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.
High-altitude saline ecosystems of the Atacama–Puna Plateau represent natural laboratories for investigating microbial adaptation and community assembly under polyextreme conditions. Despite their ecological importance, integrated assessments of microbial diversity across contrasting Andean systems remain scarce. Here, we characterized microbial mats, sediments, and saline crusts across three high-altitude sub-basins of northern Chile, including the Maricunga Salt Flat–Laguna Santa Rosa hydrological system, Laguna del Negro Francisco, and Laguna Verde. Microbial communities were analyzed using 16S rRNA gene amplicon sequencing, environmental characterization, predicted metabolic profiling, and co-occurrence network analyses. Salinity was the only environmental variable significantly associated with microbial community composition, although site identity explained a greater proportion of variation, highlighting the influence of local environmental conditions. Across ecosystems, communities were dominated by Pseudomonadota and Bacteroidota, whereas hypersaline habitats were enriched in halophilic archaeal lineages and brackish environments exhibited greater representation of photosynthetic and nitrogen-related functions. Only 15% of ASVs were shared between brackish and hypersaline habitats, indicating strong habitat specialization. Nevertheless, co-occurrence networks revealed a small set of highly connected keystone taxa shared among ecosystems, forming a regional core microbiome. Together, these findings demonstrate that salinity promotes taxonomic and functional specialization, while hydrological connectivity maintains ecological cohesion across interconnected ecosystems. By integrating lagoons, wetlands, saline crusts, and geothermal habitats within a regional framework, this study provides the first regional-scale assessment of microbial diversity, community assembly, and ecological connectivity across the southern Atacama–Puna Plateau.
María E. Alcamán-Arias, Pablo Vergara-Barros, Karina Fuentes et al.· Frontiers in Microbiology· 0 citations
Summary Sediment microbial communities in arid inland rivers are important for biogeochemical cycling, but the assembly mechanisms and network responses across the transition from irrigated oases to desert margins remain unclear. We investigated bacterial and fungal communities in Yarkand River sediments along salinity and nutrient gradients using 16S rRNA and ITS sequencing, sediment chemistry, iCAMP null-model analysis, and co-occurrence networks. Downstream increases in electrical conductivity, total nitrogen, and pH were associated with reduced bacterial α-diversity and turnover from nutrient-responsive Pseudomonadota in the oasis midstream to stress-tolerant Chloroflexota and Actinomycetota in the desert downstream. Fungal diversity showed high inter-site variability without a linear decline. Despite strong physicochemical gradients, ecological drift dominated assembly in both kingdoms, while desert networks showed higher connectivity. These findings support a hierarchical assembly model in which salinity filters community composition, but stochastic processes and network densification shape benthic microbiota in arid river sediments.
A comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome is provided and microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake are identified.
M. Macey, Velislava Ilieva, B. Stephens et al.· Environmental Microbiome· 0 citations
Microbial communities in freshwater ecosystems are structured by both natural environmental variation and anthropogenic pressures, yet how these drivers interact to shape biodiversity and ecosystem functioning remains poorly understood. Here, we assessed how biogeoclimatic regions and land-use pressures jointly structure bacterial diversity and inferred nitrogen-cycling potential in stream sediments along a broad environmental gradient across the Iberian Peninsula. We used 16S rRNA metabarcoding and functional inference across samples spanning three biogeoclimatic regions and four land-use types. Bacterial community composition and diversity showed strong regional differentiation, with pronounced taxonomic turnover and distinct alpha-diversity patterns, whereas differences among land-use types were weaker, less spatially coherent, and primarily reflected shifts in specific community components. Despite this variation, a consistent core microbiome was observed across samples, suggesting the presence of taxa shared across contrasting conditions. Inferred nitrogen-cycling functional potential partially mirrored taxonomic patterns, with Mediterranean lowlands enriched in predicted nitrification and denitrification genes, Sierra Nevada in predicted nitrogen fixation and DNRA genes, and the Cantabrian Mountains showing a more even functional profile. Land-use effects on inferred functional potential were subtle and nested within regional patterns. These results suggest that bacterial diversity and inferred nitrogen-cycling potential are more strongly shaped by biogeoclimatic conditions than by land-use, consistent with a hierarchical organization of environmental drivers. The correspondence between taxonomic composition and inferred functional potential was more evident at the regional than at the local scale. Our findings highlight the importance of incorporating regional baselines and integrating taxonomic and functional approaches into freshwater biomonitoring.
Lucía Cabello-Alemán, Víctor Carpena-Istán, E. Fenoy et al.· Microbial Ecology· 0 citations
The McMurdo Dry Valleys contain a mosaic of specialized microbial habitats structured by strong physical and chemical gradients. Blood Falls, located at the terminus of the Taylor Glacier, is a red, iron-rich outflow of deep Antarctic subglacial brine with geochemical and isotopic evidence supporting a potential ancient marine origin. Previous studies suggest the brine formed when seawater inundated the Taylor Valley over warm climatic intervals before becoming isolated beneath the advancing glacier. Here, across 167 aquatic, sediment and aeolian samples from the McMurdo Dry Valleys and marine reference sites, we identified a distinct marine micro-eukaryotic assemblage restricted to red-hued ice, mud and sediment at the Taylor Glacier terminus. Marine indicator species were identified across several phylogenetic groups including diatoms, haptophytes, dinoflagellates and ciliates. Metatranscriptomic profiles revealed transcriptionally active phototrophs with enriched pathways for photosynthesis, osmotic stress responses and cellular repair. Haplotype networks showed lineage-specific divergence between Taylor Glacier terminus and McMurdo Sound diatoms, supporting geographic isolation. These findings indicate that the subglacial brine-fed system at the Taylor Glacier terminus retains marine-derived biological signatures long after physical separation from the ocean, linking contemporary Antarctic microbial assemblages to past climatic transitions. Eukaryotic microorganisms within a subglacial brine-fed system in the McMurdo Dry Valleys of Antarctica are largely of marine origin, a legacy of past incursions of seawater into the area, according to RNA sequencing and metatranscriptomic analyses.
A. Zoumplis, Z. Füssy, D. Kaul et al.· Nature Geoscience· 0 citations
During the Phanerozoic, the ocean repeatedly experienced periods of widespread deoxygenation known as oceanic anoxic events. Geological records from these events indicate a profound shift in marine microbial ecosystems. While cyanobacterial biomarkers are found broadly, those of anoxygenic photosynthetic green sulfur bacteria are restricted to upwelling regions or topographic highs. However, the quantitative mechanisms triggering this transition and the spatial heterogeneity of primary producers remain ambiguous. Here, using a new high-resolution one-dimensional ocean biogeochemical model explicitly incorporating a marine microbial ecosystem, we systematically evaluated the global effects of increases in riverine phosphorus input rates and sea surface temperature. We show that phosphorus-driven eutrophication and ocean warming-induced reductions in both O2 solubility and export efficiency result in surface ocean deoxygenation, leading to the restructuring of the marine microbial ecosystem. The emergence of anoxic water masses enhances denitrification and establishes a nitrogen-depleted environment, promoting the proliferation of N2-fixing cyanobacteria. With further deoxygenation, euxinic water masses develop within the photic zone, allowing green sulfur bacteria to thrive below the redoxcline, resulting in a vertical ecological segregation with oxygenic photoautotrophs and N2-fixing cyanobacteria. Moreover, an abundant supply of nutrients and H2S in upwelling regions causes more severe deoxygenation within the photic zone than in the open ocean, providing a niche suitable for green sulfur bacteria and driving a more drastic restructuring of primary producers. These findings elucidate the quantitative impacts of global climate perturbations and regional upwelling on the surface ocean, offering crucial insights into how surface ocean biogeochemistry and marine microbial ecosystems fluctuated during oceanic anoxic events.
Tenga Yokoyama, E. Tajika, Yasuto Watanabe et al.· Progress in Earth and Planet...· 0 citations
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