ISME communications最新文献

Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.

Recent work highlighted the role of motility genes in dispersing fly-associated microbes and their spread between hosts. We investigated whether bacterial genes encoding motility are associated with the occurrence of bacteria above passive dispersal levels in the gut of wild Drosophila melanogaster. We revisited 16S amplicon and shotgun metagenome data of wild flies and correlated four genera of bacteria (Commensalibacter, Gluconobacter, Lactobacillus, and Tatumella) with motility genes. We plotted the microbes against neutral models of ecological drift and passive dispersal. Microbes with positive correlations to motility were exclusively found at or above neutral model predictions, suggesting motility genes are crucial for fly microbiota spread and colonization. This information is crucial for understanding how specific gene functions contribute to microbial community dispersal and colonization within the fly host. Moreover, this study's findings serve as a proof of concept for using the neutral model to predict microbial functions essential for survival and dissemination in diverse hosts.

Syntrophic interaction, driven by metabolite exchange, is widespread within microbial communities. However, co-inoculation of most auxotrophic microorganisms often fails to establish a stable metabolite exchange relationship. Here, we engineered two auxotrophic Escherichia coli strains, each dependent on the other for essential amino acid production, to investigate the dynamics of syntrophic relationships. Through invasion-from-rare experiments, we observed the rapid formation of syntrophic consortia stabilized by frequency-dependent selection, converging to a 2:1 ratio of lysine-to-arginine auxotrophs. However, laboratory evolution over 25 days revealed that syntrophic interactions were evolutionarily unstable, with cocultures collapsing as ΔL cells dominated the population. Reduced fitness in cocultures was driven by the emergence of a "selfish" ΔL phenotype, characterized by decreased arginine production and exploitation of lysine produced by ΔA cells. Dynamic metabolic assays revealed that metabolite production and utilization patterns strongly influenced the fitness of each strain. ΔL cells displayed metabolic plasticity, adjusting lysine utilization in response to lysine availability, which enabled them to outcompete ΔA cells. In contrast, ΔA cells lacked similar plasticity, resulting in their negative selection. These findings demonstrate that asymmetric metabolic responses and the emergence of selfish phenotypes destabilize syntrophic relationships. Our work underscores the importance of balanced metabolic exchanges for developing sustainable synthetic microbial consortia and offers insights into the evolutionary dynamics of microbial cooperation.

The rhizosphere is the soil region around plant roots hosting a diverse microbial community, influencing nutrient availability and how plants react to extreme conditions. However, our understanding of the fungi biodiversity and the impact of environmental variations on this biodiversity is still in its infancy. Our study investigates fungal communities' diversity and functional traits in the rhizosphere of Nothofagus pumilio, one of the few winters deciduous treeline species in the world, forming the treeline in southern South America. At four distinct locations covering 10° latitude, we collected soil samples at treeline and 200 m below over four seasons during a single year. We employed ITS metabarcoding to elucidate fungal community structures. Our results reveal that fungal diversity was mainly determined by latitudinal variation, with higher levels during warmer seasons and lower altitudes. Interestingly, we found a marked dominance of ectomycorrhizal fungi at the treeline, particularly during the winter. In contrast, saprotrophic fungi were more abundant at lower altitudes, particularly during the warmer spring and summer seasons. These findings highlight the temporal and spatial dynamics of rhizospheric fungal communities and their potential roles in ecological processes, emphasizing the value of these communities as indicators of environmental change in high-elevation forests.

Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.

Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.

Phytoplankton supports food webs in all aquatic ecosystems. Ecological studies highlighted the links between environmental variables and species successions in situ. However, the role of life cycle characteristics on phytoplankton community dynamics remains poorly characterized. In diatoms, sexual reproduction creates new genetic combinations and prevents excessive cell size miniaturization. It has been extensively studied in vitro but seldom in the natural environment. Here, analyzing metatranscriptomic data in the light of the expression patterns previously characterized in vitro, we identified a synchronized and transient sexual reproduction event during a bloom of the toxic diatom species Pseudo-nitzschia australis. Despite the complexity of environmental conditions encountered in situ, sexual reproduction appeared to be the strongest differential gene expression signal that occurred during the bloom. The potential link between environmental conditions and the initiation of sexual reproduction remain to be determined, but sexual reproduction probably had a major impact on the bloom dynamic.

The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and ¹⁸O-H₂O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial-fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.

Pteris vittata, renowned for its ability to hyperaccumulate arsenic, presents a promising solution to the escalating issue of global soil arsenic contamination. This fern cultivates a unique underground microbial community to enhance its environmental adaptability. However, our understanding of the assembly process and the long-term ecological impacts of this community remains limited, hindering the development of effective soil remediation strategies. This study addresses this gap by investigating soil-root habitats from three geographically diverse fields comprising a gradient of arsenic contamination, complemented by a time-scale greenhouse experiment. Field investigations reveal that arsenic stress influences community assembly dynamics in the rhizosphere by enhancing processes of homogeneous selection. Greenhouse experiments further reveal that arsenic exposure alters the assembly trajectory of rhizosphere communities by promoting key microbial modules. Specifically, arsenic exposure increases the enrichment of a core taxon (i.e. Rhizobiaceae) in the rhizosphere, both in field and greenhouse settings, boosting their abundance from undetectable levels to 0.02% in the soil after phytoremediation. Notably, arsenic exposure also promotes a pathogenic group (i.e. Spirochaetaceae) in the rhizosphere, increasing their abundance from undetectable levels to 0.1% in the greenhouse. This raise concerns that warrant further investigation in future phytoremediation studies. Overall, this study elucidates the assembly dynamics of the soil microbiome following the introduction of a remediation plant and emphasizes the often-overlooked impacts on soil microbial community following phytoremediation. By probing the ecological impacts of remediation plants, this work advances a more nuanced understanding of the complex ecological implications inherent in phytoremediation processes.

Earthworms are keystone animals stimulating litter decomposition and nutrient cycling. However, earthworms comprise diverse species which live in different soil layers and consume different types of food. Microorganisms in the gut of earthworms are likely to contribute significantly to their ability to digest organic matter, but this may vary among earthworm species. Here, we analyse the effect of food (litter) quality on gut microbiota and their changes during the gut passage (from foregut to hindgut) of earthworms of different ecological groups. The endogeic (soil living) species Aporrectodea caliginosa and the anecic (litter feeding) species Lumbricus terrestris were fed with high- (rape leaves) and low-quality litter (wheat straw) in a microcosm experiment for 18 weeks. Irrespective of earthworm species, alpha diversity of bacterial and fungal communities changed little during the gut passage, with the composition and diversity of microbial communities in the gut generally resembling those in soil more than in litter. In addition, the low-quality litter supported higher alpha diversity and more complex communities than high-quality litter. Further, gut microbial communities of the anecic L. terrestris changed less during gut passage than those of the endogeic A. caliginosa, especially when fed low-quality litter. Our findings indicate that earthworm gut microbial communities are predominantly shaped by the soil they ingest, but are modulated by the quality of litter they feed on and earthworm ecological group. Overall, the results suggest that earthworms primarily influence soil microbiota by mixing and spreading microorganisms from different microhabitats through bioturbation rather than by digesting microorganisms.