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[This corrects the article DOI: 10.1093/ismeco/ycag013.].
[This corrects the article DOI: 10.1093/ismeco/ycaf250.].
[This corrects the article DOI: 10.1093/ismeco/ycaf143.].
[This corrects the article DOI: 10.1093/ismeco/ycaf196.].
Environmental pollutants can profoundly influence host-associated microbiomes, with cascading effects on host health and susceptibility to disease. Here, we investigated whether nanoplastic particles (NPs), a pervasive contaminant, influence host-parasite interaction by altering the microbiome of the water flea Daphnia magna. Microbiomes from NP-exposed and control Daphnia donors were transplanted to axenic Daphnia recipients, which were subsequently challenged with the fungal parasite Australozyma monospora sp. nov. Host and parasite fitness were then compared across treatments. NP exposure induced marked shifts in bacterial community structure and increased microbial diversity in donor microbiomes. These shifts persisted after transplantation, with recipient microbiomes remaining distinct from controls throughout the host lifespan, despite the absence of direct NP exposure. Microbiome shifts associated with NP exposure corresponded to elevated parasite reproduction and reduced host fecundity, while host survival was unaffected. Our findings demonstrate that NP pollution can indirectly compromise host health by reshaping microbial communities, highlighting microbiome-mediated pathways as important mechanisms through which emerging pollutants may shape ecological and evolutionary dynamics.
Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.
Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.
Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.
Microhabitat-specific responses of soil organisms to land-use intensification remain a major blind spot in biodiversity research. Here, we assessed how protists-key regulators of microbial diversity and nutrient cycling-differ in composition and roles across litter, rhizosphere, and bulk soil along a land-use gradient of increasing management intensity, from rainforest to shrubland, rubber plantations, and oil palm plantations in Sumatra, Indonesia. High-throughput sequencing revealed that rhizosphere protists responded most strongly to land-use intensification, with a 39.6% increase in Shannon index and marked shifts in community composition. Bulk soil protists showed similar but weaker responses, while litter protists exhibited compositional shifts without significant α-diversity changes. Notably, protist community composition was differentially structured by abiotic and biotic drivers across microhabitats independent of land-use type, with biotic dominance in the rhizosphere, abiotic dominance in litter, and joint control in bulk soil. To assess functional turnover, we applied an ecological niche framework (generalist-specialist-opportunist). Generalists remained stable in litter, whereas specialists showed reduced niche breadth and richness in rhizosphere and bulk soil, particularly in oil palm plantations, and opportunists showed intermediate responses. These findings demonstrate that land-use intensification restructures belowground communities in a microhabitat-specific and functionally predictable manner. By explicitly separating litter, rhizosphere, and bulk soil microhabitats, our study reveals microhabitat-specific assembly processes overlooked in conventional bulk-soil analyses and provides new insights into protist responses to land-use intensification in tropical soils. These findings highlight the need to incorporate microhabitat-scale processes when assessing soil biodiversity and ecosystem functioning under environmental change.
Bifidobacterium species and strains are key members of the human gut microbiota, appearing soon after birth and persisting into adulthood. Resistant starch is an important dietary substrate for adult-associated bifidobacteria, where its fermentation supports host health. However, less is known about how different starch structures interact with bifidobacteria. Here we show that growth kinetics and gene expression differ depending on starch structure. Using detailed growth assays, genomics, and metabolomic analyses, bifidobacterial starch hydrolysis capabilities were closely associated with their CAZyme profiles. In one isolate of Bifidobacterium globosum, we identified a gene cluster encoding three multi-functional amylase enzymes complemented by several starch-binding modules, the genes and proteins of which were significantly upregulated in response to starch. Homologs of genes in the cluster were found in the genomes of bifidobacterial isolates from weaning infants providing insights into their role in the maturation process of the microbiota. Uncovering mechanisms of metabolic interaction between starch structures and bifidobacteria underscores the importance of this ecological function and potential health implications.
Understanding how plant-microbe-soil interactions vary across spatial scales is essential for elucidating belowground ecological dynamics, particularly in rare and ecologically sensitive species. Here, we investigated the diversity, function, and assembly of root-associated bacterial communities in Thuja sutchuenensis Franch. along continuous vertical gradients. Through an integrative multi-omics approach, morphological assessment, and soil physicochemical profiling, we uncovered a compartmentalized and spatially structured rhizosphere system. We observed a marked enrichment of soil nutrients, particularly carbon, nitrogen, and available phosphorus, in the rhizosphere compared with bulk soil. Bacterial diversity declined in the endosphere, accompanied by taxonomic and functional shifts, including enrichment of Proteobacteria and Actinobacteriota and metabolic pathways related to host interaction and xenobiotic degradation. Root and soil metabolomes also showed depth-specific signatures, with surface compartments enriched in flavonoids and defense compounds, and deeper layers characterized by core metabolic functions. Co-occurrence network and correlation analyses highlighted key bacterial hubs and revealed strong links between nutrient levels and bacterial diversity. Together, this study provides new insight into the organization of plant-soil ecosystems and offers a framework for conservation and ecological restoration strategies for endangered cliffside species.
The geomagnetic field is a fundamental environmental factor, yet the effects of its absence-termed the near-zero-magnetic field (NZMF) on microbial communities and associated ecological functions remain poorly understood. To address this, we conducted for the first time a 30-day NZMF incubation experiment using sediments and three microorganisms isolated from mangrove ecosystems. They were exposed to two magnetic conditions: the natural geomagnetic field and a near-zero-magnetic field (<3 nT), achieved using a specially designed magnetic shielding device. We analyzed the changes in microbial community composition, co-occurrence networks, and ecological functions. Our findings showed that while the overall prokaryotic and eukaryotic microbial diversity remained unaffected, NZMF exposure significantly stimulated the growth of specific taxa such as Geobacter and methanogenic archaea. Microbial co-occurrence networks revealed a reduction in inter-taxa connections under NZMF. Furthermore, NZMF significantly altered the activity of key biogeochemical enzymes, reducing the content of available potassium and organic matter, and suppressing xylosidase activity, while enhancing the activity of leucine aminopeptidase and urease. Together, these results demonstrated that NZMF could reshape microbial community structure and key ecological functions, despite minimal shifts in overall diversity. These findings highlight the importance of geomagnetic fields as an underappreciated environmental factor and underscore the need for further research into the biogeochemical and biological implications of magnetic field variations.
Warming temperatures, heat waves, and altered conditions associated with climate change affect biodiversity and ecological processes across environments, with coastal zones being particularly vulnerable. Biofilm-forming organisms in shallow coastal areas are taxonomically diverse and include bacteria, fungi, and algae that contribute to energy and nutrient cycling along with providing habitats and food for species at the base of the food web. To understand how biofilm-forming organisms respond differently to spatiotemporally changing environmental conditions, seasonal sampling was performed in a Baltic Sea bay that has undergone 50 years of thermal heating, an unaffected nearby control bay, and a temperature gradient along an exposed coastline between the bays. The diversity, composition, and seasonal dynamics of the biofilm communities differed between the three environments largely due to temperature and water chemistry, with biofilms in the heated bay being more similar across seasons compared with the control bay and the gradient, and with prokaryotes exhibiting stronger spatial heterogeneity and seasonal dynamics compared to micro-eukaryotes. In the gradient, the dominating taxonomic groups were distinct, community composition was primarily influenced by seasonal turnover and wave exposure, and alpha diversity of prokaryotes decreased with increasing temperature. Seasonal shifts in the composition of micro-eukaryotic heterotrophs, phototrophs, and mixotrophs differed between environments, with heterotrophs being more dominant at higher temperatures. In conclusion, these contrasting responses indicated that climate warming may disproportionately impact different components of coastal biofilm communities, potentially decoupling key ecological processes and reducing community resilience in Baltic Sea coastal habitats.
Conifers are a challenging host for herbivores since their tissues are very low in essential nutrients but high in chemical defenses. For herbivorous insects, such as phloem-colonizing bark beetles, mutualistic fungi may improve their diet by providing a nutritious mycelium. A recent study revealed that two filamentous fungi are mutualists of the European fir engraver beetle Pityokteines vorontzowi, but a potential nutritional contribution of the fungi, as well as their capability to degrade plant antiherbivore defenses remains unknown. We analyzed the nutrient content of the fungal mutualists Ophiostoma piceae and Geosmithia sp. F1 and examined their ability to degrade the constitutive chemical defenses of silver fir phloem in comparison to other fungi. Both mutualists turned out to be rich in amino acids, sugars, and B vitamins and were found to efficiently deplete their phloem media of several defenses. Strikingly, O. piceae not only accumulated the highest amounts of the B vitamin nicotinic acid of the 17 tested fungi but also showed a high ability to deplete its medium of chemical defenses, similar to the behavior of the Ips typographus mutualist Endoconidiophora polonica. Beetle-vectored, non-mutualistic fungi isolated from P. vorontzowi showed similar capacities to deplete defensive compounds, whereas non-fir-associated fungi were less effective in reducing their concentrations in the phloem medium. The nutritious mycelium of O. piceae and Geosmithia sp. F1 and the ability of these fungi to deplete the medium of major fir defense compounds likely facilitates the colonization of silver fir phloem by P. vorontzowi.
Skin microbiota, which is highly sensitive to environmental heterogeneity, together with skin secretions, plays a critical role in defense and communication in amphibians. However, the temporal and geographical patterns of skin microbiota, as well as the composition of the skin volatile secretions, remain largely unexplored in many amphibian species. In the present study, we collected skin bacterial samples from the Hainan frilled tree frog (Kurixalus hainanus) in the Lingshui population across four consecutive months (April-July) to assess temporal dynamics, and additionally sampled frogs from the Jinxiu and Shanglin populations to examine geographical differentiation. Skin volatile secretions were also characterized and compared among the three populations. The results showed that temporal variation in skin microbiota was primarily driven by a small fraction of rare taxa, whereas the overall evenness and dominant components of the core skin microbiota remained relatively stable over time. In contrast, pronounced differentiation in microbiota composition was observed among populations, indicating a strong influence of habitat heterogeneity. We also found that skin secretions were largely similar among the three populations. Decanal and 1-octanol were identified as candidate compounds underlying disturbance odors in K. hainanus, and three terpenoid compounds detected exclusively in individuals from the Shanglin population may be derived from environmental sources or synthesized by the resident skin microbiota. Together, our findings characterize the temporal and spatial variation of skin microbiota in K. hainanus, while simultaneously identifying population-level variation in skin volatile secretions among populations and establishing a framework for future research to address the interplay between these two critical skin components.
The Kerguelen Islands, one of the most isolated lands on Earth, represent an ideal open-air laboratory to explore patterns of microbial biogeography under minimal human influence. Fellfields, in particular, are near pristine habitats dominated by endemic plant species with few introduced ones. Using metabarcoding, we characterized 70 bulk soil and 70 root-associated fungal communities from two native plant species and one introduced one, in four distant fellfield sites. Comparative analyses of Kerguelen fungal sequences with global reference databases (GlobalFungi and UNITE) revealed that 60% to 76% of the recovered operational taxonomic units (OTUs) had a close match at ≥97% sequence identity, which indicates the presence of a majority of species with wide distribution ranges that have already been observed elsewhere on the globe. Although evidence of endemism is difficult to establish, haplotype networks created for OTUs already observed elsewhere in the world illustrate in a number of cases the presence of dominant amplified sequenced variants specific to Kerguelen, suggesting intraspecific endemism. A global analysis of the already known fungal OTUs showed they were predominantly associated to high-latitude and cold environments. A spatial analysis further affiliated known Kerguelen's fungi to two distinct endemicity zones, one that encompassed Southern South America/Antarctic Peninsula and one in Central and Northern Europe that potentially contributed to alien species that may have invaded this remote archipelago. Our results indicate that the mycoflora of one of the most isolated islands in the world has been shaped by repeated episodes of colonization from different parts of the globe.
The principles governing microbial community assembly and the interplay between deterministic selection and stochasticity remain central debates in ecology. We investigated how chemically diverse carbon sources act as ecological filters, shaping soil bacterial communities. Using replicated microcosms amended with distinct substrates (glucose, succinate, naphthalene, phenanthrene, or γ-hexachlorocyclohexane (γ-HCH)) or under starvation, we tracked community trajectories via high-frequency 16S ribosomal RNA (rRNA) gene sequencing (29 timepoints, triplicate) and quantitative ecological modeling. Null model analysis confirmed the carbon source as the primary deterministic filter, enforcing high reproducibility (homogeneous selection governing ~74% of assembly among replicates) and overriding stochastic effects. Crucially, abundant (>1%) and rare (<0.1%) taxa exhibited decoupled assembly mechanisms. While abundant taxa were driven largely by dispersal limitation (~59%) and variable selection, the rare biosphere displayed a temporal regime shift. Unlike the immediate response of dominant taxa, rare taxa transitioned from stochastic isolation to strong deterministic selection (surging to ~50%) only during later successional stages. This reframes the rare biosphere as a "latent responder" reservoir recruited by metabolic byproducts rather than the primary substrate. Additionally, time-resolved interaction networks revealed that under severe stress from toxicity or starvation, interactions shifted from competitive exclusion to facilitation (e.g. necromass scavenging). These patterns provide strong empirical support for the Stress Gradient Hypothesis in a microbial context. Collectively, our findings demonstrate how deterministic filtering and stress-mediated cooperation jointly structure ecosystems, providing a high-resolution temporal dataset to further interrogate these fundamental ecological principles.
Gingivitis and periodontitis are caused by oral microbiome dysbiosis. Post-treatment alterations in bacterial community structure are uncharacterized in situ, including how these alterations may differ between resolved and unresolved disease states. Understanding these treatment-induced microbial shifts and identifying prognostic markers in situ associated with favorable or unfavorable outcomes are crucial for developing diagnostic tools and refining therapeutic strategies. Therefore, we performed metatranscriptomic analysis on subgingival plaque samples from the anterior teeth of individuals, including healthy, gingivitis, and periodontitis sites, before and after non-surgical treatment in 28 patients. We revealed a new bacteriological characteristic of periodontitis, where periodontal pathogens emerge within the bacterial network alongside excessive and skewed associations among bacterial taxa, such as those in the Streptococcus and Actinomyces genera. Furthermore, these imbalances were found improvable through non-surgical treatment. However, even in clinically resolved gingivitis or periodontitis, the bacterial networks did not fully revert to the state observed in healthy sites. This was due to the persistence of periodontal pathogens, absent in the networks at healthy sites. By comparing groups in which periodontitis resolved and those in which it did not, specific bacterial taxa, such as Neisseria elongata and Rothia aeria, were suggested to play a role in the periodontitis healing process, while increases in genes related to glycine degradation and bacterial adhesion, including glycine dehydrogenase β-subunit and cleaved adhesin domain were implicated in inhibiting the healing process. These findings provide insights for the development of treatment strategies targeting specific bacteria and functional genes involved in the resolution of periodontitis.
Many microbiological outcomes are shaped by the determinants of community composition, including the factors that allow pathogens to invade healthy microbiota and the processes that maintain the diversity that underpins soil function. Community ecology provides a rich conceptual toolset to investigate patterns of coexistence that can be adapted to explain and manage these outcomes. However, these concepts have complex histories of controversy and debate that must be considered when applying them to the microbial context. Microorganisms also have distinctive characteristics that must be accounted for when studied using ideas that were originally developed to describe macroscopic ecosystems. Here, we provide a concise overview for microbiologists to five key frameworks from community ecology: Niche theory, Trophic levels, Keystone species, Succession, and Metacommunities. We discuss the historical context and controversies surrounding each framework and outline existing and potential applications to microbial systems. This work therefore provides a practical guide for microbiologists who wish to use community ecology to understand and manipulate microbial community composition.
Oxidative stress arises when cells fail to maintain redox balance. Among marine microalgae, oxidative stress is a hallmark of interaction with pathogenic bacteria. In co-culture of Emiliania huxleyi algae with pathogenic bacteria of the species Phaeobacter inhibens, algal intracellular levels of reactive oxygen species (ROS) increase prior to bacterial-induced population collapse. Here, we tested whether antioxidant amendments can alter the pathogenic outcome. Screening several environmentally relevant antioxidants revealed that low-nanomolar levels of selenite [Se (IV)] prevented algal death in co-culture. Time-resolved ROS measurements showed that selenite-treated co-cultures maintained lower intracellular ROS levels during exponential growth, while bacterial growth dynamics were comparable with and without selenite. Together, these results show that selenite availability shifts the outcome of the E. huxleyi-P. inhibens interaction and link host oxidative stress to resilience in co-culture.