Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau.

The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg(2+), K(+), Cl(-), Na(+), SO4 (2-), and Ca(2+)) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO4 (3-) concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.

Psychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake.

Two Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-motile, moderately halophilic bacteria (strains X15M-6T and X15M-8T) were isolated from Lake Xiaochaidan, a salt lake in Qaidam basin, Qinghai Province, China. Cells of X15M-6T were rod-like or coccoid, 0.5-0.9 µm wide and 0.9-1.5 µm long; cells of X15M-8T were rods, 0.3-0.6 µm wide and 1.2-2.2 µm long. Growth was observed in the presence of 0.5-14.0 % (w/v) NaCl (optimum, 3.0 %) and at pH 6.5-10.0 (optimum, pH 7.0-7.5) for both. X15M-6T and X15M-8T grew at 10-35 °C (optimum, 20-25 °C) and 4-35 °C (optimum, 25 °C), respectively. Both contained iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, phosphatidylethanolamine and an unknown lipid as the major polar lipids, and menaquinone MK-6 as the major respiratory quinone. The DNA G+C contents were 32.8 and 35.0 mol% for X15M-6T and X15M-8T, respectively. Phylogenetic trees based on 16S rRNA gene sequences showed that both strains belonged to the genus Psychroflexus and formed a separate lineage. In addition, strains X15M-6T and X15M-8T shared 96.8 % 16S rRNA gene sequence similarity and showed highest similarities to members of the genus Psychroflexus (92.7-93.5 and 91.8-93.1 %, respectively). Based on the above data, it is concluded that strains X15M-6T and X15M-8T represent two novel species of the genus Psychroflexus, for which the names Psychroflexus salis sp. nov. (type strain X15M-6T = CGMCC 1.12925T = JCM 30615T) and Psychroflexus planctonicus sp. nov. (type strain X15M-8T = CGMCC 1.12931T = JCM 30616T) are proposed.

Aquisalinus flavus gen. nov., sp. nov., a member of the family Parvularculaceae isolated from a saline lake.

A Gram-stain-negative bacterium, strain D11M-2T, was isolated from a saline lake (Lake Dasugan) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, 0.5-0.7 µm wide and 1.2-1.6 µm long, and motile by means of a single subpolar or lateral flagellum. Strain D11M-2T was strictly heterotrophic and aerobic, and catalase- and oxidase-positive. Growth was observed in the presence of 0-14.0% (w/v) NaCl (optimum, 2.0%), and at 10-35 °C (optimum, 30 °C) and pH 6.0-10.5 (optimum, pH 8.0). Strain D11M-2T contained Q-10 and Q-11 as the respiratory quinones and three unknown glycolipids as the major polar lipids. The major cellular fatty acids (>10.0%) were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D11M-2T belonged to the family Parvularculaceae and formed a separate lineage that was independent of the two genera within the family Parvularculaceae. Strain D11M-2T exhibited 92.8-93.4% 16S rRNA gene sequence similarity to members of the genus Parvularcula (highest to Parvularcula bermudensis HTCC 2503T), and 90.2% to a member of the genus Amphiplicatus. The DNA G+C content was 59 mol% (Tm). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain D11M-2T is considered to represent a novel species of a new genus in the family Parvularculaceae, for which the name Aquisalinus flavus gen. nov., sp. nov. is proposed. The type strain of Aquisalinus flavus is D11M-2T (=CGMCC 1.12921T=KCTC 42673T).

Planktosalinus lacus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a salt lake.

A Gram-staining-negative bacterium, strain X14M-14T, was isolated from a salt lake (Lake Xiaochaidan) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain X14M-14T were non-spore-forming, non-motile rods. Strain X14M-14T was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain X14M-14T belonged to the family Flavobacteriaceae and formed a distinct lineage that was independent of the most closely related genera: Aequorivita (16S rRNA gene sequence similarities, 91.8-93.1 %) and Salinimicrobium (91.5-92.4 %). Strain X14M-14T contained MK-6 as the major respiratory quinone, and phosphatidylethanolamine and two unknown lipids as the major polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The presence of iso-C15 : 1 G as a predominant fatty acid could distinguish this strain clearly from the most closely related genera in the family Flavobacteriaceae. The DNA G+C content was 36.6 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain X14M-14T represents a novel genus and species of the family Flavobacteriaceae, for which the name Planktosalinus lacus gen. nov., sp. nov. is proposed. The type strain is X14M-14T ( = CGMCC 1.12924T = KCTC 42675T).

Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake.

A Gram-stain-negative, facultatively aerobic bacterium, strain X13M-12T, was isolated from a salt lake (Lake Xiaochaidan) in the Qaidam basin, Qinghai Province, PR China. Cells of strain X13M-12T were slightly curved, rod-shaped, 0.5-0.8 µm wide and 1.2-2.3 µm long, and motile by means of a polar flagellum. Strain X13M-12T was catalase- and oxidase-positive. Growth was observed in the presence of 0-15.0 % (w/v) NaCl (optimum 3.0-5.0 %), and at 4-40 °C (optimum 25-30 °C) and pH 6.0-11.0 (optimum pH 8.5). Strain X13M-12T contained Q-8 as the sole respiratory quinone, and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The major cellular fatty acids (>10 % of totals) were C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c, and C18 : 1ω7c and/or C18 : 1ω6c. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain X13M-12T belonged to the family Alteromonadaceae and formed a distinct lineage, showing low gene sequence similarities to closely related genera: Bowmanella, Aestuariibacter and Salinimonas (16S rRNA gene sequence similarities, 93.0-93.1 %, 92.3-93.1 % and 92.6-92.7 %, respectively). In addition, strain X13M-12T showed < 92.7 % gene sequence similarities to other species of the family Alteromonadaceae. The DNA G+C content of strain X13M-12T was 49 mol% (Tm). Based on the data presented above, strain X13M-12T is considered to represent a novel genus and species of the family Alteromonadaceae, for which the name Lacimicrobium alkaliphilum gen. nov., sp. nov. is proposed. The type strain is X13M-12T ( = CGMCC 1.12923T = KCTC 42674T).

Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake.

A Gram-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8-1.4 µm wide and 1.9-4.0 µm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5-11.0 % (w/v) NaCl (optimum 3.0 %), and at 10-35 °C (optimum 25 °C) and pH 6.5-10.0 (optimum pH 8.5). Strain TS-T30T contained C18 : 1ω7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2-95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8-94.9 %), Marivita (93.6-94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9-94.7 %), Oceanicola (92.6-94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T ( = CGMCC 1.12477T = NBRC 110969T).

Thalassotalea marina sp. nov., isolated from a marine recirculating aquaculture system, reclassification of Thalassomonas eurytherma as Thalassotalea eurytherma comb. nov. and emended description of the genus Thalassotalea.

A Gram-stain-negative, facultatively anaerobic bacterium, strain QBLM2T, was isolated from rearing water of a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated through a polyphasic approach. Cells of strain QBLM2T were non-spore-forming rods, motile by means of a single polar flagellum. Positive for oxidase and catalase. Growth occurred at 15-40 °C (optimum 30 °C), at pH 6.5-10.5 (optimum pH 7.5-8.5) and in the presence of 0-5.0 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QBLM2T formed a distinct lineage within the genus Thalassotalea and exhibited sequence similarities of 94.5-96.3 % to members of the genus Thalassotalea. The predominant fatty acids (>10 %) were C17 : 1ω8c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the major ubiquinone. The DNA G+C content was 37.1 mol%. Based on the data above, strain QBLM2T is considered to represent a novel species of the genus Thalassotalea, for which the name Thalassotalea marina sp. nov. is proposed. The type strain is QBLM2T ( = CGMCC 1.12814T = KCTC 42731T). Phylogenetic analyses indicated that Thalassomonas eurytherma Za6a-12T fell within the genus Thalassotalea, so it is reclassified as Thalassotalea eurytherma comb. nov. and the description of the genus Thalassotalea is emended.

Maritimibacter lacisalsi sp. nov., isolated from a salt lake, and emended description of the genus Maritimibacter Lee et al. 2007.

A Gram-staining-negative, non-motile, strictly aerobic bacterium, strain X12M-4T, was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9 %, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Strain X12M-4T was catalase- and oxidase-positive. Cells were rod-shaped, 0.5­0.8 µm wide and 1.1­1.6 µm long. Growth was observed in the presence of 0­11.0 % (w/v) NaCl (optimum, 5.0­6.0 %) and at 15­40 °C (optimum, 25 °C) and pH 6.5­9.5 (optimum, pH 7.0). No growth occurred at 10 °C or 45 °C. Strain X12M-4T contained C18 : 1ω7c, C19 : 0 cyclo ω8c and C16 : 0 as the major fatty acids (>10.0 %). The predominant respiratory quinone was Q-10.The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidglycerol, an unknown aminolipid and an unidentified lipid. The DNA G+C content was 65.7 mol% (determined using T m). Strain X12M-4T showed highest 16S rRNA gene sequence similarities to Maritimibacter alkaliphilus HTCC2654T (96.7 %), Roseibacterium elongatum DSM 19469T (96.4 %), Tropicimonas aquimaris DPG-21T (95.6 %), 'Roseibacterium beibuensis' JLT1202r (95.6 %) and Tropicimonas sediminicola M97T (95.5 %) and < 95.5 % to others. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain X12M-4T formed a robust cluster with M. alkaliphilus HTCC2654T. On the basis of the data, it is concluded that strain X12M-4T represents a novel species of the genus Maritimibacter, for which the name Maritimibacter lacisalsi sp. nov. is proposed. The type strain is X12M-4T ( = CGMCC 1.12922T = JCM 30555T). To accommodate the novel species, the description of the genus Maritimibacter was emended.

Vibrio salilacus sp. nov., a new member of the Anguillarum clade with six alleles of the 16S rRNA gene from a saline lake.

A Gram-stain-negative, catalase- and oxidase-positive, facultatively aerobic bacterium, strain DSG-S6T, was isolated from Dasugan Lake (salinity 3.1%, w/w), China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S6T were non-spore-forming, slightly bent rods, and motile by means of a single polar flagellum. Growth occurred in the presence of 0-7.0% (w/v) NaCl (optimum, 2.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.0-10.5 (optimum, pH 8.0-8.5). C16 : 0, C18 : 1ω7c and C16 : 1ω7c and/or C16 : 1ω6c were the major fatty acids. Six alleles of the 16S rRNA gene sharing 98.9-99.9  % similarity were detected in strain DSG-S6T, which showed highest 16S rRNA gene sequence similarity to Vibrio aestuarianus ATCC 35048T (97.7 %), then to Vibrio pacinii LMG 19999T (97.6%) and Vibrio metschnikovii CIP 69.14T (96.8%). Multilocus sequence analysis of four housekeeping genes and 16S rRNA genes clearly clustered it as a member of the Anguillarum clade. Mean DNA-DNA relatedness between strain DSG-S6T and V. aestuarianus NBRC 15629T, V. pacinii CGMCC 1.12557T and V. metschnikovii JCM 21189T was 20.6 ± 2.3, 38.1 ± 3.5 and 24.2 ± 2.8%, respectively. The DNA G+C content was 46.8 mol% (Tm). Based on the data, it is concluded that strain DSG-S6T represents a novel species of the genus Vibrio, for which the name Vibrio salilacus sp. nov. is proposed. The type strain is DSG-S6T ( = CGMCC 1.12427T = JCM 19265T).

Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake.

A Gram-staining-negative bacterium, strain XCD-X12(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X12(T) were non-spore-forming rods, 0.4-0.7 µm wide, 2.1-3.2 µm long and motile with a single polar flagellum. Strain XCD-X12(T) was strictly aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-20.0% (w/v) NaCl (optimum, 4.0-8.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.5-10.5 (optimum, pH 8.5). It contained Q-9 as the predominant respiratory quinone. The major fatty acids (>10.0%) were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and an uncharacterized aminophospholipid. The DNA G+C content was 55.6 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X12(T) was associated with the genus Marinobacter, and showed the highest 16S rRNA gene sequence similarity to Marinobacter hydrocarbonoclasticus ATCC 49840(T) (97.4%), M. vinifirmus FB1(T) (96.8%), M. excellens KMM 3809(T) (96.8%) and M. antarcticus ZS2-30(T) (96.7%). DNA-DNA relatedness of strain XCD-X12(T) to M. hydrocarbonoclasticus CGMCC 1.7683(T) was 34 ± 5%. Based on these data, it is concluded that strain XCD-X12(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter halophilus sp. nov. is proposed. The type strain is XCD-X12(T) ( = CGMCC 1.12481(T)= JCM 30472(T)).

Belliella aquatica sp. nov., isolated from a saline lake.

A Gram-staining-negative bacterium, strain TS-T86(T), was isolated from Lake Tuosu, a saline lake (salinity 5.4%, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86(T) was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4-0.6 µm wide and 1.2-2.3 µm long. Growth was observed in the presence of 0-9.0% (w/v) NaCl (optimum, 2.0%), at 4-35 °C (optimum, 25 °C) and at pH 7.0-10.5 (optimum, pH 8.5-9.0). Strain TS-T86(T) contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10%) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86(T) was associated with the genus Belliella, and showed the highest sequence similarity to Belliella baltica BA134(T) (98.5 %) and then to Belliella kenyensis No.164(T) (95.7%) and Belliella pelovolcani CC-SAL-25(T) (95.3 %). DNA-DNA relatedness of strain TS-T86(T) to Belliella baltica DSM 15883(T) was 32 ± 3%. It is concluded that strain TS-T86(T) represents a novel species of the genus Belliella, for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86(T) ( = CGMCC 1.12479(T) = JCM 19468(T)).

Pseudomonas salina sp. nov., isolated from a salt lake.

A Gram-staining-negative, facultatively aerobic bacterium, strain XCD-X85(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/v) in Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X85(T) were non-endospore-forming rods, 0.4-0.6 µm wide and 1.0-1.6 µm long, and motile by means of a single polar flagellum. Strain XCD-X85(T) was catalase- and oxidase-positive. Growth was observed in the presence of 0-12.0% (w/v) NaCl (optimum, 1.0-2.0%) and at 4-35 °C (optimum, 25-30 °C) and pH 6.5-10.5 (optimum, pH 8.0-8.5). Strain XCD-X85(T) contained (>10%) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major respiratory quinone was ubiquinone 9 (Q-9). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 57.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X85(T) was associated with the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas pelagia CL-AP6(T) (99.0%) and Pseudomonas bauzanensis BZ93(T) (96.8%). DNA-DNA relatedness of strain XCD-X85T to P. pelagia JCM 15562(T) was 19 ± 1%. On the basis of the data presented above, it is concluded that strain XCD-X85(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salina sp. nov. is proposed. The type strain is XCD-X85(T) ( = CGMCC 1.12482(T) = JCM 19469(T)).

Marivita lacus sp. nov., isolated from a saline lake.

A Gram-staining-negative, strictly heterotrophic and aerobic bacterium, strain TS-T44T, was isolated from a saline lake, Tuosu Lake in Qaidam basin, Qinghai province, China. Its taxonomic position was investigated using a polyphasic approach. Cells of strain TS-T44T were non-endospore-forming, non-motile rods, 0.8-1.2 µm wide and 1.2-3.0 µm long. Catalase- and oxidase-positive. Growth occurred in the presence of up to 8 % (w/v) NaCl (optimum, 3.0 %) and at 15-35 °C (optimum, 25 °C) and pH 7.0-10.0 (optimum, pH 7.5-8.5). C18 : 1ω7c was the predominant fatty acid. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unknown lipid. The DNA G+C content was 65.5 mol% [determined from the melting temperature (Tm)]. Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T44T was associated with the genus Marivita and showed highest sequence similarity to Marivita cryptomonadis CL-SK44T (97.7 %), Marivita litorea CL-JM1T (97.5 %) and Marivita geojedonensis DPG-138T (97.3 %), and < 97 % to other species. DNA-DNA relatedness of strain TS-T44T to M. cryptomonadis JCM 15447T, M. litorea JCM 15446T and M. geojedonensis KCTC 23882T was 23 ± 3 %, 33 ± 4 % and 35 ± 2 %, respectively. Based on the data presented, it is concluded that strain TS-T44T represents a novel species of the genus Marivita, for which the name Marivita lacus sp. nov. is proposed. The type strain is TS-T44T ( = CGMCC 1.12478T = JCM 19516T).

Idiomarina planktonica sp. nov., isolated from a saline lake.

A Gram-stain-negative bacterium, strain TS-T11(T), was isolated from Tuosu lake, a saline lake (salinity 5.4%, w/v) in the Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T11(T) were non-spore-forming rods, 0.6-0.8 µm wide and 0.8-2.2 µm long, and motile by means of a single polar flagellum. Strain TS-T11(T) was strictly heterotrophic and aerobic. Cells were positive for catalase and oxidase. Growth was observed in the presence of 0.5-11.0% (w/v) NaCl (optimum 4.0-6.0%), at 4-40 °C (optimum 30-35 °C) and at pH 6.0-10.5 (optimum pH 7.5-8.5). Strain TS-T11(T) contained iso-C15:0, iso-C17:0 and iso-C17:1ω9c as the predominant fatty acids (>10%). The major respiratory quinone was Q-8. The polar lipids consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and nine uncharacterized phospholipids. The G+C content of genomic DNA was 46.8 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T11(T) was associated with the genus Idiomarina, and showed highest 16S rRNA gene sequence similarity to Idiomarina aestuarii KYW314(T) (97.4%) and Idiomarina salinarum ISL-52(T) (97.4%). DNA-DNA relatedness of strain TS-T11(T) to I. aestuarii JCM 16344(T) and I. salinarum DSM 21900(T) was 22.2 ± 2.4 and 11.5 ± 1.6%, respectively. Based on the data presented above, it was concluded that strain TS-T11(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina planktonica sp. nov. is proposed. The type strain is TS-T11(T) ( = CGMCC 1.12458(T) = JCM 19263(T)).

Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system.

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated S1(T), was isolated from the Cynoglossus semilaevis culture pond in a recirculating mariculture system in Tianjin, China. The taxonomy of strain S1(T) was studied by using a polyphasic approach. Cells of strain S1(T) were non-spore-forming, curved rods, 0.4-0.6 µm wide and 1.2-2.0 µm long, and motile by means of a single polar flagellum. The strain was positive for oxidase and catalase activities. Strain S1(T) was able to grow at 4-30 °C (optimum, 25 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.5) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain S1(T) contained Q-8 as the sole respiratory quinone and C16 : 1ω7c/C16 : 1ω6c and C16 : 0 as the predominant cellular fatty acids. The genomic DNA G+C content was 40.1 mol% (Tm). Phylogenetic analysis based on 16S rRNA gene sequences placed strain S1(T) in the genus Colwellia, and it formed a distinct lineage in the phylogenetic tree together with Colwellia meonggei MA1-3(T), Colwellia aestuarii SMK-10(T), Colwellia polaris 537(T) and Colwellia chukchiensis BCw111(T), with 97.7, 96.1, 95.9 and 95.0 % 16S rRNA gene sequence similarity to these strains, respectively. DNA-DNA relatedness of strain S1(T) to Colwellia meonggei MA1-3(T) was 23.5±3.6 %. On the basis of the phylogenetic and phenotypic evidence, strain S1(T) is considered to represent a novel species of the genus Colwellia, for which the name Colwellia aquaemaris sp. nov. is proposed. The type strain is S1(T) ( = CGMCC 1.12165(T) = JCM 18479(T)).

Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system.

A Gram-negative bacterium, strain CZ-AM5(T), was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5(T) were non-spore-forming rods, 0.5-0.8 µm wide and 1.2-2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5(T) was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15-40 °C (optimum, 30-35 °C), at pH 6.5-10.5 (optimum, pH 7.0-7.5) and in the presence of 0-12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5(T) showed the highest 16S rRNA gene sequence similarity (96.5 %) to Phaeobacter caeruleus LMG 24369(T); it exhibited 16S rRNA gene sequence similarity of 95.0-96.5, 95.2-96.3, 96.2, 94.6-95.7 and 94.8-95.8 % to members of the genera Phaeobacter, Ruegeria, Citreimonas, Leisingera and Donghicola, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5(T) did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5(T) is considered to represent a novel genus and species of the family Rhodobacteraceae, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5(T) ( = CGMCC 1.13219(T) = JCM 19401(T)).

Rheinheimera tuosuensis sp. nov., isolated from a saline lake.

A Gram-staining-negative bacterium, strain TS-T4(T), was isolated from Tuosu Lake, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, Qinghai, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T4(T) were non-spore-forming rods, 0.4-0.8 µm wide and 1.7-2.3 µm long, and motile by means of a single polar flagellum. Strain TS-T4(T) was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-7.0 % (w/v) NaCl (optimum, 3.0-4.0 %) and at 4-40 °C (optimum, 30-35 °C) and pH 7.0-10.5 (optimum, pH 8.5-9.0). Strain TS-T4(T) contained Q-8 as the sole respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids, as for other members of the genus Rheinheimera. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The DNA G+C content was 50.2 mol% (Tm). Phylogenetic trees based on sequences of the 16S rRNA gene and a conserved portion of the gyrase B gene (gyrB) showed that strain TS-T4(T) was associated with the genus Rheinheimera; the strain showed the highest 16S rRNA gene sequence similarity to Rheinheimera longhuensis LH2-2(T) (97.1 %) and then to Rheinheimera pacifica KMM 1406(T) (97.0 %). DNA-DNA relatedness of strain TS-T4(T) with R. longhuensis LH2-2(T) and R. pacifica NBRC 103167 was 53±2.5 and 48±2 %, respectively. Based on the data presented, it is concluded that TS-T4(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera tuosuensis sp. nov. is proposed. The type strain is TS-T4(T) ( = CGMCC 1.12461(T) = JCM 19264(T)).

Roseibium aquae sp. nov., isolated from a saline lake.

A Gram-staining-negative bacterium, strain DSG-S4-2(T), was isolated from Dasugan Lake, a saline lake (salinity 3.1%, w/v) in Qaidam basin, Qinghai, China and its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S4-2(T) were non-spore-forming rods, 0.5-0.8 µm wide and 1.2-3.8 µm long and motile by means of a single polar flagellum. Strain DSG-S4-2(T) was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. PufLM and coxL genes were present, bacteriochlorophyll a (BChl a) and a carotenoid pigment were produced. Growth was observed in the presence of 0-8.0% (w/v) NaCl (optimum, 1.0-2.0%), at 20-40 °C (optimum, 35 °C) and pH 6.5-10.5 (optimum, pH 7.5-8.0). Strain DSG-S4-2(T) contained Q-10 as the sole respiratory quinone. The polar lipids contained two aminolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sulphoquinovosyldiacylglyceride, phosphatidylcholine and some unknown phospholipids, like the other members of the genus Roseibium. The predominant fatty acid (>70%) was summed feature 8 (C(18 : 1)ω7c and/or C(18 : 1)ω6c). The DNA G+C content was 61.4 mol% (determined from melting temperature). Phylogenetic trees (neighbour-joining, maximum-likelihood and maximum-parsimony) based on 16S rRNA gene sequences showed that strain DSG-S4-2(T) was associated with the members of the genus Roseibium, with highest 16S rRNA gene sequence similarity to Roseibium denhamense OCh 254(T) (96.3%) and Roseibium hamelinense OCh 368(T) (96.3%). Based on the data presented above, it is concluded that strain DSG-S4-2(T) represents a novel species of the genus Roseibium, for which the name Roseibium aquae sp. nov. is proposed. The type strain is DSG-S4-2(T) ( = CGMCC 1.12426(T) = JCM 19310(T)).

Viral potential to modulate microbial methane metabolism varies by habitat.

Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines.

BACKGROUND: Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. RESULTS: We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. CONCLUSIONS: Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.