@article {pmid36739554,
year = {2022},
author = {Hoysted, GA and Field, KJ and Sinanaj, B and Bell, CA and Bidartondo, MI and Pressel, S},
title = {Direct nitrogen, phosphorus and carbon exchanges between Mucoromycotina 'fine root endophyte' fungi and a flowering plant in novel monoxenic cultures.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18630},
pmid = {36739554},
issn = {1469-8137},
support = {BB/M026825/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Most plants form mycorrhizal associations with mutualistic soil fungi. Through these partnerships, resources are exchanged including photosynthetically fixed carbon for fungal-acquired nutrients. Recently, it was shown that the diversity of associated fungi is greater than previously assumed, extending to Mucoromycotina fungi. These Mucoromycotina 'fine root endophytes' (MFRE) are widespread and generally co-colonise plant roots together with Glomeromycotina 'coarse' arbuscular mycorrhizal fungi (AMF). Until now, this co-occurrence has hindered the determination of the direct function of MFRE symbiosis. To overcome this major barrier, we developed new techniques for fungal isolation and culture and established the first monoxenic in vitro cultures of MFRE colonising a flowering plant, clover. Using radio- and stable-isotope tracers in these in vitro systems, we measured the transfer of [33] P, [15] N and [14] C between MFRE hyphae and the host plant. Our results provide the first unequivocal evidence that MFRE fungi are nutritional mutualists with a flowering plant by showing that clover gained both [15] N and [33] P tracers directly from fungus in exchange for plant-fixed C in the absence of other micro-organisms. Our findings and methods pave the way for a new era in mycorrhizal research, firmly establishing MFRE as both mycorrhizal and functionally important in terrestrial ecosystems.},
}

@article {pmid36739313,
year = {2023},
author = {Kruasuwan, W and Lohmaneeratana, K and Munnoch, JT and Vongsangnak, W and Jantrasuriyarat, C and Hoskisson, PA and Thamchaipenet, A},
title = {Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces.},
journal = {Rice (New York, N.Y.)},
volume = {16},
number = {1},
pages = {6},
pmid = {36739313},
issn = {1939-8425},
abstract = {Plant growth-promoting endophytic (PGPE) actinomycetes have been known to enhance plant growth and mitigate plant from abiotic stresses via their PGP-traits. In this study, PGPE Streptomyces sp. GKU 895 promoted growth and alleviated salt tolerance of salt-susceptible rice cultivar IR29 by augmentation of plant weight and declined ROS after irrigation with 150 mM NaCl in a pot experiment. Transcriptome analysis of IR29 exposed to the combination of strain GKU 895 and salinity demonstrated up and downregulated differentially expressed genes (DEGs) classified by gene ontology and plant reactome. Streptomyces sp. GKU 895 induced changes in expression of rice genes including transcription factors under salt treatment which involved in growth and development, photosynthesis, plant hormones, ROS scavenging, ion transport and homeostasis, and plant-microbe interactions regarding pathogenesis- and symbiosis-related proteins. Taken together, these data demonstrate that PGPE Streptomyces sp. GKU 895 colonized and enhanced growth of rice IR29 and triggered salt tolerance phenotype. Our findings suggest that utilisation of beneficial endophytes in the saline fields could allow for the use of such marginal soils for growing rice and possibly other crops.},
}

@article {pmid36738602,
year = {2023},
author = {Elsaeed, E and Enany, S and Solyman, S and Shohayeb, M and Hanora, A},
title = {Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites.},
journal = {Marine genomics},
volume = {68},
number = {},
pages = {101017},
doi = {10.1016/j.margen.2023.101017},
pmid = {36738602},
issn = {1876-7478},
abstract = {Many secondary metabolites with medicinal potential are produced by various animals, plants, and microorganisms. Because marine creatures have a greater proportion of unexplored biodiversity than their terrestrial counterparts, they have emerged as a key research focus for the discovery of natural product drugs. Several studies have revealed that bacteria isolated from Chromodoris quadricolor (C. quadricolor) have antibiotic and anticancer properties. In this study, meta-transcriptomics and meta-proteimic analysis were combined to identify biosynthetic gene clusters (BGCs) in the symbiotic bacteria of the C. quadricolor mantle. Symbiotic bacteria were separated from the host by differential pelleting, and then total RNA was extracted, purified, and sequenced. Meta-transcriptomic analysis was done using different natural product mining tools to identify biosynthetic transcript clusters (BTCs). Furthermore, proteins were extracted from the same cells and then analyzed by LC-MS. A meta-proteomic analysis was performed to find proteins that are translated from BCGs. Finally, only 227 proteins have been translated from 40,742 BTCs. The majority of these clusters were polyketide synthases (PKSs) with antibacterial activity. Ten novel potential metabolic clusters with the ability to produce antibiotics have been identified in Novosphingobium and Microbacteriaceae, including members of the ribosomal synthesized and post-translationally modified peptides (RiPPs), polyketide synthases, and others. We realized that using a meta-proteomic approach to identify BGCs that have already been translated makes it easier to concentrate on BGCs that are utilized by bacteria. The symbiotic bacteria associated with C. quadricolor could be a source of novel antibiotics.},
}

@article {pmid36737831,
year = {2023},
author = {Nocelli, N and Cossovich, S and Primo, E and Sorroche, F and Nievas, F and Giordano, W and Bogino, P},
title = {Coaggregative interactions between rhizobacteria are promoted by exopolysaccharides from Sinorhizobium meliloti.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jobm.202200552},
pmid = {36737831},
issn = {1521-4028},
abstract = {Bacterial surface components and extracellular compounds such as exopolysaccharides (EPSs) are crucial for interactions between cells, tolerance to different types of stress, and host colonization. Sinorhizobium meliloti produces two EPSs: Succinoglycan (EPS I), which is involved in the establishment of symbiosis with Medicago sativa, and galactoglucan (EPS II), associated with biofilm formation and the promotion of aggregation. Here, we aimed to assess their role in aggregative interactions between cells of the same strain of a given species (auto-aggregation), and between genetically different strains of the same or different species (intra- or intergeneric coaggregation). To do this, we used S. meliloti mutants which are defective in the production of EPS I, EPS II, or both. Macroscopic and microscopic coaggregation tests were performed with combinations or pairs of different bacterial strains. The EPS II-producing strains were more capable of coaggregation than those that cannot produce EPS II. This was true both for coaggregations between different S. meliloti strains, and between S. meliloti and other common rhizobacteria of agricultural relevance, such as Pseudomonas fluorescens and Azospirillum brasilense. The exogenous addition of EPS II strongly promoted coaggregation, thus confirming the polymer's importance for this phenotype. EPS II may therefore be a key factor in events of physiological significance for environmental survival, such as aggregative interactions and biofilm development. Furthermore, it might be a connecting molecule with relevant properties at an ecological, biotechnological, and agricultural level.},
}

@article {pmid36737826,
year = {2023},
author = {Forgie, AJ and Pepin, DM and Ju, T and Tollenaar, S and Sergi, CM and Gruenheid, S and Willing, BP},
title = {Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {21},
pmid = {36737826},
issn = {2049-2618},
abstract = {BACKGROUND: Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge.

RESULTS: Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of naïve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence.

CONCLUSIONS: Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of naïve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract.},
}

@article {pmid36736568,
year = {2023},
author = {Zhang, B and Wu, L and Guo, Y and Lens, PNL and Shi, W},
title = {Rapid establishment of algal-bacterial granular sludge system by applying mycelial pellets in a lab-scale photo-reactor under low aeration conditions: Performance and mechanism analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {121183},
doi = {10.1016/j.envpol.2023.121183},
pmid = {36736568},
issn = {1873-6424},
abstract = {Light-driven algal-bacterial granular sludge (ABGS) is an innovative low-carbon technology with significant merits in treating municipal wastewater, but how to shorten the photogranulation process, especially under low aeration conditions, is largely unknown. Herein, two strategies were proposed to accelerate the start-up of the ABGS system in photo-sequencing batch reactors (PSBRs) with a low superficial gas velocity of 0.5 cm/s. Compared to directly dosing mycelial pellets (MPs), applying MPs to flocculate algae and using the formed algal-mycelial pellets (AMPs) as carriers enhanced the establishment of the algal-bacterial symbiosis. The ABGS system developed rapidly within 20 days, with a large particle diameter (mean diameter of 321 μm) and excellent settleability (SVI30 of 55.4 mL/g). More importantly, this system could be stably operated for at least 100 days, mainly attributed to the reinforced secretion of protein with unique secondary structure and elevated hydrophobic functional groups. As for the reactor performance, the average removal efficiencies of the ABGS system were 97.8% for organic matter, 80.0% for total nitrogen, and 84.4% for phosphorus. The enrichment of functional bacteria and algae, and the up-regulation of functional genes and enzymes involved in electron production and transport processes likely drove the transformation of the pollutants, underlining the inherent mechanism for the excellent nutrient removal performance. This study provides a promising approach to solve the problem of a long ABGS start-up period and unstable granular structure under low aeration conditions, which is significant for achieving effective wastewater treatment without energy intensive aeration.},
}

@article {pmid36735729,
year = {2023},
author = {Li, X and Liu, M and Cai, M and Chiasson, D and Groth, M and Heckmann, AB and Wang, TL and Parniske, M and Downie, JA and Xie, F},
title = {RPG interacts with E3-ligase CERBERUS to mediate rhizobial infection in Lotus japonicus.},
journal = {PLoS genetics},
volume = {19},
number = {2},
pages = {e1010621},
doi = {10.1371/journal.pgen.1010621},
pmid = {36735729},
issn = {1553-7404},
abstract = {Symbiotic interactions between rhizobia and legumes result in the formation of root nodules, which fix nitrogen that can be used for plant growth. Rhizobia usually invade legume roots through a plant-made tunnel-like structure called an infection thread (IT). RPG (Rhizobium-directed polar growth) encodes a coiled-coil protein that has been identified in Medicago truncatula as required for root nodule infection, but the function of RPG remains poorly understood. In this study, we identified and characterized RPG in Lotus japonicus and determined that it is required for IT formation. RPG was induced by Mesorhizobium loti or purified Nodulation factor and displayed an infection-specific expression pattern. Nodule inception (NIN) bound to the RPG promoter and induced its expression. We showed that RPG displayed punctate subcellular localization in L. japonicus root protoplasts and in root hairs infected by M. loti. The N-terminal predicted C2 lipid-binding domain of RPG was not required for this subcellular localization or for function. CERBERUS, a U-box E3 ligase which is also required for rhizobial infection, was found to be localized similarly in puncta. RPG co-localized and directly interacted with CERBERUS in the early endosome (TGN/EE) compartment and near the nuclei in root hairs after rhizobial inoculation. Our study sheds light on an RPG-CERBERUS protein complex that is involved in an exocytotic pathway mediating IT elongation.},
}

@article {pmid36734377,
year = {2023},
author = {Berasategui, A and Salem, H},
title = {Synergy in symbiosis.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.85565},
pmid = {36734377},
issn = {2050-084X},
abstract = {Honeybees rely on their microbial gut symbionts to overcome a potent toxin found in pollen and nectar.},
}

@article {pmid36733772,
year = {2022},
author = {Zheng, H and Zhang, P and Qin, J and Guo, J and Deng, J},
title = {High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1092552},
pmid = {36733772},
issn = {1664-302X},
abstract = {Gastrodia elata f.glauca (G. elata) is a commonly used Chinese Medicinal Materials with great medicinal value. The medicinal plant and its endophytic bacteria are a symbiotic whole, and the endophytic bacteria are rich in species, and their metabolites are a treasure trove of natural compounds. However, there is a relative lack of analysis on the diversity, flora composition and network interactions of the endophytic bacteria of G. elata. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to reveal the core microbiota by examining the diversity and community structures of tuber endophytic bacteria in G. elata grown under different regions and exploring the effect of region on its endophytic bacteria. Here, 1,265 endophytic ASVs were found to coexist with G. elata tuber in Guizhou and Hubei. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria and Acdobacteriota. At the family level, the dominant family were Comamonadaceae, Nocardicaece, Xanthobacteraceae, and Burkholderiaceae. At the genus level, Delftia and Rhodococcus were represented the core microbiota in G. elata tuber, which served as the dominant genera that coexisted in all samples tested. Moreover, we found that the beta diversity of endophytic bacteria in G. elata tuber was higher level in the Guizhou region than Hubei region. Overall, this study results to provide a reference for screening active strains and interaction between plants and endophytic bacteria.},
}

@article {pmid36733592,
year = {2022},
author = {Liu, M and Kameoka, H and Oda, A and Maeda, T and Goto, T and Yano, K and Soyano, T and Kawaguchi, M},
title = {The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {995589},
pmid = {36733592},
issn = {1664-462X},
abstract = {Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.},
}

@article {pmid36733588,
year = {2022},
author = {Han, S and Wang, X and Cheng, Y and Wu, G and Dong, X and He, X and Zhao, G},
title = {Multidimensional analysis reveals environmental factors that affect community dynamics of arbuscular mycorrhizal fungi in poplar roots.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1068527},
pmid = {36733588},
issn = {1664-462X},
abstract = {INTRODUCTION: Poplar is a tree species with important production and application value. The symbiotic relationship between poplar and arbuscular mycorrhizal fungi (AMF) has a key role in ecosystem functioning. However, there remain questions concerning the seasonal dynamics of the AMF community in poplar roots, the relationship between AMF and the soil environment, and its ecological function.

METHOD: Poplar roots and rhizosphere soil were sampled at the end of April and the end of October. The responses of AMF communities to season, host age, and host species were investigated; the soil environmental factors driving community changes were analyzed.

RESULTS: The diversity and species composition of the AMF community were higher in autumn than in spring. Season, host age, host species, and soil environmental factors affected the formation of the symbiotic mycorrhizal system and the AMF community. Differences in the communities could be explained by soil pH, total nitrogen, total phosphorus, total potassium, available potassium, and glomalin content.

DISCUSSION: The AMF community was sensitive to changes in soil physicochemical properties caused by seasonal dynamics, particularly total potassium. The change in the mycorrhizal symbiotic system was closely related to the growth and development of poplar trees.},
}

@article {pmid36727668,
year = {2023},
author = {Bartl, A and Ipsmiller, W},
title = {Fast fashion and the Circular Economy: Symbiosis or antibiosis?.},
journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X221149639},
doi = {10.1177/0734242X221149639},
pmid = {36727668},
issn = {1096-3669},
}

@article {pmid36727281,
year = {2023},
author = {Quach, QN and Clay, K and Lee, ST and Gardner, DR and Cook, D},
title = {Phylogenetic patterns of bioactive secondary metabolites produced by fungal endosymbionts in morning glories (Ipomoeeae, Convolvulaceae).},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18785},
pmid = {36727281},
issn = {1469-8137},
abstract = {Heritable fungal endosymbiosis is under-investigated in plant biology and documented in only three plant families (Convolvulaceae, Fabaceae, Poaceae). An estimated 40% of morning glory species in the tribe Ipomoeeae (Convolvulaceae) have associations with one of two distinct heritable, endosymbiotic fungi (Periglandula and Chaetothyriales) that produce the bioactive metabolites ergot alkaloids, indole diterpene alkaloids, and swainsonine, which have been of interest for their toxic effects on animals and potential medical applications. Here, we report the occurrence of ergot alkaloids, indole diterpene alkaloids, and swainsonine in the Convolvulaceae; and the fungi that produce them based on synthesis of previous studies and new indole diterpene alkaloid data from 27 additional species in a phylogenetic, geographic, and life-history context. We find that individual morning glory species host no more than one metabolite-producing fungal endosymbiont (with one possible exception), possibly due to costs to the host and overlapping functions of the alkaloids. The symbiotic morning glory lineages occur in distinct phylogenetic clades and host species have significantly larger seed size than non-symbiotic species. The distinct and widely distributed endosymbiotic relationships in the morning glory family and their alkaloids provide an accessible study system for understanding heritable plant-fungal symbiosis evolution and their potential functions for host plants.},
}

@article {pmid36726985,
year = {2022},
author = {Wang, M and Zhang, L and Chang, W and Zhang, Y},
title = {The crosstalk between the gut microbiota and tumor immunity: Implications for cancer progression and treatment outcomes.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1096551},
pmid = {36726985},
issn = {1664-3224},
abstract = {The gastrointestinal tract is inhabited by trillions of commensal microorganisms that constitute the gut microbiota. As a main metabolic organ, the gut microbiota has co-evolved in a symbiotic relationship with its host, contributing to physiological homeostasis. Recent advances have provided mechanistic insights into the dual role of the gut microbiota in cancer pathogenesis. Particularly, compelling evidence indicates that the gut microbiota exerts regulatory effects on the host immune system to fight against cancer development. Some microbiota-derived metabolites have been suggested as potential activators of antitumor immunity. On the contrary, the disequilibrium of intestinal microbial communities, a condition termed dysbiosis, can induce cancer development. The altered gut microbiota reprograms the hostile tumor microenvironment (TME), thus allowing cancer cells to avoid immunosurvelliance. Furthermore, the gut microbiota has been associated with the effects and complications of cancer therapy given its prominent immunoregulatory properties. Therapeutic measures that aim to manipulate the interplay between the gut microbiota and tumor immunity may bring new breakthroughs in cancer treatment. Herein, we provide a comprehensive update on the evidence for the implication of the gut microbiota in immune-oncology and discuss the fundamental mechanisms underlying the influence of intestinal microbial communities on systemic cancer therapy, in order to provide important clues toward improving treatment outcomes in cancer patients.},
}

@article {pmid36726674,
year = {2022},
author = {Chen, W and Ye, T and Sun, Q and Niu, T and Zhang, J},
title = {Arbuscular mycorrhizal fungus alleviates anthracnose disease in tea seedlings.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1058092},
pmid = {36726674},
issn = {1664-462X},
abstract = {Tea has been gaining increasing popularity all over the world in recent years, and its yield and quality depend on the growth and development of tea plants [Camellia sinensis (L.) Kuntze] in various environments. Nowadays, biotic stress and extreme weather, such as high temperature, drought, waterlogging, pests, and diseases, bring about much pressure on the production of tea with high quality. Wherein anthracnose, which is the most common and serious disease of tea plants, has earned more and more attention, as its control mainly relies on chemical pesticides. Arbuscular mycorrhizal fungi (AMF), forming symbiosis with most terrestrial plants, participate in plant resistance against the anthracnose disease, which was found by previous studies in a few herbaceous plants. However, there are a few studies about arbuscular mycorrhizal (AM) fungal regulation of the resistance to the anthracnose pathogen in woody plants so far. In this paper, we investigated the effect of AMF on the development of anthracnose caused by Colletotrichum camelliae and tried to decipher the pertinent mechanism through transcriptome analysis. Results showed that inoculating AMF significantly reduced the damage of anthracnose on tea seedlings by reducing the lesion area by 35.29% compared to that of the control. The content of superoxide anion and activities of catalase and peroxidase significantly increased (P < 0.05) in mycorrhizal treatment in response to the pathogen with 1.23, 2.00, and 1.39 times higher, respectively, than those in the control. Pathways of plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling, and phenylpropanoid biosynthesis might play roles in this regulation according to the transcriptomic results. Further redundancy analysis (RDA) and partial least squares structural equation modeling (PLS-SEM) analysis found that plant hormones, such as auxin and ethylene, and the antioxidant system (especially peroxidase) were of great importance in the AM fungal alleviation of anthracnose. Our results preliminarily indicated the mechanisms of enhanced resistance in mycorrhizal tea seedlings to the anthracnose pathogen and provided a theoretical foundation for the application of AMF as one of the biological control methods in tea plantations.},
}

@article {pmid36726570,
year = {2022},
author = {Zhang, Y and Feng, S and Zhu, L and Li, M and Xiang, X},
title = {Population dynamics of Brachionus calyciflorus driven by the associated natural bacterioplankton.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1076620},
pmid = {36726570},
issn = {1664-302X},
abstract = {Zooplankton provides bacteria with a complex microhabitat richen in organic and inorganic nutrients, and the bacteria community also changes the physiochemical conditions for zooplankton, where the symbiotic relationship between them plays an important role in the nutrient cycle. However, there are few studies on the effect of associated bacteria on the population dynamics of rotifers. In order to make clear their relationships, we reconstructed the associated bacterial community in Brachionus calyciflorus culture, and examined the life history and population growth parameters, and analyzed the diversity and community composition of the associated bacteria at different growth stages of B. calyciflorus. The results showed that the addition of bacteria from natural water can promote the population growth and asexual reproduction of B. calyciflorus, but has no significant effect on sexual reproduction, exhibited by the improvement of its life expectancy at hatching, net reproduction rates and intrinsic growth rate, no significant effects on the generation time and mixis ratio of offspring. It was found that the B. calyciflorus-associated bacterial community was mainly composed of Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria and Firmicutes. Through correlation network analysis, the members of Burkholderiales, Pseudomonadales, Micrococcales, Caulobacterales and Bifidobacteriales were the keystone taxa of B. calyciflorus-associated bacteria. In addition, the relative abundance of some specific bacteria strains increased as the population density of B. calyciflorus increased, such as Hydrogenophaga, Acidovorax, Flavobacterium, Rheinheimera, Novosphingobium and Limnobacter, and their relative abundance increased obviously during the slow and exponential phases of population growth. Meanwhile, the relative abundance of adverse taxa (such as Elizabethkingia and Rickettsiales) decreased significantly with the increase in rotifer population density. In conclusion, the closely associated bacteria are not sufficient for the best growth of B. calyciflorus, and external bacterioplankton is necessary. Furthermore, the function of keystone and rare taxa is necessary for further exploration. The investigation of the symbiotic relationship between zooplankton-associated bacterial and bacterioplankton communities will contribute to monitoring their roles in freshwater ecosystems, and regulate the population dynamics of the micro-food web.},
}

@article {pmid36726189,
year = {2023},
author = {Wu, Z and Zhang, Q and Yang, J and Zhang, J and Fu, J and Dang, C and Liu, M and Wang, S and Lin, Y and Hao, J and Weng, M and Xie, D and Li, A},
title = {Correction: Significant alterations of intestinal symbiotic microbiota induced by intraperitoneal vaccination mediate changes in intestinal metabolism of NEW Genetically Improved Farmed Tilapia (NEW GIFT, Oreochromis niloticus).},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {20},
pmid = {36726189},
issn = {2049-2618},
}

@article {pmid36725821,
year = {2023},
author = {Vitiello, A and Ferrara, F and Zovi, A},
title = {The direct correlation between microbiota and SARS-CoV-2 infectious disease.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {36725821},
issn = {1568-5608},
abstract = {The human microbiota is the good part of the human organism and is a collection of symbiotic microorganisms which aid in human physiological functions. Diseases that can be generated by an altered microbiota are continuously being studied, but it is quite evident how a damaged microbiota is involved in chronic inflammatory diseases, psychiatric diseases, and some bacterial or viral infections. However, the role of the microbiota in the host immune response to bacterial and viral infections is still not entirely understood. Metabolites or components which are produced by the microbiota are useful in mediating microbiota-host interactions, thus influencing the host's immune capacity. Recent evidence shows that the microbiota is evidently altered in patients with viral infections such as post-acute COVID-19 syndrome (PACS). In this review, the associations between microbiota and COVID-19 infection are highlighted in terms of biological and clinical significance by emphasizing the mechanisms through which metabolites produced by the microbiota modulate immune responses to COVID-19 infection.},
}

@article {pmid36725749,
year = {2023},
author = {Sullivan, TJ and Roberts, H and Bultman, TL},
title = {Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36725749},
issn = {1432-184X},
abstract = {Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.},
}

@article {pmid36722409,
year = {2023},
author = {Weng, BB and Yuan, HD and Chen, LG and Chu, C and Hsieh, CW},
title = {Soy yoghurts produced with efficient GABA (γ-aminobutyric acid)-producing Lactiplantibacillus plantarum ameliorate hyperglycaemia and re-establish gut microbiota in streptozotocin (STZ)-induced diabetic mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo02708a},
pmid = {36722409},
issn = {2042-650X},
abstract = {Soy yogurt has been gaining popularity as a vegan food produced simply by soymilk fermentation with proper microbial manipulation. It is well known that soy containing rich isoflavones is beneficial for ameliorating hyperglycaemic disorders. Soy fermentation can improve the bioavailability of these precious nutrients. Lactiplantibacillus plantarum is one of the most abundant and frequently isolated species in soymilk manufacturing. Soy yogurts produced with efficient GABA (γ-aminobutyric acid)-producing L. plantarum and the deglycosylating activity of L. plantarum were functionally assessed in a STZ-induced hyperglycaemic mouse model. Hyperglycaemic mice were assigned into groups and treated with daily gavage of either dH2O, soymilk, soy yoghurts produced with high GABA-producing L. plantarum GA30 (LPGA30), low GABA-producing L. plantarum PV30 (LPPV30) or the soy yoghurts fortified with additional 30 mg g[-1] GABA counterparts (GA + GABA and PV + GABA groups). Except the dH2O group, all soy yoghurt groups retained body weight with improved glucose homeostasis, glucose tolerance test results and renal tissue integrity, while the soymilk group shows partial benefits. Plasma GABA concentrations in the daily soy yoghurt-supplemented groups (LPGA30 and LPPV30) plateaued at 5 times higher than the average 0.5 μM in dH2O and soymilk groups, and their GABA-fortified soy yoghurt counterparts (GA + GABA and PV + GABA) groups were accountable for the restored plasma insulin levels. Gut microbiome analysis revealed dysbiosis in STZ-induced hyperglycemic mice of the dH2O group with breached out facultative anaerobic Proteobacteria over the normal phyla Firmicutes and Bacteroidetes. Restored gut microbiota with transitionally populated Actinobacteria was demonstrated in the LPGA30 group but not in the LPPV30 group. Soy yoghurts produced with efficient GABA-producing L. plantarum GA30 showed exceptional benefits in modulating gut microbiota with dominant genera of Enterococcus, Lactobacillus and Bifidobacterium, and the presence of some minor beneficial microbial communities including Akkermansia muciniphila, Butyricicoccus pullicaecorum, Corynebacterium spp. and Adlercreutzia spp. Efficient GABA-producing L. plantarum GA30 fermented soymilk to produce soy yoghurts that exhibit profound synergistic protections over rich soy isoflavones to restore pancreatic β-cell functions for insulin production in STZ-induced hyperglycaemic mice. Additionally, the probiotic role of GABA-producing L. plantarum in re-establishing healthy gut microbiota in hyperglycaemic mice implies a possible symbiotic relationship, awaiting further exploration.},
}

@article {pmid36722175,
year = {2023},
author = {Wang, T and Gasciolli, V and Gaston, M and Medioni, L and Cumener, M and Buendia, L and Yang, B and Bono, JJ and He, G and Lefebvre, B},
title = {LysM receptor-like kinases involved in immunity perceive lipo-chitooligosaccharides in mycotrophic plants.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiad059},
pmid = {36722175},
issn = {1532-2548},
abstract = {Symbiotic microorganisms such as arbuscular mycorrhizal fungi (AMF) produce both conserved microbial molecules that activate plant defense and lipo-chitooligosaccharides (LCOs) that modulate plant defense. Beside a well-established role of LCOs in activation of a signaling pathway required for AMF penetration in roots, LCO perception and defense modulation during arbuscular mycorrhiza is not well understood. Here we show that members of the LYRIIIA phylogenetic group from the multigenic Lysin Motif Receptor-Like Kinase family have a conserved role in dicotyledons as modulators of plant defense and regulate AMF colonization in the Solanaceae species Nicotiana benthamiana. Interestingly, these proteins have high-affinity for LCOs in plant species able to form a symbiosis with AMF but have lost this property in species that have lost this ability. Our data support the hypothesis that LYRIIIA proteins modulate plant defense upon LCO perception to facilitate AMF colonization in mycotrophic plant species and that only their role in plant defense, but not their ability to be regulated by LCOs, has been conserved in non-mycotrophic plants.},
}

@article {pmid36722159,
year = {2023},
author = {Molla, F and Kundu, A and DasGupta, M},
title = {Sucrose-induced auxin conjugate hydrolase restores symbiosis in a Medicago cytokinin perception mutant.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiad045},
pmid = {36722159},
issn = {1532-2548},
abstract = {Rhizobia-legume interactions recruit cytokinin for the induction of nodule primordia in the cortex. Cytokinin signaling regulates auxin transport and biosynthesis, causing local auxin accumulation which triggers cortical cell division. Since sugar signaling can trigger auxin responses, we explored whether sugar treatments could rescue symbiosis in the Medicago truncatula Cytokinin Response 1 mutant (cre1.) Herein we demonstrate that sucrose and its nonmetabolizable isomer turanose can trigger auxin response and recover functional symbiosis in cre1, indicating sucrose signaling to be necessary for restoration of symbiosis. In both M. truncatula A17 (wild-type) and cre1, sucrose signaling significantly upregulated IAA-Ala Resistant 3 (IAR33), encoding an auxin conjugate hydrolase, in rhizobia-infected as well as in uninfected roots. Knockdown of IAR33 (IAR33-KD) significantly reduced nodulation in A17, highlighting the importance of deconjugation-mediated auxin accumulation during nodule inception. In cre1, IAR33-KD restricted the sucrose mediated restoration of functional symbiosis, suggesting deconjugation-mediated auxin accumulation plays a key role in the absence of CRE1-mediated auxin biosynthesis and transport control. Overexpression of IAR33 also restored functional symbiosis in cre1, further suggesting thatIAR33 mediates auxin accumulation in response to sucrose signaling. Since all the observed sucrose mediated responses were common to A17 and cre1, deconjugation-mediated auxin response appeared to be independent of CRE1, whichnormally governs local auxin accumulation in the presence of rhizobia. We propose that sucrose-dependent restoration of symbiosis in cre1 occurs by the activation of IAR33-mediated auxin deconjugation.},
}

@article {pmid36721785,
year = {2022},
author = {Lee, JE and Eom, AH},
title = {Diversity and community structure of ectomycorrhizal mycorrhizal fungi in roots and rhizosphere soil of Abies koreana and Taxus cuspidata in Mt. Halla.},
journal = {Mycobiology},
volume = {50},
number = {6},
pages = {448-456},
pmid = {36721785},
issn = {1229-8093},
abstract = {In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.},
}

@article {pmid36719456,
year = {2023},
author = {Lin, Z and Zheng, X and Chen, J},
title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-023-02183-0},
pmid = {36719456},
issn = {1432-184X},
abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.},
}

@article {pmid36719273,
year = {2023},
author = {Lobo-da-Cunha, A and Alves, Â and Rodrigues, A},
title = {Gill histology and ultrastructure in Aplysia depilans (Mollusca, Euopisthobranchia).},
journal = {Journal of morphology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jmor.21562},
pmid = {36719273},
issn = {1097-4687},
abstract = {The gill of Aplysia depilans consists of several wedge shaped pinnules with a highly folded structure, differing from the typical ctenidial gills of mollusks. Light microscopy and transmission electron microscopy were used to investigate this organ in juveniles and adults. In this species, the gill epithelium comprised ciliated, unciliated and secretory cells. The ultrastructural analysis suggests other functions for the gill besides respiration. The deep cell membrane invaginations associated with mitochondria in the basal region of epithelium point to a role in ion regulation. Endocytosis and intracellular digestion were other activities detected in epithelial cells. In juveniles, an intranuclear crystalline structure was seen in some ciliated cells. The presence of an intranuclear crystalline structure was frequently associated with chromatin decondensation, swelling of the nuclear envelope and endoplasmic reticulum cisternae, and abundance of Golgi stacks. As these intranuclear inclusions were not found in the gill of the adult specimens, their occurrence in the two juveniles seems likely to be an anomalous condition whose cause cannot be established at the moment. Mucous cells were the most abundant secretory cells in the epithelium, but a few epithelial serous cells were also found. In addition, large protein secreting subepithelial cells had the main cell body inserted in the connective tissue and a long thin neck crossing the epithelium. Mucous cells can be considered responsible for the production of the mucus layer that protects the epithelium, but the specific functions of the epithelial and subepithelial protein secreting cells remain elusive. Below the epithelium, a layer of connective tissue with muscle cells lined the narrow haemolymph space. The connective tissue included cells with a large amount of rough endoplasmic reticulum cisternae. Bacteria were found on the surface of the gill, and the most abundant had a thin stalk for attachment to the epithelial cells. This article is protected by copyright. All rights reserved.},
}

@article {pmid36718526,
year = {2023},
author = {Matsuda, H and Yamazaki, Y and Moriyoshi, E and Nakayasu, M and Yamazaki, S and Aoki, Y and Takase, H and Okazaki, S and Nagano, AJ and Kaga, A and Yazaki, K and Sugiyama, A},
title = {Apoplast-localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcad012},
pmid = {36718526},
issn = {1471-9053},
abstract = {Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing β-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the root apoplastic fraction of ichg mutants, the isoflavone glycosides contents were significantly increased while isoflavone aglycone contents were decreased, indicating that ICHG hydrolyzes isoflavone glycosides into aglycones in the root apoplast. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and WTs. Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions, either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential in isoflavone-mediated plant-microbe interactions.},
}

@article {pmid36717758,
year = {2023},
author = {Mohd-Radzman, NA and Drapek, C},
title = {Compartmentalization - a strategy for optimizing symbiosis and tradeoff management.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.14553},
pmid = {36717758},
issn = {1365-3040},
abstract = {Plant root architecture is developmentally plastic in response to fluctuating nutrient levels in the soil. Part of this developmental plasticity is the formation of dedicated root cells and organs to host mutualistic symbionts. Structures like nitrogen-fixing nodules serve as alternative nutrient acquisition strategies during starvation conditions. Some root systems can also form myconodules - globular root structures that can host mycorrhizal fungi. The myconodule association is different from the wide-spread arbuscular mycorrhization. This range of symbiotic associations provides different degrees of compartmentalization, from the cellular to organ scale, which allows the plant host to regulate the entry and extent of symbiotic interactions. In this review, we discuss the degrees of symbiont compartmentalization by the plant host as a developmental strategy and speculate how spatial confinement mitigates risks associated with root symbiosis. This article is protected by copyright. All rights reserved.},
}

@article {pmid36717442,
year = {2022},
author = {Zorov, DB and Andrianova, NV and Babenko, VA and Zorova, LD and Zorov, SD and Pevzner, IB and Sukhikh, GT and Silachev, DN},
title = {Isn't It Time for Establishing Mitochondrial Nomenclature Breaking Mitochondrial Paradigm?.},
journal = {Biochemistry. Biokhimiia},
volume = {87},
number = {12},
pages = {1487-1497},
doi = {10.1134/S0006297922120069},
pmid = {36717442},
issn = {1608-3040},
abstract = {In this work, we decided to initiate a discussion concerning heterogeneity of mitochondria, suggesting that it is time to build classification of mitochondria, like the one that exists for their progenitors, α-proteobacteria, proposing possible separation of mitochondrial strains and maybe species. We continue to adhere to the general line that mitochondria are friends and foes: on the one hand, they provide the cell and organism with the necessary energy and signaling molecules, and, on the other hand, participate in destruction of the cell and the organism. Current understanding that the activity of mitochondria is not only limited to energy production, but also that these alternative non-energetic functions are unique and irreplaceable in the cell, allowed us to speak about the strong subordination of the entire cellular metabolism to characteristic functional manifestations of mitochondria. Mitochondria are capable of producing not only ATP, but also iron-sulfur clusters, steroid hormones, heme, reactive oxygen and nitrogen species, participate in thermogenesis, regulate cell death, proliferation and differentiation, participate in detoxification, etc. They are a mandatory attribute of eukaryotic cells, and, so far, no eukaryotic cells performing a non-parasitic or non-symbiotic life style have been found that lack mitochondria. We believe that the structural-functional intracellular, intercellular, inter-organ, and interspecific diversity of mitochondria is large enough to provide grounds for creating a mitochondrial nomenclature. The arguments for this are given in this analytical work.},
}

@article {pmid36716543,
year = {2023},
author = {Ge, H and Peng, Z and Fang, Y and Liu, X and Li, H},
title = {Revealing the key species for pyrene degradation in Vallisneria natans rhizosphere sediment via triple chamber rhizome-box experiments.},
journal = {Journal of environmental management},
volume = {332},
number = {},
pages = {117340},
doi = {10.1016/j.jenvman.2023.117340},
pmid = {36716543},
issn = {1095-8630},
abstract = {To identify key species associated with pyrene degradation in Vallisneria natans (V.natans) rhizosphere sediment, this work investigated the temporal and spatial changes in the rhizosphere microbial community and the relationship between the changes and the pyrene degradation process through a three-compartment rhizome-box experiment under pyrene stress. The degradation kinetics of pyrene showed that the order of degradation rate was rhizosphere > near-rhizosphere > non-rhizosphere. The difference in the pyrene degradation behavior in the sediments corresponded to the change in the proportions of dominant phyla (Firmicutes and Proteobacteria) and genera (g_Massilia f_Comamonadaceae, g_Sphingomonas). The symbiosis networks and hierarchical clustering analysis indicated that the more important phyla related to the pyrene degradation in the rhizosphere was Proteobacteria, while g_Sphigomonas, f_Comamonadaceae, and especially g_Massilia were the core genera. Among them, f_Comamonadaceae was the genus most affected by rhizosphere effects. These findings strengthened our understanding of the PAHs-degradation microorganisms in V.natans rhizosphere and are of great significance for enhancing phytoremediation on PAHs-contaminated sediment.},
}

@article {pmid36715806,
year = {2023},
author = {Shan, H and Guo, Q and Wei, J},
title = {The impact of disclosure of risk information on risk propagation in the industrial symbiosis network.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {1-18},
pmid = {36715806},
issn = {1614-7499},
abstract = {The interdependent symbiotic relationship between enterprises may bring potential risks to the stability of the industrial symbiosis network (ISN). In order to reduce the damage caused by further risk propagation to the system, this paper establishes the multiplex network to study the impact of disclosure of risk information on risk propagation. In the multiplex network, we use a small-world network to simulate a social network and propose an evolutionary model with scale-free characteristics to simulate the symbiotic relationships between enterprises. Then we establish a risk propagation model by defining transition rules among various states. Through theoretical analysis using the Microscopic Markov Chain Approach (MMCA), we find that the proportion of disclosed enterprises, the network structure of the ISN, the recovery rate of enterprises, and the degree of symbiotic dependence affect the risk propagation threshold of the ISN. Numerical simulation results show that increasing the disclosure probability of risk information can reduce the scope of risk propagation. Moreover, once the disclosure probability of risk information reaches a certain value, the risk propagation threshold can be increased. Finally, relevant suggestions are put forward: (i) strengthening the information communication between symbiotic enterprises may reduce risks caused by information asymmetry. (ii) In addition to the authenticity and integrity of risk information, it is necessary to prevent risk information from being over-interpreted or exaggerated. (iii) Enterprises should strengthen the ability to recover from risks, appropriately reduce the degree of symbiotic dependence, and enhance risk awareness to reduce the possibility of risk occurrence.},
}

@article {pmid36714835,
year = {2022},
author = {Niehs, SP and Scherlach, K and Dose, B and Uzum, Z and Stinear, TP and Pidot, SJ and Hertweck, C},
title = {A highly conserved gene locus in endofungal bacteria codes for the biosynthesis of symbiosis-specific cyclopeptides.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac152},
pmid = {36714835},
issn = {2752-6542},
abstract = {The tight association of the pathogenic fungus Rhizopus microsporus and its toxin-producing, bacterial endosymbionts (Mycetohabitans spp.) is distributed worldwide and has significance for agriculture, food production, and human health. Intriguingly, the endofungal bacteria are essential for the propagation of the fungal host. Yet, little is known about chemical mediators fostering the symbiosis, and universal metabolites that support the mutualistic relationship have remained elusive. Here, we describe the discovery of a complex of specialized metabolites produced by endofungal bacteria under symbiotic conditions. Through full genome sequencing and comparative genomics of eight endofungal symbiont strains from geographically distant regions, we discovered a conserved gene locus (hab) for a nonribosomal peptide synthetase as a unifying trait. Bioinformatics analyses, targeted gene deletions, and chemical profiling uncovered unprecedented depsipeptides (habitasporins) whose structures were fully elucidated. Computational network analysis and labeling experiments granted insight into the biosynthesis of their nonproteinogenic building blocks (pipecolic acid and β-phenylalanine). Deletion of the hab gene locus was shown to impair the ability of the bacteria to enter their fungal host. Our study unveils a common principle of the endosymbiotic lifestyle of Mycetohabitans species and expands the repertoire of characterized chemical mediators of a globally occurring mutualistic association.},
}

@article {pmid36714746,
year = {2022},
author = {Zhang, H and Lin, R and Liu, Q and Lu, J and Qiao, G and Huang, X},
title = {Transcriptomic and proteomic analyses provide insights into host adaptation of a bamboo-feeding aphid.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1098751},
pmid = {36714746},
issn = {1664-462X},
abstract = {INTRODUCTION: Salivary glands and their secreted proteins play an important role in the feeding process of sap-sucking aphids. The determination of saliva composition is an important step in understanding host plant adaptation of aphids. Pseudoregma bambucicola is a severe bamboo pest in subtropical areas and the only aphid species that can exclusively feed on hard stalks of bamboos. How this species can penetrate and degrade hard bamboo cell walls and utilize a very specialized niche are important unanswered questions.

METHODS: In this study, comprehensive analyses based on transcriptome sequencing, RT-qPCR, liquid chromatography-tandem spectrometry (LC-MS/MS) and bioinformatics were conducted on dissected salivary glands and secreted saliva of P. bambucicola to characterize the overall gene expression and salivary protein composition, and to identify putative effector proteins important for aphid-plant interactions.

RESULTS AND DISCUSSION: Some secretory proteins homologous to known aphid effectors important for aphid-plant interactions, such as digestive enzymes, detoxifying and antioxidant enzymes and some effectors modulating plant defenses, are also detected in salivary gland transcriptome and salivary gland and/or saliva secretomes in P. bambucicola. This indicates that these effectors are probably be essential for enabling P. bambucicola feeding on bamboo host. Although several plant cell wall degrading enzymes (PCWDEs) can be identified from transcriptome, most of the enzymes identified in salivary glands showed low expression levels and they only represent a small fraction of the complete set of enzymes for degrading cellulose and hemicellulose. In addition, our data show that P. bambucicola has no its own ability to produce pectinases. Overall, our analyses indicate that P. bambucicola may lose its own ability to express and secrete key PCWDEs, and its adaptation to unique feeding habit may depend on its symbiotic bacteria.},
}

@article {pmid36714549,
year = {2023},
author = {Chot, E and Suravajhala, P and Medicherla, KM and Reddy, MS},
title = {Characterization and genome-wide sequence analysis of an ectomycorrhizal fungus Pisolithus albus, a potential source for reclamation of degraded lands.},
journal = {3 Biotech},
volume = {13},
number = {2},
pages = {58},
pmid = {36714549},
issn = {2190-572X},
abstract = {UNLABELLED: Pisolithus albus is a ubiquitous ectomycorrhizal fungus that establishes symbiosis with a wide range of woody plants around the globe. The symbiotic association of this fungus plays a crucial role in the nutrient cycling of their host plants and enables them to thrive in adverse environmental conditions. Based on its ecological importance and lack of genomic studies, whole-genome sequencing was carried out to analyze P. albus sequences through an Illumina HiSeq X system. The functional annotations were performed against various databases to explore genomic patterns and traits possibly attributing to its specialization. Comparative genomics of P. albus with phylogenetically related Pisolithus microcarpus and Pisolithus tinctorius (only available genomes of Pisolithus at NCBI till now) led to the identification of their unique and shared basic functional and stress adaptation capabilities. The de novo assembled genome of 56.15 Mb with 91.8% BUSCO completeness is predicted to encode 23,035 genes. The study is aimed to generate solid genomic data resources for P. albus, forming the theoretical basis for future transcriptomic, proteomic and metabolomic studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03483-5.},
}

@article {pmid36714504,
year = {2022},
author = {Jaman, S and Islam, MZ and Sojib, MSI and Hasan, MS and Khandakar, MMH and Bari, MS and Sarker, MAH and Habib, R and Siddiki, MSR and Islam, MA and Harun-Ur-Rashid, M},
title = {Physicochemical characteristics, sensory profile, probiotic, and starter culture viability of synbiotic yogurt.},
journal = {Journal of advanced veterinary and animal research},
volume = {9},
number = {4},
pages = {694-701},
pmid = {36714504},
issn = {2311-7710},
abstract = {OBJECTIVES: This study aimed to envisage the effectiveness of adding three particular prebiotics (inulin, β-glucan, and Hi-maize) to synbiotic yogurt's physicochemical properties, sensory characteristics, and survivability of the probiotic and starter cultures.

MATERIALS AND METHODS: The yogurt's gross composition, syneresis, water-holding capacity (WHC), viscosity, sensorial properties, and probiotic and starter cell stability were analyzed. The Lactobacillus delbrueckii subsp. bulgaricus M240-5 and Streptococcus thermophilus M140-2 were employed as yogurt starter bacteria, and Lactobacillus acidophilus LA-5 as probiotic culture. The synbiotic yogurt was formulated with 5% sucrose and 0.7% artificial vanilla flavor.

RESULTS: The findings showed that when prebiotic ingredients were added to synbiotic yogurt, it had a significant impact on its sensory qualities, WHC, syneresis, and viscosity when compared to plain yogurt samples. The prebiotics did not affect the pH and titratable acidity of the yogurt samples. Additionally, the prebiotic supplementation did not influence the protein and fat content of synbiotic yogurt (p < 0.05). Prebiotics had an impact on the probiotic cell viability and total viable count (p < 0.05) compared to the plain sample, the 2.5% β-glucan, 1.5% and 2.5% Hi-maize samples had the highest mean viability (8.95 Log CFU/ml). The starter culture ratio remained stable in response to the prebiotic levels.

CONCLUSION: In summary, the production of synbiotic yogurts supplemented with Hi-maize and β-glucan at 1.5% and 2.5%, respectively, is highly advised because these supplementations provide yogurt with acceptable syneresis, viscosity, WHC, and sensory attributes.},
}

@article {pmid36714306,
year = {2022},
author = {Barman, M and Samanta, S and Ahmed, B and Dey, S and Chakraborty, S and Deeksha, MG and Dutta, S and Samanta, A and Tarafdar, J and Roy, D},
title = {Transcription dynamics of heat-shock proteins (Hsps) and endosymbiont titres in response to thermal stress in whitefly, Bemisia tabaci (Asia-I).},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1097459},
pmid = {36714306},
issn = {1664-042X},
abstract = {The sweet potato whitefly, Bemisia tabaci (Gennadius), is one of the several species complexes of whitefly that are currently significant agricultural pests. Bemisia tabaci infests more than 600 plant species and thrives under a wide range of temperature conditions. In addition to the direct damage caused by sucking plant sap, it vectors several plant viruses. Heat-shock proteins play a pivotal role in enabling the insect to extend its geographical location, survival, and reproduction under different stress conditions. B. tabaci harbours several endosymbionts under the genera Portiera, Rickettsia, Hamiltonella, Wolbachia, Arsenophonus, Cardinium, and Fritschea that directly or indirectly affect its fitness. By accelerating cuticle biosynthesis and sclerotisation, symbiotic microbes can reduce or enhance tolerance to extreme temperatures and detoxify heavy metals. Thus, symbionts or microbial communities can expand or constrain the abiotic niche space of their host and affect its ability to adapt to changing conditions. The present study delineates the effect of thermal stress on the expression of heat-shock genes and endosymbionts in B. tabaci. Studies of the expression level of heat-shock proteins with the help of quantitative real-time polymerase chain reaction (qRT-PCR) showed that heat- and cold-shock treatment fuels the increased expression of heat-shock proteins (Hsp40 and Hsp70). However, Hsp90 was not induced by a heat- and cold-shock treatment. A significant decrease in the relative titre of secondary endosymbionts, such as Rickettsia, Arsenophonus, and Wolbachia, were recorded in B. tabaci upon heat treatment. However, the titre of the primary symbiont, C. Portiera, was relatively unaffected by both cold and heat treatments. These results are indicative of the fact that Hsp genes and endosymbionts in B. tabaci are modulated in response to thermal stress, and this might be responsible for the adaptation of whitefly under changing climatic scenario.},
}

@article {pmid36714060,
year = {2023},
author = {Xia, Y and He, C and Yan, S and Liu, J and Huang, H and Li, X and Su, Q and Jiang, W and Pang, Y},
title = {New dual functional CYP450 gene involves in isoflavone biosynthesis in Glycine max L.},
journal = {Synthetic and systems biotechnology},
volume = {8},
number = {1},
pages = {157-167},
pmid = {36714060},
issn = {2405-805X},
abstract = {Glycine max L. accumulates a large amount of isoflavonoid compounds, which is beneficial for plant defense, plant-microbe symbiotic interactions, and human health. Several CYP450 subfamily genes are involved in the flavonoid biosynthetic pathway in plants. In the present study, we found 24 CYP82 subfamily genes were differentially expressed in various tissues of soybean, in Phytophthora sojae-infected soybean varieties and in soybean hairy roots treated with cell wall glucan elicitor. Six of them (GmCYP82A2, GmCYP82A3, GmCYP82A4, GmCYP82A23, GmCYP82C20 and GmCYP82D26) were co-expressed with other known isoflavonoid pathway genes in soybean. Their enzymatic activity in yeast feeding assays showed that only GmCYP82D26 was able to convert naringenin to daidzein with both aryl migration and dehydration function. When GmCYP82D26 was over-expressed in soybean hairy roots, the contents of the two major isoflavonoid aglycones in soybean (daidzein and genistein) were reduced, but total flavonoids were not affected. When GmCYP82D26 was suppressed by RNAi in the hairy roots, daidzein content was decreased but genistein content was increased, with unchanged total flavonoid content. GmCYP82D26 was found to be localized in the endoplasmic reticulum at subcellular level when transiently expressed in tobacco leaf epidermis. GmCYP82D26 gene was preferentially expressed in roots, with low expression level in other tissues in soybean. Homology modeling and molecular docking showed that GmCYP82D26 could form hydrogen bond with both HEM and naringenin at C5-OH and C4 carbonyl. All these results indicated that GmCYP82D26 possesses new and dual enzymatic activity, which bridges the two branches (daidzein and genistein branch) of isoflavonoid pathway in soybean.},
}

@article {pmid36713225,
year = {2022},
author = {Xiao, Y and Yan, F and Cui, Y and Du, J and Hu, G and Zhai, W and Liu, R and Zhang, Z and Fang, J and Chen, L and Yu, X},
title = {A symbiotic bacterium of Antarctic fish reveals environmental adaptability mechanisms and biosynthetic potential towards antibacterial and cytotoxic activities.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1085063},
pmid = {36713225},
issn = {1664-302X},
abstract = {Antarctic microbes are important agents for evolutionary adaptation and natural resource of bioactive compounds, harboring the particular metabolic pathways to biosynthesize natural products. However, not much is known on symbiotic microbiomes of fish in the Antarctic zone. In the present study, the culture method and whole-genome sequencing were performed. Natural product analyses were carried out to determine the biosynthetic potential. We report the isolation and identification of a symbiotic bacterium Serratia myotis L7-1, that is highly adaptive and resides within Antarctic fish, Trematomus bernacchii. As revealed by genomic analyses, Antarctic strain S. myotis L7-1 possesses carbohydrate-active enzymes (CAZymes), biosynthetic gene clusters (BGCs), stress response genes, antibiotic resistant genes (ARGs), and a complete type IV secretion system which could facilitate competition and colonization in the extreme Antarctic environment. The identification of microbiome gene clusters indicates the biosynthetic potential of bioactive compounds. Based on bioactivity-guided fractionation, serranticin was purified and identified as the bioactive compound, showing significant antibacterial and antitumor activity. The serranticin gene cluster was identified and located on the chrome. Furthermore, the multidrug resistance and strong bacterial antagonism contribute competitive advantages in ecological niches. Our results highlight the existence of a symbiotic bacterium in Antarctic fish largely represented by bioactive natural products and the adaptability to survive in the fish living in Antarctic oceans.},
}

@article {pmid36713209,
year = {2022},
author = {Solanki, MK and Mandal, A and Medeiros, FHV and Awasthi, MK},
title = {Editorial: Emerging frontiers of microbial functions in sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1128267},
pmid = {36713209},
issn = {1664-302X},
}

@article {pmid36713208,
year = {2022},
author = {Chen, R and Luo, J and Zhu, X and Wang, L and Zhang, K and Li, D and Gao, X and Niu, L and Huangfu, N and Ma, X and Ji, J and Cui, J},
title = {Dynamic changes in species richness and community diversity of symbiotic bacteria in five reproductive morphs of cotton aphid Aphis gossypii Glover (Hemiptera: Aphididae).},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1086728},
pmid = {36713208},
issn = {1664-302X},
abstract = {INTRODUCTION: Reproductive polymorphism and symbiotic bacteria are commonly observed in aphids, but their interaction remains largely unclear. In polymorphic aphid species (Aphis gossypii), offspring of parthenogenetic females (PFs) develops into sexuparae which produces gynoparae and males successively. Gynoparae further produces sexual females (SFs), and these sexual females mate with males to produce offspring.

METHODS: In this study, we investigated the dynamic changes of symbiotic bacteria during the above-mentioned five reproductive morph switch in A. gossypii via 16S rRNA sequencing technology.

RESULTS: The results showed that species richness and community diversity of symbiotic bacteria in males were the highest. Proteobacteria was absolutely dominant bacterial phylum (with relative abundance of more than 90%) in the five reproductive morphs of A. gossypii, and Buchnera was absolutely dominant genus (with relative abundance of >90%), followed by Rhodococcus, Pseudomonas, and Pantoea. Male-killing symbiont Arsenophonus presented the highest relative abundance in gynoparae, a specific morph whose offsprings were exclusively sexual females. Both principal component analysis (PCA) and clustering analysis showed trans-generation similarity in microbial community structure between sexuparae and sexual females, between PFs and gynoparae. PICRUSt 2 analysis showed that symbiotic bacteria in the five reproductive morphs were mainly enriched in metabolic pathways.

DISCUSSION: Reproductive morph switch induced by environmental changes might be associated with bacterial community variation and sexual polymorphism of aphids. This study provides a new perspective for further deciphering the interactions between microbes and reproductive polymorphism in host aphids.},
}

@article {pmid36713196,
year = {2022},
author = {Goffredi, SK and Appy, RG and Hildreth, R and deRogatis, J},
title = {Marine vampires: Persistent, internal associations between bacteria and blood-feeding marine annelids and crustaceans.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1113237},
pmid = {36713196},
issn = {1664-302X},
abstract = {Persistent bacterial presence is believed to play an important role in host adaptation to specific niches that would otherwise be unavailable, including the exclusive consumption of blood by invertebrate parasites. Nearly all blood-feeding animals examined so far host internal bacterial symbionts that aid in some essential aspect of their nutrition. Obligate blood-feeding (OBF) invertebrates exist in the oceans, yet symbiotic associations between them and beneficial bacteria have not yet been explored. This study describes the microbiome of 6 phylogenetically-diverse species of marine obligate blood-feeders, including leeches (both fish and elasmobranch specialists; e.g., Pterobdella, Ostreobdella, and Branchellion), isopods (e.g., Elthusa and Nerocila), and a copepod (e.g., Lernanthropus). Amplicon sequencing analysis revealed the blood-feeding invertebrate microbiomes to be low in diversity, compared to host fish skin surfaces, seawater, and non-blood-feeding relatives, and dominated by only a few bacterial genera, including Vibrio (100% prevalence and comprising 39%-81% of the average total recovered 16S rRNA gene sequences per OBF taxa). Vibrio cells were localized to the digestive lumen in and among the blood meal for all taxa examined via fluorescence microscopy. For Elthusa and Branchellion, Vibrio cells also appeared intracellularly within possible hemocytes, suggesting an interaction with the immune system. Additionally, Vibrio cultivated from four of the obligate blood-feeding marine taxa matched the dominant amplicons recovered, and all but one was able to effectively lyse vertebrate blood cells. Bacteria from 2 additional phyla and 3 families were also regularly recovered, albeit in much lower abundances, including members of the Oceanospirillaceae, Flavobacteriacea, Porticoccaceae, and unidentified members of the gamma-and betaproteobacteria, depending on the invertebrate host. For the leech Pterobdella, the Oceanospirillaceae were also detected in the esophageal diverticula. For two crustacean taxa, Elthusa and Lernanthropus, the microbial communities associated with brooded eggs were very similar to the adults, indicating possible direct transmission. Virtually nothing is known about the influence of internal bacteria on the success of marine blood-feeders, but this evidence suggests their regular presence in marine parasites from several prominent groups.},
}

@article {pmid36713161,
year = {2022},
author = {Zhou, J and Liao, Z and Liu, Z and Guo, X and Zhang, W and Chen, Y},
title = {Urbanization increases stochasticity and reduces the ecological stability of microbial communities in amphibian hosts.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1108662},
pmid = {36713161},
issn = {1664-302X},
abstract = {Urbanization not only profoundly alters landscape profiles, ecosystems and vertebrate faunal diversity but also disturbs microbial communities by increasing stochasticity, vulnerability, biotic homogenization, etc. However, because of the buffering effect of host species, microbial communities are expected to be influenced by both host species and urbanization stresses. Therefore, the impacts of urbanization on animals' microbial symbionts could be more complex and uncertain. In this study, we quantified the urbanization degree of sampling sites and surveyed the gut and skin microbes of three amphibian host species in different sites in urban parks and nearby villages of Chengdu, Southwest China. Furthermore, a co-occurrence network analysis, the phylogenetic normalized stochasticity ratio and Sloan neutral community models were applied to infer the impact of urbanization on symbiotic microbial communities. For the three host species, urbanization increased the diversity of symbiotic microbes and the number of keystone microbial taxa. However, the negative effects of such increased diversification were evident, as the community stochasticity and co-occurrence network structure vulnerability also increased, while the network structure complexity and stability were reduced. Finally, the community stochasticity had positive associations with the network vulnerability, implying that the existence of many transient symbiotic rare microbial taxa in urban parks makes the symbiotic microbial community structure more fragile. Conclusively, urbanization increased the symbiotic microbial diversity at the cost of community stability; the results provide a new perspective for better understanding the complex triangulated environment-host-microbe relationship.},
}

@article {pmid36712793,
year = {2022},
author = {Kogawa, M and Miyaoka, R and Hemmerling, F and Ando, M and Yura, K and Ide, K and Nishikawa, Y and Hosokawa, M and Ise, Y and Cahn, JKB and Takada, K and Matsunaga, S and Mori, T and Piel, J and Takeyama, H},
title = {Single-cell metabolite detection and genomics reveals uncultivated talented producer.},
journal = {PNAS nexus},
volume = {1},
number = {1},
pages = {pgab007},
pmid = {36712793},
issn = {2752-6542},
abstract = {The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), 1 of the oldest metazoans. However, most bacterial members of sponge microbiomes have not been cultivated or sequenced, and therefore, remain unrecognized. Unequivocally linking metabolic functions to a cellular source in sponge microbiomes is, therefore, a challenge. Here, we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge (sponge that hosts a rich bacterial community) Theonella swinhoei, previously shown to contain 'Entotheonella' symbionts that produce most of the bioactive substances isolated from the sponge. As an exception, the antifungal aurantosides had remained unassigned to a source. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, 'Candidatus Poriflexus aureus' from a new Chloroflexi lineage as the aurantoside producer. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.},
}

@article {pmid36712386,
year = {2023},
author = {Madva, A and Kelly, D and Brownstein, M},
title = {Change the People or Change the Policy? On the Moral Education of Antiracists.},
journal = {Ethical theory and moral practice : an international forum},
volume = {},
number = {},
pages = {1-20},
pmid = {36712386},
issn = {1386-2820},
abstract = {While those who take a "structuralist" approach to racial justice issues are right to call attention to the importance of social practices, laws, etc., they sometimes go too far by suggesting that antiracist efforts ought to focus on changing unjust social systems rather than changing individuals' minds. We argue that while the "either/or" thinking implied by this framing is intuitive and pervasive, it is misleading and self-undermining. We instead advocate a "both/and" approach to antiracist moral education that explicitly teaches how social structures influence ideas about race and how ideas about race shape, sustain, and transform social structures. Ideally, antiracist moral education will help people see how social change and moral progress depend on the symbiotic relations between individuals and structures. We articulate a conception of "structure-facing virtue" that exemplifies this hybrid approach to illuminate the pivotal role moral education plays in the fight for racial justice.},
}

@article {pmid36712336,
year = {2022},
author = {Kuroyanagi, T and Bulasag, AS and Fukushima, K and Ashida, A and Suzuki, T and Tanaka, A and Camagna, M and Sato, I and Chiba, S and Ojika, M and Takemoto, D},
title = {Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac274},
pmid = {36712336},
issn = {2752-6542},
abstract = {The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in >400 plant species, but it is not known how this pathogen evolved this polyxenous nature. Botrytis cinerea can metabolize a wide range of phytoalexins, including the stilbenoid resveratrol in grape, and the sesquiterpenoids capsidiol in tobacco and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone, which was then further oxidized, while rishitin was directly oxidized to epoxy- or hydroxyrishitins, indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNA-seq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are found in taxonomically distant Ascomycota fungi but not in related Leotiomycetes species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.},
}

@article {pmid36711506,
year = {2023},
author = {Lindsey, AR and Parish, AJ and Newton, IL and Tennessen, JM and Jones, MW and Stark, N},
title = {Wolbachia is a nutritional symbiont.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.20.524972},
pmid = {36711506},
abstract = {UNLABELLED: Approximately a quarter of eukaryotes are infected with the bacterium Wolbachia . Its broad success as a vertically transmitted infection has been historically difficult to explain given the myriad of parasitic impacts characterized across Wolbachia 's host range. Using the Drosophila model and their natively associated Wolbachia , we show that Wolbachia infection supports fly development and buffers against nutritional stress. Wolbachia infection across several fly genotypes and a range of nutrient conditions resulted in reduced pupal mortality, increased adult emergence, and larger size. We determined that the exogenous supplementation of pyrimidines rescued these phenotypes in the Wolbachia -free, flies suggesting that Wolbachia plays a role in providing this metabolite that is normally limiting for insect growth. Additionally, Wolbachia was sensitive to host pyrimidine metabolism: Wolbachia titers increased upon transgenic knockdown of the Drosophila de novo pyrimidine synthesis pathway but not knockdown of the de novo purine synthesis pathway. We propose that Wolbachia acts as a nutritional symbiont to supplement insect development and increase host fitness: a selective advantage that could contribute to its high frequency in nature.

SIGNIFICANCE STATEMENT: Wolbachia is a bacterial symbiont of ∼1/4 of all eukaryotic species on earth, often deemed a "parasite" due to selfish manipulations of arthropod reproduction. However, many have theorized there must be more to this symbiosis: parasitic and reproductive impacts alone cannot explain the success and ubiquity of this bacterium. Here, we use Drosophila and their native Wolbachia infections to show that Wolbachia supports fly development and significantly buffers flies against nutritional stress. Additionally, we show that this advantage is likely mediated by pyrimidines: a biosynthetic pathway that all Wolbachia lineages encode for. These developmental advantages might help explain the ubiquity of Wolbachia infections.},
}

@article {pmid36710517,
year = {2023},
author = {Pichler, G and Muggia, L and Candotto Carniel, F and Grube, M and Kranner, I},
title = {How to build a lichen: from metabolite release to symbiotic interplay.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18780},
pmid = {36710517},
issn = {1469-8137},
abstract = {Exposing their vegetative bodies to the light, lichens are outstanding amongst other fungal symbioses. Not requiring a pre-established host, 'lichenized fungi' build an entirely new structure together with microbial photosynthetic partners that neither can form alone. The signals involved in the transition of a fungus and a compatible photosynthetic partner from a free-living to a symbiotic state culminating in thallus formation, termed 'lichenization', and in the maintenance of the symbiosis, are poorly understood. Here, we synthesise the puzzle pieces of the scarce knowledge available into an updated concept of signalling involved in lichenization, comprising five main stages, 1) the 'pre-contact stage', 2) the 'contact stage', 3) 'envelopment' of algal cells by the fungus, 4) their 'incorporation' into a pre-thallus and 5) 'differentiation' into a complex thallus. Considering the involvement of extracellularly released metabolites in each phase we propose that compounds such as fungal lectins and algal cyclic peptides elicit early contact between the symbionts-to-be, whereas phytohormone signalling, antioxidant protection and carbon exchange through sugars and sugar alcohols are of continued importance throughout all stages. In the fully formed lichen thallus, secondary lichen metabolites and mineral nutrition are suggested to stabilize the functionalities of the thallus, including the associated microbiota.},
}

@article {pmid36709382,
year = {2023},
author = {Maor-Landaw, K and Eisenhut, M and Tortorelli, G and van de Meene, A and Kurz, S and Segal, G and van Oppen, MJH and Weber, APM and McFadden, GI},
title = {A candidate transporter allowing symbiotic dinoflagellates to feed their coral hosts.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {7},
pmid = {36709382},
issn = {2730-6151},
abstract = {The symbiotic partnership between corals and dinoflagellate algae is crucial to coral reefs. Corals provide their algal symbionts with shelter, carbon dioxide and nitrogen. In exchange, the symbiotic algae supply their animal hosts with fixed carbon in the form of glucose. But how glucose is transferred from the algal symbiont to the animal host is unknown. We reasoned that a transporter resident in the dinoflagellate cell membrane would facilitate outward transfer of glucose to the surrounding host animal tissue. We identified a candidate transporter in the cnidarian symbiont dinoflagellate Breviolum minutum that belongs to the ubiquitous family of facilitative sugar uniporters known as SWEETs (sugars will eventually be exported transporters). Previous gene expression analyses had shown that BmSWEET1 is upregulated when the algae are living symbiotically in a cnidarian host by comparison to the free-living state [1, 2]. We used immunofluorescence microscopy to localise BmSWEET1 in the dinoflagellate cell membrane. Substrate preference assays in a yeast surrogate transport system showed that BmSWEET1 transports glucose. Quantitative microscopy showed that symbiotic B. minutum cells have significantly more BmSWEET1 protein than free-living cells of the same strain, consistent with export during symbiosis but not during the free-living, planktonic phase. Thus, BmSWEET1 is in the right place, at the right time, and has the right substrate to be the transporter with which symbiotic dinoflagellate algae feed their animal hosts to power coral reefs.},
}

@article {pmid36709299,
year = {2023},
author = {Yun, Z and Xianghong, L and Qianhua, G and Qin, D},
title = {Copper ions inhibit Streptococcus mutans-Veillonella parvula dual biofilm by activating Streptococcus mutans reactive nitrogen species.},
journal = {BMC oral health},
volume = {23},
number = {1},
pages = {48},
pmid = {36709299},
issn = {1472-6831},
abstract = {BACKGROUND: To investigate the inhibition mechanism of copper ions on Streptococcus mutans-Veillonella parvula dual biofilm.

METHODS: S. mutans-V. parvula dual biofilm was constructed and copper ions were added at different concentrations. After the biofilm was collected, RNA-seq and qRT-PCR were then performed to get gene information.

RESULTS: The coculture of S. mutans and V. parvula formed a significantly better dual biofilm of larger biomass than S. mutans mono biofilm. And copper ions showed a more significant inhibitory effect on S. mutans-V. parvula dual biofilm than on S. mutans mono biofilm when copper ions concentration reached 100 µM, and copper ions showed a decreased inhibitory effect on S. gordonii-V. parvula dual biofilm and S. sanguis-V.parvula dual biofilm than on the two mono biofilms as the concentration of copper ions increased. And common trace elements such as iron, magnesium, and zinc showed no inhibitory effect difference on S. mutans-V. parvula dual biofilm. The RNA-seq results showed a significant difference in the expression of a new ABC transporter SMU_651c, SMU_652c, SMU_653c, and S. mutans copper chaperone copYAZ. SMU_651c, SMU_652c, and SMU_653c were predicted to function as nitrite/nitrate transporter-related proteins, which suggested the specific inhibition of copper ions on S. mutans-V. parvula dual biofilm may be caused by the activation of S. mutans reactive nitrogen species.

CONCLUSIONS: Streptococcus mutans and Veillonella parvula are symbiotic, forming a dual biofilm of larger biomass to better resist the external antibacterial substances, which may increase the virulence of S. mutans. While common trace elements such as iron, magnesium, and zinc showed no specific inhibitory effect on S. mutans-V. parvula dual biofilm, copper ion had a unique inhibitory effect on S. mutans-V. parvula dual biofilm which may be caused by activating S. mutans RNS when copper ions concentration reached 250 µM.},
}

@article {pmid36709253,
year = {2023},
author = {van Creij, J and Auxier, B and An, J and Wijfjes, RY and Bergin, C and Rosling, A and Bisseling, T and Pan, Z and Limpens, E},
title = {Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {53},
pmid = {36709253},
issn = {1471-2164},
support = {ERC 678792/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.

RESULTS: Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.

CONCLUSION: Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.},
}

@article {pmid36708672,
year = {2023},
author = {Ferreira de Miranda, J and Martins Pereira Belo, G and Silva de Lima, L and Alencar Silva, K and Matsue Uekane, T and Gonçalves Martins Gonzalez, A and Naciuk Castelo Branco, V and Souza Pitangui, N and Freitas Fernandes, F and Ribeiro Lima, A},
title = {Arabic coffee infusion based kombucha: Characterization and biological activity during fermentation, and in vivo toxicity.},
journal = {Food chemistry},
volume = {412},
number = {},
pages = {135556},
doi = {10.1016/j.foodchem.2023.135556},
pmid = {36708672},
issn = {1873-7072},
abstract = {In this study, arabic coffee infusion was used to produce a fermented beverage known as kombucha. The physicochemical, antioxidant and antimicrobial activities, as well as in vivo toxicity were evaluate throughout 21 days of fermentation. Reduction in pH and sugar levels were observed throughout the fermentation period. There was no significant difference in the content of total phenolic compounds between the unfermented and fermented beverage, nor between the fermentation times, as well as in the antioxidant activity. The 5-caffeoylquinic acid was identified at all fermentation times evaluated, and no significant difference was observed regarding its concentration. It showed antibacterial and antifungal activity against all strains tested. No toxic effect of the beverages was observed in the in vivo model (Galleria mellonella) studied. These results demonstrated that coffee infusion is a possible alternative for kombucha production since the physicochemical changes prove the metabolic activity of Symbiotic Culture of Bacteria and Yeast.},
}

@article {pmid36708392,
year = {2023},
author = {Figueiredo, MA and da Silva, TH and Pinto, OHB and Leite, MGP and de Oliveira, FS and Messias, MCTB and Rosa, LH and Câmara, PEAS and Lopes, FAC and Kozovits, AR},
title = {Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36708392},
issn = {1432-184X},
abstract = {Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.},
}

@article {pmid36705037,
year = {2023},
author = {Chiu, CY and Chang, KC and Chang, LC and Wang, CJ and Chung, WH and Hsieh, WP and Su, SC},
title = {Phenotype-specific signatures of systems-level gut microbiome associated with childhood airway allergies.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {34},
number = {1},
pages = {e13905},
doi = {10.1111/pai.13905},
pmid = {36705037},
issn = {1399-3038},
abstract = {BACKGROUND: Perturbation of gut symbiosis has been linked to childhood allergic diseases. However, the underlying host-microbe interaction connected with specific phenotypes is poorly understood.

METHODS: To address this, integrative analyses of stool metagenomic and metabolomic profiles associated with IgE reactions in 56 children with mite-sensitized airway allergies (25 with rhinitis and 31 with asthma) and 28 nonallergic healthy controls were conducted.

RESULTS: We noted a decrease in the number and abundance of gut microbiome-encoded carbohydrate-active enzyme (CAZyme) genes, accompanied with a reduction in species richness, in the asthmatic gut microflora but not in that from allergic rhinitis. Such loss of CAZymes was consistent with the observation that a CAZyme-linked decrease in fecal butyrate was found in asthmatics and negatively correlated with mite-specific IgE responses. Different from the CAZymes, we demonstrated an increase in α diversity at the virulome levels in asthmatic gut microbiota and identified phenotype-specific variations of gut virulome. Moreover, use of fecal metagenomic and metabolomic signatures resulted in distinct effects on differentiating rhinitis and asthma from nonallergic healthy controls.

CONCLUSION: Overall, our integrative analyses reveal several signatures of systems-level gut microbiome in robust associations with fecal metabolites and disease phenotypes, which may be of etiological and diagnostic implications in childhood airway allergies.},
}

@article {pmid36704166,
year = {2022},
author = {Chang, W and Zhang, Y and Ping, Y and Li, K and Qi, DD and Song, FQ},
title = {Label-free quantitative proteomics of arbuscular mycorrhizal Elaeagnus angustifolia seedlings provides insights into salt-stress tolerance mechanisms.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1098260},
pmid = {36704166},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil salinization has become one of the most serious environmental issues globally. Excessive accumulation of soluble salts will adversely affect the survival, growth, and reproduction of plants. Elaeagnus angustifolia L., commonly known as oleaster or Russian olive, has the characteristics of tolerance to drought and salt. Arbuscular mycorrhizal (AM) fungi are considered to be bio-ameliorator of saline soils that can enhance the salt tolerance of the host plants. However, there is little information on the root proteomics of AM plants under salt stress.

METHODS: In this study, a label-free quantitative proteomics method was employed to identify the differentially abundant proteins in AM E. angustifolia seedlings under salt stress.

RESULTS: The results showed that a total of 170 proteins were significantly differentially regulated in E.angustifolia seedlings after AMF inoculation under salt stress. Mycorrhizal symbiosis helps the host plant E. angustifolia to respond positively to salt stress and enhances its salt tolerance by regulating the activities of some key proteins related to amino acid metabolism, lipid metabolism, and glutathione metabolism in root tissues.

CONCLUSION: Aspartate aminotransferase, dehydratase-enolase-phosphatase 1 (DEP1), phospholipases D, diacylglycerol kinase, glycerol-3-phosphate O-acyltransferases, and gamma-glutamyl transpeptidases may play important roles in mitigating the detrimental effect of salt stress on mycorrhizal E. angustifolia . In conclusion, these findings provide new insights into the salt-stress tolerance mechanisms of AM E. angustifolia seedlings and also clarify the role of AM fungi in the molecular regulation network of E. angustifolia under salt stress.},
}

@article {pmid36702408,
year = {2023},
author = {Zheng, L and Ren, M and Liu, T and Ding, A and Xie, E},
title = {Base type determines the effects of nucleoside monophosphates on microalgae-bacteria symbiotic systems.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {137943},
doi = {10.1016/j.chemosphere.2023.137943},
pmid = {36702408},
issn = {1879-1298},
abstract = {Microalgae are promising sources of clean energy. Bioflocculation by cocultured bacteria is an effective way to harvest microalgae. As a key foundation for microorganisms, phosphorus is theoretically effective in shaping microalgae production and flocculation. In this study, the impacts of 23 nucleoside monophosphates on Auxenochlorella pyrenoidosa growth, lipid synthesis, and self-settlement and on the symbiotic bacterial system were investigated. Adenosine monophosphate was the most effective in enhancing microalgae development (2.14-3.16 × 10[8] cells/mL) and lipid production (average 10.48%) and resulted in a low settling velocity. Samples were divided into two groups, purine and pyrimidine feeding, according to a random forest analysis (OOB = 0%, p < 0.001). Purine feeding resulted in the highest soluble extracellular protein and polysaccharide secretion (p < 0.01). KEGG ortholog count prediction of functional genes related to biofilm formation was conducted using PICRUSt2, and significant upregulation (FC ≥ 1.77, p < 0.05) of the extracellular polymeric substance formation functional group was observed in the adenosine and guanosine treatments. The symbiotic bacterial community structure differed substantially between purine- and pyrimidine-feeding systems. In summary, these results indicated that the effect of nucleoside monophosphates on the microalgae-bacteria system is determined by the base type (purine or pyrimidine) rather than the molecular structure (cyclic or noncyclic).},
}

@article {pmid36700963,
year = {2023},
author = {Vohník, M and Réblová, M},
title = {Fungi in hair roots of Vaccinium spp. (Ericaceae) growing on decomposing wood: colonization patterns, identity, and in vitro symbiotic potential.},
journal = {Mycorrhiza},
volume = {},
number = {},
pages = {},
pmid = {36700963},
issn = {1432-1890},
abstract = {Most of our knowledge on the ericoid mycorrhizal (ErM) symbiosis comes from temperate heathlands characterized by acidic peaty soils and many experiments with a few ascomycetous fungi. However, ericaceous plants thrive in many other ecosystems and in temperate coniferous forests, their seedlings often prosper on decomposing wood. While wood is typically exploited by basidiomycetous ectomycorrhizal (EcM) and saprobic fungi, the role of ErM fungi (ErMF) is much less clear. We explored the cultivable mycobiota of surface sterilized hair roots of Vaccinium spp. growing on decomposing wood in two coniferous forests in Mid-Norway (Scandinavia) and Northern Bohemia (Central Europe). Obtained isolates were identified using molecular tools and their symbiotic potential was tested in vitro. While the detected community lacked the archetypal ErMF Hyaloscypha hepaticicola and the incidence of dark septate endophytes and EcM fungi was negligible, it comprised other frequent asexual ascomycetous ErMF, namely H. variabilis and Oidiodendron maius, together with several isolates displaying affinities to sexual saprobic H. daedaleae and H. fuckelii. Ascomycete-suppressing media revealed representatives of the saprobic basidiomycetous genera Coprinellus, Gymnopilus, Mycena (Agaricales), and Hypochnicium (Polyporales). In the resyntheses, the tested basidiomycetes occasionally penetrated the rhizodermal cells of their hosts but never formed ericoid mycorrhizae and in many cases overgrew and killed the inoculated seedlings. In contrast, a representative of the H. daedaleae/H. fuckelii-related isolates repeatedly formed what morphologically appears as the ErM symbiosis and supported host's growth. In conclusion, while basidiomycetous saprobic fungi have a potential to colonize healthy-looking ericaceous hair roots, the mode(-s) of their functioning remain obscure. For the first time, a lineage in Hyaloscypha s. str. (corresponding to the former Hymenoscyphus ericae aggregate) where sexual saprobes are intermingled with root symbionts has been revealed, shedding new light on the ecology and evolution of these prominent ascomycetous ErMF.},
}

@article {pmid36700628,
year = {2023},
author = {Kim, JH and Scherer, G and Lumpkin, DS and Rao, K and Puentes Flores, CD and Van Arnam, EB},
title = {Amycolatopsis from Desert Specialist Fungus-Growing Ants Suppresses Contaminant Fungi Using the Antibiotic ECO-0501.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0183822},
doi = {10.1128/aem.01838-22},
pmid = {36700628},
issn = {1098-5336},
abstract = {Symbiotic Actinobacteria help fungus-growing ants suppress fungal pathogens through the production of antifungal compounds. Trachymyrmex ants of the southwest desert of the United States inhabit a unique niche far from the tropical rainforests in which most fungus-growing ant species are found. These ants may not encounter the specialist fungal pathogen Escovopsis known to threaten colonies of other fungus-growing ants. It is unknown whether Actinobacteria associated with these ants antagonize contaminant fungi and, if so, what the chemical basis of such antagonism is. We find that Pseudonocardia and Amycolatopsis strains isolated from three desert specialist Trachymyrmex species do antagonize diverse contaminant fungi isolated from field-collected ant colonies. We did not isolate the specialist fungal pathogen Escovopsis in our sampling. We trace strong antifungal activity from Amycolatopsis isolates to the molecule ECO-0501, an antibiotic that was previously under preclinical development as an antibacterial agent. In addition to suppression of contaminant fungi, we find that this molecule has strong activity against ant-associated Actinobacteria and may also play a role in bacterial competition in this niche. By studying interspecies interactions in a previously unexplored niche, we have uncovered novel bioactivity for a structurally unique antibiotic. IMPORTANCE Animal hosts often benefit from chemical defenses provided by microbes. These molecular defenses are a potential source of novel antibiotics and offer opportunities for understanding how antibiotics are used in ecological contexts with defined interspecies interactions. Here, we recover contaminant fungi from nests of Trachymyrmex fungus-growing ants of the southwest desert of the United States and find that they are suppressed by Actinobacteria isolated from these ants. The antibiotic ECO-0501 is an antifungal agent used by some of these Amycolatopsis bacterial isolates. This antibiotic was previously investigated in preclinical studies and known only for antibacterial activity.},
}

@article {pmid36699720,
year = {2022},
author = {Guizzo, MG and Hatalová, T and Frantová, H and Zurek, L and Kopáček, P and Perner, J},
title = {Ixodes ricinus ticks have a functional association with Midichloria mitochondrii.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1081666},
pmid = {36699720},
issn = {2235-2988},
abstract = {In addition to being vectors of pathogenic bacteria, ticks also harbor intracellular bacteria that associate with ticks over generations, aka symbionts. The biological significance of such bacterial symbiosis has been described in several tick species but its function in Ixodes ricinus is not understood. We have previously shown that I. ricinus ticks are primarily inhabited by a single species of symbiont, Midichloria mitochondrii, an intracellular bacterium that resides and reproduces mainly in the mitochondria of ovaries of fully engorged I. ricinus females. To study the functional integration of M. mitochondrii into the biology of I. ricinus, an M. mitochondrii-depleted model of I. ricinus ticks was sought. Various techniques have been described in the literature to achieve dysbiosed or apo-symbiotic ticks with various degrees of success. To address the lack of a standardized experimental procedure for the production of apo-symbiotic ticks, we present here an approach utilizing the ex vivo membrane blood feeding system. In order to deplete M. mitochondrii from ovaries, we supplemented dietary blood with tetracycline. We noted, however, that the use of tetracycline caused immediate toxicity in ticks, caused by impairment of mitochondrial proteosynthesis. To overcome the tetracycline-mediated off-target effect, we established a protocol that leads to the production of an apo-symbiotic strain of I. ricinus, which can be sustained in subsequent generations. In two generations following tetracycline administration and tetracycline-mediated symbiont reduction, M. mitochondrii was gradually eliminated from the lineage. Larvae hatched from eggs laid by such M. mitochondrii-free females repeatedly performed poorly during blood-feeding, while the nymphs and adults performed similarly to controls. These data indicate that M. mitochondrii represents an integral component of tick ovarian tissue, and when absent, results in the formation of substandard larvae with reduced capacity to blood-feed.},
}

@article {pmid36699610,
year = {2022},
author = {Pu, J and Li, Z and Tang, H and Zhou, G and Wei, C and Dong, W and Jin, Z and He, T},
title = {Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1070876},
pmid = {36699610},
issn = {1664-302X},
abstract = {Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN60: green manure couple with 60% nitrogen fertilizer, MN80: green manure couple with 80% nitrogen fertilizer; and MN100: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN100 treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20-40% for rice production. Graphical Abstract.},
}

@article {pmid36698910,
year = {2022},
author = {Chen, PY and Chen, CW and Su, YJ},
title = {Gangrenous cellulitis caused by coagulase‑negative Staphylococcus infection: A case report.},
journal = {Medicine international},
volume = {2},
number = {5},
pages = {31},
pmid = {36698910},
issn = {2754-1304},
abstract = {A 40-year-old male with a history of alcohol and drug addiction presented with fever for 1 day in the emergency room. He reported the abuse of drugs via intravenous injection and consumed alcohol excessively. Upon arrival to the emergency room, his body temperature was 39.4˚C. Upon a physical examination, generalized skin gangrene over the trunk and four limbs were found. Laboratory tests revealed thrombocytopenia (platelets, 67,000/µl) and elevated C-reactive protein (30.4 mg/dl), creatine kinase (>20,000 IU/l), D-Dimer (>10,000 ng/ml) levels. The urinary drug screen test was positive for ketamine and benzodiazepine. The blood culture on day 4 of admission yielded coagulase-negative Staphylococcus (CoNS). The patient was diagnosed with CoNS induced by the venous injection of ketamine. He was admitted and received treatment with parenteral antibiotics with serial debridement due to the progressive necrosis of the skin gangrene. He was discharged 2 months later with clinical improvement. CoNS generally has a symbiotic association with the hosts in the cutaneous ecosystem, which frequently contaminates blood culture and occasionally causes diseases. CoNS should be thus considered opportunistic pathogens rather than contaminants. These organisms can cause occasional infection if the cutaneous organ system has been damaged by trauma, the direct implantation of foreign bodies or inoculation by needles. Predisposing factors for CoNS infections include an older age, immunosuppression and the implantation of medical devices, which may serve as a nidus for CoNS growth. Long-term alcoholism, drug addiction and malnutrition may have caused a decline in the immunity of the patient described herein. To date, at least to the best of our knowledge, there has been no report describing local skin necrosis induced by CoNS infection. In the case in the present study, treatment with parenteral antibiotics and serial debridement was successful. In summary, physicians need to be aware of the potential pathogenicity of CoNS in the skin and soft tissue infections.},
}

@article {pmid36696762,
year = {2023},
author = {Wang, L and Zhang, Q and Zhang, G and Wang, D and Liu, C},
title = {Can industrial symbiosis policies be effective? Evidence from the nationwide industrial symbiosis system in China.},
journal = {Journal of environmental management},
volume = {331},
number = {},
pages = {117346},
doi = {10.1016/j.jenvman.2023.117346},
pmid = {36696762},
issn = {1095-8630},
abstract = {Policies directly or indirectly influence the development of industrial symbiosis (IS). Quantitatively analyzing the effects of policies on IS at a national level is necessary, but current research has lagged. Focusing on the symbiotic system that includes the thermal power industry, cement industry, iron and steel industry, and social sector in China, this paper assesses the efficacy of policies on this nationwide IS system between 2015 and 2022. A policy influence framework is proposed, combining a cost-benefit analysis, agent-based model, and comparative analysis. Results show: (1) the symbiosis probability of the nationwide IS system experiences a fluctuating increase. The maximum increments of the symbiosis probability are 5%, and the resulting environmental benefits are equivalent to an emission reduction of 6.99 Mt from blast furnace slag, 20.97 Mt from iron mine tailing, 36.02 Mt from household waste, 25.01 Mt from steel slag, and 22.95 Mt from fly ash. However, the stimulation effects of policies vary across different subsystems. (2) Thermal power-chemical subsystems, thermal power-environmental protection subsystems, iron and steel-environmental protection subsystems, and social sector-cement subsystems need policy support in the future. (3) Approximately 50% of fields in this nationwide IS system is insensitive to current policies; policy approaches should shift from economic stimulation to symbiotic guidance. This paper fills the research gap by quantitatively studying the IS policy efficacy from a national level. The findings can contribute to the improvement of the Chinese IS policy system.},
}

@article {pmid36696455,
year = {2023},
author = {Zhang, B and Chandran Sandaran, S and Feng, J},
title = {The ecological discourse analysis of news discourse based on deep learning from the perspective of ecological philosophy.},
journal = {PloS one},
volume = {18},
number = {1},
pages = {e0280190},
doi = {10.1371/journal.pone.0280190},
pmid = {36696455},
issn = {1932-6203},
abstract = {Recently, ecological damage and environmental pollution have become increasingly serious. Experts in various fields have started to study related issues from diverse points of view. To prevent the accelerated deterioration of the ecological environment, ecolinguistics emerged. Eco-critical discourse analysis is one of the important parts of ecolinguistics research, that is, it is a critical discourse analysis of the use of language from the perspective of the language's ecological environment. Firstly, an ecological tone and modality system are constructed from an ecological perspective. Under the guidance of the ecological philosophy of "equality, harmony, and symbiosis", this study conducts an ecological discourse analysis on the Sino-US trade friction reports, aiming to present the similarities and differences between the two newspapers' trade friction discourses and to reveal the ecological significance of international ecological factors in the discourse. Secondly, this method establishes a vector expression of abstract words based on emotion dictionary resources and introduces emotion polarity and part-of-speech features of words. Then the word vector is formed into the text feature matrix, which is used as the input of the Convolutional Neural Network (CNN) model, and the Back Propagation algorithm is adopted to train the model. Finally, in the light of the trained CNN model, the unlabeled news is predicted, and the experimental results are analyzed. The results reveal that during the training process of Chinese and English datasets, the accuracy of the training set can reach nearly 100%, and the loss rate can be reduced to 0. On the test set, the classification accuracy of Chinese text can reach 83%, while that of English text can reach 90%, and the experimental results are ideal. This study provides an explanatory approach for ecological discourse analysis on the news reports of Sino-US trade frictions and has certain guiding significance for the comparative research on political news reports under different ideologies between China and the United States.},
}

@article {pmid36694719,
year = {2022},
author = {Afonnikova, SD and Komissarov, AS and Kuchur, PD},
title = {Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {26},
number = {8},
pages = {810-818},
doi = {10.18699/VJGB-22-98},
pmid = {36694719},
issn = {2500-0462},
abstract = {Many plants and animals have symbiotic relationships with microorganisms, including bacteria. The interactions between bacteria and their hosts result in different outcomes for the host organism. The outcome can be neutral, harmful or have beneficial effects for participants. Remarkably, these relationships are not static, as they change throughout an organism's lifetime and on an evolutionary scale. One of the structures responsible for relationships in bacteria is O-antigen. Depending on the characteristics of its components, the bacteria can avoid the host's immune response or establish a mutualistic relationship with it. O-antigen is a key component in Gram-negative bacteria's outer membrane. This component facilitates interaction between the bacteria and host immune system or phages. The variability of the physical structure is caused by the genomic variability of genes encoding O-antigen synthesis components. The genes and pathways of O-polysaccharide (OPS) synthesis were intensively investigated mostly for Enterobacteriaceae species. Considering high genetic and molecular diversity of this structure even between strains, these findings may not have caught the entire variety possibly presented in non-model species. The current study presents a comparative analysis of genes associated with O-antigen synthesis in bacteria of the Oxalobacteraceae family. In contrast to existing studies based on PCR methods, we use a bioinformatics approach and compare O- antigens at the level of clusters rather than individual genes. We found that the O-antigen genes of these bacteria are represented by several clusters located at a distance from each other. The greatest similarity of the clusters is observed within individual bacterial genera, which is explained by the high variability of O-antigens. The study describes similarities of OPS genes inherent to the family as a whole and also considers individual unique cases of O-antigen genetic variability inherent to individual bacteria.},
}

@article {pmid36694551,
year = {2023},
author = {de Gier, W},
title = {Phylomorphometrics reveal ecomorphological convergence in pea crab carapace shapes (Brachyura, Pinnotheridae).},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9744},
pmid = {36694551},
issn = {2045-7758},
abstract = {Most members of the speciose pea crab family (Decapoda: Brachyura: Pinnotheridae) are characterized by their symbioses with marine invertebrates in various host phyla. The ecology of pea crabs is, however, understudied, and the degree of host dependency of most species is still unclear. With the exception of one lineage of ectosymbiotic echinoid-associated crabs, species within the subfamily Pinnotherinae are endosymbionts, living within the body cavities of mollusks, ascidians, echinoderms, and brachiopods. By contrast, most members of the two other subfamilies are considered to have an ectosymbiotic lifestyle, sharing burrows and tubes with various types of worms and burrowing crustaceans (inquilism). The body shapes within the family are extremely variable, mainly in the width and length of the carapace. The variation of carapace shapes in the family, focusing on pinnotherines, is mapped using landmark-based morphometrics. Mean carapace shapes of species groups (based on their host preference) are statistically compared. In addition, a phylomorphometric approach is used to study three different convergence events (across subfamilies; between three genera; and within one genus), and link these events with the associated hosts.},
}

@article {pmid36692332,
year = {2023},
author = {Sun, X and Liu, BQ and Chen, ZB and Li, CQ and Li, XY and Hong, JS and Luan, JB},
title = {Vitellogenin Facilitates Associations between the Whitefly and a Bacteriocyte Symbiont.},
journal = {mBio},
volume = {},
number = {},
pages = {e0299022},
doi = {10.1128/mbio.02990-22},
pmid = {36692332},
issn = {2150-7511},
abstract = {Integration between animal reproduction and symbiont inheritance is fundamental in symbiosis biology, but the underlying molecular mechanisms are largely unknown. Vitellogenin (Vg) is critical for oogenesis, and it is also a pathogen pattern recognition molecule in some animals. Previous studies have shown that Vg is involved in the regulation of symbiont abundance and transmission. However, the mechanisms by which an insect and its symbiont contribute to the function of Vg and how Vg impacts the persistence of insect-microbe symbiosis remain largely unclear. Symbionts are transovarially transmitted via maternal inheritance of the bacteriocytes in the whitefly Bemisia tabaci. Surprisingly, Vg is localized in bacteriocytes of whiteflies. Vg could be synthesized in whitefly bacteriocytes by the gene Vg expressed in these cells or exported into bacteriocytes from hemolymph via the Vg receptor. We further found that the juvenile hormone and "Candidatus Portiera aleyrodidarum" (here termed Portiera) control the level and localization of Vg in whiteflies. Immunocapture PCR revealed interactions between Vg and Portiera. Suppressing Vg expression reduced Portiera abundance as well as whitefly oogenesis and fecundity. Thus, we reveal that Vg facilitated the persistence of whitefly-bacteriocyte symbiont associations. This study will provide insight into the key role of Vg in the coevolution of insect reproduction and symbiont inheritance. IMPORTANCE Intracellular heritable symbionts have been incorporated into insect reproductive and developmental biology by various mechanisms. All Bemisia tabaci species harbor the obligate symbiont Portiera in specialized insect cells called bacteriocytes. We report that the whitefly juvenile hormone and Portiera determined vitellogenin (Vg) localization in bacteriocytes of whiteflies. In turn, Vg affected whitefly fecundity as well as fitness and transmission of the symbiont. Our findings show that Vg, a multifunctional protein, is indispensable for symbiont integration into the reproduction and development of insects. This reflects the outcome of long-term coevolution of the insect-microbe symbiosis.},
}

@article {pmid36690340,
year = {2023},
author = {Loudon, AH and Park, J and Parfrey, LW},
title = {Identifying the core microbiome of the sea star Pisaster ochraceus in the context of sea star wasting disease.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad005},
pmid = {36690340},
issn = {1574-6941},
abstract = {Sea stars are keystone species and their mass die-offs due to sea star wasting disease (SSWD) impact marine communities and have fueled recent interest in the microbiome of sea stars. We assessed the host-specificity of the microbiome associated with three body regions of the sea star Pisaster ochraceus using 16S rRNA gene amplicon surveys of the bacterial communities living on and in Pisaster, their environment, and sympatric marine hosts across three populations in British Columbia, Canada. Overall, the bacterial communities on Pisaster are distinct from their environment and differ by both body region and geography. We identified core bacteria specifically associated with Pisaster across populations and nearly absent in other hosts and the environment. We then investigated the distribution of these core bacteria on SSWD-affected Pisaster from one BC site and by reanalyzing a study of SSWD on Pisaster from California. We find no differences in the distribution of core bacteria in early disease at either site and two core taxa differ in relative abundance in advanced disease in California. Using phylogenetic analyses, we find that most core bacteria have close relatives on other sea stars and marine animals, suggesting these clades have evolutionary adaptions to an animal-associated lifestyle.},
}

@article {pmid36688656,
year = {2023},
author = {Rosado, PM and Cardoso, PM and Rosado, JG and Schultz, J and Nunes da Rocha, U and Keller-Costa, T and Peixoto, RS},
title = {Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0092122},
doi = {10.1128/msystems.00921-22},
pmid = {36688656},
issn = {2379-5077},
abstract = {Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.},
}

@article {pmid36688592,
year = {2023},
author = {Miyata, K and Hosotani, M and Akamatsu, A and Takeda, N and Wendi, J and Sugiyama, T and Takaoka, R and Matsumoto, K and Abe, S and Shibuya, N and Kaku, H},
title = {OsSYMRK Plays an Essential Role in AM Symbiosis in Rice (Oryza sativa).},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcad006},
pmid = {36688592},
issn = {1471-9053},
abstract = {Arbuscular mycorrhizal (AM) fungi establish mutualistic symbiosis with a wide range of terrestrial plants, including rice. However, the mechanisms underlying the initiation of AM symbiosis have yet to be elucidated, particularly in nonleguminous plants. We previously demonstrated that OsCERK1, a lysin motif (LysM) receptor-like kinase essential for chitin-triggered immunity, also plays a key role in AM symbiosis in rice. However, the mechanisms underlying the regulation of switching between immunity and symbiosis by OsCERK1 have yet to be fully elucidated. SYMRK/DMI2 is a leucine-rich repeat receptor-like kinase associated with both root nodule symbiosis and AM symbiosis in legumes. The homologue of SYMRK in rice, OsSYMRK, has a shorter form than in legumes because OsSYMRK lacks a malectin-like domain (MLD). The MLD reportedly contributes to symbiosis in Lotus japonicus; however, the contribution of OsSYMRK to AM symbiosis in rice remains unclear. Phylogenetic analyses indicated that the MLD of SYMRK/DMI2 is widely conserved even in mosses and ferns but absent in commelinids, including rice. To understand the function of OsSYMRK, we produced an Ossymrk knockout mutant using CRISPR/Cas9 technology. AM colonization was mostly abolished in Ossymrk with a more severe phenotype than Oscerk1. Ca2+ spiking against chitin tetramer was also diminished in Ossymrk. In contrast, comparable defense responses against chitin heptamer to wild type were observed in Ossymrk. Bimolecular fluorescence complementation studies demonstrating an interaction between OsSYMRK and OsCERK1 indicate OsSYMRK may play an important role in switching from immunity to symbiosis through the interaction with OsCERK1 in rice.},
}

@article {pmid36688400,
year = {2023},
author = {Rainey, PB},
title = {Major evolutionary transitions in individuality between humans and AI.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {378},
number = {1872},
pages = {20210408},
doi = {10.1098/rstb.2021.0408},
pmid = {36688400},
issn = {1471-2970},
abstract = {That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central to my argument is recognition that heritable variance in fitness at higher levels of organization can be externally imposed (scaffolded) by specific ecological structures and cultural practices. While ETIs to eusociality seem highly improbable, ETIs involving symbioses between humans and artificial intelligence (AI) can be readily envisaged. A necessary requirement is that fitness-affecting interactions between humans and AI devices are inherited by offspring. The Mendelian nature of human reproduction ensures that offspring resemble parents. Reproduction of AI devices requires nothing more than transference of algorithms from parental AI devices to devices that are assigned to offspring. This simple copying, combined with societal structures that require humans to carry AI devices, ensures heritable variance in fitness at the level of both interacting partners. Selection at the collective level will drive alignment of replicative fates and increase co-dependency, thus alleviating need for continual imposition of externally imposed scaffolds. I conclude by drawing attention to the immediacy of such transitions and express concern over possibilities for malevolent manipulation. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.},
}

@article {pmid36687730,
year = {2022},
author = {Guo, Y and Song, L and Huang, Y and Li, X and Xiao, Y and Wang, Z and Ren, Z},
title = {Latilactobacillus sakei Furu2019 and stachyose as probiotics, prebiotics, and synbiotics alleviate constipation in mice.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1039403},
pmid = {36687730},
issn = {2296-861X},
abstract = {INTRODUCTION: Slow transit constipation (STC) is a common disorder in the digestive system. This study aimed to evaluate the effects of stachyose (ST) and Latilactobacillus sakei Furu 2019 (L. sakei) alone or combined on diphenoxylate-induced constipation and explore the underlying mechanisms using a mouse model.

METHODS: ICR mice were randomly divided into five groups. The normal and constipation model groups were intragastrically administrated with PBS. The ST, L. sakei, and synbiotic groups were intragastrically administrated with ST (1.5 g/kg body weight), alive L. sakei (3 × 10[9] CFU/mouse), or ST + L. sakei (1.5 g/kg plus 3 × 10[9] CFU/mouse), respectively. After 21 days of intervention, all mice except the normal mice were intragastrically administrated with diphenoxylate (10 mg/kg body weight). Defecation indexes, constipation-related intestinal factors, serum neurotransmitters, hormone levels, short-chain fatty acids (SCFAs), and intestinal microbiota were measured.

RESULTS: Our results showed that three interventions with ST, L. sakei, and synbiotic combination (ST + L. sakei) all alleviated constipation, and synbiotic intervention was superior to ST or L. sakei alone in some defecation indicators. The RT-PCR and immunohistochemical experiment showed that all three interventions relieved constipation by affecting aquaporins (AQP4 and AQP8), interstitial cells of Cajal (SCF and c-Kit), glial cell-derived neurotrophic factor (GDNF), and Nitric Oxide Synthase (NOS). The three interventions exhibited a different ability to increase the serum excitatory neurotransmitters and hormones (5-hydroxytryptamine, substance P, motilin), and reduce the serum inhibitory neurotransmitters (vasoactive intestinal peptide, endothelin). The result of 16S rDNA sequencing of feces showed that synbiotic intervention significantly increased the relative abundance of beneficial bacteria such as Akkermansia, and regulated the gut microbes of STC mice. In conclusion, oral administration of ST or L. sakei alone or combined are all effective to relieve constipation and the symbiotic use may have a promising preventive effect on STC.},
}

@article {pmid36687653,
year = {2022},
author = {Zhao, M and Liu, L and Liu, F and Liu, L and Liu, Z and Gao, Y and Cao, J},
title = {Traditional Chinese medicine improves myasthenia gravis by regulating the symbiotic homeostasis of the intestinal microbiota and host.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1082565},
pmid = {36687653},
issn = {1664-302X},
abstract = {Myasthenia gravis (MG) is an autoimmune disease caused by autoantibodies that is dependent on T-cell immunity and complement participation and mainly involves neuromuscular junctions. In this study, 30 patients with myasthenia gravis were selected and divided into pretreatment (Case group) and posttreatment (Treatment group) and 30 healthy volunteers (CON group) were included. Among them, the treatment group was treated with Modified Buzhong Yiqi Decoction (MBZYQD), and the levels of antibodies such as AChR, Musk and Titin in blood and intestinal microbiota were compared before treatment (Case group), after treatment (Treatment group) and in healthy volunteers (CON group). The results showed that after treatment with MBZYQD, the antibody levels of AChR, MuSK, and Titin and the inflammatory factor level of IL-6, IL-1β, and IL-22 in MG patients decreased significantly and nearly returned to a healthy level. In addition, after treatment with MBZYQD, the diversity, structure and function of intestinal microorganisms in MG patients also recovered to a healthy level. At the phylum level, the relative abundance of Proteobacteria in the Case group increased significantly, accompanied by a significant decrease in the relative abundance of Bacteroides compared with that in the CON group, the relative abundance of Proteobacteria and Bacteroides in the Treatment group was similar to that in the CON group. At the genus level, the relative abundance of Shigella in the Case group was significantly increased, accompanied by a significant decrease in the relative abundance of Prevotella, and the relative abundance of Shigella and Prevotella in Treatment group was similar to that in the CON group. Moreover, the fluorobenzoate degradation pathway (KO00364) was significantly increased in the Case group, while this pathway was significantly decreased in the Treatment group. In conclusion, MBZYQD can improve the immune function of the host by regulating the diversity, structure and function of the intestinal microbiota to treat myasthenia gravis.},
}

@article {pmid36687603,
year = {2022},
author = {Tang, M and Wang, H and Qi, X and He, T and Zhang, B and Wang, E and Yu, M and Wang, B and Wang, F and Liu, Z and Liu, X},
title = {Diversification of Sinorhizobium populations associated with Medicago polymorpha and Medicago lupulina in purple soil of China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1055694},
pmid = {36687603},
issn = {1664-302X},
abstract = {The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S-23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.},
}

@article {pmid36686690,
year = {2022},
author = {Büttiker, P and Weissenberger, S and Esch, T and Anders, M and Raboch, J and Ptacek, R and Kream, RM and Stefano, GB},
title = {Dysfunctional mitochondrial processes contribute to energy perturbations in the brain and neuropsychiatric symptoms.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {1095923},
pmid = {36686690},
issn = {1663-9812},
abstract = {Mitochondria are complex endosymbionts that evolved from primordial purple nonsulfur bacteria. The incorporation of bacteria-derived mitochondria facilitates a more efficient and effective production of energy than what could be achieved based on previous processes alone. In this case, endosymbiosis has resulted in the seamless coupling of cytochrome c oxidase and F-ATPase to maximize energy production. However, this mechanism also results in the generation of reactive oxygen species (ROS), a phenomenon that can have both positive and negative ramifications on the host. Recent studies have revealed that neuropsychiatric disorders have a pro-inflammatory component in which ROS is capable of initiating damage and cognitive malfunction. Our current understanding of cognition suggests that it is the product of a neuronal network that consumes a substantial amount of energy. Thus, alterations or perturbations of mitochondrial function may alter not only brain energy supply and metabolite generation, but also thought processes and behavior. Mitochondrial abnormalities and oxidative stress have been implicated in several well-known psychiatric disorders, including schizophrenia (SCZ) and bipolar disorder (BPD). As cognition is highly energy-dependent, we propose that the neuronal pathways underlying maladaptive cognitive processing and psychiatric symptoms are most likely dependent on mitochondrial function, and thus involve brain energy translocation and the accumulation of the byproducts of oxidative stress. We also hypothesize that neuropsychiatric symptoms (e.g., disrupted emotional processing) may represent the vestiges of an ancient masked evolutionary response that can be used by both hosts and pathogens to promote self-repair and proliferation via parasitic and/or symbiotic pathways.},
}

@article {pmid36685945,
year = {2022},
author = {Mogilicherla, K and Roy, A},
title = {Epigenetic regulations as drivers of insecticide resistance and resilience to climate change in arthropod pests.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1044980},
pmid = {36685945},
issn = {1664-8021},
abstract = {Arthropod pests are remarkably capable of rapidly adapting to novel forms of environmental stress, including insecticides and climate change. The dynamic interplay between epigenetics and genetics explains the largely unexplored reality underlying rapid climatic adaptation and the development of insecticide resistance in insects. Epigenetic regulation modulates gene expression by methylating DNA and acetylating histones that play an essential role in governing insecticide resistance and adaptation to climate change. This review summarises and discusses the significance of recent advances in epigenetic regulation that facilitate phenotypic plasticity in insects and their symbiotic microbes to cope with selection pressure implied by extensive insecticide applications and climate change. We also discuss how epigenetic changes are passed on to multiple generations through sexual recombination, which remains enigmatic. Finally, we explain how these epigenetic signatures can be utilized to manage insecticide resistance and pest resilience to climate change in Anthropocene.},
}

@article {pmid36685208,
year = {2022},
author = {Jang, S and Matsuura, Y and Ishigami, K and Mergaert, P and Kikuchi, Y},
title = {Symbiont coordinates stem cell proliferation, apoptosis, and morphogenesis of gut symbiotic organ in the stinkbug-Caballeronia symbiosis.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1071987},
pmid = {36685208},
issn = {1664-042X},
abstract = {The bean bug Riptortus pedestris obtains a specific bacterial symbiont, Caballeronia insecticola (Burkholderia insecticola), from the environmental soil and harbors it in the posterior midgut region that is composed of hundreds of crypts. While newly hatched aposymbiotic insects possess primordial midgut crypts with little or no lumen, colonization of C. insecticola triggers swift development of the symbiotic organ, forming enlarged and opened crypts, and the symbiont subsequently fills the luminal cavities of those mature crypts. The cellular processes of crypt development triggered by C. insecticola colonization are poorly understood. Here we identified a fundamental mechanism of the symbiont-mediated midgut development by investigating cell cycles of intestinal epithelial cells. Intestinal stem cells of the bean bug are located and proliferate at the crypt base. Differentiated enterocytes migrate upward along the epithelial cell layer of the crypt as the midgut develops, induction of apoptosis in enterocytes primarily occurred on the tip side of the crypts, and apoptotic cells then eventually were shed from the crypts into the hemolymph. The proliferation rate of the stem cells at the base of the crypts was low while a high apoptotic rate was observed at the crypt tip in aposymbiotic insects, resulting in undeveloped short crypts. On the contrary, the gut-colonizing C. insecticola promoted the proliferation of the stem cells at the base of crypts and simultaneously inhibited apoptosis at the tip of crypts, resulting in a net growth of the crypts and the generation of a crypt lumen that becomes colonized by the bacterial symbiont. These results demonstrated that the Caballeronia symbiont colonization induces the development of the midgut crypts via finely regulating the enterocyte cell cycles, enabling it to stably and abundantly colonize the generated spacious crypts of the bean bug host.},
}

@article {pmid36684723,
year = {2022},
author = {Lidoy, J and Berrio, E and García, M and España-Luque, L and Pozo, MJ and López-Ráez, JA},
title = {Flavonoids promote Rhizophagus irregularis spore germination and tomato root colonization: A target for sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1094194},
pmid = {36684723},
issn = {1664-462X},
abstract = {The use of arbuscular mycorrhizal (AM) fungi has great potential, being used as biostimulants, biofertilizers and bioprotection agents in agricultural and natural ecosystems. However, the application of AM fungal inoculants is still challenging due to the variability of results when applied in production systems. This variability is partly due to differences in symbiosis establishment. Reducing such variability and promoting symbiosis establishment is essential to improve the efficiency of the inoculants. In addition to strigolactones, flavonoids have been proposed to participate in the pre-symbiotic plant-AM fungus communication in the rhizosphere, although their role is still unclear. Here, we studied the specific function of flavonoids as signaling molecules in AM symbiosis. For that, both in vitro and in planta approaches were used to test the stimulatory effect of an array of different subclasses of flavonoids on Rhizophagus irregularis spore germination and symbiosis establishment, using physiological doses of the compounds. We show that the flavone chrysin and the flavonols quercetin and rutin were able to promote spore germination and root colonization at low doses, confirming their role as pre-symbiotic signaling molecules in AM symbiosis. The results pave the way to use these flavonoids in the formulation of AM fungal-based products to promote the symbiosis. This can improve the efficiency of commercial inoculants, and therefore, help to implement their use in sustainable agriculture.},
}

@article {pmid36684181,
year = {2022},
author = {Wang, L and Deng, S and Meng, F and Zhang, L and Min, Z and Li, J and Wang, J},
title = {Comprehensive analysis of global research on overactive bladder: A scientometric approach.},
journal = {Frontiers in surgery},
volume = {9},
number = {},
pages = {1078052},
pmid = {36684181},
issn = {2296-875X},
abstract = {BACKGROUND: Overactive bladder, a syndrome marked by an urgent need to urinate, is a globally prevalent ailment. Human health and quality of life are seriously affected. Therefore, it is essential to investigate the current progress and trends in this field.

OBJECTIVE: No bibliometric analysis of overactive bladder has been conducted. Through the use of bibliometrics and visualization, this study intends to examine the current progress and development trend of this field.

METHODS: Global publications on overactive bladder between January 2004 and August 2022 were extracted from the Web of Science core collection database. A bibliometric and visual analysis was carried out using VOSviewer software and CiteSpace.

RESULTS: Over the last 20 years, publications have grown rapidly, but after 2019, they started to fall. According to the collaboration network, the United States, Univ Pittsburgh AND NEUROUROLOGY AND URODYNAMICS are the most active countries, institutes AND journals in the field, respectively. All keywords were categorized by the symbiosis analysis into four categories: experimental study, symptoms, clinical use, and quality of life. The most prevalent keyword across all clusters is "overactive bladder."

CONCLUSION: Year after year, there have been more publications in the field of overactive bladder research in many countries, and there has been a deeper level of cooperation and exchange. Researchers will still be interested in overactive bladder in the future. Currently, the clinical application of the disease and the safety and effectiveness of medications are being investigated. However, radical innovation in relevant experimental technologies is a significant obstacle in this field.},
}

@article {pmid36683391,
year = {2023},
author = {Gao, JP and Liang, W and Jiang, S and Yan, Z and Zhou, C and Wang, E and Murray, JD},
title = {NODULE INCEPTION activates gibberellin biosynthesis genes during rhizobial infection.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18759},
pmid = {36683391},
issn = {1469-8137},
}

@article {pmid36682940,
year = {2023},
author = {Stefanovska, T and Luckhart, S and Ripa, L and Stevens, G and Lewis, E},
title = {Steinernema carpocapsae.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2023.01.002},
pmid = {36682940},
issn = {1471-5007},
}

@article {pmid36681711,
year = {2023},
author = {Pesenti, M and Invernizzi, G and Mazzella, J and Bocciolone, M and Pedrocchi, A and Gandolla, M},
title = {IMU-based human activity recognition and payload classification for low-back exoskeletons.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1184},
pmid = {36681711},
issn = {2045-2322},
abstract = {Nowadays, work-related musculoskeletal disorders have a drastic impact on a large part of the world population. In particular, low-back pain counts as the leading cause of absence from work in the industrial sector. Robotic exoskeletons have great potential to improve industrial workers' health and life quality. Nonetheless, current solutions are often limited by sub-optimal control systems. Due to the dynamic environment in which they are used, failure to adapt to the wearer and the task may be limiting exoskeleton adoption in occupational scenarios. In this scope, we present a deep-learning-based approach exploiting inertial sensors to provide industrial exoskeletons with human activity recognition and adaptive payload compensation. Inertial measurement units are easily wearable or embeddable in any industrial exoskeleton. We exploited Long-Short Term Memory networks both to perform human activity recognition and to classify the weight of lifted objects up to 15 kg. We found a median F1 score of [Formula: see text] (activity recognition) and [Formula: see text] (payload estimation) with subject-specific models trained and tested on 12 (6M-6F) young healthy volunteers. We also succeeded in evaluating the applicability of this approach with an in-lab real-time test in a simulated target scenario. These high-level algorithms may be useful to fully exploit the potential of powered exoskeletons to achieve symbiotic human-robot interaction.},
}

@article {pmid36681696,
year = {2023},
author = {Aalipour, H and Nikbakht, A and Sabzalian, MR},
title = {Essential oil composition and total phenolic content in Cupressus arizonica G. in response to microbial inoculation under water stress conditions.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1209},
pmid = {36681696},
issn = {2045-2322},
abstract = {Arizona Cypress is one of the drought-resistant, aromatic, and aesthetically pleasing trees having several pharmacological uses. Certain microorganisms contribute to the secondary metabolism and synthesis of bioactive compounds in aromatic and medicinal plants. This study aimed to determine the photosynthetic pigments, total phenolic content, antioxidant capacity, and essential oil composition of Arizona cypress under two irrigation regimes and microbial inoculations. We established a factorial experiment with three mycorrhizae inoculations (Rhizophagus irregularis, Funneliformis mosseae, and a mixture of R. irregularis and F. mosseae), a rhizobacterium inoculation (Pseudomonas fluorescens), and two irrigation regimes (well-watered and water stress). Under the water stress regime, seedlings inoculated with F. mosseae (0.46%) and non-inoculated control plants (0.29%) had the highest and lowest essential oil contents, respectively. GC-MS analysis revealed that limonen, a-pinene, terpinen-4-ol, and umbellulone were the most abundant compounds in the seedlings and treatments under study. The water stress regime had a significant and dominant effect on essential oil and antioxidant capacity, whereas seedling growth and photosynthetic pigments tended to decrease under stress conditions. However, co-inoculation of seedlings with mycorrhizae and the bacterium resulted in an increase in phenolic compounds and carotenoids. Under conditions of water stress and mycorrhizal symbiosis, the results of the current study may help increase the level of valuable compounds in Arizona cypress for further pharmaceutical applications.},
}

@article {pmid36681082,
year = {2023},
author = {Cervantes-Pérez, SA and Thibivilliers, S and Laffont, C and Farmer, AD and Frugier, F and Libault, M},
title = {Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2023.01.002},
pmid = {36681082},
issn = {1752-9867},
}

@article {pmid36680640,
year = {2023},
author = {Singh, J and Varshney, V and Mishra, V},
title = {AUR1 and its pals: orchestration of intracellular rhizobia infection in legume for nitrogen fixation.},
journal = {Plant cell reports},
volume = {},
number = {},
pages = {},
pmid = {36680640},
issn = {1432-203X},
abstract = {We highlight the newly emerged regulatory role of a mitotic kinase AUR1, its activator, and its microtubule-associated proteins (MAPs) in infection thread formation for root nodule symbiosis.},
}

@article {pmid36679113,
year = {2023},
author = {Chiaranunt, P and White, JF},
title = {Plant Beneficial Bacteria and Their Potential Applications in Vertical Farming Systems.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/plants12020400},
pmid = {36679113},
issn = {2223-7747},
abstract = {In this literature review, we discuss the various functions of beneficial plant bacteria in improving plant nutrition, the defense against biotic and abiotic stress, and hormonal regulation. We also review the recent research on rhizophagy, a nutrient scavenging mechanism in which bacteria enter and exit root cells on a cyclical basis. These concepts are covered in the contexts of soil agriculture and controlled environment agriculture, and they are also used in vertical farming systems. Vertical farming-its advantages and disadvantages over soil agriculture, and the various climatic factors in controlled environment agriculture-is also discussed in relation to plant-bacterial relationships. The different factors under grower control, such as choice of substrate, oxygenation rates, temperature, light, and CO2 supplementation, may influence plant-bacterial interactions in unintended ways. Understanding the specific effects of these environmental factors may inform the best cultural practices and further elucidate the mechanisms by which beneficial bacteria promote plant growth.},
}

@article {pmid36679027,
year = {2023},
author = {Xie, X and Huang, Z and Lv, W and Zhu, H and Hui, G and Li, R and Lei, X and Li, Z},
title = {Influence of Nitrogen Application Rate on the Importance of NO3[-]-N and NH4[+]-N Transfer via Extramycelia of Arbuscular Mycorrhiza to Tomato with Expression of LeNRT2.3 and LeAMT1.1.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/plants12020314},
pmid = {36679027},
issn = {2223-7747},
abstract = {Arbuscular mycorrhizal fungi (AMF) form mutualistic symbiotic relationships with many land plants and play a key role in nitrogen (N) acquisition. NO3[-]-N and NH4[+]-N are the main sources of soil mineral N, but how extraradical mycelial transfer affects the different N forms and levels available to tomato plants is not clear. In the present study, we set up hyphal compartments (HCs) to study the efficiency of N transfer from the extramycelium to tomato plants treated with different N forms and levels of fertilization. Labeled [15]NO3[-]-N or [15]NH4[+]-N was placed in hyphal compartments under high and low N application levels. [15]N accumulation in shoots and the expression of LeNRT2.3, LeAMT1.1, and LeAMT1.2 in the roots of tomato were measured. According to our results, both [15]NO3[-]-N and [15]NH4[+]-N were transported via extraradical mycelia to the shoots of plants. [15]N accumulation in shoots was similar, regardless of the N form, while a higher [15]N concentration was found in shoots with low N application. Compared with the control, inoculation with AMF significantly increased the expression of LeAMT1.1 under high N and LeNRT2.3 under low N. The expression of LeAMT1.1 under high N was significantly increased when NO3[-]N was added, while the expression of LeNRT2.3 was significantly increased when NH4[+]-N was added under low N. Taken together, our results suggest that the N transfer by extraradical mycelia is crucial for the acquisition of both NO3[-]-N and NH4[+]-N by the tomato plant; however, partial N accumulation in plant tissue is more important with N deficiency compared with a higher N supply. The expression of N transporters was influenced by both the form and level of N supply.},
}

@article {pmid36678989,
year = {2023},
author = {Liu, B and Liu, K and Chen, X and Xiao, D and Wang, T and Yang, Y and Shuai, H and Wu, S and Yuan, L and Chen, L},
title = {Comparative Transcriptome Analysis Reveals the Interaction of Sugar and Hormone Metabolism Involved in the Root Hair Morphogenesis of the Endangered Fir Abies beshanzuensis.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/plants12020276},
pmid = {36678989},
issn = {2223-7747},
abstract = {Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone-sucrose-root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth.},
}

@article {pmid36678361,
year = {2022},
author = {Doty, SL and Joubert, PM and Firrincieli, A and Sher, AW and Tournay, R and Kill, C and Parikh, SS and Okubara, P},
title = {Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/pathogens12010013},
pmid = {36678361},
issn = {2076-0817},
abstract = {The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.},
}

@article {pmid36677548,
year = {2023},
author = {Aziz, T and Naveed, M and Makhdoom, SI and Ali, U and Mughal, MS and Sarwar, A and Khan, AA and Zhennai, Y and Sameeh, MY and Dablool, AS and Alharbi, AA and Shahzad, M and Alamri, AS and Alhomrani, M},
title = {Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {2},
pages = {},
doi = {10.3390/molecules28020491},
pmid = {36677548},
issn = {1420-3049},
abstract = {All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus&nbsp;plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites' characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.},
}

@article {pmid36677491,
year = {2023},
author = {Mazoyon, C and Hirel, B and Pecourt, A and Catterou, M and Gutierrez, L and Sarazin, V and Dubois, F and Duclercq, J},
title = {Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010199},
pmid = {36677491},
issn = {2076-2607},
abstract = {The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.},
}

@article {pmid36677447,
year = {2023},
author = {Fujishima, M and Kawano, H and Miyakawa, I},
title = {A 63-kDa Periplasmic Protein of the Endonuclear Symbiotic Bacterium Holospora obtusa Secreted to the Outside of the Bacterium during the Early Infection Process Binds Weakly to the Macronuclear DNA of the Host Paramecium caudatum.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010155},
pmid = {36677447},
issn = {2076-2607},
abstract = {The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and high salt resistances. In addition, an infectious form of H. obtusa-specific 63-kDa periplasmic protein with a DNA-binding domain in its amino acid sequence is secreted into the host macronucleus after invasion into the macronucleus and remain within the nucleus. These facts suggest that binding of the 63-kDa protein to the host macronuclear DNA causes changes in the host gene expressions and enhances an environmental adaptability of the host cells. This 63-kDa protein was renamed as periplasmic region protein 1 (PRP1) to distinguish it from other proteins with similar molecular weights. To confirm whether PRP1 indeed binds to the host DNA, SDS-DNA PAGE and DNA affinity chromatography with calf thymus DNA and P. caudatum DNA were conducted and confirmed that PRP1 binds weakly to the P. caudatum DNA with a monoclonal antibody raised for the 63-kDa protein.},
}

@article {pmid36677361,
year = {2022},
author = {Liu, Y and He, G and He, T and Saleem, M},
title = {Signaling and Detoxification Strategies in Plant-Microbes Symbiosis under Heavy Metal Stress: A Mechanistic Understanding.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010069},
pmid = {36677361},
issn = {2076-2607},
abstract = {Plants typically interact with a variety of microorganisms, including bacteria, mycorrhizal fungi, and other organisms, in their above- and below-ground parts. In the biosphere, the interactions of plants with diverse microbes enable them to acquire a wide range of symbiotic advantages, resulting in enhanced plant growth and development and stress tolerance to toxic metals (TMs). Recent studies have shown that certain microorganisms can reduce the accumulation of TMs in plants through various mechanisms and can reduce the bioavailability of TMs in soil. However, relevant progress is lacking in summarization. This review mechanistically summarizes the common mediating pathways, detoxification strategies, and homeostatic mechanisms based on the research progress of the joint prevention and control of TMs by arbuscular mycorrhizal fungi (AMF)-plant and Rhizobium-plant interactions. Given the importance of tripartite mutualism in the plant-microbe system, it is necessary to further explore key signaling molecules to understand the role of plant-microbe mutualism in improving plant tolerance under heavy metal stress in the contaminated soil environments. It is hoped that our findings will be useful in studying plant stress tolerance under a broad range of environmental conditions and will help in developing new technologies for ensuring crop health and performance in future.},
}

@article {pmid36677351,
year = {2022},
author = {Liu, Y and Lin, Y and Guan, N and Song, Y and Li, Y and Xie, X},
title = {A Lipopolysaccharide Synthesis Gene rfaD from Mesorhizobium huakuii Is Involved in Nodule Development and Symbiotic Nitrogen Fixation.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010059},
pmid = {36677351},
issn = {2076-2607},
abstract = {Rhizobium lipopolysaccharide (LPS) is an important component of the cell wall of gram-negative bacteria and serves as a signal molecule on the surface of rhizobia, participating in the symbiosis during rhizobia-legume interaction. In this study, we constructed a deletion mutant of ADP-L-glycerol-D-mannoheptosyl-6-exoisomerase (rfaD) of Mesorhizobium huakuii 7653R and a functional complementary strain. The results showed that the deletion of rfaD did not affect the free-living growth rate of 7653R, but that it did affect the LPS synthesis and that it increased sensitivity to abiotic stresses. The rfaD promoter-GUS reporter assay showed that the gene was mainly expressed in the infection zone of the mature nodules. The root nodules formation of the rfaD mutant was delayed during symbiosis with the host plant of Astragalus sinicus. The symbiotic phenotype analyses showed that the nodules of A. sinicus lost symbiotic nitrogen fixation ability, when inoculated with the rfaD mutant strain. In conclusion, our results reveal that the 7653R rfaD gene plays a crucial role in the LPS synthesis involved in the symbiotic interaction between rhizobia and A. sinicus. This study also provides new insights into the molecular mechanisms by which the rhizobia regulate their own gene expression and cell wall components enabling nodulation in legumes.},
}

@article {pmid36677342,
year = {2022},
author = {Prado-Tarango, DE and Mata-Gonzalez, R and Hovland, M},
title = {Drought and Competition Mediate Mycorrhizal Colonization, Growth Rate, and Nutrient Uptake in Three Artemisia Species.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010050},
pmid = {36677342},
issn = {2076-2607},
abstract = {The genus Artemisia includes several keystone shrub species that dominate the North American sagebrush steppe. Their growth, survival, and establishment are negatively affected by exotic invasive grasses such as Taeniatherum caput-medusae. While the outcomes of symbiotic relationships between Artemisia spp. and arbuscular mycorrhizal fungi (AMF) are ambiguous, the benefits of ameliorated nutrient and drought stress may be cryptic and better revealed under competition. We evaluated the effects of a commercial AMF inoculum on ameliorating biotic (competition with T. caput-medusae) and abiotic (drought) stress of Artemisia tridentata ssp. wyomingensis, Artemisia arbuscula, and Artemisia nova when grown in sterile and microbially active field soil. Stress amelioration was measured as an increase in biomass production and nutrient acquisition. Mycorrhizal colonization of roots was lower in Artemisia plants grown in competition, while T. caput-medusae colonization was higher in plants with greater moisture. Both types of stress negatively affected plant biomass. Commercial AMF inoculation did not increase biomass. Colonization from field soil increased average phosphorous concentration under drought for A. tridentata ssp. wyomingensis by 36% and A. nova by 125%. While commercial inoculum and live soil led to AMF colonization of T. caput-medusae, only the commercial inoculum increased average phosphorus uptake by 71%.},
}

@article {pmid36677293,
year = {2022},
author = {Betancur-Murillo, CL and Aguilar-Marín, SB and Jovel, J},
title = {Prevotella: A Key Player in Ruminal Metabolism.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010001},
pmid = {36677293},
issn = {2076-2607},
abstract = {Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.},
}

@article {pmid36675931,
year = {2023},
author = {de Menezes, TA and Aburjaile, FF and Quintanilha-Peixoto, G and Tomé, LMR and Fonseca, PLC and Mendes-Pereira, T and Araújo, DS and Melo, TS and Kato, RB and Delabie, JHC and Ribeiro, SP and Brenig, B and Azevedo, V and Drechsler-Santos, ER and Andrade, BS and Góes-Neto, A},
title = {Unraveling the Secrets of a Double-Life Fungus by Genomics: Ophiocordyceps australis CCMB661 Displays Molecular Machinery for Both Parasitic and Endophytic Lifestyles.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010110},
pmid = {36675931},
issn = {2309-608X},
abstract = {Ophiocordyceps australis (Ascomycota, Hypocreales, Ophiocordycipitaceae) is a classic entomopathogenic fungus that parasitizes ants (Hymenoptera, Ponerinae, Ponerini). Nonetheless, according to our results, this fungal species also exhibits a complete set of genes coding for plant cell wall degrading Carbohydrate-Active enZymes (CAZymes), enabling a full endophytic stage and, consequently, its dual ability to both parasitize insects and live inside plant tissue. The main objective of our study was the sequencing and full characterization of the genome of the fungal strain of O. australis (CCMB661) and its predicted secretome. The assembled genome had a total length of 30.31 Mb, N50 of 92.624 bp, GC content of 46.36%, and 8,043 protein-coding genes, 175 of which encoded CAZymes. In addition, the primary genes encoding proteins and critical enzymes during the infection process and those responsible for the host-pathogen interaction have been identified, including proteases (Pr1, Pr4), aminopeptidases, chitinases (Cht2), adhesins, lectins, lipases, and behavioral manipulators, such as enterotoxins, Protein Tyrosine Phosphatases (PTPs), and Glycoside Hydrolases (GHs). Our findings indicate that the presence of genes coding for Mad2 and GHs in O. australis may facilitate the infection process in plants, suggesting interkingdom colonization. Furthermore, our study elucidated the pathogenicity mechanisms for this Ophiocordyceps species, which still is scarcely studied.},
}

@article {pmid36675920,
year = {2023},
author = {Otero, A and Barcenas-Peña, A and Lumbsch, HT and Grewe, F},
title = {Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota).},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010099},
pmid = {36675920},
issn = {2309-608X},
abstract = {Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.},
}

@article {pmid36675911,
year = {2023},
author = {Mathew, SA and Helander, M and Saikkonen, K and Vankova, R and Dobrev, PI and Dirihan, S and Fuchs, B},
title = {Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010090},
pmid = {36675911},
issn = {2309-608X},
abstract = {Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.},
}

@article {pmid36675907,
year = {2023},
author = {Novotná, A and Mennicken, S and de Paula, CCP and Vogt-Schilb, H and Kotilínek, M and Těšitelová, T and Šmilauer, P and Jersáková, J},
title = {Variability in Nutrient Use by Orchid Mycorrhizal Fungi in Two Medium Types.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010088},
pmid = {36675907},
issn = {2309-608X},
abstract = {Orchid mycorrhizal fungi (OMF) from the rhizoctonia aggregate are generally considered to be soil saprotrophs, but their ability to utilize various nutrient sources has been studied in a limited number of isolates cultivated predominantly in liquid media, although rhizoctonia typically grow on the surface of solid substrates. Nine isolates representing the key OMF families (Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae), sampled in Southern France and the Czech Republic, were tested for their ability to utilize carbon (C), nitrogen (N) and phosphorus (P) sources in vitro in both liquid and solid media. The isolates showed significant inter- and intra-familiar variability in nutrient utilization, most notably in N sources. Isolates produced generally larger amounts of dry biomass on solid medium than in liquid one, but some isolates showed no or limited biomass production on solid medium with particular nutrient sources. The largest amount of biomass was produced by isolates from the family Ceratobasidiaceae on most sources in both medium types. The biomass production of Tulasnellaceae isolates was affected by their phylogenetic relatedness on all sources and medium types. The ability of isolates to utilize particular nutrients in a liquid medium but not a solid one should be considered when optimizing solid media for symbiotic orchid seed germination and in understanding of OMF functional traits under in situ conditions.},
}

@article {pmid36675877,
year = {2022},
author = {Silva-Castro, GA and Cano, C and Moreno-Morillas, S and Bago, A and García-Romera, I},
title = {Inoculation of Indigenous Arbuscular Mycorrhizal Fungi as a Strategy for the Recovery of Long-Term Heavy Metal-Contaminated Soils in a Mine-Spill Area.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010056},
pmid = {36675877},
issn = {2309-608X},
abstract = {Symbiotic associations with arbuscular mycorrhizal fungi (AMF) offer an effective indirect mechanism to reduce heavy metal (HM) stress; however, it is still not clear which AMF species are more efficient as bioremediating agents. We selected different species of AMF: Rhizoglomus custos (Custos); Rhizoglomus sp. (Aznalcollar); and Rhizophagus irregularis (Intraradices), in order to study their inoculation in wheat grown in two soils contaminated with two levels of HMs; we tested the phytoprotection potential of the different AMF symbioses, as well as the physiological responses of the plants to HM stress. Plants inoculated with indigenous Aznalcollar fungus exhibited higher levels of accumulation, mainly in the shoots of most of the HM analyzed in heavily contaminated soil. However, the plants inoculated with the non-indigenous Custos and Intraradices showed depletion of some of the HM. In the less-contaminated soil, the Custos and Intraradices fungi exhibited the greatest bioaccumulation capacity. Interestingly, soil enzymatic activity and the enzymatic antioxidant systems of the plant increased in all AMF treatments tested in the soils with both degrees of contamination. Our results highlight the different AMF strategies with similar effectiveness, whereby Aznalcollar improves phytoremediation, while both Custos and Intraradices enhance the bioprotection of wheat in HM-contaminated environments.},
}

@article {pmid36675845,
year = {2022},
author = {Li, L and Guo, N and Zhang, Y and Yuan, Z and Lu, A and Li, S and Wang, Z},
title = {Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010024},
pmid = {36675845},
issn = {2309-608X},
abstract = {The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.},
}

@article {pmid36675835,
year = {2022},
author = {Kalske, A and Saikkonen, K and Helander, M},
title = {Endophytic Fungus Negatively Affects Salt Tolerance of Tall Fescue.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/jof9010014},
pmid = {36675835},
issn = {2309-608X},
abstract = {Vertically transmitted endophytic fungi can mitigate the negative effects of salinity encountered by their host grass and alter the competitive interactions between plant individuals. To experimentally study the interactive effects of the fungal endophyte Epichloë coenophiala on salt tolerance and intraspecific competition of its host plant, tall fescue Festuca arundinacea, we subjected 15 maternal lines of each Epichloë associated (E+) and Epichloë free (E-) tall fescue to salt treatment and competition in the greenhouse and common garden. Then, to explore variation in endophyte incidence in natural populations of tall fescue, we surveyed 23 natural populations occurring on or near the Baltic Sea coast in Aland islands in southwestern Finland for endophyte incidence, distance to shore, and competitive environment. Under salinity in the greenhouse, E- plants grew larger than E+ plants, but there was no size difference in the control treatment. E- plants grew taller and were more likely to flower than E+ plants when grown in benign conditions in the common garden but not with salinity or competition. The frequency of Epichloë incidence was high (90%) in natural populations, and it decreased towards the shore and risk of salt exposure. These results demonstrate a negative effect of Epichloë endophyte on the salt tolerance of its host. The high incidence of Epichloë in natural populations of tall fescue in the northern part of the species distribution range is likely due to factors other than salinity.},
}