The ISME Journal

During host-microbe symbioses, the fitness of mutualistic microbes is determined by the interactions that concurrently occur, throughout their life cycle, with their host and other members of the surrounding microbial community. Disentangling how these multiple interactions shape the fitness of microbial symbionts is challenging, but is essential to understand the diversity and functioning of mutualisms. Here we examined the different fitness components of rhizobial symbionts of the legume plant Mimosa pudica across the multiple stages of their symbiotic life cycle. By comparing rhizobial symbiotic fitness in single and pairwise inoculations, we found that inter-bacterial interactions causing significant fitness effects are common, transitive and can have major consequences, sometimes leading to the extinction of a strain. These interactions predominantly occur at the root infection (nodulation) step, but smaller post-infection interaction effects, involving yet uncharacterized mechanisms, were also detected. Furthermore, considering pairwise interactions was sufficient to predict fitness ranks in more complex rhizobial communities consisting of 6 or 8 strains, indicating that higher-order interaction effects do not play a significant role in these communities. Overall, our results provide a quantitative framework to describe the main drivers of rhizobial symbiotic fitness in a simple community context.

Phytoplankton-bacteria interactions are pivotal in marine ecosystems, influencing primary production and biogeochemical cycles. Diatoms, in particular, engage in diverse relationships with bacteria, ranging from mutualism to pathogenicity. However, the mechanisms governing the shift between these interactions and how they are shaped by host physiology and environmental context, remain unclear. To address this, we investigated how the diatom growth phase influences the interaction between a newly isolated Alteromonas macleodii strain from the Equatorial Pacific and the model diatom Thalassiosira pseudonana. We demonstrated that A. macleodiis algicidal activity depends on the diatoms growth phase, defensive capacity, and substrate availability. The algicidal effect manifests either during the diatoms stationary phase or with an external source of organic carbon, implicating organic matter availability as a key driver. Transcriptomic analysis revealed that A. macleodii shifts from motility-associated to growth-associated gene expression patterns in response to the diatoms growth phase and co-culture duration. Filtrate assays and fluorescence microscopy suggest a two-stage infection model: initial bacterial motility and exudate secretion induce diatom death, followed by bacterial aggregation around cellular debris. Comparative transcriptomics of A. macleodii with other algal hosts highlights host-specific bacterial responses, underscoring the context-dependent nature of these interactions. Together, these findings reveal how bacterial behavior and gene expression are modulated by host state and environmental cues, providing a molecular basis for the dynamic roles of diatom-bacteria interactions in shaping microbial community structure.

Nitrobacter strain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacterium Nitrosospira AHB1, a consortium that nitrifies under acidic conditions. Here we characterise the growth of isolated Nitrobacter strain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA) in co-culture. NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2- concentrations of 500 {micro}M. However, the optimum decreases to pH 5.0 at lower initial NO2- concentrations closer to those found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2- with an apparent-half-saturation constant (54 {micro}M) one order of magnitude lower than its closest relative, the neutrophilic strain Nitrobacter hamburgensis X14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically, Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2 are sensitive to NO2--derived compounds and only oxidise [~]200-300 {micro}M ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by [~]0.5 pH units and both strains could oxidise up to 2.7-2.9 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3 and utilising AOA-derived NO2-. Removal of NO2- is likely crucial for nitrifier growth in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals that NHB1 is distinct from validated species and the name Nitrobacter laanbroekii is proposed.

Marine sponges are critical components of marine benthic fauna assemblages where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont Candidatus Taurinisymbion ianthellae residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. Candidatus Taurinisymbion ianthellae incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont Candidatus Nitrosospongia ianthellae. Metaproteogenomic analyses also indicate that Candidatus Taurinisymbion ianthellae likely imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

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.

Anaerobic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Growth of the prokaryotes and protists within the microcosms respond differently to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrioaceae and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.

The transfer of virulence factors into eukaryotic cells is a hallmark of bacterial pathogenesis. We report the expression, interspecies transfer, subcellular localization, and potential functions of three unusually large virulence factor-like proteins that underlie a bipartite mutualistic bacterial symbiosis. These proteins are synthesized by green sulfur bacterial epibionts surrounding a central motile chemoheterotroph in the multicellular phototrophic consortium Chlorochromatium aggregatum. While symbiosis-proteins remain intracellular during axenic epibiont growth, they are transferred to the partner bacterium in the association. An RTX-like protein secreted towards the central bacterium is capable of degrading its alginate capsule, thereby promoting direct cell-to-cell contact. Two gigantic hemagglutinin-like proteins are predicted to fold when binding extracellular Ca2+ to form Type 6-like auto injection needles, explaining their observed transfer into the central bacterium. These functionalities extend far beyond the known pathogenic interactions of bacteria with eukaryotes and provide new perspectives on the evolution of bacterial virulence factors.

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.

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling revealed both clade II nosZ flavobacterial isolates and whole sand communities exhibit a low affinity for N2O, contrary to previous reports that clade II N2O reducers generally have a high substrate affinity. This indicates adaptation to the high residence times of N2O within production and consumption zones in the sands. Collectively, these N2O reducers remove most N2O produced in permeable sediments, supporting lower-than-expected coastal emissions predicted by biogeochemical models. We conclude that permeable sediments host specialised microbial communities that mitigate N2O emissions and buffer marine nitrogen cycling amid rising nutrient pollution.

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.

The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the worlds soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in worlds soils, our findings have implications for global nitrogen cycles and agricultural research.

Most microbes that live in or on hosts are not obligate symbionts. Instead, they often cycle between host-associated and free-living phases and experience selection in both environments. The benefits that microbes confer to hosts are often assumed to be a product of host-microbe (co)evolution, but microbial benefits to hosts may also evolve independent of the host-microbe interaction, while the microbe is free-living. We investigated this hypothesis by experimentally evolving a beneficial Allorhizobium bacterium we had previously isolated from duckweed (Lemna japonica). We evolved this Allorhizobium strain in the absence of any host at high and low salinity and at high and low nitrogen, and then tested how the evolved strains performed as symbionts when host-associated. Microbial salinity adaptation drove the emergence of novel benefits to host plants in high-salinity environments. However, these locally adaptive benefits emerged only when microbes evolved under low-nitrogen conditions; microbial adaptation to high nitrogen reduced plant growth. Bacterial phenotyping indicated that the same microbial traits that underlie salinity adaptation mediate host benefits. Whole-genome sequencing of the evolved strains revealed significant genomic shifts between selective treatments, including plasmid variation and point mutations associated with osmotic regulation. The emergence of the microbial benefits to hosts, as a byproduct of microbial adaptation, highlights that these benefits do not require targeted host-microbe co-evolution. Rather, predicting the evolutionary trajectory of these symbioses may require understanding both the abiotic and biotic selective agents acting on key microbial traits mediating the host-microbe interaction.

Metabolically-active obligate aerobes are unheard-of in tightly-anoxic environments. Present culture-independent and culture-dependent investigations revealed aerobic microbial communities along two, ~3-meter-long sediment-cores underlying the eastern Arabian Sea oxygen minimum zone, where high H2S disallows O2 influx from the water-column. While genes for aerobic respiration by aa3-/cbb3-type cytochrome-c oxidases and cytochrome-bd ubiquinol oxidase, and aerobic oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were present across the cores, so were live aerobic, sulfur-chemolithoautotrophs and chemoorganoheterotrophs. The 8820-years-old, highly-sulfidic, methane-containing sediment-sample from 275 cmbsf of 530 mbsl yielded many such obligately-aerobic bacterial-isolates that died upon anaerobic incubation with alternative electron-acceptors/fermentative-substrates. Several metatranscriptomic reads from this sediment-sample matched aerobic-respiration-/oxidase-reaction-/transcription-/translation-/DNA-replication-/membrane-transport-/cell-division-related genes of the obligately-aerobic isolates, thereby corroborating their active aerobic metabolic-status in situ. Metagenomic and metatranscriptomic detection of perchlorate-/chlorate-reduction genes, plus anaerobic growth of an obligately-aerobic Halothiobacillus isolate in the presence of perchlorate and perchlorate-reducing-consortia, suggested that cryptic O2 produced by perchlorate-respirers could be sustaining obligately-aerobes in this environment.

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.

Glycolate is a major product of phytoplankton photorespiration, but its fate in the microbial food web is not well constrained. Here, we used stable isotope probing and mass spectrometry combined with genomic analyses and microscopy to quantify glycolate metabolism by a taxonomically diverse set of heterotrophic marine bacteria. We found that 9 of 16 tested strains with the genomic capability to metabolize glycolate directly assimilated and respired glycolate carbon in monoculture. We next co-cultivated glycolate-incorporating strains with non-incorporating strains and found that several cross-feeders incorporated more glycolate carbon into their biomass than direct incorporators. Carbon use efficiency, reflecting proportional differences in movement of glycolate carbon into biomass versus into carbon dioxide, were distinct across co-cultures and ranged from 0.01 -3.15% depending on the strain mixtures. These results suggest that the fate of glycolate carbon is not limited to microbial taxa with the genetic capability for direct assimilation, and that bacterial metabolic interactions via cross-feeding play a critical role in influencing the efficiency of carbon transfer. Such information is critical to refine conceptual and numerical models of heterotrophic processing and transfer of organic carbon in an era of global change with predicted increases in photorespiration.

Chemosynthetic symbioses between animals and bacteria are known to underpin productivity in the deep sea, yet the diversity of energy and carbon sources sustaining these associations in shallow-water environments remains poorly understood. Dimethylsulfoniopropionate (DMSP) is highly abundant in coastal habitats, where it is produced by seagrasses, phytoplankton, and heterotrophic bacteria, and occurs together with its breakdown product dimethyl sulfide (DMS) in shallow-water sediments. Here we show, supported by genomic and transcriptomic evidence, that DMSP and DMS cycling are integral to the energy and carbon metabolism of the gutless oligochaete Olavius algarvensis and its chemosynthetic symbionts. By assigning DMSP degradation pathways to individual members of the hosts microbial community, we reconstructed a network integrating demethylation and cleavage with energy conservation, methionine biosynthesis, and acetate assimilation into polyhydroxyalkanoates. We also identified a host-encoded methanethiol oxidase (MtoX) suggesting host participation in MeSH detoxification. Comparative metagenomic analyses of more than 60 gutless oligochaete species from globally distributed habitats showed that key DMSP- and DMS-processing genes (dddP, dmdA, tmm, dmsA) are widespread, indicating that organosulfur metabolism is a conserved feature of these symbioses. Our findings expand the recognized metabolic repertoire of shallow-water chemosynthetic symbioses and provide evidence that these associations directly contribute to marine DMSP and DMS cycling.

Nitrification occurs widely from the deep sea to animal holobionts, but the eco-evolutionary forces shaping the niches and dynamics of the lineages of the chemoautotrophic bacteria and archaea responsible remain largely unknown. To make strides towards this goal in a rapidly changing, exemplar marine ecosystem, the Baltic Sea, we studied basin-scale nitrifier spatio-temporal dynamics, coupled with enrichment-enabled comparative genomics. Based on metagenomes and rRNA gene sequencing, we found nitrifiers to be persistently relatively abundant throughout deep depths (>25 m), and from late-fall to spring in surface waters, as revealed by twice-weekly sampling across two years in the southwest Baltic Sea surface waters. In these surface waters, we observed time-lagged dynamics between ammonia- and nitrite-oxidizers, which were positively correlated with nitrite, nitrate, and diverse other prokaryotes, and negatively correlated with day length, light, and chlorophyll. For the dominant nitrifiers, ammonia-oxidizing archaea (AOA), we enriched five novel species including the dominant deep Baltic Sea species, and obtained genomes from all dominant AOA phylotypes. Among these genomes, which enabled fine-scale niche-differentiation, we observed a high degree of gene conservation, with most differences related to genes associated with interactions with the external environment, including genes involved in signal transduction, cell wall/membrane biogenesis, and inorganic ion transport, indicating these may be the primary drivers of strain-variability. We also observed differences in nitrogen and phosphorus metabolism between two dominant surface types. Together our study provides key insights into the niche of nitrifiers, and begins the process of understanding the mechanisms and functional implications of these patterns.

Symbiotic interactions are an ecologically and evolutionary significant phenomenon pertaining to virtually every organism on Earth. For eukaryotes inhabiting extreme environments, syntrophic symbioses with microbes may be key to successfully colonizing new niches, such as globally expanding oxygen-depleted habitats. Multi-domain symbioses between microbial eukaryotes and intracellular methanogenic archaea are crucial to understanding the origins and mechanisms of eukaryotic anaerobiosis. Nearly all anaerobic ciliates, ecologically important protists found in diverse oxygen-depleted environments, host methanogenic endosymbionts, sometimes alongside bacterial partners, that facilitate their anaerobic metabolism. Although vertical symbiont transmission necessarily occurs during ciliate cell division, symbionts might occasionally be acquired horizontally. However, patterns of host-symbiont specificity and intraspecific variability remain poorly understood. Here, we present the first intra-specific genomic analysis of both host and symbionts in such partnerships, providing key insights into the fidelity of eukaryotic-prokaryotic liaisons in anoxia. We assessed the symbiont-host co-diversification and genetic variation across eleven populations of a single undescribed Metopus species hosting Methanocorpusculum cultured from intertidal sediment locations separated by meters to 1000s of kilometers. Our results show incongruency in host mitochondrial and symbiont phylogenies, indicating a mixed transmission mode. On a genomic level, both host and symbiont populations formed distinct location-specific clusters exhibiting no signs of isolation-by-distance. Instead, ecological factors appear to have driven population genomic divergence at least partly and likely led to differences in metabolic traits. Symbiont comparative and population genomics enable us to further comprehend the complex nature of these multi-partner syntrophic symbioses, crucial to interpreting cell-cell interactions across the domains of life.

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. Efforts to increase conventional agricultural output come with significant environmental impacts stemming from deforestation and excessive use of chemicals, including soil salinization, erosion, and nutrient runoffs. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. For instance, much of our knowledge of beneficial and detrimental microbial communities vis-a-vis crop productivity comes from studies on plant-microbiome interactions in soil. Here, we investigated how the practice of continued transfer of microbial communities from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa) growth in aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Strikingly, L. sativa plant and root growth was significantly reduced across all replicates inoculated with the established microbiome. Further analyses revealed the reduced productivity was potentially a consequence of plant-specific pathogen enrichment, including Pseudomonas, through transfer of microbiomes from pre-existing systems - a phenomenon consistent with negative feedbacks in soil ecology. These findings underscore the need for diagnostic tools to monitor microbiome composition, detect negative feedbacks early, and minimize pathogen accumulation in aquaponic systems.