed evidence for frequent intra-lineage co-infections, highlighting the potential for niche divergence after initial domestication. Nearly all symbionts showed evidence for occasional host switching, but four may, more often, co-diversify with their hosts. Through our further assessment of symbiont localization and genomic functional profiles, we demonstrate distinct niches for symbionts with shared evolutionary histories, prompting further questions on the forces underlying the evolution of hosts and their gut microbiomes.},
}

@article {pmid39003318,
year = {2024},
author = {Kodama, Y and Kitatani, A and Morita, Y},
title = {Characterization of Crystals in Ciliate Paramecium bursaria Harboring Endosymbiotic Chlorella variabilis.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {265},
pmid = {39003318},
issn = {1432-0991},
support = {(Grant-in-Aid for Scientific Research (C) (Grant No. 20K06768))//Japan Society for the Promotion of Science/ ; (Grant-in-Aid for Scientific Research (B) (Grant No. 23H02529))//Japan Society for the Promotion of Science/ ; },
mesh = {*Chlorella/chemistry/metabolism ; *Paramecium/metabolism ; *Symbiosis ; Crystallization ; Cytoplasm/chemistry ; },
abstract = {Protists, including ciliates retain crystals in their cytoplasm. However, their functions and properties remain unclear. To comparatively analyze the crystals of Paramecium bursaria, a ciliate, associated with and without the endosymbiotic Chlorella variabilis, we investigated the isolated crystals using a light microscope and analyzed their length and solubility. A negligible number of crystals was found in P. bursaria cells harboring symbiotic algae. The average crystal length in alga-free and algae-reduced cells was about 6.8 μm and 14.4 μm, respectively. The crystals of alga-free cells were spherical, whereas those of algae-reduced cells were angular in shape. The crystals of alga-free cells immediately dissolved in acids and bases, but not in water or organic solvents, and were stable at - 20 °C for more than 3 weeks. This study, for the first time, reveals that the characteristics of crystals present in the cytoplasm of P. bursaria vary greatly depending on the amount of symbiotic algae.},
}

*Chlorella/chemistry/metabolism
*Paramecium/metabolism
*Symbiosis
Crystallization
Cytoplasm/chemistry

@article {pmid39003030,
year = {2024},
author = {Park, Y and Kim, W and Cha, Y and Kim, M and Park, W},
title = {Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa.},
journal = {Harmful algae},
volume = {137},
number = {},
pages = {102680},
doi = {10.1016/j.hal.2024.102680},
pmid = {39003030},
issn = {1878-1470},
mesh = {*Hydrogen Peroxide/metabolism ; *Microcystis/genetics ; *Catalase/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {High levels of environmental H2O2 represent a threat to many freshwater bacterial species, including toxic-bloom-forming Microcystis aeruginosa, particularly under high-intensity light conditions. The highest extracellular catalase activity-possessing Pseudoduganella aquatica HC52 was chosen among 36 culturable symbiotic isolates from the phycosphere in freshly collected M. aeruginosa cells. A zymogram for catalase activity revealed the presence of only one extracellular catalase despite the four putative catalase genes (katA1, katA2, katE, and srpA) identified in the newly sequenced genome (∼6.8 Mb) of P. aquatica HC52. Analysis of secreted catalase using liquid chromatography-tandem mass spectrometry was identified as KatA1, which lacks a typical signal peptide, although the underlying mechanism for its secretion is unknown. The expression of secreted KatA1 appeared to be induced in the presence of H2O2. Proteomic analysis also confirmed the presence of KatA1 inside the outer membrane vesicles secreted by P. aquatica HC52 following exposure to H2O2. High light intensities (> 100 µmol m[-2] s[-1]) are known to kill catalase-less axenic M. aeruginosa cells, but the present study found that the presence of P. aquatica cells supported the growth of M. aeruginosa, while the extracellular catalases in supernatant or purified form also sustained the growth of M. aeruginosa under the same conditions. Our results suggest that the extracellular catalase secreted by P. aquatica HC52 enhances the tolerance of M. aeruginosa to H2O2, thus promoting the formation of M. aeruginosa blooms under high light intensities.},
}

*Hydrogen Peroxide/metabolism
*Microcystis/genetics
*Catalase/metabolism/genetics
*Bacterial Proteins/metabolism/genetics

@article {pmid39003022,
year = {2024},
author = {Li, R and Deng, Y and Shang, L and Liu, Y and Tao, Z and Chai, Z and Tang, YZ},
title = {Evidence for the production of asexual resting cysts in a free-living species of Symbiodiniaceae (Dinophyceae).},
journal = {Harmful algae},
volume = {137},
number = {},
pages = {102658},
doi = {10.1016/j.hal.2024.102658},
pmid = {39003022},
issn = {1878-1470},
mesh = {*Dinoflagellida/physiology/genetics/classification ; Reproduction, Asexual ; Geologic Sediments ; Phylogeny ; Coral Reefs ; },
abstract = {Coral reef ecosystems are the most productive and biodiverse marine ecosystems, with their productivity levels highly dependent on the symbiotic dinoflagellates belonging to the family Symbiodiniaceae. As a unique life history strategy, resting cyst production is of great significance in the ecology of many dinoflagellate species, those HABs-causing species in particular, however, there has been no confirmative evidence for the resting cyst production in any species of the family Symbiodiniaceae. Based on morphological and life history observations of cultures in the laboratory and morpho-molecular detections of cysts from the marine sediments via fluorescence in situ hybridization (FISH), cyst photography, and subsequent singe-cyst PCR sequencing, here we provide evidences for the asexual production of resting cysts by Effrenium voratum, the free-living, red tide-forming, and the type species of the genus Effrenium in Symbiodiniaceae. The evidences from the marine sediments were obtained through a sequential detections: Firstly, E. voratum amplicon sequence variants (ASVs) were detected in the cyst assemblages that were concentrated with the sodium polytungstate (SPT) method from the sediments collected from different regions of China Seas by high-throughput next generation sequencing (NGS); Secondly, the presence of E. voratum in the sediments was detected by PCR using the species-specific primers for the DNA directly extracted from sediment; Thirdly, E. voratum cysts were confirmed by a combined approach of FISH using the species-specific probes, light microscopic (LM) photography of the FISH-positive cysts, and a subsequent single-cyst PCR sequencing for the FISH-positive and photographed cysts. The evidences from the laboratory-reared clonal cultures of E. voratum include that: 1) numerous cysts formed in the two clonal cultures and exhibited a spherical shape, a smooth surface, absence of ornaments, and a large red accumulation body; 2) cysts could maintain morphologically intact for a storage of two weeks to six months at 4 °C in darkness and of which 76-92 % successfully germinated through an internal development processes within a time period of 3-21 days after being transferred back to the normal culturing conditions; 3) two or four germlings were released from each cyst through the cryptopylic archeopyle in all cysts with continuous observations of germination processes; and 4) while neither sexual mating of gametes nor planozygote (cells with two longitudinal flagella) were observed, the haploidy of cysts was proven with flow cytometric measurements and direct LM measurements of fluorescence from cells stained with either propidium iodide (PI) or DAPI, which together suggest that the cysts were formed asexually. All evidences led to a conclusion that E. voratum is capable of producing asexual resting cysts, although its sexuality cannot be completely excluded, which guarantees a more intensive investigation. This work fills a gap in the knowledge about the life cycle, particularly the potential of resting cyst formation, of the species in Symbiodiniaceae, a group of dinoflagellates having unique life forms and vital significance in the ecology of coral reefs, and may provide novel insights into understanding the recovery mechanisms of coral reefs destructed by the global climate change and suggest various forms of resting cysts in the cyst assemblages of dinoflagellates observed in the field sediments, including HABs-causing species.},
}

*Dinoflagellida/physiology/genetics/classification
Reproduction, Asexual
Geologic Sediments
Phylogeny
Coral Reefs

@article {pmid39002459,
year = {2024},
author = {Yu, Q and Chen, J and Ye, M and Wei, Y and Zhang, C and Ge, Y},
title = {N-acyl homoserine lactones (AHLs) enhanced removal of cadmium and other pollutants by algae-bacteria consortia.},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121792},
doi = {10.1016/j.jenvman.2024.121792},
pmid = {39002459},
issn = {1095-8630},
abstract = {Signal transduction is an important mode of algae-bacteria interaction, in which bacterial quorum sensing (QS) may affect microalgal growth and metabolism. Currently, little is known whether acyl homoserine lactones (AHLs) released by bacteria can affect the pollutant removal by algae-bacteria consortia (ABC). In this study, we constructed ABC using Chlorella vulgaris (Cv) with two AHLs-producing bacteria and investigated their performance in the removal of multiple pollutants, including chemical oxygen demand (COD), total nitrogen (TN), phosphorus (P), and cadmium (Cd). The AHLs-producing bacteria, namely Agrobacterium sp. (Ap) and Ensifer adherens (Ea), were capable of forming a symbiosis with C. vulgaris. Consortia of Cv and Ap with ratio of 2:1 (Cv2-Ap1) showed the optimal growth promotion and higher removal of Cd, COD, TN, and P compared to the C. vulgaris monoculture. Cv2-Ap1 ABC removed 36.1-47.5% of Cd, 94.5%-94.6% COD, 37.1%-56.0% TN, and 90.4%-93.5% P from the culture medium. In addition, increase of intracellular neutral lipids and extracellular protein, as well as the types of functional groups on cell surface contributed to Cd removal and tolerance in the Cv2-Ap1 ABC. Six AHLs were detected in the Cv2-Ap1 culture. Among these, 3OC8-HSL and 3OC12-HSL additions promoted the ABC growth and enhanced their Cd accumulation. These findings may contribute to further understanding of AHL-mediated communication between algae and bacteria and provide support bioremediation efforts of metal-containing wastewater.},
}

@article {pmid39006488,
year = {2020},
author = {Smith, J and Yeluripati, J and Smith, P and Nayak, DR},
title = {Potential yield challenges to scale-up of zero budget natural farming.},
journal = {Nature sustainability},
volume = {3},
number = {},
pages = {247-252},
pmid = {39006488},
issn = {2398-9629},
abstract = {Under current trends, 60% of India's population (>10% of people on Earth) will experience severe food deficiencies by 2050. Increased production is urgently needed, but high costs and volatile prices are driving farmers into debt. Zero budget natural farming (ZBNF) is a grassroots movement that aims to improve farm viability by reducing costs. In Andhra Pradesh alone, 523,000 farmers have converted 13% of productive agricultural area to ZBNF. However, sustainability of ZBNF is questioned because external nutrient inputs are limited, which could cause a crash in food production. Here, we show that ZBNF is likely to reduce soil degradation and could provide yield benefits for low-input farmers. Nitrogen fixation, either by free-living nitrogen fixers in soil or symbiotic nitrogen fixers in legumes, is likely to provide the major portion of nitrogen available to crops. However, even with maximum potential nitrogen fixation and release, only 52-80% of the national average nitrogen applied as fertilizer is expected to be supplied. Therefore, in higher-input systems, yield penalties are likely. Since biological fixation from the atmosphere is possible only with nitrogen, ZBNF could limit the supply of other nutrients. Further research is needed in higher-input systems to ensure that mass conversion to ZBNF does not limit India's capacity to feed itself.},
}

@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae129},
pmid = {39001714},
issn = {1751-7370},
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.},
}

@article {pmid39000497,
year = {2024},
author = {Kozlova, AP and Muntyan, VS and Vladimirova, ME and Saksaganskaia, AS and Kabilov, MR and Gorbunova, MK and Gorshkov, AN and Grudinin, MP and Simarov, BV and Roumiantseva, ML},
title = {Soil Giant Phage: Genome and Biological Characteristics of Sinorhizobium Jumbo Phage.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000497},
issn = {1422-0067},
support = {24-26-00274//RSF/ ; },
mesh = {*Genome, Viral ; *Bacteriophages/genetics/isolation & purification/classification/physiology ; *Phylogeny ; *Sinorhizobium/genetics/virology/physiology ; *Soil Microbiology ; Open Reading Frames ; },
abstract = {This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage-microbe interactions with nitrogen-fixing symbiotic microorganisms.},
}

*Genome, Viral
*Bacteriophages/genetics/isolation & purification/classification/physiology
*Phylogeny
*Sinorhizobium/genetics/virology/physiology
*Soil Microbiology
Open Reading Frames

@article {pmid39000176,
year = {2024},
author = {Daminova, AG and Leksin, IY and Khabibrakhmanova, VR and Gurjanov, OP and Galeeva, EI and Trifonova, TV and Khamatgalimov, AR and Beckett, RP and Minibayeva, FV},
title = {The Roles of the Anthraquinone Parietin in the Tolerance to Desiccation of the Lichen Xanthoria parietina: Physiology and Anatomy of the Pale and Bright-Orange Thalli.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000176},
issn = {1422-0067},
support = {23-14-00327//Russian Science Foundation/ ; },
mesh = {*Lichens/metabolism ; *Desiccation ; Emodin/analogs & derivatives/metabolism ; Anthraquinones/metabolism/chemistry ; },
abstract = {Lichens are symbiotic organisms that effectively survive in harsh environments, including arid regions. Maintaining viability with an almost complete loss of water and the rapid restoration of metabolism during rehydration distinguishes lichens from most eukaryotic organisms. The lichen Xanthoria parietina is known to have high stress tolerance, possessing diverse defense mechanisms, including the presence of the bright-orange pigment parietin. While several studies have demonstrated the photoprotective and antioxidant properties of this anthraquinone, the role of parietin in the tolerance of lichens to desiccation is not clear yet. Thalli, which are exposed to solar radiation and become bright orange, may require enhanced desiccation tolerance. Here, we showed differences in the anatomy of naturally pale and bright-orange thalli of X. parietina and visualized parietin crystals on the surface of the upper cortex. Parietin was extracted from bright-orange thalli by acetone rinsing and quantified using HPLC. Although acetone rinsing did not affect PSII activity, thalli without parietin had higher levels of lipid peroxidation and a lower membrane stability index in response to desiccation. Furthermore, highly pigmented thalli possess thicker cell walls and, according to thermogravimetric analysis, higher water-holding capacities than pale thalli. Thus, parietin may play a role in desiccation tolerance by stabilizing mycobiont membranes, providing an antioxidative defense, and changing the morphology of the upper cortex of X. parietina.},
}

*Lichens/metabolism
*Desiccation
Emodin/analogs & derivatives/metabolism
Anthraquinones/metabolism/chemistry

@article {pmid39000087,
year = {2024},
author = {Dong, M and He, J and Tang, X and Liu, S and Xing, J and Chen, X and Chen, L and Li, Y and Sun, H},
title = {Genome-Wide Identification of the Sulfate Transporters Gene Family in Blueberry (Vaccinium spp.) and Its Response to Ericoid Mycorrhizal Fungi.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000087},
issn = {1422-0067},
support = {20220508099RC//Jilin Province Science and Technology Department/ ; 2023C035-4//Jilin Province Development and Reform Commission/ ; 202205AF150029//Yunnan Province Science and Technology Talents and Platform Plan (Academician Expert Work-station)/ ; },
mesh = {*Mycorrhizae/genetics ; *Blueberry Plants/genetics/microbiology/metabolism ; *Gene Expression Regulation, Plant ; *Sulfate Transporters/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Phylogeny ; Multigene Family ; Sulfates/metabolism ; Symbiosis/genetics ; Genome, Plant ; },
abstract = {Sulfur metabolism plays a major role in plant growth and development, environmental adaptation, and material synthesis, and the sulfate transporters are the beginning of sulfur metabolism. We identified 37 potential VcSULTR genes in the blueberry genome, encoding peptides with 534 to 766 amino acids. The genes were grouped into four subfamilies in an evolutionary analysis. The 37 putative VcSULTR proteins ranged in size from 60.03 to 83.87 kDa. These proteins were predicted to be hydrophobic and mostly localize to the plasma membrane. The VcSULTR genes were distributed on 30 chromosomes; VcSULTR3;5b and VcSULTR3;5c were the only tandemly repeated genes. The VcSULTR promoters contained cis-acting elements related to the fungal symbiosis and stress responses. The transcript levels of the VcSULTRs differed among blueberry organs and changed in response to ericoid mycorrhizal fungi and sulfate treatments. A subcellular localization analysis showed that VcSULTR2;1c localized to, and functioned in, the plasma membrane and chloroplast. The virus-induced gene knock-down of VcSULTR2;1c resulted in a significantly decreased endogenous sulfate content, and an up-regulation of genes encoding key enzymes in sulfur metabolism (VcATPS2 and VcSiR1). These findings enhance our understanding of mycorrhizal-fungi-mediated sulfate transport in blueberry, and lay the foundation for further research on blueberry-mycorrhizal symbiosis.},
}

*Mycorrhizae/genetics
*Blueberry Plants/genetics/microbiology/metabolism
*Gene Expression Regulation, Plant
*Sulfate Transporters/genetics/metabolism
*Plant Proteins/genetics/metabolism
*Phylogeny
Multigene Family
Sulfates/metabolism
Symbiosis/genetics
Genome, Plant

@article {pmid38999609,
year = {2024},
author = {Markova, O and Garipova, S and Chistoedova, A and Matyunina, V and Lubyanova, A and Lastochkina, O and Garipov, A and Shpirnaya, I and Pusenkova, L},
title = {Predicting Field Effectiveness of Endophytic Bacillus subtilis Inoculants for Common Bean Using Morphometric and Biochemical Markers.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {13},
pages = {},
pmid = {38999609},
issn = {2223-7747},
support = {23-24-00602//Russian Science Foundation/ ; },
abstract = {According to four field experiments, after the inoculation of Phaseolus vulgaris L. cultivar Ufimskaya with the commercial strain Bacillus subtilis 26D and the promising strain B. subtilis 10-4, it was found that inoculation with B. subtilis 10-4 improved seed productivity (SP) by 31-41% per plant, but only in dry years. In contrast, all 4 years of inoculation with B. subtilis 26D were ineffective or neutral. It was intended to determine the growing and biochemical characteristics of inoculated 7-day-old plants, which correlate with the field SP of bacterial preparations. The SP of inoculated plants (average of 4 years) correlated with root length (0.83), MDA content (-0.98), and catalase (CAT) activity in roots (-0.96) of week-old seedlings. High correlation coefficients between the H2O2 content in the roots and SP (0.89 and 0.77), as well as between the H2O2 content in shoots and SP (0.98 and 0.56), were observed only in two dry years, when the influence of bacteria was detected. These physiological indicators were identified as potential markers for predicting the effectiveness of the endophytic symbiosis between bean plants and B. subtilis strains. The findings may be used to develop effective microbial-based, eco-friendly technologies for bean production.},
}

@article {pmid38998667,
year = {2024},
author = {Morales, D and de la Fuente-Nieto, L and Marco, P and Tejedor-Calvo, E},
title = {Elaboration and Characterization of Novel Kombucha Drinks Based on Truffles (Tuber melanosporum and Tuber aestivum) with Interesting Aromatic and Compositional Profiles.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {13},
pages = {},
pmid = {38998667},
issn = {2304-8158},
support = {"Mejora de la Eficiencia de la Producción y la Innovación Agroalimentaria de la Trufa en la Pro-vincia de Zaragoza"//Diputación Provincial de Zaragoza (DPZ)/ ; JDC2022-048252-I//MICIU/AEI/10.13039/501100011033 and European Union NextGenerationEU/PRTR/ ; },
abstract = {The organoleptic and bioactive properties of truffles place these fungi as interesting materials for use in the of design functional foods based on fruiting bodies outside commercial standards. Moreover, kombucha beverages have become more popular in the Western world, leading to novel drinks using alternative substrates instead of tea leaves. In this work, two truffle species (Tuber melanosporum, TMEL; Tuber aestivum, TAES) and three different symbiotic consortia of bacteria and yeasts (SCOBYs: SC1, SC2, and SC3) were tested. Fermentation (21 days) was monitored in terms of physicochemical (pH, viscosity), biochemical (total carbohydrates, alcohol, soluble proteins, phenolic compounds), and sensory attributes (volatile organic compounds, VOCs). The obtained pH ranges were adequate, alcohol levels were undetectable or very low, and sugar content was lower than in traditional kombuchas or other beverages. In most cases, the usual bottling time could be applied (7-10 days), although longer fermentations are recommended (14 days) to reach higher protein and phenolic compounds contents. Truffle kombuchas produced up to 51 volatile organic compounds (alcohols, acids, esters, ketones, and aldehydes, among others), with TMEL showing a more complex profile than TAES. During the first week, acidic compound production was observed, especially acetic acid. Similar behavior in the VOC profile was reported with different SCOBYs.},
}

@article {pmid38998500,
year = {2024},
author = {Wu, D and Hao, L and Liu, X and Li, X and Zhao, G},
title = {The Anti-Biofilm Properties of Phloretin and Its Analogs against Porphyromonas gingivalis and Its Complex Flora.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {13},
pages = {},
pmid = {38998500},
issn = {2304-8158},
support = {21978101//National Natural Science Foundation of China/ ; 22278159//National Natural Science Foundation of China/ ; },
abstract = {Porphyromonas gingivalis is crucial for the pathogenesis of periodontitis. This research investigated the effects of the fruit-derived flavonoid phloretin and its analogs on the growth of pure P. gingivalis and the flora of P. gingivalis mixed with the symbiotic oral pathogens Fusobacterium nucleatum and Streptococcus mitis. The results showed that the tested flavonoids had little effect on the biofilm amount of pure P. gingivalis, but significantly reduced the biofilm amount of mixed flora to 83.6~89.1%. Biofilm viability decreased to 86.7~92.8% in both the pure- and mixed-bacterial groups after naringenin and phloretin treatments. SEM showed that phloretin and phlorizin displayed a similar and remarkable destructive effect on P. gingivalis and the mixed biofilms. Transcriptome analysis confirmed that biofilm formation was inhibited by these flavonoids, and phloretin significantly regulated the transcription of quorum sensing. Phlorizin and phloretin reduced AI-2 activity to 45.9% and 55.4%, respectively, independent of the regulation of related gene transcription. This research marks the first finding that these flavonoids possess anti-biofilm properties against P. gingivalis and its intricate bacterial community, and the observed performance variations, driven by structural differences, underscore the existence of intriguing structure-activity relationships.},
}

@article {pmid38997041,
year = {2024},
author = {Xu, C and Zhao, X and Duan, H and Gu, W and Zhang, D and Wang, R and Lu, X},
title = {Synergistic enzymatic mechanism of lepidolite leaching enhanced by a mixture of Bacillus mucilaginosus and Bacillus circulans.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174711},
doi = {10.1016/j.scitotenv.2024.174711},
pmid = {38997041},
issn = {1879-1026},
abstract = {Numerous studies have demonstrated that the co-leaching of ores by different silicate bacteria significantly improves the performance of bioleaching systems. Nevertheless, the mechanism of different silicate bacteria synergistically or complementarily enhanced the leaching process of lithium-containing silicate remains unclear. This study discussed the leaching impact of the combined presence of two metabolically distinct silicate bacteria on lepidolite, with the aim of comprehending the synergistic effect resulting from the presence of Bacillus mucilaginosus and Bacillus circulans in the leaching process. The results indicated that the polysaccharides and proteins secreted by bacteria-containing functional groups such as -OH and -COOH, which played an important role in the complex decomposition of ores. Organic acids played the role of acid etching and complexation. Bacillus mucilaginosus and Bacillus circulans exhibited low individual leaching efficiency, primarily due to their weak organic acid secretion. Moreover, the prolific polysaccharide production by Bacillus mucilaginosus led to bacterial aggregation, diminishing contact capability with minerals. Bacillus circulans decomposed the excessive polysaccharides produced by Bacillus mucilaginosus through enzymatic hydrolysis in the co-bioleaching process, providing later nutrient supply for both strains. The symbiosis of the two strains enhanced the synthesis and metabolic capabilities of both strains, resulting in increased organic acid secretion. In addition, protein and humic acid production by Bacillus mucilaginosus intensified, collectively enhancing the leaching efficiency. These findings suggested that the primary metabolic products secreted by different bacterial strains in the leaching process differ. The improvement in bioleaching efficiency during co-leaching was attributed to their effective synergistic metabolism. This work contributes to the construction of an efficient engineering microbial community to improve the efficiency of silicate mineral leaching, and reveals the feasibility of microbial co-culture to improve bioleaching.},
}

@article {pmid38996605,
year = {2024},
author = {Qian, F and Liu, Y and He, L and Dong, Z and Chen, M and Liu, W},
title = {Metagenomic insights into microbial metabolic mechanisms of a combined solid-phase denitrification and anammox process for nitrogen removal in mainstream wastewater treatment.},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121797},
doi = {10.1016/j.jenvman.2024.121797},
pmid = {38996605},
issn = {1095-8630},
abstract = {To overcome the significant challenges associated with nitrite supply and nitrate residues in mainstream anaerobic ammonium oxidation (anammox)-based processes, this study developed a combined solid-phase denitrification (SPD) and anammox process for low-strength nitrogen removal without the addition of nitrite. The SPD step was performed in a packed-bed reactor containing poly-3-hydroxybutyrate-co-3-hyroxyvelate (PHBV) prior to employing the anammox granular sludge reactor in the continuous-flow mode. The removal efficiency of total inorganic nitrogen reached 95.7 ± 1.2% under a nitrogen loading rate of 0.18 ± 0.01 kg N·m[3]·d[-1], and it required 1.02 mol of nitrate to remove 1 mol of ammonium nitrogen. The PHBV particles not only served as biofilm carriers for the symbiosis of hydrolytic bacteria (HB) and denitrifying bacteria (DB), but also carbon sources that facilitated the coupling of partial denitrification and anammox in the granules. Metagenomic sequencing analysis indicated that Burkholderiales was the most abundant HB genus in SPD. The metabolic correlations between DB (Betaproteobacteria, Rhodocyclaceae, and Anaerolineae) and anammox bacteria (Candidatus Brocadiac and Kuenenia) in the granules were confirmed through microbial co-occurrence networks analysis and functional gene annotations. Additionally, the genes encoding nitrate reductase (Nap) and nitrite reductase (Nir) in DB primarily facilitated nitrate reduction, thereby supplying nitric oxide to anammox bacteria for subsequent nitrogen removal with hydrazine synthase (Hzs) and hydrazine dehydrogenase (Hdh). The findings provide insights into microbial metabolism within combined SPD and anammox processes, thus advancing the development of mainstream anammox-based processes in engineering applications.},
}

@article {pmid38995042,
year = {2024},
author = {da Silva, AF and Machado, LC and da Silva, LMI and Dezordi, FZ and Wallau, GL},
title = {Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0008324},
doi = {10.1128/jvi.00083-24},
pmid = {38995042},
issn = {1098-5514},
abstract = {UNLABELLED: Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments.

IMPORTANCE: Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.},
}

@article {pmid38995034,
year = {2024},
author = {Jandl, B and Dighe, S and Gasche, C and Makristathis, A and Muttenthaler, M},
title = {Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0013323},
doi = {10.1128/cmr.00133-23},
pmid = {38995034},
issn = {1098-6618},
abstract = {SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.},
}

@article {pmid38994934,
year = {2024},
author = {Almalla, A and Alzain, N and Elomaa, L and Richter, F and Scholz, J and Lindner, M and Siegmund, B and Weinhart, M},
title = {Hydrogel-Integrated Millifluidic Systems: Advancing the Fabrication of Mucus-Producing Human Intestinal Models.},
journal = {Cells},
volume = {13},
number = {13},
pages = {},
pmid = {38994934},
issn = {2073-4409},
support = {431232613//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) for CRC 1449/ ; 375876048//DFG CRC-TRR 241-B01 and Z02/ ; 50474582//DFG CRU 5023/ ; 372486779//DFG CRC 1340-B06/ ; },
mesh = {Humans ; *Mucus/metabolism ; *Hydrogels/chemistry ; Tissue Scaffolds/chemistry ; Intestinal Mucosa/metabolism ; HT29 Cells ; Models, Biological ; Stem Cells/metabolism/cytology ; Cell Differentiation/drug effects ; Printing, Three-Dimensional ; Tissue Engineering/methods ; },
abstract = {The luminal surface of the intestinal epithelium is protected by a vital mucus layer, which is essential for lubrication, hydration, and fostering symbiotic bacterial relationships. Replicating and studying this complex mucus structure in vitro presents considerable challenges. To address this, we developed a hydrogel-integrated millifluidic tissue chamber capable of applying precise apical shear stress to intestinal models cultured on flat or 3D structured hydrogel scaffolds with adjustable stiffness. The chamber is designed to accommodate nine hydrogel scaffolds, 3D-printed as flat disks with a storage modulus matching the physiological range of intestinal tissue stiffness (~3.7 kPa) from bioactive decellularized and methacrylated small intestinal submucosa (dSIS-MA). Computational fluid dynamics simulations were conducted to confirm a laminar flow profile for both flat and 3D villi-comprising scaffolds in the physiologically relevant regime. The system was initially validated with HT29-MTX seeded hydrogel scaffolds, demonstrating accelerated differentiation, increased mucus production, and enhanced 3D organization under shear stress. These characteristic intestinal tissue features are essential for advanced in vitro models as they critically contribute to a functional barrier. Subsequently, the chamber was challenged with human intestinal stem cells (ISCs) from the terminal ileum. Our findings indicate that biomimicking hydrogel scaffolds, in combination with physiological shear stress, promote multi-lineage differentiation, as evidenced by a gene and protein expression analysis of basic markers and the 3D structural organization of ISCs in the absence of chemical differentiation triggers. The quantitative analysis of the alkaline phosphatase (ALP) activity and secreted mucus demonstrates the functional differentiation of the cells into enterocyte and goblet cell lineages. The millifluidic system, which has been developed and optimized for performance and cost efficiency, enables the creation and modulation of advanced intestinal models under biomimicking conditions, including tunable matrix stiffness and varying fluid shear stresses. Moreover, the readily accessible and scalable mucus-producing cellular tissue models permit comprehensive mucus analysis and the investigation of pathogen interactions and penetration, thereby offering the potential to advance our understanding of intestinal mucus in health and disease.},
}

Humans
*Mucus/metabolism
*Hydrogels/chemistry
Tissue Scaffolds/chemistry
Intestinal Mucosa/metabolism
HT29 Cells
Models, Biological
Stem Cells/metabolism/cytology
Cell Differentiation/drug effects
Printing, Three-Dimensional
Tissue Engineering/methods

@article {pmid38994870,
year = {2024},
author = {Heidari, H and Lawrence, DA},
title = {An integrative exploration of environmental stressors on the microbiome-gut-brain axis and immune mechanisms promoting neurological disorders.},
journal = {Journal of toxicology and environmental health. Part B, Critical reviews},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/10937404.2024.2378406},
pmid = {38994870},
issn = {1521-6950},
abstract = {The microbiome-gut-brain axis is altered by environmental stressors such as heat, diet, and pollutants as well as microbes in the air, water, and soil. These stressors might alter the host's microbiome and symbiotic relationship by modifying the microbial composition or location. Compartmentalized mutualistic microbes promote the beneficial interactions in the host leading to circulating metabolites and hormones such as insulin and leptin that affect inter-organ functions. Inflammation and oxidative stress induced by environmental stressors may alter the composition, distribution, and activities of the microbes in the microbiomes such that the resultant metabolite and hormone changes are no longer beneficial. The microbiome-gut-brain axis and immune adverse changes that may accompany environmental stressors are reviewed for effects on innate and adaptive immune cells, which may make host immunity less responsive to pathogens and more reactive to self-antigens. Cardiovascular and fluid exchanges to organs might adversely alter organ functionality. Organs, especially the brain, need a consistent supply of nutrients and clearance of debris; disruption of these exchanges by stressors, and involvement of gut microbiome are discussed regarding neural dysfunctions with Alzheimer's disease, autistic spectrum disorders, viral infections, and autoimmune diseases. The focus of this review includes the manner in which environmental stressors may disrupt gut microbiota leading to adverse immune and hormonal influences on development of neuropathology related to hyperhomocysteinemia, inflammation, and oxidative stress, and how certain therapeutics may be beneficial. Strategies are explored to lessen detrimental effects of environmental stressors on central and peripheral health navigated toward (1) understanding neurological disorders and (2) promoting environmental and public health and well-being.},
}

@article {pmid38994865,
year = {2024},
author = {Zeghina, I and El Ouar, I and Tartouga, MA and Mokhtari, MB and Elieh-Ali-Komi, D and Gali, L and Bensouici, C},
title = {GC-MS Profiling and Pharmacological Potential of Physconia venusta (Ach.) Poelt.},
journal = {Turkish journal of pharmaceutical sciences},
volume = {21},
number = {3},
pages = {243-251},
doi = {10.4274/tjps.galenos.2023.91126},
pmid = {38994865},
issn = {2148-6247},
abstract = {OBJECTIVES: Lichens are complex symbiotic organisms that generate various bioactive compounds with significant therapeutic value. We investigated the chemical composition and bioactivity of the acetone extract of the Algerian lichen Physconia venusta (Ach.) poet.

MATERIALS AND METHODS: Phytochemical screening was performed using gas chromatography-mass spectrometry (GC-MS). The antibacterial activity was assessed against Escherichia coli, Pseudomonas aeruginosa, Salmonella enteritidis, Salmonella typhi, Staphylococcus aureus, Listeria monocytogenes, and Bacillus subtilis using an agar diffusion test with the determination of the minimal inhibition concentration (MIC), while the antioxidant activity was determined using different chemical methods (DPPH, ABTS, CUPRAC, reducing power, superoxide anion scavenging, β-carotene bleaching, and metal chelate). In addition, cytotoxic activity was tested using Artemia salina (Brine shrimp) bioassay.

RESULTS: The studied extract exhibited intense antibacterial activity against E. coli and S. aureus with inhibition diameters of 28 ± 0.01 and 22 ± 0.01 mm, respectively, with a MIC value of 6.25 mg/mL and a selectivity index of 2.8. The obtained extract showed different antioxidant trends depending on the selected assay. GC-MS analysis revealed many secondary metabolites.

CONCLUSION: P. venusta, a type of lichen, is a potential source of bioactive substances that could be used in pharmaceuticals.},
}

@article {pmid38992783,
year = {2024},
author = {Klimov, PB and Hubert, J and Erban, T and Alejandra Perotti, M and Braig, HR and Flynt, A and He, Q and Cui, Y},
title = {Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2024.07.001},
pmid = {38992783},
issn = {1879-0135},
abstract = {Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.},
}