@article {pmid38069003,
year = {2023},
author = {Wójcik, M and Koper, P and Żebracki, K and Marczak, M and Mazur, A},
title = {Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil.},
journal = {International journal of molecular sciences},
volume = {24},
number = {23},
pages = {},
doi = {10.3390/ijms242316679},
pmid = {38069003},
issn = {1422-0067},
support = {MN/2021/4; MN/2022/2//Institute of Biological Sciences of the Maria Curie-Skłodowska University, Lublin, Poland/ ; },
abstract = {The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.},
}

@article {pmid38068759,
year = {2023},
author = {Wu, W and Zhao, Z and Zhao, Z and Zhang, D and Zhang, Q and Zhang, J and Fang, Z and Bai, Y and Guo, X},
title = {Structure, Health Benefits, Mechanisms, and Gut Microbiota of Dendrobium officinale Polysaccharides: A Review.},
journal = {Nutrients},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/nu15234901},
pmid = {38068759},
issn = {2072-6643},
abstract = {Dendrobium officinale polysaccharides (DOPs) are important active polysaccharides found in Dendrobium officinale, which is commonly used as a conventional food or herbal medicine and is well known in China. DOPs can influence the composition of the gut microbiota and the degradation capacity of these symbiotic bacteria, which in turn may determine the efficacy of dietary interventions. However, the necessary analysis of the relationship between DOPs and the gut microbiota is lacking. In this review, we summarize the extraction, structure, health benefits, and related mechanisms of DOPs, construct the DOPs-host axis, and propose that DOPs are potential prebiotics, mainly composed of 1,4-β-D-mannose, 1,4-β-D-glucose, and O-acetate groups, which induce an increase in the abundance of gut microbiota such as Lactobacillus, Bifidobacterium, Akkermansia, Bacteroides, and Prevotella. In addition, we found that when exposed to DOPs with different structural properties, the gut microbiota may exhibit different diversity and composition and provide health benefits, such as metabolism regulations, inflammation modulation, immunity moderation, and cancer intervention. This may contribute to facilitating the development of functional foods and health products to improve human health.},
}

@article {pmid38067739,
year = {2023},
author = {Luo, J and Wang, Q and Zou, R and Wang, Y and Liu, F and Zheng, H and Du, S and Yuan, C},
title = {A Heart Image Segmentation Method Based on Position Attention Mechanism and Inverted Pyramid.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {23},
pages = {},
doi = {10.3390/s23239366},
pmid = {38067739},
issn = {1424-8220},
support = {2023I0025//External Collaboration Project of Science and Technology Department of Fujian Province/ ; 2021J011086, 2023J01964, 2023J01965, 2023J01966//Natural Science Foundation of Fujian Province/ ; },
abstract = {In the realm of modern medicine, medical imaging stands as an irreplaceable pillar for accurate diagnostics. The significance of precise segmentation in medical images cannot be overstated, especially considering the variability introduced by different practitioners. With the escalating volume of medical imaging data, the demand for automated and efficient segmentation methods has become imperative. This study introduces an innovative approach to heart image segmentation, embedding a multi-scale feature and attention mechanism within an inverted pyramid framework. Recognizing the intricacies of extracting contextual information from low-resolution medical images, our method adopts an inverted pyramid architecture. Through training with multi-scale images and integrating prediction outcomes, we enhance the network's contextual understanding. Acknowledging the consistent patterns in the relative positions of organs, we introduce an attention module enriched with positional encoding information. This module empowers the network to capture essential positional cues, thereby elevating segmentation accuracy. Our research resides at the intersection of medical imaging and sensor technology, emphasizing the foundational role of sensors in medical image analysis. The integration of sensor-generated data showcases the symbiotic relationship between sensor technology and advanced machine learning techniques. Evaluation on two heart datasets substantiates the superior performance of our approach. Metrics such as the Dice coefficient, Jaccard coefficient, recall, and F-measure demonstrate the method's efficacy compared to state-of-the-art techniques. In conclusion, our proposed heart image segmentation method addresses the challenges posed by diverse medical images, offering a promising solution for efficiently processing 2D/3D sensor data in contemporary medical imaging.},
}

@article {pmid38066630,
year = {2023},
author = {Baud, GLC and Prasad, A and Ellegaard, KM and Engel, P},
title = {Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {283},
pmid = {38066630},
issn = {1474-760X},
support = {714804//H2020 European Research Council/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 179487//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZSTZ0_189496//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {BACKGROUND: Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.

RESULTS: Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states.

CONCLUSIONS: Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.},
}

@article {pmid38065515,
year = {2023},
author = {Ren, M and Bai, Y and Su, J and Min, Y and Wang, Y and Ali, A},
title = {Immobilized bioreactor for enhanced ammonia, phosphorus, and phenol removal and effects of phenol on microbial communities, potential functions, and nitrogen metabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130161},
doi = {10.1016/j.biortech.2023.130161},
pmid = {38065515},
issn = {1873-2976},
abstract = {In the present study, an immobilized bioreactor was established to remove ammonia (NH4[+]-N), phosphate (PO4[3-]-P), and phenol using composite mycelium spheres (CMP) as the immobilization material in combination with Pseudomonas sp. Y1. Under optimal operating conditions, the bioreactor achieved 98.07, 91.71, and 92.57 % removal of NH4[+]-N, PO4[3-]-P, and phenol, respectively. The results showed that the bioreactor removed PO4[3-]-P by biomineralization and co-precipitation. Phenol removal relied on a Fenton-like reaction achieved by CMP-induced quinone redox cycling. High-throughput sequencing analysis and functional gene prediction indicated that Pseudomonas was the dominant genus and that the bioreactor had much potential for nitrogen removal, respectively. In addition, phenol affected the performance of functional genes and the associated enzymes, which influenced the nitrogen metabolism process in the bioreactor. This work serves as a guideline for the development of more stable and sustainable composite pollution removal technologies and fungal-bacterial symbiotic systems.},
}

@article {pmid38065507,
year = {2023},
author = {Geng, J and Yan, H and Liu, C and Han, T and Liu, S and Zhao, N and Wen, H and Yang, H and Zhou, P and Wang, G and Dodson, J},
title = {Reconstruction of ENSO variability using the standardized growth index of a Tridacna shell from Yongshu Reef, South China Sea.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {169118},
doi = {10.1016/j.scitotenv.2023.169118},
pmid = {38065507},
issn = {1879-1026},
abstract = {El Niño-Southern Oscillation (ENSO) is the strongest signal of global interannual climate anomaly and reconstructing past ENSO variations using high-resolution paleoclimate archives can improve our understanding of ENSO variability, as well as improve our ability to predict future climate changes. Here, a daily resolution standardized growth index (SGI) was established using a giant clam (Tridacna spp.) shell specimen MD2 (life span: 1994-2013 CE), collected from the Yongshu Reef, southern South China Sea (SCS). The cross-spectral and correlation analysis indicated that the SGI variation of MD2 was strongly influenced by ENSO variability on an interannual timescale. Tridacna spp. is in symbiosis with zooxanthellae, and its growth index is usually modulated by the photosynthetic efficiency of zooxanthellae. During the El Niño (La Niña) period, the convective anomalies stimulated in western Pacific would increase (decrease) the effective solar radiation on Yongshu Reef, and in turn influence the photosynthesis rate of zooxanthellae and enzyme activity for the calcification site and thus the SGI of giant clam MD2. The SGI can explain 54.7 % of ENSO variance, demonstrating the potential for Tridacna SGI in ENSO reconstruction. Compared with conventional ENSO reconstruction using high-resolution geochemical proxies, the method of giant clam SGI is rapid and economical.},
}

@article {pmid38064548,
year = {2023},
author = {Veličković, D and Zemaitis, KJ and Bhattacharjee, A and Anderton, CR},
title = {Mass spectrometry imaging of natural carbonyl products directly from agar-based microbial interactions using 4-APEBA derivatization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0080323},
doi = {10.1128/msystems.00803-23},
pmid = {38064548},
issn = {2379-5077},
abstract = {The metabolic profiles within microbial biofilms and interkingdom interactions are extremely complex and serve a variety of functions, which include promoting colonization, growth, and survival within competitive and symbiotic environments. However, measuring and differentiating many of these molecules, especially in an in situ fashion, remains a significant analytical challenge. We demonstrate a chemical derivatization strategy that enabled highly sensitive, multiplexed mass spectrometry imaging of over 300 metabolites from a model microbial co-culture. Notably, this approach afforded us to visualize over two dozen classes of ketone-, aldehyde-, and carboxyl-containing molecules, which were previously undetectable from colonies grown on agar. We also demonstrate that this chemical derivatization strategy can enable the discrimination of isobaric and isomeric metabolites without the need for orthogonal separation (e.g., online chromatography or ion mobility). We anticipate that this approach will further enhance our knowledge of metabolic regulation within microbiomes and microbial systems used in bioengineering applications.},
}

@article {pmid38064511,
year = {2023},
author = {Ramanan, D and Chowdhary, K and Candéias, SM and Sassone-Corsi, M and Gelineau, A and Mathis, D and Benoist, C},
title = {Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {50},
pages = {e2311566120},
doi = {10.1073/pnas.2311566120},
pmid = {38064511},
issn = {1091-6490},
support = {AI125603//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI150686//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; DRG 2300-17//Damon Runyon Cancer Research Foundation (DRCRF)/ ; T32GM007753//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM144273//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Foxp3[+] regulatory T cells (Tregs) in the colon are key to promoting peaceful coexistence with symbiotic microbes. Differentiated in either thymic or peripheral locations, and modulated by microbes and other cellular influencers, colonic Treg subsets have been identified through key transcription factors (TFs; Helios, Rorγ, Gata3, and cMaf), but their interrelationships are unclear. Applying a multimodal array of immunologic, genomic, and microbiological assays, we find more overlap than expected between populations. The key TFs (Rorγ, Helios, Gata3, and cMaf) play different roles, some essential for subset identity, others driving functional gene signatures. Functional divergence was clearest under challenge. Single-cell genomics revealed a spectrum of phenotypes between the Helios+ and Rorγ+ poles, different Treg-inducing bacteria inducing the same Treg phenotypes to varying degrees, not distinct populations. TCR repertoires in monocolonized mice revealed that Helios+ and Rorγ+ Tregs are related and cannot be uniquely equated to tTreg and pTreg. Comparison of spleen and colon repertoires revealed that 2 to 5% of clonotypes are shared between the locations. We propose that rather than the origin of their differentiation, tissue-specific cues dictate the spectrum of colonic Treg phenotypes.},
}

@article {pmid38064371,
year = {2023},
author = {Kawamura, K and Shoguchi, E and Nishitsuji, K and Sekida, S and Narisoko, H and Zhao, H and Shu, Y and Fu, P and Yamashita, H and Fujiwara, S and Satoh, N},
title = {In Vitro Phagocytosis of Different Dinoflagellate Species by Coral Cells.},
journal = {Zoological science},
volume = {40},
number = {6},
pages = {444-454},
doi = {10.2108/zs230045},
pmid = {38064371},
issn = {0289-0003},
abstract = {Coral-dinoflagellate symbiosis is a unique biological phenomenon, in which animal cells engulf single-celled photosynthetic algae and maintain them in their cytoplasm mutualistically. Studies are needed to reveal the complex mechanisms involved in symbiotic processes, but it is difficult to answer these questions using intact corals. To tackle these issues, our previous studies established an in vitro system of symbiosis between cells of the scleractinian coral Acropora tenuis and the dinoflagellate Breviolum minutum, and showed that corals direct phagocytosis, while algae are likely engulfed by coral cells passively. Several genera of the family Symbiodiniaceae can establish symbioses with corals, but the symbiotic ratio differs depending on the dinoflagellate clades involved. To understand possible causes of these differences, this study examined whether cultured coral cells show phagocytotic activity with various dinoflagellate strains similar to those shown by intact A. tenuis. We found that (a) A. tenuis larvae incorporate Symbiodinium and Breviolum, but not Cladocopium, and very few Effrenium, (b) cultured coral cells engulfed all four species but the ratio of engulfment was significantly higher with Symbiodinium and Breviolum than Cladocopium and Effrenium, (c) cultured coral cells also phagocytosed inorganic latex beads differently than they do dinoflagellates . It is likely that cultured coral cells preferentially phagocytose Symbiodinium and Breviolum, suggesting that specific molecular mechanisms involved in initiation of symbiosis should be investigated in the future.},
}

@article {pmid38063979,
year = {2023},
author = {de Oliveira, KB and Goes, AC and Silva, AD and Vieira, PC and Rodrigues, A},
title = {Fungal Cultivars of Higher Attine Ants Promote Escovopsis Chemotropism.},
journal = {Current microbiology},
volume = {81},
number = {1},
pages = {37},
pmid = {38063979},
issn = {1432-0991},
support = {2019/03746-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/12481-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2012/25299-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 305269/2018-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {In varied environments, microorganisms search for partners or nutritional resources using chemical signals. Microbes are drawn (chemotaxis) or grow directionally (chemotropism) towards the chemical source, enabling them to establish and maintain symbiosis. The hypocrealean fungi Escovopsis enhance their growth towards the basidiomycete fungus Leucoagaricus gongylophorus, which is cultivated by leaf-cutting attine ants for food. Although directional growth is well documented in this symbiosis, it is unclear whether non-volatile or volatile organic compounds participate in the interaction between cultivar and Escovopsis, and which specific chemical compounds might attract and induce chemotropism. In this study, we examined the growth responses of Escovopsis isolates to non-volatile and volatile organic compounds produced by fungal cultivars of higher attine ants. We also isolated and identified molecules released by the ant-cultivar and assessed the chemotropism of Escovopsis towards them. Our results indicate that the growth of Escovopsis is stimulated in the presence of both non-volatile and volatile compounds from fungal cultivars. We also identified three isomeric diketopiperazines molecules from crude extracts of the ant cultivar, suggesting that these might play a role in Escovopsis chemotropism. Our findings provide insights into the complex chemical interactions that govern the association between Escovopsis and fungal cultivars.},
}

@article {pmid38063396,
year = {2023},
author = {Makhulu, EE and Onchuru, TO and Gichuhi, J and Otieno, FG and Wairimu, AW and Muthoni, JN and Koekemoer, L and Herren, JK},
title = {Localization and tissue tropism of the symbiont Microsporidia MB in the germ line and somatic tissues of Anopheles arabiensis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0219223},
doi = {10.1128/mbio.02192-23},
pmid = {38063396},
issn = {2150-7511},
abstract = {Microsporidia MB is a symbiont with a strong malaria transmission-blocking phenotype in Anopheles arabiensis. It spreads in mosquito populations through mother-to-offspring and sexual transmission. The ability of Microsporidia MB to block Plasmodium transmission, together with its ability to spread within Anopheles populations and its avirulence to the host, makes it a very attractive candidate for developing a key strategy to stop malaria transmissions. Here, we report tissue tropism and localization patterns of Microsporidia MB, which are relevant to its transmission. We find that Microsporidia MB accumulates in Anopheles arabiensis tissues, linked to its sexual and vertical transmission. Its prevalence and intensity in the tissues over the mosquito life cycle suggest adaptation to maximize transmission and avirulence in Anopheles arabiensis. These findings provide the foundation for understanding the factors that may affect Microsporidia MB transmission efficiency. This will contribute to the development of strategies to maximize Microsporidia MB transmission to establish and sustain a high prevalence of the symbiont in Anopheles mosquito populations for malaria transmission blocking.},
}

@article {pmid38062903,
year = {2023},
author = {Zhang, K and Wang, H and Tappero, R and Bhatnagar, JM and Vilgalys, R and Barry, K and Keymanesh, K and Tejomurthula, S and Grigoriev, IV and Kew, WR and Eder, EK and Nicora, CD and Liao, HL},
title = {Ectomycorrhizal fungi enhance pine growth by stimulating iron-dependent mechanisms with trade-offs in symbiotic performance.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19449},
pmid = {38062903},
issn = {1469-8137},
support = {DE-SC0012704//Biological and Environmental Research/ ; DE-SC0020403//Biological and Environmental Research/ ; 2029168//Division of Integrative Organismal Systems/ ; 1026825//National Institute of Food and Agriculture/ ; 7001162//National Institute of Food and Agriculture/ ; },
abstract = {Iron (Fe) is crucial for metabolic functions of living organisms. Plants access occluded Fe through interactions with rhizosphere microorganisms and symbionts. Yet, the interplay between Fe addition and plant-mycorrhizal interactions, especially the molecular mechanisms underlying mycorrhiza-assisted Fe processing in plants, remains largely unexplored. We conducted mesocosms in Pinus plants inoculated with different ectomycorrhizal fungi (EMF) Suillus species under conditions with and without Fe coatings. Meta-transcriptomic, biogeochemical, and X-ray fluorescence imaging analyses were applied to investigate early-stage mycorrhizal roots. While Fe addition promoted Pinus growth, it concurrently reduced mycorrhiza formation rate, symbiosis-related metabolites in plant roots, and aboveground plant carbon and macronutrient content. This suggested potential trade-offs between Fe-enhanced plant growth and symbiotic performance. However, the extent of this trade-off may depend on interactions between host plants and EMF species. Interestingly, dual EMF species were more effective at facilitating plant Fe uptake by inducing diverse Fe-related functions than single-EMF species. This subsequently triggered various Fe-dependent physiological and biochemical processes in Pinus roots, significantly contributing to Pinus growth. However, this resulted in a greater carbon allocation to roots, relatively reducing the aboveground plant carbon content. Our study offers critical insights into how EMF communities rebalance benefits of Fe-induced effects on symbiotic partners.},
}

@article {pmid38062896,
year = {2023},
author = {Zhang, X and Chen, JX and Lian, WT and Zhou, HW and He, Y and Li, XX and Liao, H},
title = {Molecular module GmPTF1a/b-GmNPLa regulates rhizobia infection and nodule formation in soybean.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19462},
pmid = {38062896},
issn = {1469-8137},
support = {2021YFF1000500//National Key Research and Development Program/ ; 32072661//National Natural Science Foundation of China/ ; },
abstract = {Nodulation begins with the initiation of infection threads (ITs) in root hairs. Though mutual recognition and early symbiotic signaling cascades in legumes are well understood, molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis remain largely unexplored. We functionally investigated a novel pectate lyase enzyme, GmNPLa, and its transcriptional regulator GmPTF1a/b in soybean (Glycine max), where their regulatory roles in IT development and nodule formation were elucidated through investigation of gene expression patterns, bioinformatics analysis, biochemical verification of genetic interactions, and observation of phenotypic impacts in transgenic soybean plants. GmNPLa was specifically induced by rhizobium inoculation in root hairs. Manipulation of GmNPLa produced remarkable effects on IT and nodule formation. GmPTF1a/b displayed similar expression patterns as GmNPLa, and manipulation of GmPTF1a/b also severely influenced nodulation traits. LI soybeans with low nodulation phenotypes were nearly restored to HI nodulation level by complementation of GmNPLa and/or GmPTF1a. Further genetic and biochemical analysis demonstrated that GmPTF1a can bind to the E-box motif to activate transcription of GmNPLa, and thereby facilitate nodulation. Taken together, our findings potentially reveal novel mediation of cell wall gene expression involving the basic helix-loop-helix transcription factor GmPTF1a/b acts as a key early regulator of nodulation in soybean.},
}

@article {pmid38062814,
year = {2023},
author = {Yuan, Z and Liu, F and Yuan, Y and Pan, H},
title = {Structural Composition and Diversity of Bacterial Communities in High- and Low-Yielding Moso Bamboo Forests.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {28},
number = {11},
pages = {290},
doi = {10.31083/j.fbl2811290},
pmid = {38062814},
issn = {2768-6698},
support = {2021FKJ07//Forestry Science and Technology Project of Fujian Province/ ; },
abstract = {BACKGROUND: Bacterial communities play an important role in helping plants absorb nutrients, promoting plant development, and preventing diseases. Moso bamboo (Phyllostachys edulis [Carriere] J. Houzeau) has a long history of cultivation and important economic value.

METHODS: In this study, high-throughput sequencing technology was utilized to analyze the differences in the diversity of endophytic and root zone soil bacterial communities between high-yielding (HY) and low-yielding (LY) P. edulis forests in subtropical China.

RESULTS: Notably, the soil conditions and bacterial communities in Yong'an (YA) and Jiangle (JL) differed, but the bacterial community structures in the root zone soil of both regions were similar with the dominant bacterial phyla composed of Proteobacteria, Acidobacteriota, and Actinobacteriota. The Chao1 and Shannon indices of the root zone soil and endophytic bacterial communities in the LY were higher than those in the HY. Moreover, the bacterial community structures of HY and LY were significantly different. Notably, the relative abundances of Actinobacteriota, Myxococcota, and Cyanobacteria were higher in the HY soil samples. The bacterial community differences between the tissues and root zone soil of HY and LY indicated that healthy HY P. edulis plants were enriched with specific bacterial communities, suggesting associations between yield and both endophytic and root zone soil bacterial communities.

CONCLUSIONS: The findings of this study provide a basis to regulate artificial bacterial communities to benefit the future cultivation of HY P. edulis.},
}

@article {pmid38062479,
year = {2023},
author = {Dungan, AM and Geissler, L and Williams, AS and Gotze, CR and Flynn, EC and Blackall, LL and van Oppen, MJH},
title = {DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {86},
pmid = {38062479},
issn = {2524-6372},
support = {2022ECR096//University of Melbourne/ ; DP210100630//Australian Research Council/ ; DP210100630//Australian Research Council/ ; },
abstract = {BACKGROUND: Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.

RESULTS: By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.

CONCLUSIONS: Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.},
}

@article {pmid38061081,
year = {2023},
author = {Kushwaha, AS and Ahmad, I and Lata, S and Padalia, K and Yadav, AK and Kumar, M},
title = {Mycorrhizal fungus Serendipita indica-associated acid phosphatase rescues the phosphate nutrition with reduced arsenic uptake in the host plant under arsenic stress.},
journal = {Ecotoxicology and environmental safety},
volume = {269},
number = {},
pages = {115783},
doi = {10.1016/j.ecoenv.2023.115783},
pmid = {38061081},
issn = {1090-2414},
abstract = {Symbiotic interactions play a vital role in maintaining the phosphate (Pi) nutrient status of host plants and providing resilience during biotic and abiotic stresses. Serendipita indica, a mycorrhiza-like fungus, supports plant growth by transporting Pi to the plant. Despite the competitive behaviour of arsenate (As[V]) with Pi, the association with S. indica promotes plant growth under arsenic (As) stress by reducing As bioavailability through adsorption, accumulation, and precipitation within the fungus. However, the capacity of S. indica to enhance Pi accumulation and utilization under As stress remains unexplored. Axenic studies revealed that As supply significantly reduces intracellular ACPase activity in S. indica, while extracellular ACPase remains unaffected. Further investigations using Native PAGE and gene expression studies confirmed that intracellular ACPase (isoform2) is sensitive to As, whereas extracellular ACPase (isoform1) is As-insensitive. Biochemical analysis showed that ACPase (isoform1) has a Km of 0.5977 µM and Vmax of 0.1945 Unit/min. In hydroponically cultured tomato seedlings, simultaneous inoculation of S. indica with As on the 14thday after seed germination led to hyper-colonization, increased root/shoot length, biomass, and induction of ACPase expression and secretion under As stress. Arsenic-treated S. indica colonized groups (13.33 µM As+Si and 26.67 µM As+Si) exhibited 8.28-19.14 and 1.71-3.45-fold activation of ACPase in both rhizospheric media and root samples, respectively, thereby enhancing Pi availability in the surrounding medium under As stress. Moreover, S. indica (13.33 µM As+Si and 26.67 µM As+Si) significantly improved Pi accumulation in roots by 7.26 and 9.46 times and in shoots by 4.36 and 8.85 times compared to the control. Additionally, S. indica induced the expression of SiPT under As stress, further improving Pi mobilization. Notably, fungal colonization also restricted As mobilization from the hydroponic medium to the shoot, with a higher amount of As (191.01 ppm As in the 26.67 µM As+Si group) accumulating in the plant's roots. The study demonstrates the performance of S. indica under As stress in enhancing Pi mobilization while limiting As uptake in the host plant. These findings provide the first evidence of the As-Pi interaction in the AM-like fungus S. indica, indicating reduced As uptake and regulation of PHO genes (ACPase and SiPT genes) to increase Pi acquisition. These data also lay the foundation for the rational use of S. indica in agricultural practices.},
}

@article {pmid38060423,
year = {2024},
author = {Winslow, ER},
title = {Invited Commentary: Symbiotic Relationship between the Pancreatic Surgeon and the Pancreatic Imager: Necessity of Reciprocal Communication.},
journal = {Radiographics : a review publication of the Radiological Society of North America, Inc},
volume = {44},
number = {1},
pages = {e230225},
doi = {10.1148/rg.230225},
pmid = {38060423},
issn = {1527-1323},
}

@article {pmid38059992,
year = {2023},
author = {Wang, M and Zhang, W and He, T and Rong, L and Yang, Q},
title = {Degradation of polycyclic aromatic hydrocarbons in aquatic environments by a symbiotic system consisting of algae and bacteria: green and sustainable technology.},
journal = {Archives of microbiology},
volume = {206},
number = {1},
pages = {10},
pmid = {38059992},
issn = {1432-072X},
support = {2015ZX07406-005//National Science and Technology Major Project/ ; 2016YFC0209205//National Science and Technology Major Project/ ; 50578151//National Natural Science Foundation of China/ ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are genotoxic, carcinogenic, and persistent in the environment and are therefore of great concern in the environmental protection field. Due to the inherent recalcitrance, persistence and nonreactivity of PAHs, they are difficult to remediate via traditional water treatment methods. In recent years, microbial remediation has been widely used as an economical and environmentally friendly degradation technology for the treatment of PAH-contaminated water. Various bacterial and microalgal strains are capable of potentially degrading or transforming PAHs through intrinsic metabolic pathways. However, their biodegradation potential is limited by the cytotoxic effects of petroleum hydrocarbons, unfavourable environmental conditions, and biometabolic limitations. To address this limitation, microbial communities, biochemical pathways, enzyme systems, gene organization, and genetic regulation related to PAH degradation have been intensively investigated. The advantages of algal-bacterial cocultivation have been explored, and the limitations of PAHs degradation by monocultures of algae or bacteria have been overcome by algal-bacterial interactions. Therefore, a new model consisting of a "microalgal-bacterial consortium" is becoming a new management strategy for the effective degradation and removal of PAHs. This review first describes PAH pollution control technologies (physical remediation, chemical remediation, bioremediation, etc.) and proposes an algal-bacterial symbiotic system for the degradation of PAHs by analysing the advantages, disadvantages, and PAH degradation performance in this system to fill existing research gaps. Additionally, an algal-bacterial system is systematically developed, and the effects of environmental conditions are explored to optimize the degradation process and improve its technical feasibility. The aim of this paper is to provide readers with an effective green and sustainable remediation technology for removing PAHs from aquatic environments.},
}

@article {pmid38057446,
year = {2023},
author = {Asrat, A and Sitotaw, B and Dawoud, TM and Nafidi, HA and Bourhia, M and Mekuriaw, A and Wondmie, GF},
title = {Effect of glyphosate on the growth and survival of rhizobia isolated from root nodules of grass pea (Lathyrus sativus L.).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21535},
pmid = {38057446},
issn = {2045-2322},
abstract = {Grass pea (L. sativus L.) is a widely cultivated crop worldwide, forming a symbiotic relationship with nitrogen-fixing rhizobia. Glyphosate is commonly used by farmers for weed control during agricultural processes. However, the application of this chemical herbicide negatively impacts soil fertility by affecting the nitrogen-fixing rhizobia. This study aimed to assess the effects of glyphosate on rhizobia isolated from healthy and robust Grass pea plants. Specifically, Grass pea plants exhibiting vigorous growth and a healthy appearance were intentionally selected to isolate rhizobia from their root nodules. The isolated rhizobia were then characterized based on their morphological features, biochemical properties, and resistance to abiotic traits. Rhizobial isolates from grass peas exhibited Gram-negative, rod-shaped morphology, milky colony color, and variable colony sizes. Additionally, the majority displayed smooth colony surfaces on yeast extract mannitol agar medium. Based on morphological and biochemical characteristics, the isolates could be grouped under the genus Rhizobium. Optimum growth conditions for these isolates were observed at temperatures between 28 and 38 °C, pH levels ranging from 5 to 8, and salt (NaCl) concentrations of 0.5% and 1%. At a concentration of 20 mL L[-1], glyphosate inhibited 5.52-47% of the Rhizobium population. The inhibition percentage increased to 17.1-53.38% at a concentration of 40 mL L[-1]. However, when exposed to a higher concentration (60 mL/L) of glyphosate, 87% of the isolates were inhibited. The number of colonies after glyphosate exposure was significantly dependent on concentration, and there were notable differences between treatments with varying glyphosate concentrations (p < 0.05). Glyphosate negatively impacted the survival of grass pea rhizobia, leading to a reduction in the Rhizobium population (CFU). However, the effect varied between Rhizobium isolated from grass pea root nodules.},
}

@article {pmid38057302,
year = {2023},
author = {Sexauer, M and Bhasin, H and Schön, M and Roitsch, E and Wall, C and Herzog, U and Markmann, K},
title = {A micro RNA mediates shoot control of root branching.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8083},
pmid = {38057302},
issn = {2041-1723},
support = {Az:7533-30-20/1//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg)/ ; CRC101, project 07//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Plants extract mineral nutrients from the soil, or from interactions with mutualistic soil microbes via their root systems. Adapting root architecture to nutrient availability enables efficient resource utilization, particularly in patchy and dynamic environments. Root growth responses to soil nitrogen levels are shoot-mediated, but the identity of shoot-derived mobile signals regulating root growth responses has remained enigmatic. Here we show that a shoot-derived micro RNA, miR2111, systemically steers lateral root initiation and nitrogen responsiveness through its root target TML (TOO MUCH LOVE) in the legume Lotus japonicus, where miR2111 and TML were previously shown to regulate symbiotic infections with nitrogen fixing bacteria. Intriguingly, systemic control of lateral root initiation by miR2111 and TML/HOLT (HOMOLOGUE OF LEGUME TML) was conserved in the nonsymbiotic ruderal Arabidopsis thaliana, which follows a distinct ecological strategy. Thus, the miR2111-TML/HOLT regulon emerges as an essential, conserved factor in adaptive shoot control of root architecture in dicots.},
}

@article {pmid38055153,
year = {2023},
author = {Fasel, C and Chiapperino, L},
title = {Between the genotype and the phenotype lies the microbiome: symbiosis and the making of 'postgenomic' knowledge.},
journal = {History and philosophy of the life sciences},
volume = {45},
number = {4},
pages = {43},
pmid = {38055153},
issn = {1742-6316},
support = {PZ00P1_185822//FNS Ambizione/ ; },
mesh = {Humans ; Animals ; *Drosophila melanogaster/genetics ; Symbiosis ; Genotype ; Phenotype ; *Microbiota ; },
abstract = {Emphatic claims of a "microbiome revolution" aside, the study of the gut microbiota and its role in organismal development and evolution is a central feature of so-called postgenomics; namely, a conceptual and/or practical turn in contemporary life sciences, which departs from genetic determinism and reductionism to explore holism, emergentism and complexity in biological knowledge-production. This paper analyses the making of postgenomic knowledge about developmental symbiosis in Drosophila melanogaster by a specific group of microbiome scientists. Drawing from both practical philosophy of science and Science and Technology Studies, the paper documents epistemological questions of artefactuality and representativeness of model organisms as they emerge in the day-to-day labour producing and being produced by the "microbiome revolution." Specifically, the paper builds on all the written and editorial exchanges involved in the troubled publication of a research paper studying the symbiotic role of the microbiota in the flies' development. These written materials permit us to delimit the network of justifications, evidence, standards of knowledge-production, trust in the tools and research designs that make up the conditions of possibility of a postgenomic fact. More than reframing the organism as a radically novel multiplicity of reactive genomes, we conclude, doing postgenomic research on the microbiota and symbiosis means producing a story that deviates from the scripts embedded into the sociotechnical experimental systems of post-Human Genome Project life sciences.},
}

Humans
Animals
*Drosophila melanogaster/genetics
Symbiosis
Genotype
Phenotype
*Microbiota

@article {pmid38053772,
year = {2023},
author = {Martin, ML and Pervent, M and Lambert, I and Colella, S and Tancelin, M and Severac, D and Clément, G and Tillard, P and Frugier, F and Lepetit, M},
title = {Localized osmotic stress activates systemic responses to N limitation in Medicago truncatula-Sinorhizobium symbiotic plants.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1288070},
pmid = {38053772},
issn = {1664-462X},
abstract = {In mature symbiotic root nodules, differentiated rhizobia fix atmospheric dinitrogen and provide ammonium to fulfill the plant nitrogen (N) demand. The plant enables this process by providing photosynthates to the nodules. The symbiosis is adjusted to the whole plant N demand thanks to systemic N signaling controlling nodule development. Symbiotic plants under N deficit stimulate nodule expansion and activate nodule senescence under N satiety. Besides, nodules are highly sensitive to drought. Here, we used split-root systems to characterize the systemic responses of symbiotic plants to a localized osmotic stress. We showed that polyéthylène glycol (PEG) application rapidly inhibited the symbiotic dinitrogen fixation activity of nodules locally exposed to the treatment, resulting to the N limitation of the plant supplied exclusively by symbiotic dinitrogen fixation. The localized PEG treatment triggered systemic signaling stimulating nodule development in the distant untreated roots. This response was associated with an enhancement of the sucrose allocation. Our analyses showed that transcriptomic reprogramming associated with PEG and N deficit systemic signaling(s) shared many targets transcripts. Altogether, our study suggests that systemic N signaling is a component of the adaptation of the symbiotic plant to the local variations of its edaphic environment.},
}

@article {pmid38053218,
year = {2023},
author = {Prioux, C and Tignat-Perrier, R and Gervais, O and Estaque, T and Schull, Q and Reynaud, S and Béraud, E and Mérigot, B and Beauvieux, A and Marcus, MI and Richaume, J and Bianchimani, O and Cheminée, A and Allemand, D and Ferrier-Pagès, C},
title = {Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {271},
pmid = {38053218},
issn = {2049-2618},
mesh = {Animals ; Bacteria/genetics ; *Anthozoa/microbiology ; *Microbiota ; Temperature ; Forests ; Coral Reefs ; },
abstract = {BACKGROUND: Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.

RESULTS: Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.

CONCLUSIONS: Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.},
}

Animals
Bacteria/genetics
*Anthozoa/microbiology
*Microbiota
Temperature
Forests
Coral Reefs

@article {pmid38053000,
year = {2023},
author = {Pena, R and Bluhm, SL and Ammerschubert, S and Agüi-Gonzalez, P and Rizzoli, SO and Scheu, S and Polle, A},
title = {Mycorrhizal C/N ratio determines plant-derived carbon and nitrogen allocation to symbiosis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {1230},
pmid = {38053000},
issn = {2399-3642},
support = {Cluster of Excellence: Functional Biodiversity Research//Niedersächsische Ministerium für Wissenschaft und Kultur (Lower Saxony Ministry of Science and Culture)/ ; PE 2256/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; PE 2256/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Mycorrhizae/physiology ; Symbiosis ; Nitrogen ; Carbon ; Ecosystem ; Plants ; },
abstract = {Carbon allocation of trees to ectomycorrhizas is thought to shape forest nutrient cycling, but the sink activities of different fungal taxa for host resources are unknown. Here, we investigate fungal taxon-specific differences in naturally composed ectomycorrhizal (EM) communities for plant-derived carbon and nitrogen. After aboveground dual labeling of young beech with [15]N and [13]C, ectomycorrhizas formed with different fungal taxa exhibit strong differences in label enrichment. Secondary Ion Mass Spectrometry (SIMS) imaging of nitrogen in cross sections of ectomycorrhizas demonstrates plant-derived [15]N in both root and fungal structures. Isotope enrichment in ectomycorrhizas correlates with that in the corresponding ectomycorrhiza-attached lateral root, supporting fungal taxon-specific N and C fluxes in ectomycorrhizas. The enrichments with [13]C and [15]N in the symbiosis decrease with increasing C/N ratio of ectomycorrhizas, converging to zero at high C/N. The relative abundances of EM fungal species on roots are positively correlated with [13]C enrichment, demonstrating higher fitness of stronger than of less C-demanding symbioses. Overall, our results support that differences among the C/N ratios in ectomycorrhizas formed with different fungal species regulate the supply of the symbioses with host-derived carbon and provide insights on functional traits of ectomycorrhizas, which are important for major ecosystem processes.},
}

*Mycorrhizae/physiology
Symbiosis
Nitrogen
Carbon
Ecosystem
Plants

@article {pmid38051239,
year = {2023},
author = {Cohen, PR and Parish, LC and Lambert, WC and Gaspari, AA},
title = {Editors and Journals: Part II-Relationship between the Editor-in-Chief and the Owner of the Journal: The Consequences When Editorial Independence Dissolves.},
journal = {Skinmed},
volume = {21},
number = {6},
pages = {411-415},
pmid = {38051239},
issn = {1751-7125},
abstract = {A symbiotic relationship between the editor and the owner of a medical journal is important for the journal to fulfill successfully the expectations of its readers and authors. Editorial freedom and transparency by owner of the journal are important qualities that enable the editor to provide valid scientific information in an unbiased manner. Unresolved impedance of editorial freedom or the persistent lack of transparency or both frequently results in untenable consequences for editor and often a substantial defamation of the journal's credibility. Unfortunately, misguided and inappropriate behavior by a medical society or the publication owner repeatedly occurs with the same devastating effect for the editor: prompt, unanticipated, and unjustified termination of the position at the journal. Alternatively, conditions imposed by a journal's owner may lead to the resignation of the editor because of untenable conditions. Because the owner does not have to account for its actions and there is no recourse for the editor, currently there seems to be no effective measures to prevent this tragic sequence of events in the future.},
}

@article {pmid38047691,
year = {2023},
author = {Nakabachi, A and Suzaki, T},
title = {Ultrastructure of the bacteriome and bacterial symbionts in the Asian citrus psyllid, Diaphorina citri.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0224923},
doi = {10.1128/spectrum.02249-23},
pmid = {38047691},
issn = {2165-0497},
abstract = {Omics analyses suggested a mutually indispensable tripartite association among the host D. citri and organelle-like bacteriome associates, Carsonella and Profftella, which are vertically transmitted through host generations. This relationship is based on the metabolic complementarity among these organisms, which is partly enabled by horizontal gene transfer between partners. However, little was known about the fine morphology of the symbionts and the bacteriome, the interface among these organisms. As a first step to address this issue, the present study performed transmission electron microscopy, which revealed previously unrecognized ultrastructures, including aggregations of ribosomes in Carsonella, numerous tubes and occasional protrusions of Profftella, apparently degrading Profftella, and host organelles with different abundance and morphology in distinct cell types. These findings provide insights into the behaviors of the symbionts and host cells to maintain the symbiotic relationship in D. citri.},
}

@article {pmid38047686,
year = {2023},
author = {Zhang, W and Wang, J and Huang, Z and He, X and Wei, C},
title = {Symbionts in Hodgkinia-free cicadas and their implications for co-evolution between endosymbionts and host insects.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0137323},
doi = {10.1128/aem.01373-23},
pmid = {38047686},
issn = {1098-5336},
abstract = {Obligate symbionts in sap-sucking hemipterans are harbored in either the same or different organs, which provide a unique perspective for uncovering complicated insect-microbe symbiosis. Here, we investigated the distribution of symbionts in adults of 10 Hodgkinia-free cicada species of 2 tribes (Sonatini and Polyneurini) and the co-phylogeny between 65 cicada species and related symbionts (Sulcia and YLSs). We revealed that YLSs commonly colonize the bacteriome sheath besides the fat bodies in these two tribes, which is different with that in most other Hodgkinia-free cicadas. Co-phylogeny analyses between cicadas and symbionts suggest that genetic variation of Sulcia occurred in Sonatini and some other cicada lineages and more independent replacement events in the loss of Hodgkinia/acquisition of YLS in Cicadidae. Our results provide new information on the complex relationships between auchenorrhynchans and related symbionts.},
}

@article {pmid38046823,
year = {2023},
author = {Gotoh, A and Hidaka, M and Sakurama, H and Nishimoto, M and Kitaoka, M and Sakanaka, M and Fushinobu, S and Katayama, T},
title = {Substrate recognition mode of a glycoside hydrolase family 42 β-galactosidase from Bifidobacterium longum subspecies infantis (BiBga42A) revealed by crystallographic and mutational analyses.},
journal = {Microbiome research reports},
volume = {2},
number = {3},
pages = {20},
pmid = {38046823},
issn = {2771-5965},
abstract = {Aim: Bifidobacterium longum subsp. infantis uses a glycoside hydrolase (GH) family 42 β-galactosidase (BiBga42A) for hydrolyzing lacto-N-tetraose (LNT), which is the most abundant core structure of human milk oligosaccharides (HMOs). As such, BiBga42A represents one of the pivotal enzymes underpinning the symbiosis between bifidobacteria and breastfed infants. Despite its importance, the structural basis underlying LNT hydrolysis by BiBga42A is not understood. Moreover, no substrate-complexed structures are available to date for GH42 family members. Methods: X-ray crystallography was used to determine the structures of BiBga42A in the apo- and liganded forms. The roles of the amino acid residues that were presumed to be involved in catalysis and substrate recognition were examined by a mutational study, in which kinetic parameters of each mutant were determined using 4-nitrophenyl-β-D-galactoside, lacto-N-biose I, LNT, and lacto-N-neotetraose (LNnT) as substrates. Conservation of those amino acid residues was examined among structure-determined GH42 β-galactosidases. Results: Crystal structures of the wild-type enzyme complexed with glycerol, the E160A/E318A double mutant complexed with galactose (Gal), and the E318S mutant complexed with LNT were determined at 1.7, 1.9, and 2.2 Å resolutions, respectively. The LNT molecule (excluding the Gal moiety at subsite +2) bound to the E318S mutant is recognized by an extensive hydrogen bond network and several hydrophobic interactions. The non-reducing end Gal moiety of LNT adopts a slightly distorted conformation and does not overlap well with the Gal molecule bound to the E160A/E318A mutant. Twelve of the sixteen amino acid residues responsible for LNT recognition and catalysis in BiBga42A are conserved among all homologs including β-1,6-1,3-galactosidase (BlGal42A) from Bifidobacterium animalis subsp. lactis. Conclusion: BlGal42A is active on 3-β-galactobiose similarly to BiBga42A but is inactive on LNT. Interestingly, we found that the entrance of the catalytic pocket of BlGal42A is narrower than that of BiBga42A and seems not easily accessible from the solvent side due to the presence of two bulky amino acid side chains. The specificity difference may reflect the structural difference between the two enzymes.},
}

@article {pmid38045608,
year = {2023},
author = {Segers, A and de Vos, WM},
title = {Mode of action of Akkermansia muciniphila in the intestinal dialogue: role of extracellular proteins, metabolites and cell envelope components.},
journal = {Microbiome research reports},
volume = {2},
number = {1},
pages = {6},
pmid = {38045608},
issn = {2771-5965},
abstract = {Akkermansia muciniphila is a promising next-generation beneficial microbe due to its natural presence in the mucus layer of the gut, its symbiotic ability to degrade mucus, and its capacity to improve the intestinal barrier function. A. muciniphila is able to counteract weight gain and immuno-metabolic disturbances in several animal models. Many of these disorders, including obesity and auto-immune diseases, have been associated with decreased gut barrier function and consequent increased inflammation. Since A. muciniphila was found to normalize these changes and strengthen the gut barrier function, it is hypothesized that other beneficial effects of A. muciniphila might be caused by this restoration. In search for A. muciniphila's mode of action in enhancing the gut barrier function and promoting health, we reasoned that secreted components or cell envelope components of A. muciniphila are interesting candidates as they can potentially reach and interact with the epithelial barrier. In this review, we focus on the potential mechanisms through which A. muciniphila can exert its beneficial effects on the host by the production of extracellular and secreted proteins, metabolites and cell envelope components. These products have been studied in isolation for their structure, signaling capacity, and in some cases, also for their effects in preclinical models. This includes the protein known as Amuc_1100, which we here rename as pilus-associated signaling (PAS) protein , the P9 protein encoded by Amuc_1631, the short-chain fatty acids acetate and propionate, and cell envelope components, such as phosphatidylethanolamine and peptidoglycan.},
}

@article {pmid38045388,
year = {2023},
author = {Cao, M},
title = {CRISPR-Cas9 genome editing in Steinernema entomopathogenic nematodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.24.568619},
pmid = {38045388},
abstract = {Molecular tool development in traditionally non-tractable animals opens new avenues to study gene functions in the relevant ecological context. Entomopathogenic nematodes (EPN) Steinernema and their symbiotic bacteria of Xenorhabdus spp are a valuable experimental system in the laboratory and are applicable in the field to promote agricultural productivity. The infective juvenile (IJ) stage of the nematode packages mutualistic symbiotic bacteria in the intestinal pocket and invades insects that are agricultural pests. The lack of consistent and heritable genetics tools in EPN targeted mutagenesis severely restricted the study of molecular mechanisms underlying both parasitic and mutualistic interactions. Here, I report a protocol for CRISPR-Cas9 based genome-editing that is successful in two EPN species, S. carpocapsae and S. hermaphroditum . I adapted a gonadal microinjection technique in S. carpocapsae , which created on-target modifications of a homologue Sc-dpy-10 (cuticular collagen) by homology-directed repair. A similar delivery approach was used to introduce various alleles in S. hermaphroditum including Sh-dpy-10 and Sh-unc-22 (a muscle gene), resulting in visible and heritable phenotypes of dumpy and twitching, respectively. Using conditionally dominant alleles of Sh-unc-22 as a co-CRISPR marker, I successfully modified a second locus encoding Sh-Daf-22 (a homologue of human sterol carrier protein SCPx), predicted to function as a core enzyme in the biosynthesis of nematode pheromone that is required for IJ development. As a proof of concept, Sh-daf-22 null mutant showed IJ developmental defects in vivo (in insecta) . This research demonstrates that Steinernema spp are highly tractable for targeted mutagenesis and has great potential in the study of gene functions under controlled laboratory conditions within the relevant context of its ecological niche.},
}

@article {pmid38044128,
year = {2023},
author = {Chiba, Y and Sasaki, M and Masuda, S and Shibata, A and Shirasu, K and Kawaharada, Y},
title = {A Novel Rhizobium sp. Chiba-1 Strain Exhibits a Host Range for Nodule Symbiosis in Lotus Species.},
journal = {Microbes and environments},
volume = {38},
number = {4},
pages = {},
doi = {10.1264/jsme2.ME23056},
pmid = {38044128},
issn = {1347-4405},
mesh = {*Rhizobium/genetics ; Host Specificity/genetics ; Symbiosis/genetics ; *Lotus/microbiology ; Plant Roots/microbiology ; Soil ; Root Nodules, Plant/microbiology ; },
abstract = {Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan. We conducted genomic and host range ana-lyses of various Lotus species. The results obtained revealed that the novel isolated Rhizobium sp. Chiba-1 was closely related to R. leguminosarum and had a wide host range that induced nodule development, including L. burttii and several L. japonicus wild-type accessions. However, L. japonicus Gifu exhibited an incompatible nodule phenotype. We also identified the formation of an epidermal infection threads that was dependent on the Lotus species and independent of nodule organ development. In conclusion, this newly isolated Rhizobium strain displays a distinct nodulation phenotype from Lotus species, and the results obtained herein provide novel insights into the functional mechanisms underlying host specificity and host ranges.},
}

*Rhizobium/genetics
Host Specificity/genetics
Symbiosis/genetics
*Lotus/microbiology
Plant Roots/microbiology
Soil
Root Nodules, Plant/microbiology

@article {pmid38044013,
year = {2023},
author = {Ray, PP},
title = {Generative Artificial Intelligence (AI) and Medical Ethics: A Symbiotic Dance for the Future.},
journal = {Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons},
volume = {81},
number = {12},
pages = {1457-1459},
doi = {10.1016/j.joms.2023.09.015},
pmid = {38044013},
issn = {1531-5053},
}

@article {pmid38042930,
year = {2023},
author = {Tagirdzhanova, G and Scharnagl, K and Yan, X and Talbot, NJ},
title = {Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21285},
pmid = {38042930},
issn = {2045-2322},
support = {BBS/E/J/000PR9798/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Lichens/genetics/microbiology ; Symbiosis/genetics ; *Ascomycota/genetics ; *Chlorophyta/genetics ; Genomics ; Phylogeny ; },
abstract = {Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae.},
}

*Lichens/genetics/microbiology
Symbiosis/genetics
*Ascomycota/genetics
*Chlorophyta/genetics
Genomics
Phylogeny

@article {pmid38042473,
year = {2023},
author = {Liu, R and Hu, B and Flemetakis, E and Dannenmann, M and Geilfus, CM and Haensch, R and Wang, D and Rennenberg, H},
title = {Antagonistic effect of mercury and excess nitrogen exposure reveals provenance-specific phytoremediation potential of black locust-rhizobia symbiosis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {342},
number = {},
pages = {123050},
doi = {10.1016/j.envpol.2023.123050},
pmid = {38042473},
issn = {1873-6424},
abstract = {Interaction of different environmental constrains pose severe threats to plants that cannot be predicted from individual stress exposure. In this context, mercury (Hg), as a typical toxic and hazardous heavy metal, has recently attracted particular attention. Nitrogen (N2)-fixing legumes can be used for phytoremediation of Hg accumulation, whereas N availability could greatly affect its N2-fixation efficiency. However, information on the physiological responses to combined Hg exposure and excess N supply of woody legume species is still lacking. Here, we investigated the interactive effects of rhizobia inoculation, Hg exposure (+Hg), and high N (+N) supply, individually and in combination (+N*Hg), on photosynthesis and biochemical traits in Robinia pseudoacacia L. seedlings of two provenances, one from Northeast (DB) and one from Northwest (GS) China. Our results showed antagonistic effects of combined + N*Hg exposure compared to the individual treatments that were provenance-specific. Compared to individual Hg exposure, combined + N*Hg stress significantly increased foliar photosynthesis (+50.6%) of inoculated DB seedlings and resulted in more negative (-137.4%) δ[15]N abundance in the roots. Furthermore, combined + N*Hg stress showed 47.7% increase in amino acid N content, 39.4% increase in NR activity, and 14.8% decrease in MDA content in roots of inoculated GS seedlings. Inoculation with rhizobia significantly promoted Hg uptake in both provenances, reduced MDA contents of leaves and roots, enhanced photosynthesis and maintained the nutrient balance of Robinia. Among the two Robinia provenances investigated, DB seedlings formed more nodules, had higher biomass and Hg accumulation than GS seedlings. For example, total Hg concentrations in leaves and roots and total biomass of inoculated DB seedlings were 1.3,1.9 and 3.4 times higher than in inoculated GS seedlings under combined + N*Hg stress, respectively. Therefore, the DB provenance is considered to possess a higher potential for phytoremediation of Hg contamination compared to the GS provenance in environments subjected to N deposition.},
}

@article {pmid38040609,
year = {2023},
author = {Anz, RI and Chung, P},
title = {Animals as healers: A historical journey through the impact of animals on human health across the ages.},
journal = {Current problems in pediatric and adolescent health care},
volume = {},
number = {},
pages = {101476},
doi = {10.1016/j.cppeds.2023.101476},
pmid = {38040609},
issn = {1538-3199},
abstract = {Animals have had a profound impact on health throughout the course of human history. Beginning with zootherapy in the ancient world, where animals were used as sources of mystical healing, animals have been crucial in the scientific discovery of human health and disease. In the modern world, the therapeutic application of emotional support animals serves as recognition for the symbiotic relationship between animals and humans. Appreciating the continued application of animals in human health serves as a reminder of the connectivity between humanity and the animal kingdom.},
}

@article {pmid38040356,
year = {2023},
author = {Sun, L and Wang, D and Liu, X and Zhou, Y and Hang, W and Guan, X and Zhang, X and Xie, Z},
title = {The volatile organic compound acetoin enhances the colonization of Azorhizobium caulinodans ORS571 on Sesbania rostrata.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {169006},
doi = {10.1016/j.scitotenv.2023.169006},
pmid = {38040356},
issn = {1879-1026},
abstract = {Chemoreceptors play a crucial role in assisting bacterial sensing and response to environmental stimuli. Genome analysis of Azorhizobium caulinodans ORS571 revealed the presence of 43 putative chemoreceptors, but their biological functions remain largely unknown. In this study, we identified the chemoreceptor AmaP (methyl-accepting protein of A. caulinodans), characterized by the presence of the CHASE3 domain and exhibited a notable response to acetoin. Thus, we investigated the effect of acetoin sensing on its symbiotic association with the host. Our findings uncovered a compelling role for acetoin as a key player in enhancing various facets of A. caulinodans ORS571's performance including biofilm formation, colonization, and nodulation abilities. Notably, acetoin bolstered A. caulinodans ORS571's efficacy in promoting the growth of S. rostrata, even under moderate salt stress conditions. This study not only broadens our understanding of the AmaP protein with its distinctive CHASE3 domain but also highlights the promising potential of acetoin in fortifying the symbiotic relationship between A. caulinodans and Sesbania rostrata.},
}

@article {pmid38039119,
year = {2023},
author = {Nouwen, N and Pervent, M and El M'Chirgui, F and Tellier, F and Rios, M and Horta Araújo, N and Klopp, C and Gressent, F and Arrighi, JF},
title = {OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiad642},
pmid = {38039119},
issn = {1532-2548},
abstract = {Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accomodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signalling pathway that activates two coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defence-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordia form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid (VLCFA)-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.},
}

@article {pmid38038797,
year = {2023},
author = {Mustaq, S and Moin, A and Pandit, B and Tiwary, BK and Alam, M},
title = {Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {38038797},
issn = {1874-9356},
abstract = {The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.},
}

@article {pmid38038369,
year = {2023},
author = {Neubauer, A and Aros-Mualin, D and Mariscal, V and Szövényi, P},
title = {Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13588},
pmid = {38038369},
issn = {1744-7909},
abstract = {Effective communication across fields and disciplines relies on well-defined terminology. Standardized use of accurate definitions has been advocated by scientists across various disciplines (Tipton et al., 2019; PySek, 1995; Dubrovsky, 2022; Rillig, 2023; Rabin and Brownson, 2017). Divergent interpretations or the application of differing terminology can negatively impact interdisciplinary exchange, leading to missed information, hampered methodology transfer, and ultimately impeding progress (Sapp, 2010; Tipton et al., 2019). An impressive example of the use of multiple terms with the same interpretation is the definition of non-native or invasive plants encompassing at least 14 different terms (PySek, 1995). An abundance of definitions for the same term can be equally confusing which is thoroughly discussed in a recent review on plant root terminology. This article is protected by copyright. All rights reserved.},
}

@article {pmid38037476,
year = {2023},
author = {Wu, YC and Yu, CW and Chiu, JY and Chiang, YH and Mitsuda, N and Yen, XC and Huang, TP and Chang, TF and Yen, CJ and Guo, WJ},
title = {The AT-hook protein AHL29 promotes Bacillus subtilis colonization by suppressing SWEET2-mediated sugar retrieval in Arabidopsis roots.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.14779},
pmid = {38037476},
issn = {1365-3040},
support = {MOST 104-2311-B-006-004-MY3//National Science and Technology Council/ ; MOST 108-2314-B-006-077-MY3//National Science and Technology Council/ ; MOST 111-2313-B-005-020//National Science and Technology Council/ ; //Ministry of Education in Taiwan/ ; },
abstract = {Beneficial Bacillus subtilis (BS) symbiosis could combat root pathogenesis, but it relies on root-secreted sugars. Understanding the molecular control of sugar flux during colonization would benefit biocontrol applications. The SWEET (Sugar Will Eventually Be Exported Transporter) uniporter regulates microbe-induced sugar secretion from roots; thus, its homologs may modulate sugar distribution upon BS colonization. Quantitative polymerase chain reaction revealed that gene transcripts of SWEET2, but not SWEET16 and 17, were significantly induced in seedling roots after 12 h of BS inoculation. Particularly, SWEET2-β-glucuronidase fusion proteins accumulated in the apical mature zone where BS abundantly colonized. Yet, enhanced BS colonization in sweet2 mutant roots suggested a specific role for SWEET2 to constrain BS propagation, probably by limiting hexose secretion. By employing yeast one-hybrid screening and ectopic expression in Arabidopsis protoplasts, the transcription factor AHL29 was identified to function as a repressor of SWEET2 expression through the AT-hook motif. Repression occurred despite immunity signals. Additionally, enhanced SWEET2 expression and reduced colonies were specifically detected in roots of BS-colonized ahl29 mutant. Taken together, we propose that BS colonization may activate repression of AHL29 on SWEET2 transcription that would be enhanced by immunity signals, thereby maintaining adequate sugar secretion for a beneficial Bacillus association.},
}

@article {pmid38037395,
year = {2023},
author = {Nguyen, PN and Rehan, SM},
title = {Wild bee and pollen microbiomes across an urban-rural divide.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad158},
pmid = {38037395},
issn = {1574-6941},
abstract = {Wild pollinators and their microbiota are sensitive to land use changes from anthropogenic activities that disrupt landscape and environmental features. As urbanization and agriculture affect bee habitats, human led disturbances are driving changes in bee microbiomes, potentially leading to dysbiosis detrimental to bee fitness. This study examines the bacterial, fungal, and plant compositions of the small carpenter bee, Ceratina calcarata, and its pollen provisions across an urban-rural divide. We performed metabarcoding of C. calcarata and provisions in Toronto by targeting the 16S rRNA, ITS, and rbcL regions. Despite similar plant composition and diversity across bees and their provisions, there was a greater microbial diversity in pollen provisions than in bees. By characterizing the differences in land use, climate, and pesticide residues that differentiate urban and rural landscapes, we find that urban areas support elevated levels of microbial diversity and more complex networks between microbes and plants than rural areas. However, urban areas may lead to lower relative abundances of known beneficial symbionts and increased levels of pathogens, such as Ascosphaera and Alternaria fungi. Further, rural pollen provisions indicate elevated pesticide residues that may dysregulate symbiosis. As anthropogenic activities continue to alter land use, ever changing environments threaten microbiota crucial in maintaining bee health.},
}

@article {pmid38034649,
year = {2023},
author = {Morales-Cortés, VI and Domínguez-Soberanes, J and Hernández-Lozano, LC and Licon, CC and Estevez-Rioja, A and Peralta-Contreras, M},
title = {Sensory characterization of functional guava symbiotic petit cheese product.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21747},
pmid = {38034649},
issn = {2405-8440},
abstract = {The consumption of functional dairy products continues to rise due to consumer needs. This study aimed to develop a dairy guava functional symbiotic petit cheese product that included probiotics (Bifidobacterium animalis subsp. lactis BB-12, Chr. Hansen, Denmark) and prebiotics (inulin), which had adequate organoleptic characteristics. Moreover, adequate physicochemical, microbiological, and sensory characteristics during its shelf life were expected. A pasteurized skim milk curd flavored with a guava pulp was stabilized with gelatin to formulate this product. As sweeteners, iso maltol, erythritol, and Luo Han Guo extract from monk fruit (Siraitia Grosvenorii) were added. The prebiotic used was inulin, and the probiotic (Bifidobacterium animalis subsp. lactis BB-12, Chr. Hansen, Denmark). The product was kept refrigerated (4 °C) during the shelf life of 28 days. For the organoleptic analysis (100 consumers), the evaluations performed were: (1) overall liking (OL), (2) CATA (Check all that apply) testing 19 attributes, and (3) purchase intention was evaluated. Results were analyzed with FIZZ Software Biosystèmes. During shelf life, (1) physicochemical, microbiological, and sensory tests were performed. The product was evaluated as "liked much'' (7.16 out of 9); it was described as a creamy (71 %) natural product (73 %) with a fruity odor (57 %). It could be suitable for marketing because 82 % of the consumers would buy it. The product's probiotic character (over 1 × 10[6]) was established through a microbiological count. On day one, the CFU was found to be 4.15 × 10[8], and after 28 days, 1.98 × 10[8] CFU of viable Bifidobacterium animalis subsp. lactis BB-12, leading us to establish its probiotic characteristics. The shelf life was estimated at 21 days.},
}

@article {pmid38034552,
year = {2023},
author = {Arifuzzaman, M and Mamidi, S and Sanz-Saez, A and Zakeri, H and Scaboo, A and Fritschi, FB},
title = {Identification of loci associated with water use efficiency and symbiotic nitrogen fixation in soybean.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1271849},
pmid = {38034552},
issn = {1664-462X},
abstract = {Soybean (Glycine max) production is greatly affected by persistent and/or intermittent droughts in rainfed soybean-growing regions worldwide. Symbiotic N2 fixation (SNF) in soybean can also be significantly hampered even under moderate drought stress. The objective of this study was to identify genomic regions associated with shoot carbon isotope ratio (δ[13]C) as a surrogate measure for water use efficiency (WUE), nitrogen isotope ratio (δ[15]N) to assess relative SNF, N concentration ([N]), and carbon/nitrogen ratio (C/N). Genome-wide association mapping was performed with 105 genotypes and approximately 4 million single-nucleotide polymorphism markers derived from whole-genome resequencing information. A total of 11, 21, 22, and 22 genomic loci associated with δ[13]C, δ[15]N, [N], and C/N, respectively, were identified in two environments. Nine of these 76 loci were stable across environments, as they were detected in both environments. In addition to the 62 novel loci identified, 14 loci aligned with previously reported quantitative trait loci for different C and N traits related to drought, WUE, and N2 fixation in soybean. A total of 58 Glyma gene models encoding for different genes related to the four traits were identified in the vicinity of the genomic loci.},
}

@article {pmid38031601,
year = {2023},
author = {Zartdinova, R and Nikitin, A},
title = {Calcium in the Life Cycle of Legume Root Nodules.},
journal = {Indian journal of microbiology},
volume = {63},
number = {4},
pages = {410-420},
pmid = {38031601},
issn = {0046-8991},
abstract = {The present review highlights both the fundamental questions of calcium localization, compartmentation, and its participation in symbiosome signaling cascades during nodule formation and functioning. Apparently, the main link of such signaling is the calmodulin…calcium- and calmodulin-dependent protein kinases…CYCLOPS…NIN…target genes cascade. The minimum threshold level of calcium as a signaling agent in the presence of intracellular reserves determines the possibility of oligotrophy and ultraoligotrophy in relation to this element. During the functioning of root nodules, the Ca[2+]-ATPases activity maintains homeostasis of low calcium concentrations in the cytosol of nodule parenchyma cells. Disturbation of this homeostasis can trigger the root nodule senescence. The same reasons determine the increase in the effectiveness of symbiosis with the help of seed priming with sources of calcium. Examples of calcium response polymorphism in components of nitrogen fixing simbiosis important in practical terms are shown.},
}

@article {pmid38031529,
year = {2023},
author = {Sanders, WB},
title = {The disadvantages of current proposals to redefine lichens: A comment on Hawksworth & Grube (2020): 'Lichens redefined as complex ecosystems'.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19321},
pmid = {38031529},
issn = {1469-8137},
}

@article {pmid38031487,
year = {2023},
author = {Hawksworth, DL and Grube, M},
title = {Reflections on lichens as ecosystems.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19418},
pmid = {38031487},
issn = {1469-8137},
}

@article {pmid38030972,
year = {2023},
author = {Wu, F and Zhao, M and Zhang, Y and Si, W and Cheng, B and Li, X},
title = {Systematic analysis of the Rboh gene family in seven gramineous plants and its roles in response to arbuscular mycorrhizal fungi in maize.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {603},
pmid = {38030972},
issn = {1471-2229},
support = {GXXT-2019-032//Collaborative Innovation Project for Universities in Anhui Province/ ; U21A20235//National Natural Science Foundation of China/ ; 202204c06020021//The key research and development Program of Anhui Province/ ; },
mesh = {*Mycorrhizae/physiology ; Zea mays/metabolism ; Phylogeny ; Symbiosis ; Plant Roots/genetics ; Gene Expression Regulation, Plant ; },
abstract = {BACKGROUND: Plant respiratory burst oxidase homolog (Rboh) gene family produces reactive oxygen species (ROS), and it plays key roles in plant-microbe interaction. Most Rboh gene family-related studies mainly focused on dicotyledonous plants; however, little is known about the roles of Rboh genes in gramineae.

RESULTS: A total of 106 Rboh genes were identified in seven gramineae species, including Zea mays, Sorghum bicolor, Brachypodium distachyon, Oryza sativa, Setaria italica, Hordeum vulgare, and Triticum aestivum. The Rboh protein sequences showed high similarities, suggesting that they may have conserved functions across different species. Duplication mode analysis detected whole-genome/segmental duplication (WGD)/(SD) and dispersed in the seven species. Interestingly, two local duplication (LD, including tandem and proximal duplication) modes were found in Z. mays, S. italica and H. vulgare, while four LD were detected in T. aestivum, indicating that these genes may have similar functions. Collinearity analysis indicated that Rboh genes are at a stable evolution state in all the seven species. Besides, Rboh genes from Z. mays were closely related to those from S. bicolor, consistent with the current understanding of plant evolutionary history. Phylogenetic analysis showed that the genes in the subgroups I and II may participate in plant-AM fungus symbiosis. Cis-element analysis showed that different numbers of elements are related to fungal induction in the promoter region. Expression profiles of Rboh genes in Z. mays suggested that Rboh genes had distinct spatial expression patterns. By inoculation with AM fungi, our transcriptome analysis showed that the expression of Rboh genes varies upon AM fungal inoculation. In particularly, ZmRbohF was significantly upregulated after inoculation with AM fungi. pZmRbohF::GUS expression analyses indicated that ZmRbohF was induced by arbuscular mycorrhizal fungi in maize. By comparing WT and ZmRbohF mutant, we found ZmRbohF had limited impact on the establishment of maize-AM fungi symbiosis, but play critical roles in regulating the proper development of arbuscules.

CONCLUSIONS: This study provides a comprehensive analysis of the evolution relationship of Rboh genes in seven gramineae species. Results showed that several Rboh genes regulate maize-AM fungal symbiosis process. This study provides valuable information for further studies of Rboh genes in gramineae.},
}

*Mycorrhizae/physiology
Zea mays/metabolism
Phylogeny
Symbiosis
Plant Roots/genetics
Gene Expression Regulation, Plant

@article {pmid38029803,
year = {2023},
author = {Zhang, Y and Liu, L and Huang, G and Yang, C and Tian, W and Ge, Z and Zhang, B and Wang, S and Zhang, H},
title = {Enhancing humification and microbial interactions during co-composting of pig manure and wine grape pomace: The role of biochar and Fe2O3.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130120},
doi = {10.1016/j.biortech.2023.130120},
pmid = {38029803},
issn = {1873-2976},
abstract = {Phenol-rich wine grape pomace (WGP) improves the conversion of pig manure (PM) into humic acid (HA) during composting. However, the impact of using combinations of Fe2O3 and biochar known to promote compost maturation remains uncertain. This research explored the individual and combined influence of biochar and Fe2O3 during the co-composting of PM and WGP. The findings revealed that Fe2O3 boosts microbial network symbiosis (3233 links), augments the HA yield to 3.38 by promoting polysaccharide C-O stretching, and improves the germination index to 124.82 %. Limited microbial interactions, increased by biochar, resulted in a lower HA yield (2.50). However, the combination weakened the stretching of aromatics and quinones, which contribute to the formation of HA, resulting in reduced the humification to 2.73. In addition, Bacillus and Actinomadura were identified as pivotal factors affecting HA content. This study highlights Fe2O3 and biochar's roles in phenol-rich compost humification, but combined use reduces efficacy.},
}

@article {pmid38029247,
year = {2023},
author = {Jiao, X and Li, Z},
title = {Temporal dynamics and composition of ocular surface microbiota in C57BL/6J mice: uncovering a 12h ultradian rhythm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1244454},
pmid = {38029247},
issn = {2235-2988},
abstract = {PURPOSE: This study aimed to investigate the presence of rhythmic fluctuations in the composition, abundance, and functions of commensal core bacteria on the ocular surface of C57BL/6J mice.

METHODS: Male C57BL/6J mice, aged 12 weeks, were subjected to a 12-hour light/12-hour dark cycle. Ocular surface tissue samples were collected at four time points (ZT) over a 24-hour period at six-hour intervals. The core ocular surface microbiota's oscillation cycles and frequencies were assessed using 16S rRNA gene sequencing targeting the V3-V4 region, along with the JTK_CYCLE algorithm. Functional predictions of these bacteria were conducted using PICRUSt2.

RESULTS: Deep sequencing of the ocular surface microbiota highlighted the high abundance of commensal bacteria, with Proteobacteria, Actinobacteriota, and Firmicutes collectively constituting over 90% of the total sample abundance. Among the 22 core bacterial genera, 11 exhibited robust 12-hour rhythms, including Halomonas, Pelagibacterium, Pseudomonas, Nesterenkonia, norank_f_Hyphomonadaceae, Stenotrophomonas, Anoxybacillus, Acinetobacter, Zoogloea, Brevibacillus, and Ralstonia. Further taxonomic analysis indicated significant intra-cluster similarities and inter-cluster differences at the order, family, and genus levels during ZT0/12 and ZT6/18. Community interaction networks and functional prediction analyses revealed synchronized 12-hour rhythmic oscillations in neural, immune, metabolic, and other pathways associated with symbiotic bacteria.

CONCLUSION: This study demonstrates the presence of ultradian rhythmic oscillations in commensal bacteria on the ocular surface of normal C57BL/6J mice, with a 12-hour cycle. These findings suggest a crucial role for ultradian rhythms in maintaining ocular surface homeostasis in the host.},
}

@article {pmid38029204,
year = {2023},
author = {Venice, F and Vizzini, A and Danti, R and Della Rocca, G and Mello, A},
title = {Responses of a soil fungal community to severe windstorm damages in an old silver fir stand.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1246874},
pmid = {38029204},
issn = {1664-302X},
abstract = {Forests are increasingly threatened by climate change and the Anthropocene seems to have favored the emergence and adaptation of pathogens. Robust monitoring methods are required to prevent biodiversity and ecosystems losses, and this imposes the choice of bioindicators of habitat health. Fungal communities are increasingly recognized as fundamental components in nearly all natural and artificial environments, and their ecosystem services have a huge impact in maintaining and restoring the functionality of ecosystems. We coupled metabarcoding and soil analyses to infer the dynamics of a fungal community inhabiting the old silver fir stand in Vallombrosa (Italy), which is known to be afflicted by both Armillaria and Annosum root rot. The forest was affected in 2015, by a windstorm which caused a partial falling and uprooting of trees. The remaining stand, not affected by the windstorm, was used as a comparison to infer the consequences of the ecosystem disturbance. We demonstrated that the abundance of pathogens alone is not able to explain the soil fungal differences shown by the two areas. The fungal community as a whole was equally rich in the two areas, even if a reduction of the core ectomycorrhizal mycobiome was observed in the wind-damaged area, accompanied by the increase of wood saprotrophs and arbuscular mycorrhizas. We hypothesize a reshaping of the fungal community and a potentially ongoing re-generation of its functionalities. Our hypothesis is driven by the evidence that key symbiotic, endophytic, and saprotrophic guilds are still present and diversified in the wind-damaged area, and that dominance of single taxa or biodiversity loss was not observed from a mycological point of view. With the present study, we aim at providing evidence that fungal communities are fundamental for the monitoring and the conservation of threatened forest ecosystems.},
}

@article {pmid38029197,
year = {2023},
author = {Zhang, Q and Chang, S and Yang, Y and Xi, C and Dong, Y and Liu, L and He, Y and Liu, Y and Cai, B and Liu, T},
title = {Endophyte-inoculated rhizomes of Paris polyphylla improve polyphyllin biosynthesis and yield: a transcriptomic analysis of the underlying mechanism.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1261140},
pmid = {38029197},
issn = {1664-302X},
abstract = {INTRODUCTION: Polyphyllin from Paris polyphylla var. yunnanensis exhibits anti-inflammatory, analgesic, antibacterial, and antiviral properties. However, the current production of polyphyllin can barely meet market demand. To improve the content of polyphyllin produced by P. polyphylla, two endophyte strains, Bacillus cereus LgD2 and Fusarium oxysporum TPB, were isolated from Paris fargesii Franch. and inoculated in the roots of P. polyphylla. Both symbiotic strains significantly promoted the accumulation of saponins in P. polyphylla.

METHODS: The content of polyphyllin in rhizomes of P. polyphylla treated with TPB with LgD2 strain was determined using High Performance Liquid Chromatography and the expressed genes were analyzed by RNA-seq. Gene Ontology and Kyoto Encyclopedia of Genes annotations were performed on the differentially expressed genes, a clustering tree of UDP-glycosyltransferase (UGT) and cytochrome P450 (CYP450) gene families was constructed, and UGT and CYP450 involved in the biosynthesis of polyphyllin were predicted using weighted correlation network analysis (WGCNA).

RESULTS: RNA-seq and qRT-PCR analyses showed that endophytic inoculation did not promote polyphyllin accumulation by enhancing the upstream terpene biosynthesis pathway, but probably by up-regulating the downstream CYP450 and UGT genes associated with polyphyllin biosynthesis. Genomes enrichment analyses of differentially expressed genes indicated that inoculation with LgD2 and TPB played a positive role in promoting the defense against pathogenic bacteria, enhancing the biosynthesis of carbohydrates, attenuating the process of nitrogen metabolism, and maintaining the equilibrium of the redox reaction homeostasis, potentially indirectly enhancing the polyphyllin yield of P. polyphylla. By combining differentially expressed genes screening, WGCNA, and phylogenetic tree analyses, 17 CYP450 and 2 UGT candidate genes involved in the biosynthesis of polyphyllin I, polyphyllin II, polyphyllin VII, polyphyllin D, and polyphyllin H were identified. These results suggest that endophytes probably effectively promote the accumulation of polyphyllin by regulating key downstream genes in biosynthetic pathways.

DISCUSSION: This study provides a new approach for investigating the regulatory mechanisms of endophytes that promote the production and accumulation of polyphyllin in P. polyphylla, providing a basis for further elucidating the mechanisms of plant-endophyte interactions.},
}

@article {pmid38029157,
year = {2023},
author = {Liu, M and Ding, J and Lu, M},
title = {Influence of symbiotic bacteria on the susceptibility of Plagiodera versicolora to Beauveria bassiana infection.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290925},
pmid = {38029157},
issn = {1664-302X},
abstract = {The symbiotic bacterial microbiota of insects has been shown to play essential roles in processes related to physiology, metabolism, and innate immunity. In this study, the symbiotic microbiome of Plagiodera versicolora at different developmental stages was analyzed using 16S rRNA high-throughput sequencing. The result showed that symbiotic bacteria community in P. versicolora was primarily made up of Actinobacteriota, Proteobacteria, Firmicutes, Bacteroidota, and Dependentiae. The bacterial composition among different age individuals were highly diverse, while 65 core genera were distributed in all samples which recommend core bacterial microbiome. The 8 species core bacteria were isolated from all samples, and all of them were classified as Pseudomonas sp. Among them, five species have been proven to promote the vegetable growth of Beauveria bassiana. Moreover, the virulence of B. bassiana against nonaxenic larvae exceeded B. bassiana against axenic larvae, and the introduction of the Pseudomonas sp. to axenic larvae augmented the virulence of fungi. Taken together, our study demonstrates that the symbiotic bacteria of P. versicolora are highly dissimilar, and Pseudomonas sp. core bacteria can promote host infection by entomopathogenic fungus. This result emphasizes the potential for harnessing these findings in the development of effective pest management strategies.},
}

@article {pmid38029104,
year = {2023},
author = {Carrouel, F and Kanoute, A and Lvovschi, VE and Bourgeois, D},
title = {Periodontal pathogens of the interdental microbiota in a 3 months pregnant population with an intact periodontium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1275180},
doi = {10.3389/fmicb.2023.1275180},
pmid = {38029104},
issn = {1664-302X},
abstract = {Steroid hormones and the oral microbiota of pregnant women both appear as cumulative risk factors for gingivitis. This cross-sectional study, using real-time PCR, investigated the composition and diversity of the microbiota in interdental spaces of 3 months pregnant women with intact periodontium according the 2018 EFP/AAP classification. Bacteria identified were belonged to the red (Porphyromonas gingivalis Treponema denticola, and Tanerella forsythia), orange (Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus, and Parvimonas micra), and green (Eikenella corrodens and A. actinomycetencomitans) Socransky complexes. Approximatively 10[9.11] bacteria were counted per interdental space in pregnant women. Bacteria from the red complex represented 33.80% versus 62.81% for the orange group versus 3.39% for the green group of the total number spread over the 3 groups. Dietary habits and physical activity did not have a significant impact on interdental microbiota, although a decrease in the median amount of 9 periodontopathogens was observed when fruit and vegetable consumption increased. Pregnant women who brushed their teeth at least twice a day had lower counts of total bacteria and 9 periodontal pathogens than those who brushed less. In 3 months pregnant women at high risk of periodontal disease (>30% bleeding sites), the dendogram revealed 2 clusters of the 9 periodontopathogens. This provides further support for the "key pathogen" hypothesis, among which Porphyromonas gingivalis plays a key role, indicating that specific bacteria in limited quantities can influence the host immune system and convert the microbiota from symbiotic to dysbiotic to induce inflammatory disorder. As a result, this study reported that 3 months pregnant women with healthy periodontium had high levels of interdental bleeding and a dysbiotic microbiota with periodontal pathogens of the Socransky orange and red complexes. These subjects were therefore potentially at increased risk of developing periodontal disease and, consequently, an adverse pregnancy outcome. So, preventive oral prophylaxis measures, in particular individual interdental prophylaxis, should be implemented as soon as pregnancy is established.},
}

@article {pmid38028661,
year = {2023},
author = {Mazarakis, A and Bernhard-Skala, C and Braun, M and Peters, I},
title = {What is critical for human-centered AI at work? - Toward an interdisciplinary theory.},
journal = {Frontiers in artificial intelligence},
volume = {6},
number = {},
pages = {1257057},
doi = {10.3389/frai.2023.1257057},
pmid = {38028661},
issn = {2624-8212},
abstract = {Human-centered artificial intelligence (HCAI) has gained momentum in the scientific discourse but still lacks clarity. In particular, disciplinary differences regarding the scope of HCAI have become apparent and were criticized, calling for a systematic mapping of conceptualizations-especially with regard to the work context. This article compares how human factors and ergonomics (HFE), psychology, human-computer interaction (HCI), information science, and adult education view HCAI and discusses their normative, theoretical, and methodological approaches toward HCAI, as well as the implications for research and practice. It will be argued that an interdisciplinary approach is critical for developing, transferring, and implementing HCAI at work. Additionally, it will be shown that the presented disciplines are well-suited for conceptualizing HCAI and bringing it into practice since they are united in one aspect: they all place the human being in the center of their theory and research. Many critical aspects for successful HCAI, as well as minimum fields of action, were further identified, such as human capability and controllability (HFE perspective), autonomy and trust (psychology and HCI perspective), learning and teaching designs across target groups (adult education perspective), as much as information behavior and information literacy (information science perspective). As such, the article lays the ground for a theory of human-centered interdisciplinary AI, i.e., the Synergistic Human-AI Symbiosis Theory (SHAST), whose conceptual framework and founding pillars will be introduced.},
}

@article {pmid38028650,
year = {2023},
author = {Carrell, AA and Clark, M and Jawdy, S and Muchero, W and Alexandre, G and Labbé, JL and Rush, TA},
title = {Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa.},
journal = {Plant direct},
volume = {7},
number = {11},
pages = {e544},
doi = {10.1002/pld3.544},
pmid = {38028650},
issn = {2475-4455},
abstract = {Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.},
}

@article {pmid38028595,
year = {2023},
author = {Adedayo, AA and Babalola, OO},
title = {Genomic mechanisms of plant growth-promoting bacteria in the production of leguminous crops.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1276003},
doi = {10.3389/fgene.2023.1276003},
pmid = {38028595},
issn = {1664-8021},
abstract = {Legumes are highly nutritious in proteins and are good food for humans and animals because of their nutritional values. Plant growth-promoting bacteria (PGPR) are microbes dwelling in the rhizosphere soil of a plant contributing to the healthy status, growth promotion of crops, and preventing the invasion of diseases. Root exudates produced from the leguminous plants' roots can lure microbes to migrate to the rhizosphere region in other to carry out their potential activities which reveals the symbiotic association of the leguminous plant and the PGPR (rhizobia). To have a better cognition of the PGPR in the rhizosphere of leguminous plants, genomic analyses would be conducted employing various genomic sequences to observe the microbial community and their functions in the soil. Comparative genomic mechanism of plant growth-promoting rhizobacteria (PGPR) was discussed in this review which reveals the activities including plant growth promotion, phosphate solubilization, production of hormones, and plant growth-promoting genes required for plant development. Progress in genomics to improve the collection of genotyping data was revealed in this review. Furthermore, the review also revealed the significance of plant breeding and other analyses involving transcriptomics in bioeconomy promotion. This technological innovation improves abundant yield and nutritional requirements of the crops in unfavorable environmental conditions.},
}

@article {pmid38027833,
year = {2023},
author = {Widodo, },
title = {A new technique inversion Time-Domain electromagnetic data.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21638},
doi = {10.1016/j.heliyon.2023.e21638},
pmid = {38027833},
issn = {2405-8440},
abstract = {Time-Domain Electromagnetic (TDEM) data modeling, especially for central-loop configurations, is often achieved through 1D inversion models. This study aims to enhance the accuracy and efficiency of TDEM data inversion by employing the Born Approximation method to address calculation and convergence speed issues. We also utilize the modified Symbiotic Organism Search (mSOS), a global optimization algorithm capable of handling multi-minimum problems in non-linear objective functions, to optimize the inversion process. Our research includes the assessment of the accuracy and performance of this approach through inversion modeling on both synthetic and field data. The accuracy of the synthetic data was evaluated based on the algorithm's capability to retrieve the values of the synthetic data, as indicated by the small relative error between the synthetic model parameters and the calculated model. In the case of field data modeling, the accuracy relied on the consistency achieved when modeling the data with different numbers of layers. Additionally, we considered the time required to perform the inversion as an evaluation metric for inversion performance. For the synthetic data case, the algorithm produced relatively accurate models with misfit values of approximately 0 % and low relative error values. In the field data case, the inversion models demonstrated consistency and reduced misfit values when the data was modeled with different numbers of layers, specifically 8.72 % for the 2-layer model, 3.92 % for the 3-layer model, and 2.61 % for the 4- and 5-layer models. Both datasets required less than 19 min for 10,000 iterations. These findings highlight the innovative nature of the mSOS algorithm and its potential for practical applications in TDEM inversion studies.},
}

@article {pmid38025720,
year = {2023},
author = {Sánchez-Matiz, JJ and Díaz-Ariza, LA},
title = {Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16151},
doi = {10.7717/peerj.16151},
pmid = {38025720},
issn = {2167-8359},
abstract = {BACKGROUND: Around the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship.

METHODS: Through a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine.

RESULTS: The literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents.

CONCLUSION: This review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world.},
}

@article {pmid38025692,
year = {2023},
author = {Li, Y and Huang, Y and Wronski, T and Huang, M},
title = {Diversity of bacteria associated with lichens in Mt. Yunmeng in Beijing, China.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16442},
doi = {10.7717/peerj.16442},
pmid = {38025692},
issn = {2167-8359},
abstract = {Lichens host highly complex and diverse microbial communities, which may perform essential functions in these symbiotic micro-ecosystems. In this research, sequencing of 16S rRNA was used to investigate the bacterial communities associated with lichens of two growth forms (foliose and crustose). Results showed that Pseudomonadota, Actinomycetota and Acidobacteriota were dominant phyla in both types of lichens, while Acetobacterales and Hyphomicrobiales were the dominant orders. Alpha diversity index showed that the richness of bacteria hosted by foliose lichens was significantly higher than that hosted by crustose ones. Principal co-ordinates analysis showed a significant difference between beta diversity of the foliose lichen-associated bacterial communities and those of crustose lichen-associated ones. Gene function prediction showed most functions, annotated by the lichen-associated bacteria, to be related to metabolism, suggesting that related bacteria may provide nutrients to their hosts. Generally, our results propose that microbial communities play important roles in fixing nitrogen, providing nutrients, and controlling harmful microorganisms, and are therefore an integral and indispensable part of lichens.},
}

@article {pmid38023845,
year = {2023},
author = {Liu, X and Feng, Z and Zhang, W and Yao, Q and Zhu, H},
title = {Exogenous myristate promotes the colonization of arbuscular mycorrhizal fungi in tomato.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1250684},
doi = {10.3389/fpls.2023.1250684},
pmid = {38023845},
issn = {1664-462X},
abstract = {Arbuscular mycorrhizal fungi (AMF) can establish symbiotic associations with the roots of most terrestrial plants, thereby improving the tolerance of the host plants to biotic and abiotic stresses. Although AMF cannot synthesize lipids de novo, they can obtain lipids from the root cells for their growth and development. A recent study reveals that AMF can directly take up myristate (C14:0 lipid) from the environment and produce a large amount of hyphae in asymbiotic status; however, the effect of environmental lipids on AM symbiosis is still unclear. In this study, we inoculated tomato (Solanum lycopersicum) with AMF in an in vitro dual culture system and a sand culture system, and then applied exogenous myristate to the substrate, in order to explore the effect of exogenous lipids on the mycorrhizal colonization of AMF. We investigated the hyphae growth, development, and colonization of AMF, and examined the gene expression involved in phosphate transport, lipid biosynthesis, and transport. Results indicate that exogenous lipids significantly stimulated the growth and branching of hyphae, and significantly increased the number of hyphopodia and mycorrhizal colonization of AMF, with arbuscular abundance and intraradical spores or vesicles being the most promoted. In contrast, exogenous myristate decreased the growth range and host tropism of the germ tubes, and largely inhibited the exchange of nutrition between symbionts. As a result, exogenous myristate did not affect the plant growth. This study suggests that lipids promote mycorrhizal colonization by enhancing the growth and development of AMF hyphae and increasing their contact opportunities with plant roots. To the best of our knowledge, this is the first report that shows that lipids promote the colonization of AMF. Our study highlights the importance of better understanding the roles of environmental lipids in the establishment and maintenance of AM symbiosis and, thus, in agricultural production.},
}

@article {pmid38023592,
year = {2023},
author = {Yun, HM and Hyun, S},
title = {Role of gut commensal bacteria in juvenile developmental growth of the host: insights from Drosophila studies.},
journal = {Animal cells and systems},
volume = {27},
number = {1},
pages = {329-339},
doi = {10.1080/19768354.2023.2282726},
pmid = {38023592},
issn = {1976-8354},
abstract = {The gut microbiome plays a crucial role in maintaining health in a variety of organisms, from insects to humans. Further, beneficial symbiotic microbes are believed to contribute to improving the quality of life of the host. Drosophila is an optimal model for studying host-commensal microbe interactions because it allows for convenient manipulation of intestinal microbial composition. Fly microbiota has a simple taxonomic composition and can be cultivated and genetically tracked. This permits functional studies and analyses of the molecular mechanisms underlying their effects on host physiological processes. In this context, we briefly introduce the principle of juvenile developmental growth in Drosophila. Then, we discuss the current understanding of the molecular mechanisms underlying the effects of gut commensal bacteria, such as Lactiplantibacillus plantarum and Acetobacter pomorum, in the fly gut microbiome on Drosophila juvenile growth, including specific actions of gut hormones and metabolites in conserved cellular signaling systems, such as the insulin/insulin-like (IIS) and the target of rapamycin (TOR) pathways. Given the similarities in tissue function/structure, as well as the high conservation of physiological systems between Drosophila and mammals, findings from the Drosophila model system will have significant implications for understanding the mechanisms underlying the interaction between the host and the gut microbiome in metazoans.},
}

@article {pmid38023456,
year = {2023},
author = {Liang, J},
title = {Harmonizing minds and machines: survey on transformative power of machine learning in music.},
journal = {Frontiers in neurorobotics},
volume = {17},
number = {},
pages = {1267561},
doi = {10.3389/fnbot.2023.1267561},
pmid = {38023456},
issn = {1662-5218},
abstract = {This survey explores the symbiotic relationship between Machine Learning (ML) and music, focusing on the transformative role of Artificial Intelligence (AI) in the musical sphere. Beginning with a historical contextualization of the intertwined trajectories of music and technology, the paper discusses the progressive use of ML in music analysis and creation. Emphasis is placed on present applications and future potential. A detailed examination of music information retrieval, automatic music transcription, music recommendation, and algorithmic composition presents state-of-the-art algorithms and their respective functionalities. The paper underscores recent advancements, including ML-assisted music production and emotion-driven music generation. The survey concludes with a prospective contemplation of future directions of ML within music, highlighting the ongoing growth, novel applications, and anticipation of deeper integration of ML across musical domains. This comprehensive study asserts the profound potential of ML to revolutionize the musical landscape and encourages further exploration and advancement in this emerging interdisciplinary field.},
}

@article {pmid38020871,
year = {2023},
author = {Li, D and Xia, W and Cui, X and Zhao, M and Huang, K and Wang, X and Shen, J and Chen, H and Zhu, L},
title = {The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome.},
journal = {Evolutionary applications},
volume = {16},
number = {10},
pages = {1708-1720},
doi = {10.1111/eva.13595},
pmid = {38020871},
issn = {1752-4571},
abstract = {Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.},
}

@article {pmid38020682,
year = {2023},
author = {McPherson, AE and Abram, PK and Curtis, CI and Wannop, ER and Dudzic, JP and Perlman, SJ},
title = {Dynamic changes in Wolbachia infection over a single generation of Drosophila suzukii, across a wide range of resource availability.},
journal = {Ecology and evolution},
volume = {13},
number = {11},
pages = {e10722},
doi = {10.1002/ece3.10722},
pmid = {38020682},
issn = {2045-7758},
abstract = {Wolbachia bacteria are maternally inherited symbionts that commonly infect terrestrial arthropods. Many Wolbachia reach high frequencies in their hosts by manipulating their reproduction, for example by causing reproductive incompatibilities between infected male and uninfected female hosts. However, not all strains manipulate reproduction, and a key unresolved question is how these non-manipulative Wolbachia persist in their hosts, often at intermediate to high frequencies. One such strain, wSuz, infects the invasive fruit pest Drosophila suzukii, spotted-wing drosophila. Here, we tested the hypothesis that wSuz infection provides a competitive benefit when resources are limited. Over the course of one season, we established population cages with varying amounts of food in a semi-field setting and seeded them with a 50:50 mixture of flies with and without Wolbachia. We predicted that Wolbachia-infected individuals should have higher survival and faster development than their uninfected counterparts when there was little available food. We found that while food availability strongly impacted fly fitness, there was no difference in development times or survival between Wolbachia-infected and uninfected flies. Interestingly, however, Wolbachia infection frequencies changed dramatically, with infections either increasing or decreasing by as much as 30% in a single generation, suggesting the possibility of unidentified factors shaping Wolbachia infection over the course of the season.},
}

@article {pmid38019961,
year = {2023},
author = {Carobene, A and Padoan, A and Cabitza, F and Banfi, G and Plebani, M},
title = {Rising adoption of artificial intelligence in scientific publishing: evaluating the role, risks, and ethical implications in paper drafting and review process.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
pmid = {38019961},
issn = {1437-4331},
abstract = {BACKGROUND: In the rapid evolving landscape of artificial intelligence (AI), scientific publishing is experiencing significant transformations. AI tools, while offering unparalleled efficiencies in paper drafting and peer review, also introduce notable ethical concerns.

CONTENT: This study delineates AI's dual role in scientific publishing: as a co-creator in the writing and review of scientific papers and as an ethical challenge. We first explore the potential of AI as an enhancer of efficiency, efficacy, and quality in creating scientific papers. A critical assessment follows, evaluating the risks vs. rewards for researchers, especially those early in their careers, emphasizing the need to maintain a balance between AI's capabilities and fostering independent reasoning and creativity. Subsequently, we delve into the ethical dilemmas of AI's involvement, particularly concerning originality, plagiarism, and preserving the genuine essence of scientific discourse. The evolving dynamics further highlight an overlooked aspect: the inadequate recognition of human reviewers in the academic community. With the increasing volume of scientific literature, tangible metrics and incentives for reviewers are proposed as essential to ensure a balanced academic environment.

SUMMARY: AI's incorporation in scientific publishing is promising yet comes with significant ethical and operational challenges. The role of human reviewers is accentuated, ensuring authenticity in an AI-influenced environment.

OUTLOOK: As the scientific community treads the path of AI integration, a balanced symbiosis between AI's efficiency and human discernment is pivotal. Emphasizing human expertise, while exploit artificial intelligence responsibly, will determine the trajectory of an ethically sound and efficient AI-augmented future in scientific publishing.},
}

@article {pmid38018541,
year = {2023},
author = {Varshney, U},
title = {Co-evolution of the translation apparatus and eukaryotes.},
journal = {Journal of biosciences},
volume = {48},
number = {},
pages = {},
pmid = {38018541},
issn = {0973-7138},
abstract = {The symbiotic evolution between the two prokaryotic domains of life (bacteria and archaea) is believed to have given rise to the third domain of life, the eukaryotes. Common to all three domains of life, is an ancient mechanism of ribosome-mediated protein synthesis (translation). Can the evolutionary history of the protein translation apparatus shed light on the evolutionary history of life forms? This commentary addresses this broad question with the spotlight on a specific component of the translation apparatus.},
}

@article {pmid38017446,
year = {2023},
author = {Wu, YH and Qin, Y and Cai, QQ and Liu, M and He, DM and Chen, X and Wang, H and Yan, ZY},
title = {Effect the accumulation of bioactive constituents of a medicinal plant (Salvia Miltiorrhiza Bge.) by arbuscular mycorrhizal fungi community.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {597},
pmid = {38017446},
issn = {1471-2229},
support = {81973416//National Natural Science Foundation of China/ ; 2021YFS0045//the Science and Technology Department of Sichuan Province/ ; },
abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with various terrestrial plants and have attracted considerable interest as biofertilizers for improving the quality and yield of medicinal plants. Despite the widespread distribution of AMFs in Salvia miltiorrhiza Bunge's roots, research on the impact of multiple AMFs on biomass and active ingredient accumulations has not been conducted. In this study, the effects of five native AMFs (Glomus formosanum, Septoglomus constrictum, Rhizophagus manihotis, Acaulospora laevis, and Ambispora gerdemannii) and twenty-six communities on the root biomass and active ingredient concentrations of S. miltiorrhiza were assessed using the total factor design method.

RESULTS: Thirty-one treatment groups formed symbiotic relationships with S. miltiorrhiza based on the pot culture results, and the colonization rate ranged from 54.83% to 89.97%. AMF communities had higher colonization rates and total phenolic acid concentration than single AMF, and communities also appeared to have higher root fresh weight, dry weight, and total phenolic acid concentration than single inoculations. As AMF richness increased, there was a rising trend in root biomass and total tanshinone accumulations (ATTS), while total phenolic acid accumulations (ATP) showed a decreasing trend. This suggests that plant productivity was influenced by the AMF richness, with higher inoculation benefits observed when the communities contained three or four AMFs. Additionally, the affinities of AMF members were also connected to plant productivity. The inoculation effect of closely related AMFs within the same family, such as G. formosanum, S. constrictum, and R. manihotis, consistently yielded lower than that of mono-inoculation when any combinations were applied. The co-inoculation of S. miltiorrhiza with nearby or distant AMFs from two families, such as G. formosanum, R. manihotis, and Ac. laevis or Am. gerdemannii resulted in an increase of ATP and ATTS by more than 50%. AMF communities appear to be more beneficial to the yield of bioactive constituents than the single AMF, but overall community inoculation effects are related to the composition of AMFs and the relationship between members.

CONCLUSION: This study reveals that the AMF community has great potential to improve the productivity and the accumulation of bioactive constituents in S. miltiorrhiza, indicating that it is an effective way to achieve sustainable agricultural development through using the AMF community.},
}

@article {pmid38016867,
year = {2023},
author = {Quevarec, L and Brasseur, G and Aragnol, D and Robaglia, C},
title = {Tracking the early events of photosymbiosis evolution.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.11.005},
pmid = {38016867},
issn = {1878-4372},
abstract = {Oxygenic photosynthesis evolved in cyanobacteria around 3.2 giga-annum (Ga) ago and was acquired by eukaryotes starting around 1.8 Ga ago by endosymbiosis. Photosymbiosis results either from integration of a photosynthetic bacteria by heterotrophic eukaryotes (primary photosymbiosis) or by successive integration of photosymbiotic eukaryotes by heterotrophic eukaryotes (secondary photosymbiosis). Primary endosymbiosis is thought to have been a rare event, whereas secondary and higher-order photosymbiosis evolved multiple times independently in different taxa. Despite its recurrent evolution, the molecular and cellular mechanisms underlying photosymbiosis are unknown. In this opinion, we discuss the primary events leading to the establishment of photosymbiosis, and we present recent research suggesting that, in some cases, domestication occurred instead of symbiosis, and how oxygen and host immunity can be involved in symbiont maintenance.},
}

@article {pmid38016543,
year = {2023},
author = {Biswas, A and Chakraborty, S},
title = {Assessment of microbial population in integrated CW-MFC system and investigation of organics and fecal coliform removal pathway.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168809},
doi = {10.1016/j.scitotenv.2023.168809},
pmid = {38016543},
issn = {1879-1026},
abstract = {The current study is focused on understanding the operational mechanism of an integrated constructed wetland-microbial fuel cell (CW-MFC) reactor emphasizing fecal coliform (FC) removal. Few studies are available in the literature investigating the inherent mechanisms of pathogen inactivation in a CW-MFC system. Raw domestic wastewater was treated in three vertical reactors, one planted constructed wetland (R1), one planted CW-MFC (R2), and one unplanted CW-MFC (R3). Spatial analysis of treated effluents showed a considerable amount of organics and fecal coliform removal at the vicinity of the anode in R2. Assessment of the microbial population inside all the reactors revealed that EABs (Firmicutes, Bacteroidetes, and Actinobacteria) were more abundant in R2 compared to R1 and R3. During the activity study, biomass obtained from R2 showed a maximum substrate utilization rate of 1.27 mg COD mgVSS[-1] d[-1]. Kinetic batch studies were carried out for FC removal in all the reactors, and the maximum first order FC removal rate was obtained at the anode of R2 as 2.13 d[-1] when operated in closed circuit mode. This value was much higher than the natural die-off rate of FCs in raw wastewater which was 1.16 d[-1]. Simultaneous bioelectricity monitoring inferred that voltage generation can be correlated to faster FC inactivation, which was probably due to EABs outcompeting other exogenous microbes in a preferable anaerobic environment with the presence of an anode. Reactor R2 was found to be functioning as a symbiotic bio-electrochemical mesocosm.},
}

@article {pmid38016408,
year = {2023},
author = {Li, J and Li, Y and Xiao, H and Li, W and Ye, F and Wang, L and Li, Y and Wang, C and Wu, Y and Xuan, R and Huang, Y and Huang, J},
title = {The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China.},
journal = {Poultry science},
volume = {103},
number = {2},
pages = {103198},
doi = {10.1016/j.psj.2023.103198},
pmid = {38016408},
issn = {1525-3171},
abstract = {Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.},
}

@article {pmid38016378,
year = {2023},
author = {Cao, X and Cheng, XW and Liu, YY and Dai, HW and Gan, RY},
title = {Inhibition of pathogenic microbes in oral infectious diseases by natural products: Sources, mechanisms, and challenges.},
journal = {Microbiological research},
volume = {279},
number = {},
pages = {127548},
doi = {10.1016/j.micres.2023.127548},
pmid = {38016378},
issn = {1618-0623},
abstract = {The maintenance of oral health is of utmost importance for an individual's holistic well-being and standard of living. Within the oral cavity, symbiotic microorganisms actively safeguard themselves against potential foreign diseases by upholding a multifaceted equilibrium. Nevertheless, the occurrence of an imbalance can give rise to a range of oral infectious ailments, such as dental caries, periodontitis, and oral candidiasis. Presently, clinical interventions encompass the physical elimination of pathogens and the administration of antibiotics to regulate bacterial and fungal infections. Given the limitations of various antimicrobial drugs frequently employed in dental practice, the rising incidence of oral inflammation, and the escalating bacterial resistance to antibiotics, it is imperative to explore alternative remedies that are dependable, efficacious, and affordable for the prevention and management of oral infectious ailments. There is an increasing interest in the creation of novel antimicrobial agents derived from natural sources, which possess attributes such as safety, cost-effectiveness, and minimal adverse effects. This review provides a comprehensive overview of the impact of natural products on the development and progression of oral infectious diseases. Specifically, these products exert their influences by mitigating dental biofilm formation, impeding the proliferation of oral pathogens, and hindering bacterial adhesion to tooth surfaces. The review also encompasses an examination of the various classes of natural products, their antimicrobial mechanisms, and their potential therapeutic applications and limitations in the context of oral infections. The insights garnered from this review can support the promising application of natural products as viable therapeutic options for managing oral infectious diseases.},
}

@article {pmid38016137,
year = {2023},
author = {Azarm, A and Koosha, M and Dalimi, A and Zahraie-Ramazani, A and Akhavan, AA and Saeidi, Z and Mohebali, M and Azam, K and Vatandoost, H and Oshaghi, MA},
title = {Association Between Wolbachia Infection and Susceptibility to Deltamethrin Insecticide in Phlebotomus papatasi (Diptera: Psychodidae), the Main Vector of Zoonotic Cutaneous Leishmaniasis.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/vbz.2023.0085},
pmid = {38016137},
issn = {1557-7759},
abstract = {Background: Phlebotomus papatasi (Diptera: Psychodidae) is the main vector of zoonotic cutaneous leishmaniasis. Wolbachia is a symbiotic alphaproteobacteria of arthropods that can be involved in susceptibility or resistance. This study aimed to investigate the relationship between Wolbachia and Deltamethrin susceptibility/resistance in Ph. papatasi. Deltamethrin filter papers (0.00002%) were used to test sand fly field collected from southern Iran. After the test, PCR amplification of the Wolbachia surface protein gene (wsp) was used to measure Wolbachia infection rate in the killed, surviving, and control groups. Result: The rates of infection by Wolbachia strain (wPap, super group A) differed between killed (susceptible) and surviving (resistant) Ph. papatasi specimens. The rate of Wolbachia infection in susceptible individuals was more than twice (2.3) (39% vs. 17%) in resistant individuals with the same genetic background. This difference was highly significant (p < 0.001), indicating a positive association between Wolbachia infection and susceptibility to Deltamethrin. In addition, the results showed that Deltamethrin can act as a PCR inhibitor during detection of Wolbachia in Ph. papatasi. Conclusion: Results of this study show that Wolbachia is associated with Deltamethrin susceptibility level in Ph. papatasi. Also, as Deltamethrin has been identified as a PCR inhibitor, great care must be taken in interpreting Wolbachia infection status in infected populations. The results of this study may provide information for a better understanding of the host-symbiont relationship, as well as application of host symbiosis in pest management.},
}

@article {pmid38014981,
year = {2023},
author = {Ball, LM and Bronstein, E and Liechti, GW and Maurelli, AT},
title = {Neisseria gonorrhoeae drives Chlamydia trachomatis into a persistence-like state during in vitro co-infection.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0017923},
doi = {10.1128/iai.00179-23},
pmid = {38014981},
issn = {1098-5522},
abstract = {Chlamydia trachomatis and Neisseria gonorrhoeae are the most prevalent bacterial sexually transmitted infections (STIs) globally. Despite frequent co-infections in patients, few studies have investigated how mono-infections may differ from co-infections. We hypothesized that a symbiotic relationship between the pathogens could account for the high rates of clinical co-infection. During in vitro co-infection, we observed an unexpected phenotype where the C. trachomatis developmental cycle was impaired by N. gonorrhoeae. C. trachomatis is an obligate intracellular pathogen with a unique biphasic developmental cycle progressing from infectious elementary bodies (EB) to replicative reticulate bodies (RB), and back. After 12 hours of co-infection, we observed fewer EBs than in a mono-infection. Chlamydial genome copy number remained equivalent between mono- and co-infections. This is a hallmark of Chlamydial persistence. Chlamydial persistence alters inclusion morphology but varies depending on the stimulus/stress. We observed larger, but fewer, Chlamydia during co-infection. Tryptophan depletion can induce Chlamydial persistence, but tryptophan supplementation did not reverse the co-infection phenotype. Only viable and actively growing N. gonorrhoeae produced the inhibition phenotype in C. trachomatis. Piliated N. gonorrhoeae had the strongest effect on C. trachomatis, but hyperpiliated or non-piliated N. gonorrhoeae still produced the phenotype. EB development was modestly impaired when N. gonorrhoeae were grown in transwells above the infected monolayer. C. trachomatis serovar L2 was not impaired during co-infection. Chlamydial impairment could be due to cytoskeletal or osmotic stress caused by an as-yet-undefined mechanism. We conclude that N. gonorrhoeae induces a persistence-like state in C. trachomatis that is serovar dependent.},
}

@article {pmid38013749,
year = {2023},
author = {Tran, TT and van Leeuwen, J and Tran, DTM and Bush, SR},
title = {Beyond compliance: public voluntary standards and their effect on state institutional capacity in Vietnam.},
journal = {Journal of environmental policy & planning},
volume = {25},
number = {5},
pages = {511-523},
pmid = {38013749},
issn = {1522-7200},
abstract = {Public certification standards have received limited scholarly attention, especially the institutional capacity of public authorities that develop and implement these standards to address complex challenges, such as the promotion of industrial ecology and industrial symbiosis for enhancing resource use efficiency. This research uses an institutional capacity assessment framework to examine the ways in which a voluntary public standard for certifying eco-industrial parks affected the Vietnamese state's capacity to coordinate and implement industrial ecology. The article draws upon the interviews and a review of official documentation to show that the benefits of public standards extend beyond compliance to the enhancement of state capacities to coordinate complex policy domains such as industrial ecology. The findings contribute to providing a basis to redesign standard-setting processes to move beyond end-user compliance and provide insights into how public actors can more effectively address 'systemic' sustainability challenges - from circular economy ambitions to the Sustainable Development Goals.},
}

@article {pmid38013635,
year = {2023},
author = {Ntui, VO and Tripathi, JN and Shah, T and Tripathi, L},
title = {Targeted knockout of early nodulin-like 3 (MusaENODL3) gene in banana reveals its function in resistance to Xanthomonas wilt disease.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14248},
pmid = {38013635},
issn = {1467-7652},
support = {//CGIAR research program for roots, tubers, and banana/ ; USAID//The United States Agency for International Development (USAID)/ ; },
abstract = {Nodulins and nodulin-like proteins play an essential role in the symbiotic associations between legumes and Rhizobium bacteria. Their role extends beyond the leguminous species, as numerous nodulin-like proteins, including early nodulin-like proteins (ENODL), have been identified in various non-leguminous plants, implying their involvement in functions beyond nodulation, such as nutrient transport and growth modulation. Some ENODL proteins have been associated with plant defense against pathogens, as evident in banana infected with Xanthomonas campestris pv. musacearum (Xcm) causing banana Xanthomonas wilt (BXW) disease. Nonetheless, the specific role of ENODL in plant defense remains to be fully elucidated. The MusaENODL3 gene was found to be repressed in BXW-resistant banana progenitor 'Musa balbisiana' and 20-fold upregulated in BXW-susceptible cultivar 'Gonja Manjaya' upon early infection with Xcm. To further unravel the role of the ENODL gene in disease resistance, the CRISPR/Cas9 system was employed to disrupt the MusaENODL3 gene in 'Gonja Manjaya' precisely. Analysis of the enodl3 edited events confirmed the accurate manipulation of the MusaENODL3 gene. Disease resistance and gene expression analysis demonstrated that editing the MusaENODL3 gene resulted in resistance to BXW disease, with 50% of the edited plants remaining asymptomatic. The identification and manipulation of the MusaENODL3 gene highlight its potential as a critical player in plant-pathogen interactions, offering new opportunities for enhancing disease resistance in crops like banana, an important staple food crop and source of income for resource-poor farmers in the tropics. This study provides the first evidence of the direct role of the ENODL3 gene in developing disease-resistant plants.},
}

@article {pmid38013492,
year = {2023},
author = {Giovannetti, M and Binci, F and Navazio, L and Genre, A},
title = {Nonbinary fungal signals and calcium-mediated transduction in plant immunity and symbiosis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19433},
pmid = {38013492},
issn = {1469-8137},
support = {PRID - BIRD180317//Dipartimento di Biologia, Università degli Studi di Padova/ ; PRID - BIRD214519//Dipartimento di Biologia, Università degli Studi di Padova/ ; //European Commission/ ; 2022NW97JX//Ministero dell'Università e della Ricerca/ ; //Università di Torino - Dipartimento di Scienze della Vita e Biologia dei Sistemi/ ; },
abstract = {Chitin oligomers (COs) are among the most common and active fungal elicitors of plant responses. Short-chain COs from symbiotic arbuscular mycorrhizal fungi activate accommodation responses in the host root, while long-chain COs from pathogenic fungi are acknowledged to trigger defence responses. The modulation of intracellular calcium concentration - a common second messenger in a wide variety of plant signal transduction processes - plays a central role in both signalling pathways with distinct signature features. Nevertheless, mounting evidence suggests that plant immunity and symbiosis signalling partially overlap at multiple levels. We here elaborate on recent findings on this topic, highlighting the nonbinary nature of chitin-based fungal signals, their perception and their interpretation through Ca[2+] -mediated intracellular signals. Based on this, we propose that plant perception of symbiotic and pathogenic fungi is less clear-cut than previously described and involves a more complex scenario in which partially overlapping and blurred signalling mechanisms act upstream of the unambiguous regulation of gene expression driving accommodation or defence responses.},
}

@article {pmid38011635,
year = {2023},
author = {Choueiry, F and Gold, A and Xu, R and Zhang, S and Zhu, J},
title = {Secondary-Electrospray Ionization Mass Spectrometry-Based Online Analyses of Mouse Volatilome Uncover Gut Microbiome-Dictated Metabolic Changes in the Host.},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {},
number = {},
pages = {},
doi = {10.1021/jasms.3c00304},
pmid = {38011635},
issn = {1879-1123},
abstract = {The symbiotic relationship between the gut microbial population is capable of regulating numerous aspects of host physiology, including metabolism. Bacteria can modulate the metabolic processes of the host by feeding on nutritional components within the lumen and releasing bioactive components into circulation. Endogenous volatile organic compound (VOC) synthesis is dependent on the availability of precursors found in mammalian metabolism. Herein, we report that microbial-mediated metabolic influences can alter the host volatilome and the prominent volatile changes can be uncovered by a novel volatile analysis technique named secondary electrospray ionization mass spectrometry. Mice were subjected to an antibiotic cocktail to deplete the microbiome and then inoculated with either single strain bacteria or fecal matter transplantation (FMT) to replete the microbial population in the gut. VOC sampling was achieved by using an advanced secondary electrospray ionization (SESI) source that directly mounted onto a Thermo Q-Exactive high-resolution mass spectrometer (HRMS). A principal component analysis summarizing the volatile profiles of the mice revealed independent clustering of each strain of the FMT-inoculated groups, suggesting unique volatile profiles. The Mummichog algorithm uncovered phenylalanine metabolism as a significantly altered metabolic profile in the volatilome of the microbiome-repleted mice. Our results indicated that the systemic metabolic changes incurred by the host are translated to unique volatile profiles correlated to the diversity of the microbial population colonized within the host. It is thus possible to take advantage of SESI-HRMS-based platforms for noninvasive screening of VOCs to determine the contribution of various microbial colonization within human gut that may impact host health.},
}

@article {pmid38010368,
year = {2023},
author = {Yeo, XY and Chae, WR and Lee, HU and Bae, HG and Pettersson, S and Grandjean, J and Han, W and Jung, S},
title = {Nuanced contribution of gut microbiome in the early brain development of mice.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2283911},
doi = {10.1080/19490976.2023.2283911},
pmid = {38010368},
issn = {1949-0984},
abstract = {The complex symbiotic relationship between the mammalian body and gut microbiome plays a critical role in the health outcomes of offspring later in life. The gut microbiome modulates virtually all physiological functions through direct or indirect interactions to maintain physiological homeostasis. Previous studies indicate a link between maternal/early-life gut microbiome, brain development, and behavioral outcomes relating to social cognition. Here we present direct evidence of the role of the gut microbiome in brain development. Through magnetic resonance imaging (MRI), we investigated the impact of the gut microbiome on brain organization and structure using germ-free (GF) mice and conventionalized mice, with the gut microbiome reintroduced after weaning. We found broad changes in brain volume in GF mice that persist despite the reintroduction of gut microbes at weaning. These data suggest a direct link between the maternal gut or early-postnatal microbe and their impact on brain developmental programming.},
}

@article {pmid38009998,
year = {2023},
author = {Naka, H and Haygood, MG},
title = {The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0074423},
doi = {10.1128/aem.00744-23},
pmid = {38009998},
issn = {1098-5336},
abstract = {This study highlights diversity in iron acquisition and regulation in bacteria. The mechanisms of iron acquisition and its regulation in Teredinibacter turnerae, as well as its connection to cellulose utilization, a hallmark phenotype of T. turnerae, expand the paradigm of bacterial iron acquisition. Two of the four TonB genes identified in T. turnerae exhibit functional redundancy and play a crucial role in siderophore-mediated iron transport. Unlike typical TonB genes in bacteria, none of the TonB genes in T. turnerae are clearly iron regulated. This unusual regulation could be explained by another important finding in this study, namely, that the two TonB genes involved in iron transport are also essential for cellulose utilization as a carbon source, leading to the expression of TonB genes even under iron-rich conditions.},
}

@article {pmid38009979,
year = {2023},
author = {Roda, C and Clúa, J and Eylenstein, A and Greco, M and Ariel, F and Zanetti, ME and Blanco, FA},
title = {The C subunit of the nuclear factor Y binds to the Cyclin P4;1 promoter to modulate nodule organogenesis and infection during symbiosis in Phaseolus vulgaris.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19419},
pmid = {38009979},
issn = {1469-8137},
support = {PICT 2019/00029;//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2020-00053//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
}

@article {pmid38009302,
year = {2023},
author = {Ferrer-Orgaz, S and Tiwari, M and Isidra-Arellano, MC and Pozas-Rodriguez, EA and Vernié, T and Rich, MK and Mbengue, M and Formey, D and Delaux, PM and Ané, JM and Valdés-López, O},
title = {Early Phosphorylated Protein 1 is required to activate the early rhizobial infection program.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19423},
pmid = {38009302},
issn = {1469-8137},
support = {OPP1172165//Bill and Melinda Gates Foundation/ ; DE-SC0018247//DOE/ ; 101001675//European Union's Horizon 2020/ ; ANR-10-LABX-41//Laboratoire d'Excellence TULIP/ ; 2010789//NSF-IOS/ ; IN201320//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; },
}

@article {pmid38008224,
year = {2023},
author = {Ruangwicha, J and Chiersilp, B and Suyotha, W},
title = {Green biorefinery of shrimp shell waste for α-chitin and high-value co-products through successive fermentation by co-lactic acid bacteria and proteolytic fungus.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130106},
doi = {10.1016/j.biortech.2023.130106},
pmid = {38008224},
issn = {1873-2976},
abstract = {Green biorefinery process was conducted to extract α-chitin and high-value co-products from shrimp shell waste through microbial fermentation using mature coconut water (MCW) as a sole nutrient source. Symbiotic co-lactic acid fermentation (Co-LAF) by Lactobacillus plantarum and Streptococcus thermophilus produced higher levels of lactic acid (LA) and protease activity than their mono-cultures, which led to greater demineralization (DM) and deproteinization (DP) of shrimp shell powder (SSP). After optimizing Co-LAF through Response Surface Methodology and successive fermentation by an acid-active proteolytic fungus Rhizopus oligosporus, the highest DM of 94.0 ± 0.91 % and DP of 86.7 ± 0.1 % were achieved. Based on FT-IR, XRD, and SEM analysis, the bio-extracted chitin had similar structural characteristics to commercial α-chitin but with better quality. These strategies not only contribute to environmentally-friendly and cost-effective extraction of α-chitin (303 ± 18 mg/g-SSP), but also co-produce LA (57.18 ± 0.89 g/L), acid protease (4.33 ± 0.5 U/mL), bio-calcium (277 ± 12 mg-CaSO4/g-SSP), protein hydrolysate (268 ± 5 mg/g-SSP), and pigments (28.78 ± 1.56 µg/g-SSP).},
}

@article {pmid38008016,
year = {2023},
author = {Zhu, J and Miao, X and Li, X and Zhang, Y and Lou, Y and Chen, H and Liu, X},
title = {Granulomatous lobular mastitis co-existing with ductal carcinoma in situ: Report of three cases and review of the literature.},
journal = {Annals of diagnostic pathology},
volume = {68},
number = {},
pages = {152241},
doi = {10.1016/j.anndiagpath.2023.152241},
pmid = {38008016},
issn = {1532-8198},
abstract = {Granulomatous lobular mastitis (GLM) is a benign and infrequent chronic breast ailment. Although this lesion can be clinically and radiographically mistaken for early-onset breast cancer, it is a rare occurrence for the two to coexist. This report describes three such cases. In all three patients, the primary signs and symptoms were related to the formation of diffuse breast masses or abscesses. Breast ultrasound and MRI revealed glandular edema and dilated breast ducts. The biopsies of all lesions exhibited both granulomatous inflammation confined to the lobules of the breast, abundant interstitial inflammatory cell infiltrates, and apparently cancerous cells located in dilated ducts with intact basement membranes. The surgically excised specimens confirmed the diagnosis of GLM and ductal carcinoma in situ (DCIS) in all three patients who underwent breast mass resection. By clinical imaging and clinical manifestations, GLM may obscure a concurrent DCIS, as highlighted by the cases reported herein.},
}

@article {pmid38007735,
year = {2023},
author = {Guo, Y and Liang, L and Liang, W},
title = {Exploring of Diverse Plant Communities and Adaptation to Drought Conditions Based on Advanced Logistics Model with Variable Growth.},
journal = {Studies in health technology and informatics},
volume = {308},
number = {},
pages = {137-145},
doi = {10.3233/SHTI230834},
pmid = {38007735},
issn = {1879-8365},
abstract = {Bio reciprocal symbiosis is very common in nature, such as soybeans providing food for rhizobia, which uses atmospheric nitrogen to synthesize nitrogen to provide nutrients to soybeans. This paper proposes an advanced Logistic model that adjusts to changes in precipitation and an environmental capacity parameter that varies with the level of symbiosis. The aim is to precisely depict the symbiotic relationship between plants and the interplay among symbiosis, competition, and independent growth of each population in the plant community, as precipitation changes by adapting finite difference method and tertiary Hermit interpolation. The model in this paper offers a comprehensive understanding of how plant populations interact with one another, providing valuable insights into the dynamics of plant growth and development. This paper finally finds that a combination of woody and herbaceous plants had the highest growth rate and total biomass, while herbaceous-only plants required 7 times longer to reach environmental capacity. This paper also reveals that irregular weather patterns, and different levels of species biomass can have different impacts on the recovery time of plant communities after drought or damage, and different types of pollution can have various effects on the community's regeneration, while the effect of overgrazing is the smallest.},
}

@article {pmid38007500,
year = {2023},
author = {Matthews, JL and Hoch, L and Raina, JB and Pablo, M and Hughes, DJ and Camp, EF and Seymour, JR and Ralph, PJ and Suggett, DJ and Herdean, A},
title = {Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20724},
pmid = {38007500},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/physiology ; Photosynthesis ; Temperature ; Bacteria ; Photosystem II Protein Complex ; *Dinoflagellida/physiology ; Symbiosis ; },
abstract = {Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.},
}

Animals
*Anthozoa/physiology
Photosynthesis
Temperature
Bacteria
Photosystem II Protein Complex
*Dinoflagellida/physiology
Symbiosis

@article {pmid38007126,
year = {2023},
author = {Förster, F and Reynaud, S and Sauzéat, L and Ferrier-Pagès, C and Samankassou, E and Sheldrake, TE},
title = {Increased coral biomineralization due to enhanced symbiotic activity upon volcanic ash exposure.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168694},
doi = {10.1016/j.scitotenv.2023.168694},
pmid = {38007126},
issn = {1879-1026},
abstract = {Coral reefs, which are among the most productive ecosystems on earth, are in global decline due to rapid climate change. Volcanic activity also results in extreme environmental changes at local to global scales, and may have significant impacts on coral reefs compared to other natural disturbances. During explosive eruptions, large amounts of volcanic ash are generated, significantly disrupting ecosystems close to a volcano, and depositing ash over distal areas (10s - 1000s of km depending on i.a. eruption size and wind direction). Once volcanic ash interacts with seawater, the dissolution of metals leads to a rapid change in the geochemical properties of the seawater column. Here, we report the first known effects of volcanic ash on the physiology and elemental cycling of a symbiotic scleractinian coral under laboratory conditions. Nubbins of the branching coral Stylophora pistillata were reared in aquaria under controlled conditions (insolation, temperature, and pH), while environmental parameters, effective quantum yield, and skeletal growth rate were monitored. Half the aquaria were exposed to volcanic ash every other day for 6 weeks (250 mg L[-1] week[-1]), which induced significant changes in the fluorescence-derived photochemical parameters (ΦPSII, Fv/Fm, NPQ, rETR), directly enhanced the efficiency of symbiont photosynthesis (Pg, Pn), and lead to increased biomineralization rates. Enhancement of symbiont photosynthesis is induced by the supply of essential metals (Fe and Mn), derived from volcanic ash leaching in ambient seawater or within the organism following ingestion. The beneficial role of volcanic ash as an important micronutrient source is supported by the fact that neither photophysiological stress nor signs of lipid peroxidation were detected. Subaerial volcanism affects micronutrient cycling in the coral ecosystem, but the implication for coral ecophysiology on a reef scale remains to be tested. Nevertheless, exposure to volcanic ash can improve coral health and thus influence resilience to external stressors.},
}

@article {pmid38006561,
year = {2024},
author = {Bordenstein, SR},
title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {337-348},
pmid = {38006561},
issn = {1940-6029},
mesh = {Animals ; *Arthropods ; *Wolbachia/genetics ; *Bacteriophages/genetics ; Prophages ; Myoviridae ; },
abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.},
}

Animals
*Arthropods
*Wolbachia/genetics
*Bacteriophages/genetics
Prophages
Myoviridae

@article {pmid38006559,
year = {2024},
author = {Cortez, CT and Murphy, RO and Owens, IM and Beckmann, JF},
title = {Use of Drosophila Transgenics to Identify Functions for Symbiont Effectors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {301-320},
doi = {10.1007/978-1-0716-3553-7_18},
pmid = {38006559},
issn = {1940-6029},
abstract = {Wolbachia, one of the most successful and studied insect symbionts, and Drosophila, one of the most understood model insects, can be exploited as complementary tools to unravel mechanisms of insect symbiosis. Although Wolbachia itself cannot be grown axenically as clonal isolates or genetically manipulated by standard methods, its reproductive phenotypes, including cytoplasmic incompatibility (CI), have been elucidated using well-developed molecular tools and precise transgenic manipulations available for Drosophila melanogaster. Current research only scratches the surface of how Drosophila can provide a tool for understanding Wolbachia's evolutionary success and the molecular roles of its genetic elements. Here, we briefly outline basic methodologies inherent to transgenic Drosophila systems that have already contributed significant advances in understanding CI, but may be unfamiliar to those who lack experience in Drosophila genetics. In the future, these approaches will continue providing significant insights into Wolbachia that undoubtedly will be extended to other insect symbionts and their biological capabilities.},
}

@article {pmid38006556,
year = {2024},
author = {Duplouy, A},
title = {Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {239-247},
pmid = {38006556},
issn = {1940-6029},
abstract = {Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.},
}

@article {pmid38006552,
year = {2024},
author = {Zhang, M and Xi, Z},
title = {Wolbachia Transinfection Via Embryonic Microinjection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {175-188},
pmid = {38006552},
issn = {1940-6029},
abstract = {The process of transferring Wolbachia from one species to another to establish a stable, maternally inherited infection in the target species is known as transinfection. The success of transinfection is primarily achieved through embryonic microinjection, which is the most direct and efficient means of delivering Wolbachia into the germline of the target species and establishing stable maternal transmission. For the fundamental studies, transinfection is often used to characterize Wolbachia-host interactions, including Wolbachia host range, the role of host or bacterial factors in symbiosis, and evolution of Wolbachia-host associations. For the applied studies, use of transinfection to generate a novel infection in the target species is the first step to build the weapon for both population replacement and population suppression for controlling insect pests or their transmitted diseases. For the primary dengue vector Aedes aegypti and Anopheles vectors of malaria, which either do not naturally carry Wolbachia or are infected with strains that lack necessary features for implementation, transinfection can be established by introducing a novel strain capable of inducing both cytoplasmic incompatibility (CI) and pathogen blocking. For A. albopictus and Culex mosquito species, which naturally harbor CI-inducing Wolbachia, transinfection can be achieved by either introducing a novel strain to generate superinfection or replacing the native infection with a different Wolbachia strain in a symbiont-free line, which is derived from antibiotic treatment of the wild type. Here, we use A. aegypti as an example to describe the Wolbachia transinfection method, which can be adapted to other insect species, such as planthoppers, according to their specific developmental requirements.},
}

@article {pmid38006547,
year = {2024},
author = {Kakumanu, ML and Hickin, ML and Schal, C},
title = {Detection, Quantification, and Elimination of Wolbachia in Bed Bugs.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {97-114},
pmid = {38006547},
issn = {1940-6029},
abstract = {Wolbachia is an obligatory nutritional symbiont of the common bed bug, Cimex lectularius, providing B-vitamins to its host. The biological significance of Wolbachia to bed bugs is investigated primarily by eliminating the symbiont with antibiotics, which is followed by confirmation with molecular assays. In this chapter, we describe a protocol for eliminating Wolbachia in bed bugs using the ansamycin antibiotic rifampicin (also known as rifampin) and three molecular methods to accurately detect and quantify the Wolbachia gene copies in bed bug samples. We describe the digital droplet PCR (ddPCR), a highly sensitive technique for absolute quantification of low abundance target genes, which has proven to be a valuable technique for confirmation of the elimination of Wolbachia.},
}

@article {pmid38006542,
year = {2024},
author = {Fallon, AM},
title = {Wolbachia: Advancing into a Second Century.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {1-13},
pmid = {38006542},
issn = {1940-6029},
abstract = {Wolbachia pipientis had its scientific debut nearly a century ago and has recently emerged as a target for therapeutic treatment of filarial infections and an attractive tool for control of arthropod pests. Wolbachia was known as a biological entity before DNA was recognized as the molecule that carries the genetic information on which life depends, and before arthropods and nematodes were grouped in the Ecdysozoa. Today, some investigators consider Wolbachia the most abundant endosymbiont on earth, given the numbers of its hosts and its diverse mutualistic, commensal, and parasitic roles in their life histories. Recent advances in molecular technologies have revolutionized our understanding of Wolbachia and its associated reproductive phenotypes. New models have emerged for its investigation, and substantial progress has been made towards Wolbachia-based interventions in medicine and agriculture. Here I introduce Wolbachia, with a focus on aspects of its biology that are covered in greater detail in subsequent chapters.},
}

@article {pmid38006236,
year = {2023},
author = {Watanabe, D},
title = {Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbad167},
pmid = {38006236},
issn = {1347-6947},
abstract = {The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.},
}

@article {pmid38006200,
year = {2023},
author = {Houldcroft, CJ and Underdown, S},
title = {Infectious disease in the Pleistocene: Old friends or old foes?.},
journal = {American journal of biological anthropology},
volume = {182},
number = {4},
pages = {513-531},
doi = {10.1002/ajpa.24737},
pmid = {38006200},
issn = {2692-7691},
support = {//Oxford Brookes University/ ; },
abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.},
}

@article {pmid38005785,
year = {2023},
author = {Amoako, FK and Sulieman, S and Mühling, KH},
title = {Mineral and Carbon Metabolic Adjustments in Nodules of Symbiotically Grown Faba Bean (Vicia faba L.) Varieties in Response to Organic Phosphorus Supplementation.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {22},
pages = {},
pmid = {38005785},
issn = {2223-7747},
abstract = {Phosphorus (P) is a major limiting factor for legume and symbiotic nitrogen fixation (SNF). Although overall adaptations of legumes to P supplementation have been extensively studied in connection with inorganic P, little information is currently available regarding nodulation or SNF responses to organic P (Po) in hydroponics. We investigated the mineral and carbon metabolism of Po-induced nodules of two contrasting faba bean varieties grown hydroponically under inorganic P (Pi), viz., in P-deficient (2 µM KH2PO4, -Pi), sufficient-P (200 µM KH2PO4, +Pi), and phytic acid (200 µM, Po) conditions, and were inoculated with Rhizobium leguminosarum bv. viciae 3841 and grown for 30 days. The results consistently reveal similar growth and biomass partitioning patterns between +Pi and Po, with both varying substantially from -Pi. In comparison, +Pi and Po observed equivalent accumulations of overall elemental P concentrations, with both increasing by 114 and 119%, respectively, relative to -Pi. A principal component analysis on metabolites showed a clear separation of the -Pi treatment from the others, with +Pi and Po correlating closely together, highlighting the nonsignificant differences between them. Additionally, the δ[15]N abundance of shoots, roots, and nodules was not significantly different between treatments and varieties and exhibited negative δ[15]N signatures for all tissues. Our study provides a novel perspective on mineral and carbon metabolism and their regulation of the growth, functioning, and reprogramming of nodules upon phytate supply.},
}

@article {pmid38004797,
year = {2023},
author = {Ngwenya, ZD and Dakora, FD},
title = {Symbiotic Functioning and Photosynthetic Rates Induced by Rhizobia Associated with Jack Bean (Canavalia ensiformis L.) Nodulation in Eswatini.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004797},
issn = {2076-2607},
abstract = {Improving the efficiency of the legume-rhizobia symbiosis in African soils for increased grain yield would require the use of highly effective strains capable of nodulating a wide range of legume plants. This study assessed the photosynthetic functioning, N2 fixation, relative symbiotic effectiveness (%RSE) and C assimilation of 22 jack bean (Canavalia ensiformis L.) microsymbionts in Eswatini soils as a first step to identifying superior isolates for inoculant production. The results showed variable nodule number, nodule dry matter, shoot biomass and photosynthetic rates among the strains tested under glasshouse conditions. Both symbiotic parameters and C accumulation differed among the test isolates at the shoot, root and whole-plant levels. Although 7 of the 22 jack bean isolates showed much greater relative symbiotic efficiency than the commercial Bradyrhizobium strain XS21, only one isolate (TUTCEeS2) was statistically superior to the inoculant strain, which indicates its potential for use in inoculant formulation after field testing. Furthermore, the isolates that recorded high %RSE elicited greater amounts of fixed N.},
}

@article {pmid38004772,
year = {2023},
author = {Zhang, P and Meng, S and Bao, G and Li, Y and Feng, X and Lu, H and Ma, J and Wei, X and Liu, W},
title = {Effect of Epichloë Endophyte on the Growth and Carbon Allocation of Its Host Plant Stipa purpurea under Hemiparasitic Root Stress.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004772},
issn = {2076-2607},
support = {2022-ZJ-715//the basic research program of science and technology of Qinghai Province, China/ ; 32060398 and U21A20239//The Natural Science Foundation of China/ ; },
abstract = {Epichloë endophytes not only affect the growth and resistance of their host plants but also confer nutrient benefits to parasitized hosts. In this study, we used Pedicularis kansuensis to parasitize Stipa purpurea, both with and without endophytic fungi, and to establish a parasitic system. In this study, endophytic fungal infection was found to increase the dry weight of the leaf, stem, and leaf sheath, as well as the plant height, root length, tiller number, aboveground biomass, and underground biomass of S. purpurea under root hemiparasitic stress. Meanwhile, the [13]C allocation of the leaf sheaths and roots of S. purpurea increased as the density of P. kansuensis increased, while the [13]C allocation of the leaf sheaths and roots of E+ S. purpurea was lower than that of E- S. purpurea. The [13]C allocation of the stem, leaf sheath, and root of E+ S. purpurea was higher than that of its E- counterpart. Furthermore, the content of photosynthetic [13]C and the [13]C partition rate of the stems, leaves, roots, and entire plant of S. purpurea and P. kansuensis transferred from S. purpurea increased as the density of P. kansuensis increased. These results will generate new insights into the potential role of symbiotic microorganisms in regulating the interaction between root hemiparasites and their hosts.},
}

@article {pmid38004718,
year = {2023},
author = {Kampen, H and Werner, D},
title = {Biting Midges (Diptera: Ceratopogonidae) as Vectors of Viruses.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004718},
issn = {2076-2607},
abstract = {Biting midges of the genus Culicoides occur almost globally and can regionally and seasonally reach high abundances. Most species are hematophagous, feeding on all groups of vertebrates, including humans. In addition to being nuisance pests, they are able to transmit disease agents, with some viruses causing high morbidity and/or mortality in ruminants, horses and humans. Despite their impact on animal husbandry, public health and tourism, knowledge on the biology and ecology of culicoid biting midges and their interactions with ingested pathogens or symbiotic microorganisms is limited. Research is challenging due to unknown larval habitats, the insects' tiny size, the inability to establish and breed most species in the laboratory and the laborious maintenance of colonies of the few species that can be reared in the laboratory. Consequently, the natural transmission of pathogens has experimentally been demonstrated for few species while, for others, only indirect evidence of vector potential exists. Most experimental data are available for Culicoides sonorensis and C. nubeculosus, the only species kept in western-world insectaries. This contribution gives an overview on important biting midge vectors, transmitted viruses, culicoid-borne viral diseases and their epidemiologies and summarizes the little knowledge on interactions between biting midges, their microflora and culicoid-borne arboviruses.},
}

@article {pmid38004678,
year = {2023},
author = {Mondal, S and Somani, J and Roy, S and Babu, A and Pandey, AK},
title = {Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/microorganisms11112665},
pmid = {38004678},
issn = {2076-2607},
support = {BT/PR45283/NER/95/1919/2022//Department of Biotechnology/ ; },
abstract = {The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.},
}

@article {pmid38004180,
year = {2023},
author = {Zhou, J and Ho, V},
title = {Role of Baseline Gut Microbiota on Response to Fiber Intervention in Individuals with Irritable Bowel Syndrome.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/nu15224786},
pmid = {38004180},
issn = {2072-6643},
support = {Investigator Initiated Funding Scheme//Nestlé Foundation/ ; },
abstract = {Irritable bowel syndrome (IBS) is one of the most prevalent functional gut disorders in the world. Partially hydrolyzed guar gum, a low-viscosity soluble fiber, has shown promise in the management of IBS-related symptoms. In this study, we aimed to determine if an individual's baseline gut microbiota impacted their response to a partially hydrolyzed guar gum intervention. Patients diagnosed with IBS undertook a 90-day intervention and follow-up. IBS symptom severity, tolerability, quality-of-life, and fecal microbiome composition were recorded during this study. Patients with normal microbiota diversity (Shannon index ≥ 3) showed significant improvements to IBS symptom scores, quality-of-life, and better tolerated the intervention compared to patients with low microbiota diversity (Shannon index < 3). Our findings suggest that an individual's baseline microbiome composition exerts a substantial influence on their response to fiber intervention. Future investigations should explore a symbiotic approach to the treatment of IBS.},
}