ISME Communications

Bacterial bloomers,populations that experience rapid and significant increases in abundance in response to environmental triggers, briefly dominate marine microbial communities, potentially impacting the ecosystem by channeling large amounts of nutrients and affecting carbon fluxes. Due to their ephemeral nature, bacterial bloomers are challenging to capture, and it remains unknown whether they are restricted to specific taxonomic groups or whether they exhibit recurrent patterns. We analyzed a decade-long time series from the Blanes Bay Microbial Observatory (BBMO, NW Mediterranean Sea) to investigate bacterial bloomers in two size fractions (free-living (0.2-3 um) and particle-attached (3-20 um) communities. We identified 57 Amplicon Sequence Variants (ASVs), less than 1% of the total bacterial richness, exhibiting recurrent or chaotic blooming-like behavior. Bloomers spanned diverse phyla, though some taxonomic coherence appeared within families containing multiple blooming taxa. Monthly sampling detected bloom events on average 4.6 +- 1.9 times per year across both size fractions. Once seasonality was accounted for, blooms showed weak associations with biological and physicochemical variables, likely a consequence of monthly sampling resolution. Nonetheless, a marked shift in the blooming community within the particle-attached size fraction coincided with ecosystem disturbances from the nearby harbour restoration, suggesting that bloomers may act as disturbance sentinels. Metagenomic data showed that blooms led to marked shifts in the community functional potential. Overall, our findings underscore the importance of investigating bloom dynamics to understand microbial contributions to biogeochemical cycles and stress the need for higher-frequency sampling to accurately capture these transient but ecologically relevant events.

Competition for light has driven extensive pigment diversification among phytoplankton species, yet how this diversity shapes their spatiotemporal distribution in the field has been little studied so far. The cyanobacterium Synechococcus is an ideal model for addressing this issue, since this group has colonized most light spectral niches in marine environments. Here, we used an approach based on marker read recruitment from metagenomes to analyze the seasonal succession of Synechococcus pigment types (PTs) at two time-series stations off French coasts exhibiting contrasting oceanic regimes. Marked seasonality was observed at both sites. The shallow, permanently mixed English Channel site SOMLIT-Astan was characterized by an alternation between green-light specialists (PT 3a) peaking in spring, and chromatic acclimaters type A (PT 3dA) accounting for most of the Synechococcus community in winter. In contrast, the pigment diversity was much higher at the deep Mediterranean station BOUSSOLE. In the upper layer, the two main PTs were the blue light specialists (PT 3c), which dominated the community in summer and fall, and PT 3dA cells, which were more abundant in spring. The third most abundant PT was chromatic acclimaters type B (PT 3dB), which accounted for up to 15% of the surface community in late fall. Strikingly, PT 3dA was dominant at depth during most of the year. Multivariate analyses between PT abundances, clade abundances and environmental factors, notably water color indexes, suggested new associations between PTs to specific clades and ecological niches. This study provides novel insights for refining distribution models of Synechococcus PTs and phytoplankton groups in general.

Virus-host interactions are fundamental drivers of microbial community structure, yet whether viral ecological niches are confined within individual host niches (nested host niche scenario) or span multiple hosts and exceed any single host niche (expanded host niche scenario) remains poorly understood. To explore these patterns, we characterized prokaryotic and viral distributions and predicted virus-host interactions along a salinity gradient at Bras del Port salterns (Spain), ranging from seawater (3.6% salinity) to salt saturation (39.0%). We analyzed metagenomes and viromes from six ponds supplemented by 27 additional published viromes from the same hypersaline system, recovering 170 metagenome-assembled genomes (MAGs) dereplicated at the genomospecies level (MAGs clustered at 95 % average nucleotide identity), approximately 55,000 viral operational taxonomic units (vOTUs), and nearly 4,000 predicted virus-host pairs. Viruses exhibited broader niches than their putative hosts at the highest salinities, while at lower salinities the pattern was reversed or inconsistent depending on the site, and niche breadths of both viruses and hosts increased steadily toward higher salinities. Host taxonomy at the class level and below was the primary driver of viral genomic clustering, explaining more variance than salinity provenance (approximately 30% vs. approximately 19%), while the contribution of salinity to viral genomic composition appeared indirect, mediated through the salinity-driven distribution of distinct host classes rather than direct environmental filtering of viral sequences. Together, these findings support the expanded host niche scenario as the predominant virus-host interaction strategy, with evolutionary and ecological dynamics jointly shaped by salinity and host identity.

Soils are recognized as reservoirs of antibiotic resistance genes (ARGs) with the potential to transfer to clinical pathogens, creating antimicrobial resistance (AMR) that poses a threat to human health. While large-scale AMR surveys have profiled how diverse biomes shape soil resistomes, less is known about the influence of specific soil properties. Here, we combined metagenomics and 16S rRNA amplicon sequencing with isolate-based approaches to investigate drivers of soil AMR across a tropical watershed from beach to mountaintop in Waimea Valley, Oahu, Hawai{square}i. We leveraged functional- and taxonomic-classification of resistances to unravel how soil properties interact with bacterial taxa to structure resistomes. Metagenomic- and isolate-resistomes showed remarkable consistency, including a general gradient of increasing AMR from ridge to beach. Resistome functional composition was significantly correlated with total bacterial community structure. The relationship between resistances and soil properties was primarily dictated by taxonomic composition of each resistance. Rifampin- and Vancomycin-ARGs associated with Actinomycetes negatively correlated with soil physical properties, while resistant genes and isolates from Gammaproteobacteria positively correlated with enzymatic activity metrics. These findings indicate that soil properties structure the resistome indirectly through taxonomic filtering of microbial hosts and challenge the notion that AMR is decoupled from phylogenetic relatedness.

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.

Streptomyces are abundant soil inhabitants with extensive secondary metabolism and antibiotic resistance traits. Yet, their ecological role in shaping soil antibiotic resistome dynamics remains understudied. Here, we investigated how two different bio-based fertilizers harbouring Streptomyces shaped soil resistome and mobilome by combining genome analysis of eight Streptomyces isolates to metagenomic profiling of soils before fertilization, within 48 hours after fertilizer application, and six weeks after. Streptomyces genomes showed linkages among antibiotic resistance genes, carbohydrate-active enzymes, and antibiotic-production-associated biosynthetic gene clusters, connecting resistance and biosynthesis to broader metabolic strategies. Relationships between carbon degradation and biosynthesis associated with specific enzyme families, indicating that carbon availability shapes secondary metabolism. We confirmed experimentally that antibacterial potential varied with carbon source, suggesting that microbial activity during manufacturing of the bio-based fertilizers may create localized selection pressures before fertilizers enter the soil. Fertilization with the studied materials induced modest but consistent shifts in resistome and mobilome without major changes in dominant taxa or overall bacterial abundances, indicating functional reorganization within soil communities. Diversity of antibiotic resistance genes and mobile genetic elements increased, whereas abundance changes were small. Mobile genetic element composition showed stronger responses that were associated with fertilizer inputs, Streptomyces abundance, and taxa linked to faecal and resistance sources. Together, our results show that bio-based fertilizers shape soil resistome primarily through ecological restructuring of resident soil communities, while carbon-dependent microbial activity within fertilizers may enrich resistance. These factors should be considered in manufacturing of bio-based fertilizer as well as in designing agricultural practices.

Cyanobacteria are key prokaryotic primary producers in diverse ecosystems, yet the role of cyanobacterial siderophores in shaping their associated microbiomes remains unexplored. Our study demonstrates the benefits provided to the heterotrophic co-habitants of filamentous cyanobacteria in terrestrial microbial biofilms, focusing on the recently discovered widespread siderophores cyanochelins. To address the acceptance of cyanochelin B (CychB) across multiple bacterial classes, we first investigated its role in providing iron to a model siderophore producer P. aeruginosa PAO1 and selected Pseudomonas natural isolates, which were found to utilize CychB under iron limiting conditions while downregulating endogenous siderophore production. In response to CychB, PAO1 expresses a siderophore internalization cluster, which is localized in multiple Pseudomonas natural isolates. Using metagenome analysis, we characterized the bacterial community recruited along with CychB producing Phormidesmis cyanobacteria under long-term iron starvation. Potential CychB acceptor bacteria associated with the CychB producer were predominantly lacking endogenous siderophore machineries. Using siderophore selective pressure, we isolated a genuine CychB acceptor, gram-negative bacterium Methyloversatilis sp. S146 and demonstrated that its genome hosts an iron processing cluster overexpressed after CychB feeding, recognizing Methyloversatilis as a candidate for further mechanistic investigation of iron acquisition-driven microbial interactions. Our results indicate that CychB supports a specific subset of co-habiting heterotrophic bacteria during iron starvation, further emphasizing the role of cyanobacteria as key drivers of nutrient flows within globally important microbial soil crust ecosystems, supporting microbial life in nutrient-limited environments. These findings provide a mechanistic foundation to elucidate the role of cyanochelins as a public good in these communities.

Harmful algal bloom (HAB) succession in eutrophic lakes arises from seasonal rebalancing of selection, dispersal, and drift across interacting microbial domains, yet process attribution remains limited due to the scarcity of cross-domain analyses. Using multi-marker eDNA metabarcoding (16S rRNA, 18S rRNA, 23S rRNA), we show that bacterioplankton, cyanobacteria, phytoplankton, and zooplankton in Lake Taihu undergo coordinated spring-summer transitions, with inter-seasonal turnover far exceeding spatial heterogeneity. Assembly regimes shifted coherently across domains: spring communities were dominated by strong homogeneous selection--especially among cyanobacteria and microeukaryotes--whereas summer communities moved toward drift- or neutrality-like dynamics under bloom-stage mixing that enhanced dispersal. Null- and neutral-model diagnostics supported these trends. Cross-domain co-occurrence networks restructured seasonally, with summer networks becoming more connected and substantially more robust, indicating that bloom conditions foster cohesive, robust interaction structures rather than destabilization. These findings provide evidence that bloom progression restructures aquatic microbiomes through a seasonal rebalance of selection, drift, and dispersal coupled with adaptive strengthening of cross-domain connectivity, providing a process-explicit framework for understanding community stability and ecosystem resilience in eutrophic lakes.

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.

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.

Sialic acids (Sias) and related nonulosonic acids are critical components of glycoconjugates involved in host-pathogen interactions, immune regulation, and cell signalling. Despite their biotechnological relevance, the diversity of enzymes involved in Sia biosynthesis remains largely underexplored due to limitations in culture-dependent methods and the lack of (ultra)high-throughput screening strategies. Here, we report the development of a highly sensitive droplet-based microfluidic screening platform enabling the functional discovery of sialic acid aldolases in environmental metagenomes. The method integrates a fluorescence-coupled enzymatic cascade compatible with fluorescence-activated droplet sorting (FADS), allowing the screening of >10 droplets per experiment, as well as a downstream validation strategy for the selected hits. Although some limitations were identified, the system demonstrated high sensitivity and was utilised for the screening of a metagenomic library from garden soil. During this campaign, a potential new sialic acid aldolase enzyme was identified. This work establishes a generalizable framework for measuring complex, multi-step enzymatic functions at ultrahigh throughput using coupled cascades in droplets

Defined microbial communities (also known as synthetic communities) are showing promising results for plant health but are lacking an efficient lab to field transition. This is the due to limited knowledge on how to efficiently modulate plant microbiota by considering complex environments and multi-kingdom interactions. In this study, we aimed to better understand the transmission and impact of multi-kingdom synthetic communities (SynComs) from the seed to seedling stage. We constructed 20 different SynComs using both a priori and random approaches, from pool of diverse strains including 24 bacteria, 11 yeasts and 10 filamentous fungi. SynComs were inoculated on Brassica napus seeds and we monitored both transmission and impact on the microbiota of 15-day-old seedlings grown in non-sterile soil. Optimization of the inoculation protocol showed that alginate coating improved bacterial, yeast and filamentous fungi concentrations by more than 2 log compared with other approaches. With this inoculation method, we observed contrasted seedling colonization profiles, with SynComs members representing between 1.1-45.7% of bacterial community and 3.2-36.6% of fungal community. Our multiple SynCom design revealed that strain selection is a more critical determinant of SynCom performance than assembly strategy. Even randomly assembled communities performed well, as long as they are drawn from a pool of ecologically relevant, well-adapted taxa. Based on these evidences, we identified key bacterial and fungal traits explaining efficient seedling colonization such as high abundance on inoculated seed and low in vitro lag-time. Despite low colonization levels, we observed that SynCom inoculation altered seeding bacterial community assembly in 14 SynComs. A total of 82 native bacterial ASVs were identified as responsive to SynCom inoculation, most likely originating from the soil. This shift indicates that SynComs influence community assembly by modulating the recruitment of environmental taxa, especially when SynCom strains were more integrated in multi-kingdom network structures. Finally, we identified four distinct SynComs profiles which either colonized strongly or not seedlings while shifting of not native microbiota. Altogether, these findings provide actionable directions for improving SynCom design, suggesting that leveraging ecological processes such as host adaptation, optimal inoculation density, and network integration could enhance both colonization efficiency and plant phenotypic outcomes.

The Arctic Ocean microbiomes experience extreme seasonal fluctuations in light, nutrient availability, and organic carbon supply. In this environment, neutral lipid storage may provide a key survival strategy. Here, we investigated the diversity, distribution, and ecological role of neutral lipid metabolism in Arctic microbiomes using metagenome-resolved analyses and global ocean comparisons. Arctic photic-zone microbiomes were strongly enriched in triacylglycerol (TAG) biosynthesis genes relative to other oceans, primarily due to picoeukaryotic phytoplankton, including the ecologically dominant Micromonas and Bathycoccus. In contrast, prokaryotic communities exhibited diverse TAG-degrading taxa and fatty acid transport systems, supporting a previously unrecognized lipotrophic bacterial guild exploiting phytoplankton-derived lipids as carbon and energy sources. Genome-resolved analyses further revealed distinct bacterial lipid-storage strategies: TAG-producing taxa preferentially encoded fatty acid uptake and carbohydrate utilization pathways, whereas polyhydroxyalkanoate-producing taxa were associated with aromatic compound degradation, linking terrestrial organic matter to lipid storage. Our results expand the known diversity of marine microbes capable of neutral lipid metabolism and identify microbial lipid cycling as a previously overlooked component of the Arctic carbon cycle. We propose that neutral lipid storage and turnover support microbial survival through the polar night while enhancing carbon transfer within Arctic microbial food webs under ongoing climate change.

We present an update to the PIGEON (Phages and Integrated Genomes Encapsidated or Not) reference database of DNA viral sequences (vOTUs, mostly dsDNA bacteriophages) from global ecosystems. To reflect the inclusion of only virus size-fractionated metagenome- (virome-)derived vOTUs, we reintroduce the database as PEONY (Phages Encapsidated ONlY) and present new data summarizing the utility of this database.

Aerobiological studies have largely focused on near-surface sampling and horizontal biogeographic patterns, while vertical structuring of airborne microbial communities within the atmospheric boundary layer (ABL) remains poorly understood. Here, we investigated microbial communities across the lower and upper ABL in a low-orography coastal site on the Antarctic Peninsula, representative of the Southern Ocean marine ABL and with low direct human influence. Airborne microorganisms were sampled simultaneously using ground-based and aerial platforms on five occasions. Community composition, abundance, and cell morphometry were assessed using metabarcoding and epifluorescence microscopy and interpreted alongside atmospheric observations. Airborne bacterial and eukaryotic communities showed consistent vertical stratification, although partial taxonomic overlap indicates vertical connectivity between atmospheric layers. Lower ABL communities were more diverse than upper ABL counterpart, compositionally homogeneous, and dominated by marine-associated taxa, reflecting strong influence from local sources and turbulent mixing. In contrast, upper ABL communities were less diverse but more heterogeneous among sampling events, enriched in stress-tolerant, terrestrial and plant-associated taxa, consistent with atmospheric filtering, selective upward transport, and long-range atmospheric inputs. Upper-layer samples also exhibited higher microbial abundance and greater prevalence of elongated cell morphologies, suggesting particle accumulation aloft and aerodynamic selection permanence. Together, these findings identify the Southern Ocean ABL as a vertically structured microbial habitat organized into two partially decoupled sublayers, in which atmospheric dynamics regulate microbial dispersal, ecosystem connectivity, and biogeographic patterns.

Phage tail-like elements (PTEs) -- tailocins, bacterial type VI secretion systems (T6SS), and extracellular contractile injection systems (eCIS) -- are contractile nanomachines that bacteria use to kill their neighbors and compete within their micro-ecosystems. PTEs help shape microbial community composition. Most PTE detection tools only detect a single PTE class. Moreover, most tailocin detection methods are largely restricted to Pseudomonas, leaving a key part of tailocin diversity uncharacterized. In this work, we present PhageTAILor (https://github.com/hjcho-bio/PhageTAILor), an integrative and fully automated pipeline that detects and classifies prophages and 3 PTE classes from bacterial genomes. PhageTAILor combines a 6-detector homology-based candidate search (geNomad, tail-gene, PHROGs-tail, SecReT6, eCIStem, and a divergence-tolerant tail-HMM detector) with a LightGBM classifier comprising 1 multiclass and 3 binary heads, trained on 6,501 bacterial genomes carrying 13,082 prophages and PTEs. A phylogeny-free feature matrix used in our model keeps predictions reproducible between model construction and user inference. PhageTAILor performs strongly at the genome level and generalizes beyond its Pseudomonas-rich training set. On a 76-strain cross-clade benchmark, PhageTAILor detected tailocins at F1 = 0.955. Furthermore, it identified 12 of 13 experimentally validated tailocins spanning five genera versus 2 of 13 for a Pseudomonas-restricted tool TattleTail. PhageTAILor also demonstrated sensitivity equivalent to viral detection tool geNomad while avoiding its higher false-positive rate. Applied to 7,925 plant- and soil-associated bacterial isolates, PhageTAILor showed that prophages in the phyllosphere and tailocins in plant-associated bacteria, whereas eCIS are enriched in soil. PhageTAILor is distributed as an open-source, modular pipeline with a command-line interface.

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

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.

The Eboliang Hu saline lakes in the hyper-arid Qaidam Basin is a high-altitude, weakly acidic hypersaline system with strong environmental gradients and limited nitrogen availability. To resolve its microbial ecology and evolutionary context, we performed genome-resolved metagenomic sequencing across four distinct habitats, reconstructing 46 medium- to high-quality metagenome-assembled genomes (MAGs) and a comprehensive gene catalog. The community shows pronounced spatial heterogeneity and is dominated by Thermodesulfobacteriota, Pseudomonadota, Bacteroidota, and archaeal lineages. Phylogenomic placement and large-scale sequence comparisons indicate that multiple dominant taxa exhibit affinity to marine- and subsurface-associated reference lineages, consistent with long-term isolation of a marine-derived ecosystem about 10-11 million years ago. Functional reconstruction reveals a distributed metabolic system in which carbon, nitrogen, and sulfur cycling are partitioned across taxa. Notably, hydrogen oxidation and arsenite oxidation are recurrent energy-producing strategies across dominant lineages, indicating redox flexibility under oligotrophic conditions. Comparative genomics further suggests lineage-specific adaptations to osmotic stress, UV exposure, and nutrient limitation. Horizontal gene transfer and phylogenetic incongruence among key metabolic genes indicate that co-evolutionary processes and gene exchange have contributed to functional innovation. These findings provide a framework for understanding microbial persistence and evolution in isolated extreme environments and offer potential analogs for extraterrestrial habitability.

Protists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity. While most commonly found protist species are well known to science, our global-scale environmental DNA survey across soil, water, and sediments reveals dozens of novel, phylum-level phylogenetic lineages that remain to be characterized for basic morphology and function. A vast majority of these undescribed taxa occur in marine water and sediments, but some are common in soil. Most of these novel taxa have distinct substrate and habitat preferences and biogeographic patterns. To accord these lineages scientific agency and enable unambiguous scientific communication, we propose formal names for 150 species to phylum-level taxa from 25 deep lineages based on eDNA and rRNA gene long-read sequence information.