The ISME Journal

How a single gram of soil harbors billions of microorganisms, each with distinct genomic variants that collectively maintain coherent ecological function(s), is one of microbiology's grand unsolved problems. A key obstacle is determining which variants contribute to individual- and community-level fitness, in which contexts, and how co-occurring ecotypes interact to divide niche space. Here, using nitrate (NO3-)-contaminated subsurface sediment as inoculum, we have performed high throughput enrichments in laboratory media of defined carbon source compositions across ecologically relevant gradients of pH and NO3-. Long-read metagenomics and link-community decomposition of co-occurrence networks of taxa across these enrichments has revealed context-specific functional interactions among dominant generalist and lower-abundance specialist denitrifier ecotypes that comprise 53 distinct enriched communities (EnComs) across 288 enrichments derived from a single sediment sample. We identified a single enzymatic difference of alternative NO3- reductases (NapAB vs. NarGHI) with differing substrate affinities that provided a mechanistic explanation for competitive niche partitioning between the two dominant taxa, Neorhizobium spp. and Allorhizobium spp., along the NO3- gradient. Genome-wide polymorphism ratios (pN/pS) revealed that selective pressures vary systematically with carbon source availability and gradients of pH and NO3-, which helps explain the natural biodiversity and functional interactions of ecotypes within denitrifying communities in the subsurface sediment. Our findings show that controlled enrichments along ecological gradients can thus uncover eco-evolutionary forces of selection, drift, and diversification that sculpt the biodiversity of microbial populations in the natural environment.

Bacterial species often harbor extensive strain-level diversity, raising the question of whether strains, rather than species, are the relevant ecological units. We quantified pairwise interactions among 12 strains from four prevalent Lactobacillus species of the honeybee gut microbiota using gnotobiotic bees. Microbiota-depleted bees were colonized with individual strains and all 66 pairwise combinations, with strain abundances measured by colony counts and strain-resolved amplicon sequencing. Negative interactions predominated, with most significant interactions involving mutual inhibition. Within-species interactions were stronger and more asymmetric than between-species interactions, producing less even community compositions. Across repeated cycles of colonization in microbiota-depleted bees, three of four within-species pairs lost one strain, whereas all four between-species pairs persisted. These results indicate that closely related strains experience greater niche overlap and stronger competition than strains from different species, supporting bacterial species as ecologically differentiated units while highlighting the importance of strain-specific traits in shaping community assembly and stability.

A plant-independent avenue for N2-fixation takes place in desert topsoils through a "C-for-N" mutualism between heterodiazotrophs and the cyanobacterium Microcoleus vaginatus. These partners come together within a diverse soil microbiome under conditions of N-limitation for the phototroph and C limitation for the heterotrophs. We hypothesized that extracellular chemical signaling might enable partner selection and collocation, though infomolecules shaping inter-microbial architecture were unknown. We show that the complex chemical composition of M. vaginatus exometabolome depends on its N-limitation status, thus potentially offering information to mutualists. In chemotactic assays, the exometabolome effectively repelled most native soil bacteria, particularly intensely when under N-limitation. Bacterial assemblages circumventing the repulsion were enriched in species that are rare in the soil microbiome, and that functionally resemble mutualistic cyanospheres (showing high N2-fixation potential, secretion of urea, and copiotrophy), setting the stage for a working symbiosis. Further, we could reproduce the enrichment of copiotrophs and nitrogen-fixers using mixtures of N-acetylglutamic acid, N-acetylmethionine, indole-3-acetic acid, and 5'-methylthioadenosine, all preferentially released by M. vaginatus under N-limitation. These signaling molecules did not result in an enrichment of urea producers, however. The results demonstrate that trans-species communication through specific infochemicals, together with already known quorum-sensing-like intraspecific communication in M. vaginatus, act as a tool to organize microbiomes spatially and to attain mutualistic partner specificity in an open, crowded background.

Microbial symbioses drive the evolutionary and functional diversification of eukaryotic clades, from single-celled protists to large invertebrates. However, our knowledge of host-associated assemblages (the "holobiont") is limited in microscopic animal phyla with a body size <1mm, due to practical challenges such as low biomass and difficult taxonomy of host species. Marine nematodes represent an ideal case study for rapidly advancing our knowledge of bacterial-animal symbioses, representing a globally abundant invertebrate group with strong links to terrestrial and model organism species within the same phylum. Here, we sequenced the holobionts of 220 marine nematodes and generated 815 metagenome-assembled genomes (MAGs) of host-associated bacteria/archaea. Our data indicates that 20-34% of marine nematodes harbor an obligate intracellular symbiont, often with multiple endosymbionts co-occurring within the same host. Three bacterial phyla (Pseudomonadota Bacteroidota, and Verrucomicrobiota) account for three-quarters of all nematode-associated MAGs, and the majority of these holobiont MAGs represent deeply divergent lineages in the prokaryotic tree of life. The Flavobacteriaceae (a core microbiome taxon in C. elegans and other terrestrial nematodes), were consistently recovered across phylogenetically diverse marine nematode lineages, suggesting evolutionary conservation of holobiont taxa across marine and terrestrial environments. We also report a novel chemoautotroph family (Ca. Thionematobacter) recovered from nematode hosts in both deep-sea and shallow-water habitats, and report the first confirmed instance of Cardinium endosymbionts from marine invertebrates. Finally, [~]65% of nematode-associated MAGs are able to degrade chitin, via hexosaminidase, implying that benthic invertebrate holobionts make significant contributions to global carbon cycling. These results underline the importance of evaluating symbiosis in microscopic marine invertebrates, and accelerating our understanding of animal evolution and ecosystem dynamics in vast benthic habitats.

Trichodesmium is a major nitrogen fixer in the nutrient-limited tropical and subtropical ocean, contributing up to 50% of new nitrogen and driving primary productivity. Trichodesmium filaments often aggregate into colonies that host a diverse consortium of microbes that can influence their activity and physiology; however, it is unclear what factors shape community structure. To address this, we used metagenomics of Trichodesmium colonies collected across the subtropical and tropical Atlantic Ocean to examine how Trichodesmium diversity and abundance shape epibiont community composition. Heterotrophic metagenome-assembled-genomes from Trichodesmium colonies and genes specific to the major Trichodesmium subclades were read mapped against Trichodesmium metagenomes from the North Atlantic, the Western Tropical South Pacific, and the Red Sea. Using this global survey of Trichodesmium subclade distribution patterns and their enriched heterotrophs, we found unique core microbiomes that are specific to Trichodesmium subclades across ocean basins. Genome characteristics of the enriched heterotrophs reveal a genomically small, slow-growing community consistently associates with colonies. Our results suggest that Trichodesmium genotype may influence epibiont community structure, indicating a role for deterministic processes in shaping the microbiome.

The roles of reactive oxygen species (ROS) as signaling molecules and inhibitors of phytoplankton growth are well documented. While phytoplankton physiological mechanisms for ROS detoxification are well characterized, the role of heterotrophic bacterial partners in ROS alleviation and outcomes for these bacteria remain poorly understood. Here, we examined how extracellular hydrogen peroxide (H2O2) shapes nutrient exchange between the diatom Phaeodactylum tricornutum and two phycosphere bacteria. From an initial screen of 20 bacteria, we identified a "helper" (Muricauda sp.) that enabled P. tricornutum to survive acute H2O2 stress and a "non-helper" (Algoriphagus sp.) that did not. Using nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked diatom-derived carbon and nitrogen (13C and 15N) transfer to each bacterial partner under ROS stress. Oxidative stress disrupted diatom metabolism and altered nutrient transfer: diatom-derived carbon and nitrogen incorporation was significantly reduced in the helper but increased in the non-helper under H2O2 stress. Growth assays revealed that the helper preferentially utilized exudates from healthy, intact hosts, whereas the non-helper did not grow on exudates but thrived on lysates from damaged or lysed cells. Together, these findings indicate the helper was better adapted to accessing resources from living hosts, while the non-helper relied on nutrients released through ROS-induced host damage. Our results highlight oxidative stress as a key driver of algal-bacterial interactions and suggest that bacterial resource-acquisition strategy underlies host protection: bacteria utilizing healthy-host exudates are more likely to protect hosts from oxidative stress, while those benefiting from host damage are not, despite retaining ROS detoxification capacity.

In marine ecosystems, phytoplankton growth is frequently limited by iron, a micronutrient, due to its poor solubility from major sources such as atmospheric dust. Many phytoplankton cannot access dust-bound iron independently, and processes that solubilize this iron remain poorly understood. Here, we investigated whether bacterial partners can enhance phytoplankton growth under iron-limited conditions by facilitating utilization of dust-bound iron. Our study focused on Phaeodactylum tricornutum, a model diatom that is adapted to low iron growth conditions, grown in co-culture with bacteria isolated from its phycosphere. In iron-limited experiments using mineral dust as the sole iron source, the addition of Marinobacter significantly enhanced diatom growth compared to axenic controls, whereas Stappia significantly suppressed it. However, under iron-replete conditions, neither bacterium affected growth. These results indicated that under low-iron conditions, Marinobacter actively alleviates iron deficiency. Co-cultured bacterial cell abundances remained at least an order of magnitude lower than diatom cells. Marinobacter also enhanced algal growth within days of dust addition to established Fe-limited co-cultures, indicating its beneficial effect on P. tricornutum was not unique to a system in which it was newly introduced. Exometabolomic profiling comparing the axenic diatom and co-cultures revealed a suite of condensed aromatic organosulfur and peptide-like compounds associated with bacterial presence, as well as compounds that appeared to be unique to each co-culture, hinting at a molecular underpinning of each strains impact. Our findings demonstrate that low-abundance members of the phycosphere community can have a significant impact on host growth by modulating the accessibility of dust-bound Fe.

Microbes in the animal gut compete to colonize spatially restricted host niches. However, whether competition for space drives inter-individual variation among hosts, and which factors determine the outcome of such competition, remain poorly understood. Here, we investigated competitive interactions of the western honeybee gut symbiont Frischella perrara with other members of the bee gut microbiota. Shotgun metagenomics analysis of individual bees revealed that F. perrara is negatively correlated with a specific species of the genus Gilliamella. Co-colonization of microbiota-depleted bees with these two bacteria resulted in their competitive exclusion. The outcome of this competition depended on the relative number of bacteria each bee received and benefited Gilliamella when one of the two type VI secretion systems of F. perrara was mutated. Using fluorescently tagged strains, high-resolution microscopy, and gut region-specific quantification, we show that both bacteria localize to the same host niche in the ileum of mono-colonized bees, indicating competition in a spatially restricted host niche. Moreover, both microbes protected against infection, promoting bee health. This competition provides an explanatory mechanism underlying variation in the occurrence of F. perrara across honeybee colonies and highlights the importance of gut spatial structure and microbial competition in shaping microbiome composition and inter-individual variability.

Pelagibacterales gMED is the dominant epipelagic genomospecies in the western Mediterranean Sea. We used the O-chain biosynthesis gene clusters, OBCs, as clonal barcodes to analyse strain-level population structure. In total, 385 OBC-defined clonal lineages were tracked across Mediterranean metagenomes spanning 14 years and depths from 5 to 90 m within the photic zone, with between 128 and 336 detected per metagenome. The relative conservation of dominant OBC types across years, seasons, and geographic locations indicated a persistently high and stable clonal diversity.

Biological nitrogen fixation converts dinitrogen gas into ammonia, supplying new bioavailable nitrogen to marine ecosystems, but the evolutionary processes shaping its distribution among heterotrophic bacteria remain unresolved. Thalassolituus, a genus within the family Oceanospirillaceae (order Oceanospirillales), is best known for hydrocarbon degradation, yet nitrogen fixation has been confirmed in only one cultured isolate. We analyzed 74 quality-filtered genomes assigned to Thalassolituus within a broader dataset of 421 Oceanospirillaceae genomes to reconstruct the distribution and evolutionary history of the minimal nifHDKENB gene set. Twenty-five genomes encoded complete or near-complete nif loci and occurred in four well-supported clades interspersed with genomes lacking the pathway. Statistical topology tests rejected the species-tree topology for concatenated NifHDK and NifHDKENB protein alignments, and eleven recombination events across nif loci were supported by at least four detection methods. The core nifHDK gene order remained broadly conserved, but accessory neighborhoods differed among clades, and structural nifHDK genes showed stronger codon adaptation than biosynthesis nifENB genes. Clade 2 combined species-gene tree congruence, conserved gene neighborhoods, and comparatively high nifH codon adaptation, whereas Clades 1 and 4 showed greater phylogenetic discordance, more recombination, and weaker codon adaptation. These results support a reticulate history in Thalassolituus, in which lateral acquisition introduced nitrogen fixation into distinct lineages, vertical inheritance preserved it within some clades, and homologous recombination continued to reshape nif loci. These processes help explain why nitrogen fixation is unevenly distributed among closely related marine heterotrophic bacteria.

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, "Candidatus Abyssoplasma scotoplanesicola", within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. "Candidatus Abyssoplasma scotoplanesicola" occupied 76.4-98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

Understanding the molecular mechanisms underlying plant-microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the complexity of natural microbial communities remains challenging. Such challenges can be addressed by employing synthetic microbial communities (SynComs) derived from well characterized microbial culture collections. Despite their importance, plant-associated microbial collections from major agricultural crops remain scarce. To bridge this gap, we established TriMic, a taxonomically and functionally representative culture collection of wheat root-associated bacteria. Complementing this collection, we include high quality genome sequences and an overview of genes involved in plant colonization, nutrient cycling, and plant growth promotion. Furthermore, we expanded this experimental toolkit by designing a reduced complexity SynCom that enables controlled dissection of plant-microbe interactions. Together, these resources lay the groundwork for mechanistic studies of plant-microbe interactions to accelerate biostimulant development aimed at enhancing agricultural productivity and sustainability. The TriMic collection and whole genomes are publicly available at the DSMZ (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/trimic) and NCBI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/740170v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@91bda0org.highwire.dtl.DTLVardef@386c49org.highwire.dtl.DTLVardef@4d455aorg.highwire.dtl.DTLVardef@1043ccb_HPS_FORMAT_FIGEXP M_FIG C_FIG Overview of the workflow for development of the wheat root bacterial collection and SynCom. (a) Bacterial isolates were recovered from roots of wheat grown in natural soil using two strategies after a root slurry was prepared: directly plating or host-mediated, which involved producing a secondary root slurry from wheat roots inoculated with the original root slurry (Ben Niu et al. 2017). Both root slurries were diluted and then plated onto four different types of media (1/10 R2A, 1/20 R2A, 1/100 R2A, and VxylG). Colonies were picked based on morphology and time of appearance. (b) Non-redundant strains of 88 purified isolates were made publicly available at the German Collection of Microorganisms and Cell cultures GmbH (DSMZ). (c) A 15-species synthetic community (SynCom) was developed after evaluating community dynamics in wheat roots inoculated with a 27-member consortium selected across genera in the collection. (d) Isolate genomes were sequenced using either short-read or hybrid assemblies with long-reads. Following functional annotation, genomes were screened for traits associated with plant-microbe interactions and secondary metabolite production.

Marine planktonic viruses play critical roles in shaping microbial communities and driving global biogeochemical cycles. However, quantitative, microbiome-wide analyses of marine prokaryoplankton-virus interactions in situ and their ecological impacts remain challenging due to the vast diversity of viral genomes and interaction modes and the limitations of existing methodologies. Here, we utilized GORG-Tropics, a global collection of 12,715 single amplified genomes (SAGs) generated from randomly sampled marine prokaryoplankton cells, to determine the frequency and modes of their interactions with viruses in the tropical surface ocean. We found 4.2% (range 1%-19% among samples) of GORG-Tropics SAGs to contain phage genomic material, with the highest frequency found in productive ocean regions. Prokaryoplankton lineages known to have high metabolic rates, including Prochlorococcus and Rhodobacterales, had a substantially larger fraction of cells associated with viruses (10-12% of SAGs) as compared to the less active but highly abundant lineages including Pelagibacterales (2.2% of SAGs). Cell-virus associations indicative of lysogeny were elevated in Alphaproteobacteria relative to other taxa. The collection of phages recovered from individual SAGs exhibited genomic diversity that bridged order-level taxonomies, indicating high diversity and genomic connectivity within wild phage populations. A substantial fraction of the observed cell-virus associations disagreed with the computationally predicted host identity of the virus, indicative of non-infective interactions. The extent of genetic exchange across tailed bacteriophages infecting different hosts, and connected to taxonomically distant phages provided further evidence for the role of non-infective phage entry in the lateral transfer between tailed phages. This study provides large-scale quantitative evidence of viral infection rates in the collective prokaryoplankton community across the global surface tropical ocean through large-scale identification and quantification of the specific phages, hosts, and modes of interaction at the resolution of individual cells. Our results confirm prior reports on the overall frequency of prokaryoplankton infections with viruses in the oligotrophic tropical surface ocean. Our findings uncover non-infective phage-cell associations that may be contributing to the lateral transfer of viral genes and the nutrition of marine prokaryoplankton.

The rhizosphere microbiome plays fundamental roles in plant health and productivity, yet the ecological rules governing microbiome assembly remain poorly understood. Here, we investigated early rhizosphere community assembly in tomato using a replicated combinatorial community coalescence framework, in which seven distinct natural bacterial communities were inoculated individually and in all possible pairwise and triplet combinations. Single inoculum communities clustered according to inoculum identity, indicating a strong effect of source community composition on assembly trajectories. However, when all communities were analyzed jointly, samples formed a continuous compositional landscape with no clear evidence of discrete community states. Despite major differences in source community composition, rhizosphere communities consistently converged toward the same uneven rank abundance structure, with two ASVs accounting for 50% and a median of nineteen ASVs for 90% of total abundance. While assembly was dominated by a very small number of Pseudomonas ASVs, limited evidence of alternative dominant states was observed. Increasing inoculum complexity did not increase stochasticity but instead promoted stronger convergence toward a global rhizosphere compositional centroid. Moreover, dominance hierarchies emerging from community coalescence closely mirrored the distance of source communities to this centroid. Communities derived from orchard soils consistently showed the highest dominance, suggesting that historical contingency and prior adaptation to horticultural crop rhizospheres may influence competitive success. Together, these results support the existence of a canonical rhizosphere attractor in both community composition and abundance architecture, with patterns consistent with assembly occurring under a limited number of dominant ecological niches imposed by the tomato rhizosphere.

Grassland microbial communities are central to mediating ecosystem function and stability, yet how long-term grazing reshapes root-associated microbiomes across contiguous soil-root habitats remains poorly understood. This limits our ability to identify robust microbial bioindicators for grassland health monitoring. In this study, we investigated the community assembly and functional variation of root-associated microbiomes of Stipa breviflora, a dominant perennial clonal grass in desert steppes, across a 17-year continuous grazing experiment with four grazing intensity treatments (no grazing, light, moderate, and heavy grazing). We show that grazing intensity induces niche-specific restructuring of microbial communities, with the most profound compositional and functional shifts occurring in the rhizosphere, followed by root endophytic compartments and bulk soil. Light and moderate grazing significantly enriches the phylum Bacillota in rhizosphere and endophytic compartments, whereas the genus Pseudomonas dominates ungrazed grassland soils and is markedly depleted under grazing conditions. Microbial community responses to grazing follow a unimodal intermediate disturbance pattern, with moderate grazing triggering the strongest microbial community differentiation, enhanced microbial network connectivity and modularity, and the highest abundance of grazing-responsive microbial biomarkers. Notably, grazing-induced microbial community variation is decoupled from intraspecific phenotypic changes in S. breviflora. Our findings demonstrate that long-term grazing acts as a strong selective filter partitioning core beneficial microbial taxon, establishing Bacillota and Pseudomonas as complementary bioindicators for evaluating desert steppe ecosystem health. This study advances the understanding of plant-microbe interactions under anthropogenic disturbance and provides microbiome-based insights for sustainable grassland management.

Viral infection is a major yet poorly quantified driver of microbial interactions and biogeochemical fluxes in the ocean. In diatoms, which are key contributors to marine primary production, the extent to which viruses reprogram host cell metabolism and alter elemental cycling remains largely unresolved. Here, we investigated how infection by a lytic single-stranded RNA virus reshapes carbon (C) and nitrogen (N) fluxes in the ecologically relevant nanoplanktonic diatom Mediolabrus comicus. Using controlled infection experiments coupled with flow cytometry, electron microscopy, PAM fluorimetry, and stable isotope probing, we resolved infection-driven changes from the population to the cellular scale. Infection induced rapid optical shifts and cellular reorganization, including the formation of membrane-bound viral replication compartments. These changes coincided with early impairment of plastidial functions, as shown by disruption of photosystem II functionality and a concomitant decline in photosynthetic carbon fixation. In contrast, nitrogen uptake was maintained and strongly enhanced during late stages of infection, indicating sustained resource acquisition to support viral replication. This decoupling led to dynamic changes in cellular stoichiometry and, overall, to substantial reductions in population-level carbon and nitrogen assimilation due to growth inhibition. Together, these findings demonstrate that diatom RNA virus infection reshapes host carbon and nitrogen metabolism, with cascading effects on elemental cycling. Our results identify diatom RNA viruses as important drivers of marine biogeochemical processes, with implications for primary production and the fate of organic matter in the ocean.

Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.

Viruses and grazers are fundamental agents of mortality in the oceans, impacting phytoplankton populations and organic matter cycling. Although viruses and grazers co-occur in nature, they are typically studied in isolation in laboratory experiments, limiting our understanding of their combined ecosystem impacts. Here, using a simplified ecosystem approach, we investigated individual and combined effects of the T7-like cyanopodovirus, P-SSP7, and the protistan grazer, Paraphysomonas bandaiensis, on the abundant marine cyanobacterium, Prochlorococcus MED4, and co-occurring non-photosynthetic heterotrophic bacteria (bacteria from here on). We observed that, individually, viruses and grazers caused substantial Prochlorococcus mortality. Viral lysis also triggered increases in damaged Prochlorococcus cells, dissolved organic matter release, and bacterial growth, while grazing reduced bacterial abundances. When grazers and viruses were combined, Prochlorococcus mortality was lower than expected from the sum of their individual effects. Contrary to expectations, this reduced Prochlorococcus mortality did not result in fewer viruses or grazers. Instead, virus-grazer-Prochlorococcus interplay resulted in greater virus production, maintenance of grazer growth, and a dramatic increase in particle aggregation. Our results reveal trophic cooperation and efficiency in which competition between viruses and grazers was likely mitigated, with virus progeny production enhanced by grazers, and grazer growth sustained through a shift to alternative food sources (bacteria, damaged cells, aggregates) secondarily derived from Prochlorococcus following viral lysis. The synergistic enhancement of particle aggregation via grazer-virus-phytoplankton interplay observed with the small buoyant Prochlorococcus phytoplankter underscores the importance of food web interactions for the flow of phytoplankton-fixed carbon within, and export from, the photic zone. SignificanceViruses and grazers both use phytoplankton as a resource for reproduction. In a simplified experimental system with Prochlorococcus, an important primary producer in the oceans, we found that the interplay between viruses and grazers led to reduced mortality of Prochlorococcus. Despite this reduced mortality, virus-grazer interactions resulted in elevated virus production and a dramatic increase in organic matter aggregation. Furthermore, grazer abundance was not affected by this interplay, likely due to the transfer of organic matter from Prochlorococcus to bacteria and aggregates, which the grazers could consume as alternative food sources. These findings provide insights into the complexity of ecosystem interactions and how they impact the fate of organic matter fixed by phytoplankton in the oceans.

Bacillus velezensis is a widely used plant growth-promoting rhizobacterium whose effectiveness under natural conditions is strongly influenced by interactions with surrounding microorganisms. While bacterial secondary metabolites are known to shape these interactions, little is known about their long-term evolutionary consequences. Here, we show that repeated exposure of B. velezensis GA1 to secondary metabolites produced by the competing rhizobacterium Pseudomonas sessilinigenes CMR12a drives the emergence of an adapted subpopulation with enhanced ecological fitness. Multi-omics analyses revealed extensive metabolomic and transcriptional changes associated with altered growth dynamics, sporulation, motility, and biofilm formation. Importantly, the evolved variant exhibited improved tomato root colonization and reduced the abundance of the competing Pseudomonas strain in planta. Together, our results demonstrate that prolonged exposure to diffusible bacterial metabolites can drive rapid adaptive diversification in rhizosphere-associated bacteria and highlight the importance of long-term interbacterial interactions in shaping the outcome of plant microbiome assembly and biocontrol performance.

Winogradsky columns are a classic model ecosystem for studying microbial biogeochemistry across steep gradients of oxygen and sulfide. They also remain widely used in microbiology education, introducing generations of students to microbial diversity. Yet, the genomic potential of their microbial communities remains uncharacterized. Here, we applied shotgun metagenomic sequencing to a Winogradsky column community at multiple depths, yielding 20 metagenome-assembled genomes (MAGs) representing diverse, largely uncultivated taxa. Genome-resolved analyses revealed metabolically diverse oxygenic and anoxygenic phototrophs that could potentially contribute to carbon and nitrogen fixation across all layers of the column. Most of these phototrophs also encoded one or more pathways for sulfur oxidation, which we speculated may support both energy conservation and/or sulfide detoxification by these populations. Complex carbon degradation capacity was also widespread across the MAGs, suggestive of the potential for the transformation of the column's amended organic matter (shredded coffee filters) into smaller depolymerization products and, through fermentation, organic acids. Together, these findings reveal how distinct microbial guilds might partition interconnected carbon, sulfur, and nitrogen transformations within redox-stratified systems.