Environmental Microbiology

Coenocytic algae are organisms that undergo karyokinesis without cytokinesis, resulting in multinucleated cells. Most research on bacterial communities in coenocytic algae has used 16S rRNA sequencing, primarily focusing on the order Bryopsidales of green coenocytic algae. Recent studies have analyzed metagenome-assembled genomes (MAGs) from algal hosts across multiple taxa, such as Chlorophyta, Phaeophyta, and Rhodophyta, revealing more about bacterial biosynthetic machinery and potential symbiotic relationships. Given the cosmopolitan distribution of coenocytic algae, such as Bryopsis, Caulerpa, Codium, and the yellow-green alga Vaucheria, and their unique morphology, there is a need to better understand their associated bacterial communities. To address this, filaments of Vaucheria bursata LB2067 were sequenced using the Illumina NovaSeq instrument, and all publicly available short- and long-read datasets from coenocytic algae were screened for MAG recovery. All recovered MAGs from both Bryopsidales and Vaucheriales showed a high dominance of Pseudomonadota at the phylum level, but no consistent patterns at the order or family levels. High completeness of specific KEGG pathways, such as bidirectional polyphosphate metabolism and riboflavin biosynthesis, was prevalent in MAGs from coenocytic orders compared to non-coenocytic ones. Notably, N-acetylglutaminylglutamine amide (NAGGN) biosynthetic gene clusters (BGCs) were found only in MAGs from coenocytic orders, whereas polysaccharide utilization loci (PULs) were present in all MAGs analyzed. These results indicate that bacterial communities associated with coenocytic algae are complex, with diverse survival strategies adapted to challenging and variable environments.

The Deep Chlorophyll Maximum (DCM) is likely the most important feature organizing the marine epipelagic environment. Within this layer, opposing gradients of light and nutrients create a stratified habitat that supports high phytoplankton biomass and a substantial fraction of oceanic primary production. Despite its ecological importance, most studies treat the DCM as a single depth, overlooking its fine-scale heterogeneity. Here we investigated prokaryotic community organization across the DCM in the northwestern Mediterranean Sea through high-resolution sampling of four profiles collected over two days. Free-living (0.2-3 {micro}m) and particle-associated (3-20 {micro}m) communities were characterized using 16S rRNA gene amplicon sequencing. Prokaryotic communities changed progressively along the vertical gradient, revealing the DCM as a microbial coenocline with continuous community turnover. Fuzzy clustering identified distinct assemblages associated with environmental transitions from warm surface waters to the chlorophyll maximum, the nitrite peak below the DCM, and deeper nitrate-rich layers. In both the free-living and particle-associated fractions, most ASVs remained consistently associated with the same depth-defined clusters across all samplings, indicating stable niche partitioning over short timescales. However, these temporally stable ASVs accounted for a substantially smaller fraction of community sequences in particle-associated communities, suggesting higher dynamism, likely driven by particle-mediated transport. Nevertheless, phylogenetic analyses revealed that closely related ASVs tended to occupy similar depth niches, indicating that habitat preferences are phylogenetically conserved in both size fractions. Our results demonstrate prokaryotic niche partitioning over scales of only a few meters within the DCM, highlighting the importance of fine-scale sampling for understanding microbial community structure and responses to ocean change.

Trichodesmium is an important oceanic N2 fixing cyanobacterial genus that has been shown to provide up to 50% of new N to oligotrophic regimes. Despite its importance, we know relatively little about the genomic potential and functional diversity of the two major clades of Trichodesmium (Clade I and Clade III, hereafter Thieb and Tery, respectively). With the expanded collection of Trichodesmium isolates in the USCTCC (University of Southern California Trichodesmium Culture Collection), we sequenced genomes from seven cultivated strains to further characterize the genomic diversity within the genus. For example, sequencing the genome of the "gigantic", red Trichodesmium contortum surprisingly shows that they are closely related to the smallest Trichodesmium clade, TeryA. The high genomic identity between TeryA and T. contortum (>98.5% ANI) and lack of implicated auxiliary genes suggests their large biovolume differences might be transcriptional or epigenetic in origin. Furthermore, these data show that using Tery-subclades are a more accurate designation than the classical Trichodesmium species delineation. Finally, we placed the analysis of these genomes in an ecological context via read mapping with globally distributed RNA and DNA datasets. Our data show that Tery clades (A&B) are both lower in relative abundance compared to Thieb in global oceans, generally co-occur when detected in the field, and are highly linked to decreased salinity and increased temperatures, especially for sampling locations in the Bay of Bengal. Lastly, even though TeryA members are undersaturated with respect to current CO2 concentrations, our phenotypic and biogeography data suggests that salinity/ocean color could limit their predicted global impact as climate changes.

Microorganisms are the key drivers of carbon cycling in coastal marine sediment ecosystems, significantly influencing carbon storage and release during Gracilariopsis lemaneiformis cultivation. This study employed 16S rRNA sequencing, a high-throughput qPCR chip, and carbon isotope labeling to assess the impact of G. lemaneiformis cultivation on carbon cycling processes in coastal sediments. A comparative analysis was conducted between cultivated zones (GZ) of G. lemaneiformis and adjacent control zones (CZ). The results indicated that macroalgae cultivation significantly modified sediment-seawater exchange dynamics and accelerated carbon cycling within coastal marine sediment ecosystems. Furthermore, G. lemaneiformis cultivation increased the abundance of genes linked to polysaccharide degradation and carbon fixation pathways, thereby enhancing carbon cycling efficiency. The ecosystem multifunctional index, calculated based on carbon fixation gene abundance, was significantly higher in GZ compared to CZ. Incubation experiments using 13C-NaHCO3 demonstrated that cultivation markedly elevated the carbon fixation rate of sediment, emphasizing a higher potential for carbon sequestration in sedimentary environments cultivated with macroalgae. Additionally, cultivation significantly altered sediment microbial communities, simplifying their structural complexity. Key microbial taxa identified via k-core species analysis--including Subgroup10 of Desulfobacterota and MBNT15, correlated strongly with carbon fixation rates, indicating their pivotal roles in sediment carbon cycling processes. This study provides critical insights into how large-scale macroalgae cultivation influences coastal carbon dynamics and informs strategies for optimizing carbon management in aquaculture ecosystems.

Chytrids are unicellular fungi that infect and degrade phytoplankton as parasites or saprotrophs. They impact not only food availability and quality in surface waters but also carbon cycling and sequestration. So far, their ecological significance has mostly been investigated for freshwater environments, whereas observations for marine environments are scarce -- even though chytrids can be highly abundant there, too (as shown for the Arctic Ocean). To test the chytrids' potential to control phytoplankton dynamics in the Arctic Ocean, we analysed metabarcoding and photosynthetic pigment data from two expeditions, Tara Polar Circle and MOSAiC; the latter providing a dense sampling transect across one year from the under-ice water column and sea ice samples. The phytoplankton communities of both environments were dominated by diatoms, with strong seasonal effects indicating blooms in the water column. Chytrids dominated fungal communities in both environments and revealed a strong cryo-pelagic coupling. They were especially abundant during the sea ice melt in water samples and in ice-associated (sympagic) samples, where they represented >2% and up to 61%, respectively, of all combined reads assigned to chytrids or phytoplankton. Co-occurrences of the two most abundant chytrid taxa with some of the most abundant diatom taxa and niche differentiation from other potential diatom parasites are consistent with the chytrids' critical role in controlling diatom blooms, especially in sympagic habitats.

Identifying discrete microbial assemblages and their environmental drivers across multiple biological fractions simultaneously remains a central challenge in aquatic microbial ecology. We applied an integrated analytical pipeline built around Latent Dirichlet Allocation (LDA) to an eight-year 16S rRNA amplicon time series from the Laurentian Great Lakes, spanning four size-fractionated biological blocks -- free-living prokaryotes, particle-associated prokaryotes, and small and large chloroplast-containing eukaryotes. LDA resolved ecologically coherent subcommunities whose taxonomic identity was consistently defined at the order and class level, with fingerprint taxa confirmed by discriminant analysis. Shannon entropy differences between blocks reflected fundamental differences in dispersal capacity and environmental filtering -- free-living prokaryotes and large eukaryotes showed higher mixing than particle-associated prokaryotes and small eukaryotes. Temperature dominated environmental structuring across all blocks, assessed through Limma and random forest with SHAP, with secondary drivers differing by size fraction. Group Compositional Analysis jointly integrating all four blocks revealed that thermal stratification and lake chemistry organize microbial communities coherently across all size fractions simultaneously. Warm stratified and cold inversely-stratified waters harbored largely non-overlapping assemblages across all four blocks, with cold water specialists -- including chemolithotrophic deep-branching lineages and silica-dependent diatoms -- having no warm water equivalents. ImportanceThe Laurentian Great Lakes are among the fastest warming lakes in the world, yet the microbial communities that drive their biogeochemical cycles remain poorly characterized across size fractions and thermal habitats. Using eight years of samples spanning all five Great Lakes, we show that free-living bacteria, particle-associated bacteria, small phytoplankton, and large phytoplankton all respond coherently to the same master environmental gradients -- thermal stratification and lake chemistry -- despite fundamental differences in organism size, trophic role, and sequencing protocol. Warm stratified and cold water habitats support distinct microbial communities, and the cold water specialists identified here have no warm water equivalents. As the Great Lakes warm and cold water habitats shrink, the microbial communities that depend on them will not simply become less abundant they will be replaced by fundamentally different assemblages.

The critically endangered Caribbean staghorn coral Acropora cervicornis hosts microbiomes frequently dominated by the putatively parasitic intracellular bacterium Candidatus Aquirickettsia rohweri, which is associated with reduced coral growth and heightened disease susceptibility. Whether this dominance can be disrupted through antibiotic treatment and a sequential disturbance of thermal stress, remains unknown. In this study, we exposed disease-susceptible A. cervicornis fragments to broad-spectrum antibiotics, sub-bleaching thermal stress, or the combination of an antibiotic pre-treatment followed by thermal stress, and tracked changes in microbiome composition and diversity across all experimental phases using 16S rRNA amplicon sequencing and quantitative PCR (qPCR). We find that while the minor microbial fraction exhibits sustained compositional shifts in response to treatment, Ca. Aquirickettsia rohweri is resilient to antibiotic and thermal perturbation and may in fact increase in abundance following antibiotic exposure, suggesting that its dominance is actively maintained and not readily displaced by current disease mitigation strategies.These results indicate that antibiotic intervention is unlikely to be a viable strategy for disrupting Ca. A. rohweri dominance in disease-susceptible A. cervicornis, underscoring the urgency of understanding its transmission routes to inform microbiome rescue efforts.

Intertidal mudflats are low hydrodynamic energy environments hosting microphytobenthic communities that experience strong spatiotemporal variability in light regimes, including changes in spectral quality and light intensity that can lead to cellular photooxidative stress. To cope with these fluctuations, autotrophs exhibit diverse and highly plastic adaptations that are often species-dependent and shaped by their ecological niches. This study investigates photophysiological responses and metabolic remodeling in a diatom assemblage originating from a natural winter microphytobenthic biofilm under contrasting red and blue light intensities. To this end, photosynthetic parameters were monitored alongside changes in lipophilic metabolites, including untargeted lipids and lipophilic pigments. While few metabolites showed temporal remodeling, rapid and contrasting changes were observed within 30 minutes in response to both spectral quality and light intensity. Red light treatments induced broader remodeling of lipophilic metabolites than blue light, whereas blue light appeared to have a greater impact on photosynthetic parameters. Moreover, red light induced xanthophyll-cycle responses comparable to those observed under blue light at equivalent incident intensity. We discuss these metabolic responses in relation to diatom photoadaptive strategies, placing these findings within the intertidal environmental framework. This work further underlines the importance of understanding rapid metabolic plasticity in coping with light fluctuations, providing new insights into the photoregulatory strategies of natural microphytobenthic communities.

Nitrogen availability is a key factor shaping microbial metabolism, ecological adaptation, and nitrogen cycling in aquatic environments. Members of the genus Vibrio are ubiquitous heterotrophic bacteria in marine and aquaculture ecosystems, yet their responses to different inorganic nitrogen sources remain poorly understood. Here, we systematically compared the growth characteristics, nitrogen transformation capacity, and molecular responses of Vibrio harveyi and Vibrio parahaemolyticus under ammonium (NH4+), nitrate (NO3-), and nitrite (NO2-) conditions using physiological assays, comparative genomic analysis, and transcriptomic profiling. V. harveyi exhibited broader nitrogen utilization capacity and was able to grow under all three nitrogen conditions, whereas V. parahaemolyticus showed a strong preference for NH4+ and limited growth under NO3- and NO2- conditions. Moreover, V. harveyi displayed rapid population expansion accompanied by reduced long-term viability, while V. parahaemolyticus maintained greater population stability. Both species showed NO3- accumulation during growth despite lacking canonical nitrification genes under NH4+ condition, suggesting the potential involvement of non-canonical heterotrophic nitrification processes. Transcriptomic analysis revealed nitrogen source-dependent metabolic specialization in V. harveyi. NH4+ availability promoted motility-associated responses and metabolic overflow, whereas NO3- induced iron acquisition-related pathways and NO2- activated assimilatory nitrite reduction coupled with oxidative stress adaptation. These findings demonstrate that inorganic nitrogen availability drives divergent metabolic and adaptive strategies in Vibrio, providing new insights into their nitrogen metabolic potential and ecological roles in aquatic environments. ImportanceThis study demonstrates that V. harveyi and V. parahaemolyticus exhibit distinct inorganic nitrogen utilization strategies, with V. harveyi displaying broader nitrogen utilization capacity. Transcriptomic and metabolomic analyses revealed that different nitrogen sources drive distinct metabolic and environmental adaptation responses in V. harveyi, including enhanced motility-associated functions and metabolic overflow responses under NH4+ condition, increased iron acquisition pathways under NO3- condition, and activation of assimilatory nitrite reduction coupled with oxidative stress adaptation under NO2- condition. Furthermore, significant nitrate accumulation was observed in both Vibrio strains during ammonium cultivation despite the absence of canonical nitrification genes, suggesting unexplored nitrogen transformation potential in vibrios. This study expands our understanding of how inorganic nitrogen availability shapes microbial adaptation strategies and ecological functions in aquatic environments.

Bacteriophages are abundant and diverse in soils, playing a major role in regulating bacterial communities and consequently affecting biogeochemical cycles. Such host-phage interactions may be influenced by fluctuations in soil moisture, as observed in wetlands soils which constitute a key feature of the ongoing climate change. Here, we investigated the spatial and temporal dynamics of both bacteria and T4-type bacteriophage community structures and diversities in soil of a freshwater wetland. Soil was sampled in three sites across a proximal soil transect presenting an increase moisture content at seven dates over an 18 months period with contrasted flooding periods. DNA was extracted and we applied amplicon sequencing of the bacterial 16S rRNA gene and viral g23 gene. Bacterial community composition varied across the proximal soil transect, with Methylomirabilia and Gammaproteobacteria being significantly enriched in the wettest site and comprising ASVs affiliated to methanotroph and denitrifying bacteria, respectively. We identified a large diversity of T4-type phages, among which a fraction was novel, while others were similar to phages previously sequenced from various biomes. These findings suggest that T4-type phages are capable of successfully colonizing diverse niches in the biosphere, contributing to their ubiquity and diversity. Viral community was however dominated by few vASVs, which were highly represented in one or two of the three studied sites supporting the Bank model. All together our results indicate that T4-type phages have broad host ranges and more likely follow bacterial population dynamics. The present study provides new insights into the role of phages in soil, highlighting their interactions with bacterial hosts involved in carbon and nitrogen cycles, interactions that are likely regulated by fluctuations in soil moisture, as observed in wetlands. HighlightsO_LIBoth bacterial and T4-type phages were structured across proximal sites C_LIO_LIBacterial 16S rRNA gene copy number was inversely correlated to the soil moisture C_LIO_LI26 viral ASVs did not cluster with reference sequences C_LIO_LIviral ASVs seem to be primarily controlled by host availability C_LIO_LISoil bacteria and phage diversities were significantly lower in the wettest site C_LI

The Southern Ocean harbors diverse marine microbial communities shaped by both local oceanographic conditions and dispersal limitations. However, this knowledge is mainly based on coastal Antarctic sites, whereas circumpolar Antarctic open sea and subantarctic ecosystems remain poorly explored. Here, we characterize marine microbial communities (using 16S rDNA high-throughput sequencing) and marine oceanographic data across two regions: the Subantarctic, involving two localities (the Magellan Strait and the Beagle Channel), and Antarctic open sea, involving two localities (Eastern Indian and Central South Pacific). We found extensive differences across regions and localities, characterized by distinct taxonomic patterns, alpha diversity, microbial composition, and enriched taxa profiles. Despite these differences, Clade Ia, Amylibacter, NS5 marine group, and NS2b marine group exhibited high prevalence across regions. Oceanographic parameters had variable relationships with microbial alpha diversity across regions: Sea surface temperature and salinity had a negative and positive correlation, respectively, in the Magellan Strait during 2024. In the Antarctic region, dissolved oxygen displayed a negative correlation in the Indian Ocean during 2024, whereas salinity displayed a more variable relationship in the Indian Ocean: positively correlated during 2024, while negatively correlated during 2025. Collectively, our results highlight a strong microbiological biogeographic structure in the Southern Ocean, both across broad scales (between Subantarctic and Antarctic regions) and within regions. Furthermore, our results show dynamic relationships between oceanographic variables and marine microbial diversity across Antarctic and Subantarctic regions.

Diatom mating activity contributes to their enormous phenotypic and genetic diversity, yet little is known about patterns in diatom reproductive compatibility across genetically diverse strains, nor the effects on offspring phenotypes that may confer adaptive evolution, niche partitioning, or trait improvement. Here a panel of 38 Arctic Cylindrotheca sp. isolates were crossed pairwise to detect mating compatibility. Positive mating patterns were identified in multiple clades, including amongst crosses of different parental rbcL genotypes. F1 isolated from three different crosses presented phenotypic variation in growth rate, plastid traits, and associated photo-physiological responses to blue and green actinic light. Offspring gliding speed and behaviour also varied, providing insights into complex motility traits that link cell morphology, bioenergetics and sensory adaptation with emergent movement patterns. Exploratory analysis of the F1 trait landscape identified a varaible mixture of individual-level and cross-dependent effects, including substantial variation in growth rate between individuals and strong effects of different crosses on morphology and motility. Experimental diatom breeding may offer a unique strategy to study ocean protist evolution and phenotypic diversification and could complement other biotechnological innovations to enhance cultivation yields and crop resilience in mass cultivation.

The marine sponge holobiont, composed of the sponge host and its microbial symbionts, is a known source of abundant and diverse ether lipids (ELs). Apart from their structural role in the cytoplasmic membrane of archaea and some bacteria, ELs have often been linked to signaling functions and defense against pathogens. Despite the relevance of ELs, their biosynthesis, as well as the identity of their producers, remain elusive. Here, we report the analysis of potential ether lipid producing genes and gene clusters, detected in marine sponge metagenomes as well as public sponge genomes. We show that the sponge holobiont has the capacity to synthesize ELs via several pathways, and suggest the ability of the sponge holobiont to synthesize ELs under different O2 levels. Finally, targeted lipidome analysis confirmed that ELs are present in the lipid profiles of all of the studied sponge holobiont samples, and indicates that the biosynthesis of the plasmalogens detected is likely restricted to the sponge host itself, based on the detected hydrocarbon chain lengths. This work provides a basis for the challenging quest to decipher intricate EL biosynthesis in marine sponges and their associated microbes.

Antarctica represents a significant, unresolved, and unstable source of methane to the atmosphere. To advance our understanding of the biological filter of methane in Antarctica, here we identify the taxa and functional genes present during methane oxidation in an Antarctic Methane Seep. Methane oxidation was present in all sediments, including in a non seep control site. Using 16S rRNA analysis alongside metagenomics, we found that ANaerobic MEthane oxidizing (ANME) archaea coupled to Sulfate-Reducing Bacteria (SRB), documented as the most important marine methane sink in other locations, were not present. Instead, we observed the presence of denitrification-dependent methane oxidizers, including the anaerobic genus Candidatus Methylomirabilis, alongside the nitrate reducing archaea Candidatus Methanoperedens through short-read metagenomic classification. In addition, we note the presence of multiple aerobic methanotrophs, with a particularly high abundance of the Methylobacter, Methylomonas, and Methyloprofundus genera. Our results support denitrification-mediated methane oxidation and aerobic methanotrophy as the primary potential methane sinks in the Ross Sea. The widespread methane oxidation, including in control sediment, combined with the possibility of anaerobic methane oxidation linked to denitrification rather than sulfate reduction highlights the ubiquity and uniqueness of the Antarctic methane cycle.

Bacterial conjugation is the primary mechanism by which antibiotic resistance genes spread in microbial populations, yet our understanding of this process has been largely based on experiments conducted under aerobic conditions. This creates a fundamental disconnect: environments that are considered hotspots for gene exchange (e.g., the gut, abscesses, chronic wounds, and wastewater systems) are predominantly anaerobic. In this study, we investigate whether oxygen availability influences the transfer rate of a set of common ESBL-IncI1- and qnrS1-IncF plasmids in commensal Escherichia coli strains from chickens. We found that oxygen availability significantly shapes conjugation dynamics in a recipient strain-specific manner, with anaerobic conditions promoting higher ESBL-IncI1- plasmid transfer rates to commensal E. coli recipients. Conjugation rates of the ESBL-IncI1- plasmids to a laboratory strain of E. coli were several orders of magnitude higher and independent of oxygen level, while two qnrS1-IncF plasmids showed higher anaerobic rates. Our study reveals critical "oxygen blind spots" in conventional conjugation assays and suggests that conventional aerobic conjugation assays underestimate plasmid transfer rates in natural environments such as the chicken caeca. These findings highlight the importance of aligning experimental conditions with the physiological and ecological environments in which gene exchange naturally occurs. Tailoring these variables is essential for generating results that accurately reflect, predict, and potentially intervene in the horizontal spread of antimicrobial resistance.

Fusarium head blight (FHB) is driven by co-occurring Fusarium species. Yet the molecular bases of their competitive interactions, particularly at the strain level, remain largely unknown. We performed an integrated multi-omic investigation of four Fusarium isolates cultivated in monoculture, self-confrontation (SC) and inter-specific confrontation (C) assays: two Fusarium graminearum strains FgrI349 and FgrPH-1, and two Fusarium avenaceum strains FaveI494 and FaLH03. Light microscopy and quantitative colorimetry revealed marked phenotypic heterogeneity. the F. graminearum strains formed expansive, red-pigmented colonies with rapid radial growth, whereas the F. avenaceum isolates grew more slowly and displayed distinct colony morphologies and pigmentation patterns. Untargeted LC-HRMS detected 1,008 metabolites in monocultures and 938 metabolites in confrontation zones. Species-level chemical signatures were confirmed, and strain-specific metabolite sets were identified, with FaLH03 producing more than 60 % of the metabolites being made exclusively by a single strain, highlighting its exceptionally unique metabolic profile. RNA-seq uncovered extensive transcriptional reprogramming during competition. In self-confrontations, strain-specific differences persisted but no major morphological or metabolic shifts were observed. Inter-specific confrontations elicited partner-dependent responses: FgrI349 up-regulated 1,492 genes against FaveI494 (including secondary-metabolite biosynthesis, oxidoreductase activity and transport) but only 407 genes against FaLH03, while down-regulating secondary-metabolite genes in the conspecific confrontation. Conversely, the F. avenaceum isolates showed opposite trends; FaLH03 strongly repressed ribosome-biogenesis and cell-wall genes while inducing oxidative-metabolism pathways, whereas FaveI494 displayed a modest transcriptional response dominated by down-regulation of cell-division and chromosome-segregation genes. Gene-ontology enrichment highlighted an opponent-specific reversal of the secondary-metabolite biosynthetic process category in F. graminearum: down-regulated in intra-specific confrontation but up-regulated in both inter-specific encounters. Collectively, our results demonstrate that competitive outcomes are shaped more by strain identity than by species identity, with each strain deploying a distinct molecular arsenal, ranging from metabolite-mediated antagonism to targeted transcriptional shutdown, when confronted with a specific opponent. These findings refine our understanding of Fusarium community dynamics and provide a framework for developing strain-targeted biocontrol strategies against FHB.

A substantial fraction of marine sediments experience elevated temperatures due to burial or hydrothermal activity. These conditions can fundamentally reshape both microbial activity and the chemical nature of sedimentary organic matter (OM). Laboratory incubations have demonstrated that moderate heating of marine sediments can lead to the production of labile organic compounds such as acetate, however, it remains unclear whether heating alters the bioavailability of the remaining OM pool. In this study, we experimentally tested the effect of temperature on the bioavailability of OM through a series of bioreactor experiments using deeply buried sediment collected from Guaymas Basin (Gulf of California). We measured acetate concentrations in sterilized Guaymas Basin sediments before and after artificial heating (70{degrees}C for 7 days) to quantify abiotic acetate generation. We then conducted incubations of a model marine bacterium with sterilized, artificially heated sediment and tracked respired CO2 production and its associated 13C and 14C signatures. Our study revealed that sediment depth and hydrothermal history strongly control abiotic acetate production, with higher acetate yields from shallower, cooler sediments. Respiration rates in control and heated sediment incubations were nearly identical, indicating that heating does not measurably alter the bioavailability of bulk sedimentary OM. Moreover, the {delta}13C values of respired CO2 were indistinguishable between control and heated sediment incubations while the {Delta}14C values were more depleted in the first 24 hours in incubations with heated sediment. This transient offset suggests that low-temperature heating mobilizes a small pool of older material due to desorption of mineral-bound OM without altering overall bioavailability. Our findings shed light on the role of thermal alteration in shaping carbon cycling in marine sediments by influencing how OM is made available to sedimentary microorganisms.

Anatoxin-producing cyanobacteria pose growing ecological and public health risks, yet the genomic organization of anatoxin biosynthesis remains poorly resolved. Using complete genome assembly of a benthic cyanobacterium of the genus Microcoleus, we show that the entire anatoxin biosynthetic gene cluster is encoded on a small circular plasmid rather than the chromosome. This unexpected localization suggests enhanced mobility of anatoxin biosynthesis and has implications for toxin evolution, release, and environmental surveillance.

Evidence from the Cassini mission confirmed that Saturn's moon Enceladus hosts a subsurface alkaline ocean where rock-water reactions may generate redox disequilibria capable of supporting microbial metabolisms. To investigate potential microbial survival under simulated Enceladus ocean conditions, we used thermodynamic modeling to develop a salt formulation consistent with one possible Enceladus ocean composition and supplemented it with putative microbial energy sources to create a growth medium. The medium was inoculated with samples from diverse ocean world analog environments on Earth to determine which microorganisms could persist under Enceladus-like conditions. The microorganisms persisting in this geochemically bounded medium were heterotrophic, metabolically versatile bacteria with low carbon requirements. Genomic and physiological analyses further showed the presence of multiple stress-response pathways, sodium- based bioenergetic systems, osmoregulation strategies, and other adaptations consistent with survival in alkaline, low-nutrient settings. These results suggest that some stress-tolerant heterotrophic bacteria may serve as useful model organisms for life in Enceladus' subsurface ocean. These findings demonstrate the value of geochemically modeled media as a framework for constraining habitability, identifying relevant biosignatures, and probing potential microbial survival strategies beyond Earth.

Quantitative stable isotope probing (qSIP) allows researchers to calculate taxon-specific carbon incorporation from sequencing of natural microbial communities, which can be used as a proxy for metabolic activity rates and subsequently as an input for biogeochemical modeling. While qSIP is widely utilized in soils to investigate the identity and metabolic activity of largely unculturable microbes, the application of qSIP in marine and aquatic ecosystems is more recent. Here, we investigated how bioreactor type (batch vs. chemostat) and carbon substrate complexity (single vs. multiple substrates) affect the incorporation of {superscript 1}3C-labeled glucose into rRNA after 24 hours using excess atomic fraction (EAF) as a proxy for metabolic activity rate. We found that the growth dynamics and community composition of the {superscript 1}3C-incorporating bacteria differed significantly for each treatment. EAF was positively correlated with both 16S gene copy number and a genomic index of copiotrophy in both batch treatments, but not in the chemostat, suggesting that chemostats dampen the competitive advantage of fast-growing copiotrophic taxa. Our results demonstrate that both substrate complexity and experimental regime influence qSIP-derived metabolic activity estimates and provide guidance for future applications of qSIP in aquatic environments.