Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake.

Two extremely halophilic strains, designated SYSU A558-1T and SYSU A121-1, were isolated from a saline sediment sample collected from Aiding salt-lake, China. Cells of strains SYSU A558-1T and SYSU A121-1 were Gram-stain-negative, coccoid, and non-motile. The strains were aerobic and grew at NaCl concentration of 10-30% (optimum, 20-22%), at 20-55 °C (optimum, 37-42 °C) and at pH 6.5-8.5 (optimum, 7.0-8.0). Cells lysed in distilled water. The polar lipids were phosphatidyl choline, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether-1 and unidentified glycolipid. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the two strains SYSU A558-1T and SYSU A121-1 were closely related to the membranes of the genus Haloterrigena. Phylogenetic and phylogenomic trees of strains SYSU A558-1T and SYSU A121-1 demonstrated a robust clade with Haloterrigena turkmenica, Haloterrigena salifodinae and Haloterrigena salina. The genomic DNA G + C content of strains SYSU A558-1T and SYSU A121-1 were 65.8 and 65.0%, respectively. Phenotypic, phylogenetic, chemotaxonomic and genome analysis suggested that the two strains SYSU A558-1T and SYSU A121-1 represent a novel species of the genus Haloterrigena, for which the name Haloterrigena gelatinilytica sp. nov. is proposed. The type strain is SYSU A558-1T (= KCTC 4259T = CGMCC 1.15953T).

Lunatibacter salilacus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a saline and alkaline lake sediment.

A non-motile, Gram-staining negative, catalase- and oxidase-positive, crescent-rod shaped bacterium, designated strain CUG 91308T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. Colonies on OSM agar were round, smooth, flat and pinkish-orange in colour. Strain CUG 91308T could grow at 15-37 °C, pH 6-12 and in the presence of up to 7.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91308T belonged to the family Cyclobacteriaceae and formed a clade with the genus Lunatimonas in the phylogenetic tree, but separated from any species of the known genera within the family. The genomic DNA G+C content is about 42.1 %. The predominant fatty acids (>10 %) were iso-C15 : 0 (21.1 %), summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c / iso-C15 : 0 2OH) (14.3 %), iso-C17 : 0 3OH (12.3 %) and summed feature 9 (iso-C17 : 1 ω9c / C16 : 0 10-methyl) (10.6 %). The polar lipids of strain CUG 91308T were phosphatidylethanolamine (PE) and four unidentified polar lipids. Strain CUG 91308T contained MK-7 as the major respiratory quinone. On the basis of phenotypic, genotypic and phylogenetic data, strain CUG 91308T represents a novel species of a novel genus in the family Cyclobacteriaceae, for which the name Lunatibacter salilacus gen. nov., sp. nov. is proposed. The type strain of the proposed new isolate is CUG 91308T (=KCTC 62636T=CGMCC 1.13593T).

Ruania rhizosphaerae sp. nov., a novel actinobacterium isolated from rhizosphere of Suaeda aralocaspica.

A Gram-stain-positive, non-motile and short rod-shaped actinobacterium, designated strain LNNU 22110T, was isolated from the rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which collected in Xinjiang, north-west China. Growth occurred at 10-45 °C, pH 6.0-10.0 and in the presence of 0-11 % NaCl (w/v). Based on the results of 16S rRNA gene sequence phylogenetic analyses, strain LNNU 22110T belonged to the genus Ruania and had 97.5 and 95.5 % sequence similarity to Ruania alba KCTC 19413T and Ruania albidiflava CGMCC 4.3142T, respectively. The digital DNA-DNA hybridization relatedness values between strain LNNU 22110T and R. alba KCTC 19413T and R. albidiflava CGMCC 4.3142T were 23.2 and 19.9 %, respectively. The highest average nucleotide identity value between strain LNNU 22110T and its closest related strain (R. alba KCTC 19413T) was 80.2 %, much lower than the species delineation threshold of 95-96 %. The genome of strain LNNU 22110T was 4.4 Mb, with a genomic DNA G+C content of 68.4 mol%. The diagnostic diamino acids in the peptidoglycan layer of strain LNNU 22110T were lysine, alanine, glycine, glutamic acid and aspartic acid. The predominant menaquinone was MK-8(H4). The major fatty acid (>10 %) was anteiso-C15 : 0. The polar lipid profile of strain LNNU 22110T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, diacylated phosphatidyl dimannoside, one unidentified glycolipid and two unidentified phospholipids. According to the phenotypic, phylogenetic and chemotaxonomic results, strain LNNU 22110T is considered to represent a novel species of the genus Ruania, for which the name Ruania rhizosphaerae sp. nov. is proposed. The type strain is LNNU 22110T (=KCTC 39807T=CGMCC 1.17105T).

Hoyosella suaedae sp. nov., a novel bacterium isolated from rhizosphere soil of Suaeda aralocaspica (Bunge) Freitag & Schütze.

A Gram-stain-positive, non-motile and coccus-shaped bacterium, designated strain LNNU 331112T, was isolated from the composite rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which was collected in Xinjiang, north-west China. Growth occurred at 10-45 °C, pH 6.0-11.0 and in the presence of 0-10 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence suggested that strain LNNU 331112T belonged to the genus Hoyosella and showed 95.6, 95.5 and 95.4 % sequence similarities to Hoyosella altamirensis DSM 45258T, Hoyosella subflava CGMCC 4.3532T and Hoyosella rhizosphaerae CGMCC 1.15478T, respectively. The estimated digital DNA-DNA hybridization relatedness values between strain LNNU 331112T and the type strains of H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 18.9, 19.3 and 18.3 %, respectively. The average nucleotide identity values between strain LNNU 331112T and H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 72.6, 72.7 and 72.3 %, respectively. The genome sequence of strain LNNU 331112T showed 69.0-72.3 % average amino acid identity values in comparison with the related genome sequences of three validly published Hoyosella species. The genome of strain LNNU 331112T was 3.47 Mb, with a DNA G+C content of 68.4 mol%. A total of 3182 genes were identified as protein-coding in strain LNNU 331112T. Genomic analysis revealed that a number of genes involved in osmotic pressure regulation, intracellular pH homeostasis and potassium (K+) uptake protein were found in strain LNNU 331112T. The predominant menaquinones were MK-8 (44.6 %) and MK-7 (55.4 %), which differentiated strain LNNU 331112T from other three recognized Hoyosella species. Major fatty acids (>10 %) were C17 : 1 ω8c (33.8 %), C16 : 0 (23.3 %), C17 : 0 (12.8 %) and summed feature 3 (12.9 %), which also clearly separated strain LNNU 331112T from three recognized Hoyosella species. The polar lipid profile of strain LNNU 331112T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. According to the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 331112T is considered to represent a novel species of the genus Hoyosella, for which the name Hoyosella suaedae sp. nov. is proposed. The type strain is LNNU 331112T (=KCTC 39808T=CGMCC 1.17107T=DSM 103463T).

Lysinibacillus cavernae sp. nov., isolated from cave soil.

A Gram-staining positive, motile, rod-shaped and subterminal endospore-forming bacterium, designated strain SYSU K30005T, was isolated from a soil sample collected from a karst cave in Libo county, Guizhou province, south-western China. Strain SYSU K30005T showed the highest 16S rRNA gene sequence similarity with Lysinibacillus fusiformis (98.6%) and Lysinibacillus sphaericus (98.2%). In phylogenetic tree, strain SYSU K30005T clade with the members of the genus Lysinibacillus. Based on the phylogenetic and 16S gene sequence result, strain SYSU K30005T was affiliated to the genus Lysinibacillus. The growth of SYSU K30005T was observed at 15-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-4% (w/v) NaCl (optimum in 3.5% NaCl). Cell wall peptidoglycan type was A4α (Lys-Asp). The cell-wall sugars of SYSU K30005T were ribose, galactose and mannose and MK-7 was the only quinone. The fatty acids (> 5% of total fatty acids) were iso-C15:0, anteiso-C15:0, iso-C16:0 and iso-C17:0. The polar lipids profile included diphosphatidylglycerol, phosphatideylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G + C content was 37.2 mol%. The average nucleotide identity values between SYSU K30005T and its closest relatives were below the cut-off level (95-96%) for species delineation. The results support the conclusion that strain SYSU K30005T represents a novel species of the genus Lysinibacillus, for which we proposed the name Lysinibacillus cavernae sp. nov. The type strain is SYSU K30005T (= KCTC 43130T = CGMCC 1.17492T).

Amycolatopsis anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis elatior.

A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15-40 °C, pH 6.0-8.0 and in the presence of 0-6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus Amycolatopsis and shared the highest sequence similarities with Amycolatopsis nigrescens JCM 14717T (97.1 %) and Amycolatopsis sacchari DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus Amycolatopsis were less than 97.0 %. The average nucleotide identity and DNA-DNA hybridization values between strain EGI 650086T and the reference strains were 78.1-79.8 % and 22.1-23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).

Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov., isolated from a saline lake.

Two novel strains, designated SYSU L10167T and SYSU L10180T, were isolated from sediment sampled at Dabancheng saline lake in Xinjiang, PR China. A polyphasic approach was used to clarify the taxonomic positions of the two strains. Cells of the isolates were curved ring-like, horseshoe-shaped or rod-shaped, non-motile and non-spore-forming. Cells were Gram-stain-negative, aerobic, heterotrophic and rose-pigmented. The phylogenetic trees based on 16S rRNA gene sequences showed that strains SYSU L10167T and SYSU L10180T formed a distinct lineage within the genus Cyclobacterium. Strains SYSU L10167T and SYSU L10180T showed highest similarities to Cyclobacterium jeungdonense KCTC 23150T (98.0 and 97.4%, respectively). Results of genomic analyses (including average nucleotide identity, digital DNA-DNA hybridization and the marker gene tree) and pan-genome analysis further confirmed that strains SYSU L10167T and SYSU L10180T were separate from each other and other species of the genus Cyclobacterium. The draft genomes of the isolates had sizes of 5.5-5.7 Mb and reflected their major physiological capabilities. Based on phenotypic, physiological, chemotaxonomic and genotypic characterization, we propose that the isolates represent two novel species, for which the names Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov. are proposed. The type strains of the species are SYSU L10167T (=KCTC 72390T=CGMCC 1.17521T) and SYSU L10180T (=KCTC 72391T=CGMCC 1.17278T).

Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample.

A novel actinobacterial strain, designated SYSU K10008T, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008T was most closely related to Streptomyces cyaneus CGMCC 4.1671T, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, ll-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H6), while the major fatty acids (>10 %) were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16  : 1 ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008T was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008T represents a novel species of the genus Streptomyces, for which the name Streptomyces cavernae sp. nov. is proposed. The type strain is SYSU K10008T (=KCTC 39850T=DSM 104115T).

Lysobacter prati sp. nov., isolated from a plateau meadow sample.

A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).

Microlunatus speluncae sp. nov., a novel actinobacterium isolated from a Karstic subterranean environment sample.

A novel actinobacterial strain, designated SYSU K12189T, was isolated from a soil sample collected from a Karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were observed to be aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K12189T is closely related to the type strains of the genus Microlunatus, Microlunatus parietis 12-Be-011T (98.5% sequence similarity), Microlunatus nigridraconis CPCC 203993T (98.4%) and Microlunatus cavernae YIM C01117T (96.6%), and is therefore considered to represent a member of the genus Microlunatus. DNA-DNA hybridization values between strain SYSU K12189T and related type strains of the genus Microlunatus were < 70%. In addition, LL-diaminopimelic acid was found to be the diagnostic diamino acid in the cell wall peptidoglycan. The major isoprenoid quinone was identified as MK-9(H4), while the major fatty acids (> 10%) were found to be anteiso-C15:0, iso-C15:0, iso-C16:0 and iso-C14:0. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, three glycolipids and two unidentified lipids. The genomic DNA G+C content of strain SYSU K12189T was determined to be 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K12189T is concluded to represent a novel species of the genus Microlunatus, for which the name Microlunatus speluncae sp. nov. is proposed. The type strain is SYSU K12189T (= KCTC 39847T = DSM 103947T).

Nocardioides speluncae sp. nov., a novel actinobacterium isolated from a karstic subterranean environment sample.

A novel actinobacterial strain, designated YIM ART13T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, South western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were found to aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence analysis, strain YIM ART13T was found to be closely related to Nocardioides pakistanensis NCCP 1340T (96.1% sequence similarity) and is therefore considered to represent a member of the genus Nocardioides. In addition, LL-diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall peptidoglycan. The whole cell sugars were found to be mannose, galactose, glucose and ribose. The major isoprenoid quinone was identified as MK-8(H4), while the major fatty acids (> 10%) were identified as iso-C16:0, C18:1ω9c and C18:0 10-methyl. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol phosphatidylinositol and phosphatidylinositol mannoside, an unidentified phospholipid. The genomic DNA G+C content of strain YIM ART13T was determined from the draft genome sequence to be 70.1 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM ART13T represents a novel species of the genus Nocardioides, for which the name Nocardioides speluncae sp. nov. is proposed. The type strain is YIM ART13T (= KCTC 39593T = DSM 100493T).

Regulation of intracellular process by two-component systems: Exploring the mechanism of plasmid-mediated conjugative transfer.

Plasmid-mediated conjugative transfer facilitates the dissemination of antibiotic resistance, yet the comprehensive regulatory mechanisms governing this process remain elusive. Herein, we established pure bacteria and activated sludge conjugation system to investigate the regulatory mechanisms of conjugative transfer, leveraging metformin as an exogenous agent. Transcriptomic analysis unveiled that substantial upregulation of genes associated with the two-component system (e.g., AcrB/AcrA, EnvZ/Omp, and CpxA/CpxR) upon exposure to metformin. Furthermore, downstream regulators of the two-component system, including reactive oxygen species (ROS), cytoplasmic membrane permeability, and adenosine triphosphate (ATP) production, were enhanced by 1.7, 1.4 and 1.1 times, respectively, compared to the control group under 0.1 mg/L metformin exposure. Moreover, flow sorting and high-throughput sequencing revealed increased microbial community diversity among transconjugants in activated sludge systems. Notably, the antibacterial potential of human pathogenic bacteria (e.g., Bacteroides, Escherichia-Shigella, and Lactobacillus) was augmented, posing a potential threat to human health. Our findings shed light on the spread of antibiotic resistance bacteria and assess the ecological risks associated with plasmid-mediated conjugative transfer in wastewater treatment systems.

Overlooked in-situ sulfur disproportionation fuels dissimilatory nitrate reduction to ammonium in sulfur-based system: Novel insight of nitrogen recovery.

Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %-61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7-210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus, and Rubrivivax, harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology.

Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria.

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes.

Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.

Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat.

The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO42-, Na+, CO32-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded saline lakes under environmental change.

Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.

Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.

Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.

BACKGROUND: Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. RESULTS: Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. CONCLUSIONS: This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.