Using long-read sequencing, high-quality genomes are recovered for six isolates that dereplicate to three independent, bona fide haloalkaliphilic lineages spanning two distant families (Halomonadaceae, Bacillaceae), whose closest relative is not its type strain but an isolate from another distant extreme habitat, including two other Mexican hypersaline systems.
Analysis revealed genes for metabolizing diverse carbohydrate sources, a complete ectoine synthesis cluster essential for halophily, and genes conferring tolerance to osmotic stress, low temperatures, and pH, underscoring its polyextremophilic capacity.
Ian Ariel Barbosa Nunes, Adan Rodrigues de Oliveira, Adonney Allan de Oliveira Veras et al.· Brazilian Journal of Microbi...· 0 citations
This study provides genome- and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.
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.
Haoran Wang, Chunhui Ai, A. Barcan et al.· bioRxiv· 0 citations
Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes.
The genusSynechococcuscomprises photosynthetic picocyanobacteria that, as autotrophic microorganisms, make a significant contribution to the production of organic matter and oxygen in marine and freshwater ecosystems. The wide distribution of representatives of the genusSynechococcusis due to their genetic diversity and ecological plasticity. Of particular interest is the study of these microorganisms in unique natural ecosystems, such as Lake Baikal – a freshwater oligotrophic deep-water lake with a high percentage of endemism among its inhabiting species. This work presents an analysis of two genomes ofSynechococcusrepresentatives recovered from metagenomic data of microbial communities from the water of Lake Baikal (MAGs):Synechococcussp. bin7 andSynechococcussp. bin8. A structural and functional characterization of the genomes is provided, and genes for antibiotic resistance and secondary metabolite synthesis are identified. Phylogenetic analysis, including 90 closely related freshwater and marine representatives of the genusSynechococcusalongside the studied MAGs, showed that the genomes belong to different, rather distant, phylogenetic clades.
O. Kaluzhnaya, D. Gutnik, A. Krasnopeev et al.· Limnology and Freshwater Bio...· 0 citations
Soda lakes represent some of the most extreme aquatic ecosystems on Earth, yet their microbial diversity and functional potential remain poorly characterized, particularly in East Africa. This study presents the first shotgun metagenomic analysis of bacterial communities inhabiting both water and sediment of Small Momela Lake, a soda lake in northern Tanzania. Samples were sequenced using Illumina NovaSeq and analyzed with MetaPhlAn4 and HUMAnN3 to resolve taxonomic composition, diversity patterns and predicted metabolic functions. Results showed 27 distinct species within Pseudomonadota, Bacteroidota, Firmicutes, Cyanobacteria and Verrucomicrobia dominated by sulfur-cycling Thioalkalivibrio denitrificans and uncultured Candidatus lineages. Notably, based on currently available literature multiple taxa were detected for the first time in soda lake environments globally, within Africa and East Africa, expanding the known biogeography of extremophiles. Functional profiling revealed a strong enrichment of nucleotide and amino acid biosynthesis pathways, alongside marker genes linked to pH homeostasis, osmotic stress tolerance, sulfur metabolism and carbon fixation. These features suggest pronounced metabolic flexibility supporting microbial persistence under extreme alkaline and saline conditions. These findings underscore Small Momela Lake as a critical reservoir of novel, functional bacterial resources with promising applications in biotechnology and bioprospecting.
A. A. Siima, Sadikiel E. Kaale, F. Mpenda et al.· Discover Life· 0 citations
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