Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the pH and salt content, highly diverse microbial communities known to be present in lake brines but microbiome of sediments received much less attention microbiologists. Here, we performed metagenomic sequencing on give first extensive overview taxonomic diversity found these complex, environments gain novel physiological insights into most abundant, uncultured prokaryote lineages. We sequenced...

Representatives of the phylum Chloroflexi, though reportedly highly abundant in extensive deep water habitats both marine (SAR202 up to 30% total prokaryotes) and freshwater (CL500-11 26% prokaryotes), remain uncultivated uncharacterized. There are few metagenomic studies on Chloroflexi representatives, while pelagic community is largely unknown except for a single metagenome-assembled genome CL500-11. Here, we provide first examination composition this cosmopolitan range (176 datasets)...

The dark ocean microbiota represents the unknown majority in global waters. SAR202 cluster belonging to phylum Chloroflexi was first microbial lineage discovered specifically inhabit aphotic realm, where they are abundant and globally distributed. absence of cultured representatives is a significant bottleneck towards understanding their metabolic capacities role marine environment. In this work, we use combination metagenome-assembled genomes from deep-sea datasets publicly available...

The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or occur spontaneously in the environment, depending on temperature and pH. Inorganic compounds serve as energy sources for specialized prokaryotes are important substrates microbial growth general. Here, we investigate dissimilatory cycling brine sediments southwestern Siberian soda lake characterized by an extremely high pH salinity, combining meta-omics analyses its uniquely adapted highly...

Abstract The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle disentangling complex web of ecological interactions spun by a diverse assortment participants (pro- and eukaryotes their viruses). In microbial communities, numerically most actors, viruses, remain elusive, especially freshwaters identities ecology unknown. Here, using ultra-deep metagenomic sequencing pelagic freshwater habitats, we recovered complete...

Abstract Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available genomic repositories. Currently, our apprehension of evolutionary ecology freshwater bacteria is hampered by the difficulty to establish organism models for most representative clades. To circumvent bottlenecks inherent cultivation-based techniques, we applied ecogenomics approaches order unravel history and processes drive genome architecture hallmark lineages...

Abstract Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts microbial assemblages during after the have been reported, genomic information on community of remains scarce. Results We performed high-resolution spatio-temporal sampling reservoir describe multitude previously unknown taxa using metagenome-assembled genomes eukaryotes, prokaryotes,...

The crossing of environmental barriers poses major adaptive challenges. Rareness freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that species rarely existed in...

The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two reservoirs located close to each other (Tous Amadorio, Spain). These metagenome-assembled (MAGs) display a remarkable taxonomic diversity inside comprise wide ranges of estimated genome sizes (from 1.8 6 Mb). Among all found some smallest Spartobacteria Opitutae classes...

We present here the findings from a study of microbiome southern basin Caspian Sea, largest water body on Earth disconnected any ocean and brackish inland sea. By high-throughput metagenomics, we were able to reconstruct genomes representative microbes. The gross community structure (at phylum level) was different typical marine freshwater communities in temperate open oceans, with Sea having freshwater-like amounts Actinobacteria Alphaproteobacteria, while Gammaproteobacteria...

Abstract Background The Black Sea is the largest brackish water body in world, although it connected to Mediterranean and presents an upper layer similar some regions of former, albeit with lower salinity temperature. Despite its well-known hydrology physicochemical features, this enormous mass remains poorly studied at microbial genomics level. Results We have sampled different masses analyzed microbiome by shotgun genome-resolved metagenomics, generating a large number metagenome-assembled...

Abstract The Persian Gulf, hosting ca. 48% of the world’s oil reserves, has been chronically exposed to natural seepage. Oil spill studies show a shift in microbial community composition response pollution; however, influence chronic exposure on remains unknown. We performed genome-resolved comparative analyses water and sediment samples along Gulf’s pollution continuum (Strait Hormuz, Asalouyeh, Khark Island). Continuous trace amounts primed intrinsic rare marine oil-degrading microbes such...

While oligotrophic deep groundwaters host active microbes attuned to the low-end of bioenergetics spectrum, ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal bacterial communities disconnected fracture fluids Fennoscandian Shield Europe. Leveraging dataset that combines metagenomes, single cell genomes, metatranscriptomes, show flowing...

Abstract Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that mainly accumulated in oil reservoirs. As the introduction all classes hydrocarbons including crude products into environment has increased significantly, pollution become a global ecological problem. However, our perception pathways for biotic degradation major HCs key enzymes these bioconversion processes been based on cultured microbes is biased by uneven taxonomic representation. Here...

A few genera of diatoms are widespread in the oceans and form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. unique feature diatom-Richelia symbioses is symbiont cellular location spans a continuum integration (epibiont, periplasmic, endobiont) that reflected genome size content. In this study we analyzed genomes derived from cultures environmental metagenome-assembled focusing on characters indicative evolution. Our results show an enrichment short length...

Lake Urmia located in Iran is a hypersaline environment with salinity of about 27% (w/v). Metagenomic analyses water samples collected from six locations the lake exhibited microbial community dominated by representatives family Haloferacaceae (69.8%), mainly those affiliated to only two genera, Haloquadratum (59.3%) and Halonotius (9.1%). Similar other lakes, bacterial was Salinibacter ruber (23.3%). Genomic variation analysis inspecting single nucleotide variations (SNVs)...

A Gram-positive, moderately halophilic rod, designated X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT a strictly aerobic, motile bacterium that produced ellipsoidal endospores at central-subterminal position non-swollen sporangia. The isolate grew pH 7.0-10.0 (optimum 7.5), 25-45 °C 35 °C) and with 2.5-15 % (w/v) NaCl 5-7.5 %). On basis 16S rRNA gene sequences, strain belonged to genus Bacillus showed highest similarity persepolensis HS136T (95.6...

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B T , was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells were rod-shaped, motile produced ellipsoidal endospores in terminal positions non-swollen sporangia. Strain strictly aerobic bacterium catalase- oxidase-positive. The able to grow at NaCl concentrations 0.5–20.0 % (w/v), with optimum growth occurring 10.0 (w/v) NaCl....

Abstract Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled or single-cell genomes. While this diversity can provide novel insights into microbial population structure, most tools available core-genome estimation are sensitive to genome completeness. Consequently, a major portion huge phylogenetic uncovered environmental genomic approaches remains excluded...

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain E33(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells E33(T) were motile rods produced ellipsoidal endospores at central or subterminal position swollen sporangia. Strain strictly aerobic catalase- oxidase-positive. The able to grow NaCl concentrations 0.5-25 % (w/v), with optimum growth occurring 5-15 (w/v) NaCl. temperature...

An extremely halophilic archaeon, strain DA50 T , was isolated from a brine sample of Urmia lake, hypersaline environment in north-west Iran. Strain orange-pigmented, motile, pleomorphic and required at least 2.5 M NaCl but not MgCl 2 for growth. Optimal growth achieved 4.0 0.3 . The optimum pH temperature were 7.0 45 °C, while it able to grow over range 6.5–8.0 25–50 °C. Analysis 16S rRNA gene sequences revealed that is member the family Halobacteriaceae showing low level similarity with...

An extremely halophilic archaeon, strain D108 T , was isolated from a brine sample of Aran-Bidgol salt lake in Iran. The novel cream-pigmented, motile, pleomorphic rod-shaped and required at least 2.5 M NaCl but not MgCl 2 for growth. Optimal growth achieved with 4.3 0.1 . optimum pH temperature were 7.5 40 °C, respectively, the able to grow over range 6.5 9.0, 30 50 °C. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that clustered type sole species genus...