It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.

The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.

Plant-associated microbial communities play a vital role in host adaptation to environmental stress, yet their contributions to plant nickel (Ni) tolerance strategies remain unclear. It is not understood whether the same microbial community elicits similar responses across different plant species or regulates stress adaptation in a host-specific manner. Although microorganisms influence plant responses to metal toxicity by altering metal bioavailability in the rhizosphere, their potential to optimize plant metal uptake is less explored. In this study, we evaluated whether synthetic microbial communities enhance (Ni) uptake in two species with contrasting metal strategies: the hyperaccumulator Odontarrhena chalcidica and the Ni-excluding Arabidopsis arenosa. We hypothesized that soil microorganisms support plant metal adaptation by improving physiological function rather than altering soil metal availability. Our results show that O. chalcidica reached its full hyperaccumulating potential only when co-cultivated with a soil-derived microbial community, regardless of the microorganisms' ability to mobilize Ni or promote plant growth. Microorganisms that enhanced Ni uptake had no effect on soil Ni availability. Microbial community analysis revealed species-specific microbiota assembly, with O. chalcidica being more responsive yet more selective. Serpentine-soil microbiota enhanced Ni uptake in O. chalcidica by upregulating iron-transporter genes, confirming reliance on Fe-transport pathways for Ni acquisition. In contrast, the same inoculum induced Zn-transporters and NRT2.1/NRT2.2 in A. arenosa, reflecting strategy of cation partitioning and nutrient-transport fine-tuning under Ni stress. These findings refine criteria for selecting microorganisms in phytoremediation and highlight that the functional impact of plant-associated microorganisms on metal handling outweigh their effects on metal solubility in soil.

Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.

Dinoflagellate algae in the family Symbiodiniaceae, symbionts of many marine cnidarians are critical for the metabolic integrity of reef ecosystems, which are increasingly threatened by environmental stress. The resilience of the cnidarian-dinoflagellate symbiosis depends on thermotolerance of the partner organisms; coral hosts that harbor heat-resistant symbionts exhibit greater resistance to bleaching. Although coral responses to heat stress are well-documented, transcriptomic adaptation/acclimation of Symbiodiniaceae to elevated temperatures are limited. Here, we compare thermal responses of two species representing two genera of Symbiodiniaceae, Symbiodinium linucheae (strain SSA01; ITS2 type A4) and Breviolum minutum (strain SSB01; ITS2 type B1). SSA01 in culture maintained photosynthetic function at elevated temperatures and mounted a rapid transcriptomic response characterized by early downregulation of a JMJ21-like histone demethylase coupled with prompt upregulation of transcripts associated with DNA repair and oxidative stress, which would likely contribute to enhanced resilience to heat stress. In contrast, SSB01 experienced a decline in photosynthetic efficiency and a delayed transcriptomic response that included upregulation of transcripts encoding proteasome subunits and reduced transcripts encoding proteins involved in photosynthesis and metabolite transport. These findings indicate that a rapid and moderate transcriptomic response that results in increased expression of genes related to the synthesis and repair of biomolecules might be crucial for thermal tolerance in the Symbiodiniaceae whereas sensitivity to elevated temperatures may be reflected by increased protein turnover and a marked decline in anabolic processes. Understanding these differences is vital for predicting coral responses to warming seas and developing strategies to mitigate heat-stress impacts on reefs.

Wood-colonizing beetles are associated with a diversity of microbes many of which are thought to act as mutualists with their beetle hosts, but the evidence is usually anecdotal. The ship-timber beetle Elateroides dermestoides, one of the few fungus-farming but non-social ambrosia beetles, is described to have a mutualistic relationship with the yeast-like fungus Alloascoidea hylecoeti. Here, we tested the hypothesis that A. hylecoeti has a high nutrient content thus allowing it to function as a valuable food source for the solitary larvae of E. dermestoides, which bore into the wood of dead trees, an extremely nutrient-poor substrate. Our analyses revealed that A. hylecoeti is rich in soluble sugars, free amino acids, ergosterol, phosphorus, and potassium compared to the other fungi measured, and also accumulates high amounts of fatty acids, B vitamins and nitrogen. We also tested whether A. hylecoeti possesses chemical mechanisms to suppress antagonistic microbes. Extracts from A. hylecoeti and chemical compounds produced or accumulated by this fungus were found to significantly inhibit the growth of potentially competing fungi. The active substances include fungal-produced monoterpenes and acetic acid, as well as phenolic compounds accumulated from host tree tissues. Moreover, sufficient acetic acid was released by A. hylecoeti to drop the medium pH to as low as 3.6, which inhibited all tested competitors, whereas the growth of A. hylecoeti was promoted. Taken together, the nutritional properties and competitive ability of A. hylecoeti may make a major contribution to the success of its insect partner, the ship-timber beetle under natural conditions.

Miniaturization, i.e., reduction in body size, happens in different organisms as an adaptation strategy under environmental stress such as warming. However, whether phytoplankton miniaturization occurs in coastal waters remains understudied due to complex environmental factors and strong spatiotemporal variability. Here, we comprehensively investigated the long-term changes in phytoplankton body size over 20 years in the coastal waters of Hong Kong through monthly sampling at 25 stations across the region. We employed a framework distinguishing two drivers of community miniaturization: (1) intraspecific size reduction (species miniaturization) and (2) shifts in community composition toward a higher proportion of small species. At the species level, miniaturization was widespread, more in diatoms than dinoflagellates, primarily driven by temperature, supporting the temperature-size relation. In contrast, community-level miniaturization was negligible across most stations (except in a semi-closed bay), which was attributed to the decreased proportion of small species. This could be explained by the declined phosphate concentration which not only directly reduced the proportion of small species but also diminished the temperature sensitivity of phytoplankton community. Our findings provide multi-scale insights into coastal phytoplankton miniaturization, with critical implications for food web dynamics and the biological carbon pump. Moreover, we highlight that anthropogenic nutrient reduction may significantly mitigate community-level phytoplankton miniaturization, though localized effects in semi-enclosed systems warrant further investigation.

Bathyarchaeia, among the most ancient and abundant microbial lineages on Earth, dominate diverse anoxic subsurface ecosystems and play a pivotal role in global carbon cycling. This review synthesizes current understanding of their physiological, metabolic, and evolutionary foundations underlying their ecological significance and environmental effects over geological timescales. Despite their global distribution in the deep biosphere, the phylogenetic diversity and total cellular abundance of Bathyarchaeia remain substantially underestimated. As uncultivated metabolic generalists, Bathyarchaeia exhibit remarkable metabolic versatility, including anaerobic organic degradation, dark carbon fixation, and putative methane and alkane metabolism. Specifically, genus Baizosediminiarchaeum has been demonstrated to adopt organomixotrophy by coupling anaerobic lignin degradation with inorganic carbon assimilation. These metabolic strategies likely enable them to thrive in energy-limited subsurface environments with dynamic geochemical fluctuation. The early evolutionary history of Bathyarchaeia appears closely linked to major geological events, including tectonic activity and plant evolution, whereas more recent lineage expansions reflect physiological adaptations to host-associated and anthropogenically influenced environments, highlighting their on-going co-evolution with Earth's modern environments. Overall, we propose carbon metabolic innovation as the central driver behind the ecological and evolutionary significance of Bathyarchaeia, putatively linking microbial ecological functions to planetary biogeochemical processes. Future efforts in isolation and cultivation remains essential for elucidating their unknown physiological and metabolic mechanisms. In parallel, advances in ecological modeling and the development of lineage-specific lipid biomarkers hold great promise for quantifying their contributions to global carbon budgets and reconstructing paleoenvironmental and paleoclimate conditions.

The keystone species concept holds that certain members of an ecological community, despite their low abundance, exert disproportionately large effects on species diversity and composition. In microbial ecology, experimental validation of this concept has been limited because targeted removal of individual species remains technically challenging. Here, we developed a procedure to test the keystone species concept within a soil microbial food web by selectively suppressing a protist predator at the microscale via UV-induced phototoxicity in a microfluidic soil chip system. We targeted a hypotrich ciliate (subclass Hypotrichia), and combined microscopy with high-throughput amplicon sequencing of microbial taxonomic markers to assess, across multiple trophic levels, how its suppression affected microbial community abundance, diversity, and composition. Over the 20-day incubation, the chip system supported complex communities of bacteria, fungi, and protists. Following Hypotrichia suppression, two distinct ecological responses were observed: first, an increase in the relative abundance of flagellates, consistent with mesopredator release, accompanied by a significant rise in overall protist diversity; second, a convergence in protist community composition, indicative of biotic homogenization. Bacterial community abundance, richness, and composition remained unchanged, likely due to compensatory predation from a relative increase in bacterivorous flagellates. In contrast, fungal diversity decreased, presumably because the altered protist community favored facultative fungal consumers. Collectively, these findings provide direct experimental evidence that low abundance microbial predators can function as keystone species, modulating predator community composition and diversity, and exerting cascading effects on lower trophic levels within microbial brown food webs.

Widespread aromatic pollutants such as benzene, toluene, ethylbenzene, and xylene are traditionally considered to drive soil carbon loss through mineralisation and ecotoxicity. Contrary to this view, our study reveals that low concentrations of these pollutants stimulate microbial carbon chain elongation-a previously overlooked carbon conversion pathway producing medium-chain fatty acids, thereby reshaping soil carbon dynamics. Using phased amplicon sequencing, metagenomics, and metaproteomics of soil microcosms amended with these compounds, we demonstrate that aromatic pollutants bidirectionally regulate carbon chain elongation at both taxonomic and molecular levels. These pollutants selectively enrich Clostridium_sensu_stricto_12 and Rummelibacillus while suppressing Acinetobacter, a key elongation taxon in natural soils. Simultaneously, they inhibit Petrimonas, a syntrophic fatty acid degrader, promoting the accumulation of medium-chain fatty acids. Carbon chain-elongating bacteria cooperate with aromatic degraders, redirecting pollutant-derived carbon towards chain elongation rather than complete mineralisation to CO₂. Among them, Bacillus occupies a pivotal niche bridging aromatic degradation and carbon elongation. At the molecular level, aromatic pollutants enhance chain elongation by accelerating substrate uptake and channelling the key intermediate acetyl-CoA into the reverse β-oxidation pathway. Additionally, aromatic pollutants restrain fatty acid biosynthesis pathway by upregulating fabR, whereas inhibiting acrR and fadR. They also maintain NADH availability to alleviate Rex-mediated repression of bcd, a critical gene in the β-oxidation pathway. However, high concentrations of aromatic pollutants disrupt metabolic homeostasis and suppress chain elongation activity. Our findings redefine the ecological impact of aromatic hydrocarbon contamination in soil, demonstrating their role in modulating anaerobic carbon fixation and retention within soil microbial communities.

Macrolide antibiotics are vital for controlling infections in humans, animals, and agriculture, yet their effectiveness is increasingly compromised by antimicrobial resistance. Macrolide esterases (MLEs) are key mediators of macrolide resistance but have only been detected in Gram-negative bacteria, with no evidence in Gram-positive species. Here, we mined over 500,000 Gram-positive genomes and identified 8,707 candidate proteins. Six representative MLEs were functionally validated, conferring resistance to 16-membered macrolides and increasing minimum inhibitory concentrations up to 16-fold in Escherichia coli and 128-fold in Bacillus subtilis. Moreover, two exhibited broad-spectrum activity against all clinically and veterinary relevant 16-membered macrolides. Temporal analysis revealed that Gram-positive MLEs originated at least 2.7 million years ago, contrasting with their emergence in Gram-negative bacteria after the introduction of antibiotics. Genomic surveys further demonstrated the global distribution of MLE-carrying Gram-positive bacteria across 97 countries and diverse ecosystems, including clinical, food, agricultural, and natural environments. These findings highlight Gram-positive MLEs as an underrecognized risk and underscore the need for a One Health-oriented strategy to monitor, assess, and mitigate the spread of macrolide resistance across interconnected ecosystems.

Host specificity of a plant pathogen is defined by its effector complement. However, it remains unclear whether the full complement is required for pathogenicity. Pseudomonas syringae pv. actinidiae (Psa) is an emerging model pathogen of kiwifruit with over 30 functional effectors, providing a unique opportunity to understand how host-mediated selection shapes pathogen evolution. The majority of Psa's effectors previously appeared non-essential in single knockout contexts. Why, then, does Psa maintain such a large repertoire? We sought to examine effector requirements, redundancies, and repertoire refinement across host genotypes through a mutated effector-leveraging evolution experiment (MELEE), serially passaging competitive populations of effector knockout strains. Competition suggests that all effectors are collectively required for successful virulence, demonstrated by the dominance of wild-type. Host-specific effector requirements identified may further explain the maintenance of this large effector repertoire, providing important insights into the dynamics of effector redundancy following incursions.

Organismal life cycles are influenced by Earth's rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms' ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.

Mesopelagic microbes and zooplankton, degrade, and attenuate >90% of the 10 billion tonnes of particulate organic carbon that sinks into the oceans' interior annually. Approaches such as particle interceptors/incubators (called c-respire) can isolate the microbial assemblage attached to particles from that of zooplankton, enabling quantification of microbially mediated particulate organic carbon flux attenuation. This metric yields patterns of particulate organic carbon degradation by microorganisms through the upper mesopelagic (200-500 m depth). Here, we investigate the temporal sequence of particulate organic carbon degradation in two steps. First, we intercept sinking particle assemblages from different depths (180-300 m) and hence with varying degrees of exposure to microbial activity. Second, we incubate these intercepted particles shipboard for 12 h (short-term) and track degradation using apparent respiratory quotients (dDIC/dDO2). We also conducted a 12-hour shipboard incubation on a particle assemblage that had already undergone a 36-hour in situ c-respire (long-term) incubation. At a subantarctic and two polar sites, ARQs from short-term incubations exhibited a significant decrease with depth, consistent with particles deeper in the upper mesopelagic being exposed to a longer period of degradation and flux attenuation (as they settle). ARQs from all long-term incubations had significantly lower ARQs, and smaller depth-dependent gradients, than the short-term incubations. We interpret these trends as being driven in part by sequential changes in the stoichiometry of the microbially altered POC substrates. ARQs of <0.5 (less than the theoretical minimum) were observed in long-term incubations suggesting a role for incomplete oxidation of dissolved substrates. This temporal sequence is used to conceptually explore what sets the limits on microbially mediated degradation of POC.

Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methylhydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal-bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.

Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transfer of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of faecal or caecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, faecal transplantation, and caecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored bacterial and viral populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transfer-recipient control mice. Although all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. Overall, faecal and caecal transplant resulted in highly similar colonization processes with some minor variation in enrichment for two specific bacterial families. This study provides valuable insights into microbial ecology, as well as the dynamics underlying experimental microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transfer in mouse models.

Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that (i) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, (ii) the identity of key chitin degraders varies with moisture level, and (iii) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.

As important members of the marine ecosystem, baleen whales are frequently managed and protected, but methodology to assess their health remains limited. Recent technological advances, such as the use of drones, support the non-invasive collection of promising health-associated data, including respiratory exhalant microbiota. Here, we considered five health metrics paired with respiratory exhalant samples to examine the utility of characterizing respiratory microorganisms for health diagnostics of North Atlantic right whales (Eubalaena glacialis), one of the most endangered baleen whale species. In 2016-2024, we used drones to collect 103 exhalant samples from 85 individuals to examine the associated microbiome, using amplicon sequencing methods targeting bacteria and archaea. The health status of sampled whales was characterized using an index of body condition derived from full-body vertical drone images, three qualitative assessments obtained from photo-identification imagery, and an existing health and vital rates model. Using an elastic net penalized regression approach, we demonstrate significant relationships between these health metrics and respiratory-associated microorganisms. Bacterial taxa that significantly contributed to the model for the body condition index differed between the thinnest and most robust males in the dataset. The thin whale harbored taxa belonging to the same genus as mammalian pathogens, Clostridium and Peptoniphilus, whereas the robust whale harbored taxa commonly observed in lipid-rich environments, Sediminispirochaeta and Candidatus Gracilibacteria. These differences warrant further investigation into the mechanisms by which bacteria contribute to whale health. Our findings demonstrate the utility of non-invasive multi-metric health models that include respiratory exhalant microbiota for whale health assessment and management.

Saccharomyces cerevisiae relies on social wasps (e.g. Vespa crabro, Polistes spp.) for dispersal and genetic mixing. Unlike most natural environments, wasp intestines provide conditions that support yeast survival, sporulation, spore germination, and mating. This study explores the mechanisms at the basis of this process by examining the wasp gut environment and yeast responses. Molecular analyses based on yeast deletion collection and transcriptomics showed that yeast sporulates in the crop, spores germinate in the gut, and cells ferment in the gut. The crop and gut differ chemically: the gut has more sugars, a higher pH, and (in workers) greater viscosity. In vitro tests confirmed yeast survival in both environments, with faster germination in gut-like conditions. Computational models based on these physicochemical traits matched the experimental results. The data obtained provide fundamental insights into yeast progression towards mating within wasps' intestines and suggest a possible relation between yeast alcoholic fermentation and wasps' alcohol tolerance, thereby enhancing our understanding of the S. cerevisiae-social wasp association.