Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau.

The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.

Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil.

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and rod-shaped actinobacterium, designated strain 10Sc9-8T, was isolated from Taklamakan desert soil sampled in the Xinjiang Uygur Autonomous Region, China. Strain 10Sc9-8T grew at 8‒37 °C (optimum, 28‒30 °C), pH 6.0‒10.0 (optimum, pH 7.0-8.0) and in the presence of 0‒15 % (w/v) NaCl (optimum, 0-3 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 10Sc9-8T was affiliated with members of the genus Georgenia and showed the highest 16S rRNA gene sequence similarity to Georgenia yuyongxinii Z443T (97.4 %). Phylogenomic analysis based on the whole genome sequences indicated that strain 10Sc9-8T should be assigned into the genus Georgenia. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole genome sequences indicated that strain 10Sc9-8T was clearly separated from other closely related species of the genus Georgenia with values below the thresholds for species delineation. Chemotaxonomic analyses showed that the cell-wall peptidoglycan was in a variant of A4α type with an interpeptide bridge comprising l-Lys-l-Ala-Gly-l-Asp. The predominant menaquinone was MK-8(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, several unidentified phospholipids, glycolipids and one unidentified lipid. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0. The genomic DNA G+C content was 72.7 mol%. On the basis of phenotypic, phylogenetic and phylogenomic data, strain 10Sc9-8T represents a novel species of the genus Georgenia, for which the name Georgenia halotolerans sp. nov. is proposed. The type strain is 10Sc9-8T (=JCM 33946T=CPCC 206219T).

Ancylobacter mangrovi sp. nov., a novel endophytic bacterium isolated from mangrove plant.

Two novel strains GSK1Z-4-2T and MQZ15Z-1 were isolated from branches of mangrove plants collected from Guangxi Zhuang Autonomous Region, China. Both strains were Gram-negative, aerobic, non-flagellated and non-spore-forming bacteria. The comparison of 16S rRNA gene sequences initially indicated that the two strains were assigned to the genus Ancylobacter with sharing the highest similarity to Ancylobacter pratisalsi DSM 102029T (97.3%). The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains GSK1Z-4-2T and MQZ15Z-1 were 99.9%, 97.4% and 77.4%, respectively, which revealed that the two strains belonged to the same species. Phylogenetic analyses based on 16S rRNA gene sequences and the core proteome showed that the two strains formed a well-supported cluster with A. pratisalsi DSM 102029T. Moreover, the ANI and isDDH values between strain GSK1Z-4-2T and A. pratisalsi DSM 102029T were 83.0% and 25.8%, respectively, demonstrating that strain GSK1Z-4-2T was a previously undescribed species. Meanwhile, strains GSK1Z-4-2T and MQZ15Z-1 exhibited most of chemotaxonomic and phenotypic features consistent with the description of the genus Ancylobacter. Based on the polyphasic data, strains GSK1Z-4-2T and MQZ15Z-1 should represent a novel species of the genus Ancylobacter, for which the name Ancylobacter mangrovi sp. nov. is proposed. The type strain is GSK1Z-4-2T (=MCCC 1K07181T = JCM 34924T).

Paenibacillus mangrovi sp. nov., a novel endophytic bacterium isolated from bark of Kandelia candel.

A endospore-forming bacterium, designated strain KQZ6P-2T, was isolated from surface-sterilized bark of the mangrove plant Kandelia candel, collected from Maowei Sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, China. Strain KQZ6P-2T was able to grow at NaCl concentrations in the range of 0-3 % (w/v) with optimum growth at 0-1 % (w/v) NaCl. Growth occurred at 20-42 °C (optimal growth at 30-37 °C) and pH 5.5-6.5 (optimal growth at pH 6.5). The 16S rRNA gene sequence similarity between strain KQZ6P-2T and its closest phylogenetic neighbour Paenibacillus chibensis JCM 9905T was 98.2 %. Phylogenetic analyses using 16S rRNA gene sequences showed that strain KQZ6P-2T formed a distinct lineage with Paenibacillus chibensis JCM 9905T. The draft genome of strain KQZ6P-2T was 5 937 633 bp in size and its DNA G+C content was 47.2mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain KQZ6P-2T and its related species were below the cut-off levels of 95, 70 and 95.5%, respec-tively. The cell-wall peptidoglycan of strain KQZ6P-2T contained meso-diaminopimelic acid as the diagnostic diamino acid. Major cellular fatty acids were anteiso-C15:0 and C16:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, four unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. Based on phylogenetic, phenotypic and chemotaxonomic data, strain KQZ6P-2T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus mangrovi sp. nov. is proposed. The type strain is KQZ6P-2T (=MCCC 1K07172T =JCM 34931T).

Jiella avicenniae sp. nov., a novel endophytic bacterium isolated from bark of Avicennia marina.

A Gram-stain-negative and short rod-shaped strain CBK1P-4T, isolated from surface-sterilized bark of Avicennia marina was investigated by a polyphasic taxonomic approach to resolve its taxonomic position. Strain CBK1P-4T grew at 10-30 °C (optimum, 25 °C), pH 5.0-9.0 (optimum, pH 5.5) and in the presence of 0-9% (w/v) NaCl (optimum, 1-2%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBK1P-4T belonged to the genus Jiella and was most closely related to species of the genus Jiella (97.4-98.3%). The genome comparisons between strain CBK1P-4T and the closely related species indicated that average nucleotide identity and digital DNA-DNA hybridization values were below the recommended thresholds for assigning strains to the same species (95-96% and 70%, respectively). The cell wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The principal fatty acids were C18:1ω7c and C19:0cycloω8c. The polar lipids were mainly comprised of phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and one unidentified glycolipid. The dominant respiratory quinone was ubiquinone-10. The DNA G + C content of strain CBK1P-4T was 66.7%. Based on the phenotypic features, phylogenetic analysis as well as genome analysis, we conclude that strain CBK1P-4T represents a novel Jiella species, for which the name Jiella avicenniae sp. nov. is proposed. The type strain is CBK1P-4T (= CGMCC 1.18742T = JCM 34330T).

Stakelama flava sp. nov., a novel endophytic bacterium isolated from a branch of Kandelia candel.

A Gram-stain-negative, aerobic, motile, non-spore-forming, short-rod-shaped strain that did not produce diffusible pigment, designated CBK3Z-3T, was isolated from a branch of Kandelia candel, collected from the Beilun Estuary National Nature Reserve in Guangxi Zhang Autonomous Region, PR China, and investigated by a polyphasic approach to determine its taxonomic position. Strain CBK3Z-3T grew at pH 5.0-10.0 (optimum, pH 8.0), 20-37 °C (optimum, 25-30 °C) and with 0-10 % (w/v) NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBK3Z-3T was closely related to species of genus Stakelama and had the highest 16S rRNA gene sequence similarity of 98.7 % to Stakelama pacifica CGMCC 1.7294T. The DNA G+C content value of strain CBK3Z-3T was 62.6 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid and the polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, an unidentified aminolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c and C16 : 0. The average nucleotide identity, estimated digital DNA-DNA hybridization and average amino acid identity values between strain CBK3Z-3T and the type strain of Stakelama pacifica CGMCC 1.7294T were 80.4, 23.1 and 81.5 %, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain CBK3Z-3T should be designated as a novel species of the genus Stakelama, for which the name Stakelama flava sp.nov. is proposed. The type strain is CBK3Z-3T (=JCM 34534T=CGMCC 1.18972T).

Hoyosella lacisalsi sp. nov., a halotolerant actinobacterium isolated from the Lake Gudzhirganskoe.

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and coccus-shaped strain, designated strain G463T, was isolated from the rhizosphere soil of Salicornia europaea L. collected from Lake Gudzhirganskoe in Siberia. Based on 16S rRNA gene phylogeny, strain G463T belonged to the genus Hoyosella, with the highest 16S rRNA gene sequence similarity to Hoyosella altamirensis DSM 45258T (96.1%). The major fatty acids were C17:1 ω8c, C16:0, C15 : 0 and C17:0. The strain contained meso-diaminopimelic acid as the cell-wall diagnostic diamino acid and arabinose, galactose and ribose as the whole-cell sugars. MK-8 and MK-7 were the predominant menaquinones. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phosphoglycolipid, two unidentified glycolipids and several unidentified lipids. Acetyl was the muramyl residue. Mycolic acids (C28-C34) were present. The G+C content of the genomic DNA was 68.3 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain G463T was considered to represent a novel species of the genus Hoyosella, for which the name Hoyosella lacisalsi sp. nov. is proposed. The type strain is G463T (=JCM 33650T=CGMCC 1.17230T).

Phycicoccus mangrovi sp. nov., a novel endophytic actinobacterium isolated from bark of Sonneratia apetala.

Two novel strains KQZ13P-1T and MAQZ13P-2 were isolated from bark of Sonneratia apetala collected from Maowei sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, China. Two strains were Gram-positive, aerobic, non-spore-forming, no diffusion pigment actinobacterial strains and investigated by a polyphasic approach to determine their taxonomic position. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 99.9% and 99.7%, respectively, suggesting that they belonged to the same species. The ANI and dDDH values between strain KQZ13P-1T and five Phycicoccus species were 74.4-95.3% and 20.1-61.5%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains were member of the genus Phycicoccus and were closely related to P. jejuensis NRRL B-24460T (99.2% sequence similarity), followed by P. ginsengisoli DCY87T (97.5-97.6%). Moreover, based on 88 core genes, the phylogenomic tree indicated that the two strains clustered with P. jejuensis NRRL B-24460T. The cell-wall peptidoglycan of both strains contained meso-diaminopimelic acid. The major fatty acids in two strains were C17:1ω8c, iso-C15:0 and iso-C16:0. The major polar lipids included diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylinositol (PI). Based on phylogenetic, phenotypic and chemotaxonomic analysis, strains KQZ13P-1T and MAQZ13P-2 represent a novel species of the genus Phycicoccus, for which the name Phycicoccus mangrovi sp. nov. is proposed. The type strain is KQZ13P-1T (=CGMCC 1.18973T = JCM 34556T).

Jiella mangrovi sp. nov., a novel endophytic bacterium isolated from leaf of Rhizophora stylosa.

A Gram-stain negative, non-motile, brilliant yellow and non-spore forming, coccoid- or short rod-shaped bacterium, designated strain KSK16Y-1T, was isolated from surface-sterilised leaf of Rhizophora stylosa collected from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. Genome of strain KSK16Y-1T is 4.93 Mb with 68.1% DNA G + C content and encoded 4359 predicted proteins, 4 rRNAs, 45 tRNAs and 4 ncRNA. Comparative 16S rRNA gene sequence analysis showed that the strain KSK16Y-1T has 98.1%, 97.9% and 96.9% 16S rRNA gene similarities with Jiella aquimaris JCM 30119T, J. endophytica CBS5Q-3T and J. pacifica 40Bstr34T, respectively. Whole-genome comparisons between strain KSK16Y-1T and J. aquimaris 22II-16-19i, J. endophytica CBS5Q-3T, J. pacifica 40Bstr34T, using average nucleotide identity (ANI) values (< 82.0%) and digital DNA-DNA hybridization (dDDH) values (< 25.1%), confirmed low genome relatedness. Strain KSK16Y-1T grew at 20-30 °C (optimum, 30 °C), pH 6.0-11.0 (optimum, pH 6.0-7.0) and with 0-10% (w/v) NaCl (optimum, 0-2%). Cell wall contained meso-diaminopimelic acid and the major fatty acid was C18:1ω7c. The polar lipid profile consists of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unknown phospholipid, one unknown aminolipid, one unknown aminophospholipid and four unidentified lipids. The predominant respiratory quinone is ubiquinone-10 (Q-10). The polyphasic characterization indicated that strain KSK16Y-1T represents a novel Jiella species. The name Jiella mangrovi sp. nov., type strain KSK16Y-1T (= CGMCC 1.18745T = JCM 34332T) is proposed.

Phycicoccus flavus sp. nov., a novel endophytic actinobacterium isolated from branch of Kandelia candel.

A Gram-stain-positive, aerobic, non-motile, non-endospore-forming and rod-shaped actinobacterium, designated strain CMS6Z-2T, was isolated from a surface-sterilized branch of Kandelia candel collected from the Maowei Sea, Guangxi Zhuang Autonomous Region, PR China. Strain CMS6Z-2T grew at 10-37 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-10.0 % (w/v) NaCl (optimum, 0-1.0 %). Strain CMS6Z-2T possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan and MK-8 (H4) as the predominant menaquinone. The major fatty acids were iso-C15 : 0, C16 : 0 and C18 : 1 ω9c. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The G+C content of the genomic DNA was 74.1 mol%. Comparative analysis of 16S rRNA genes showed that strain CMS6Z-2T should be assigned to the genus Phycicoccus and its closest relative was Phycicoccus endophyticus IP6SC6T with 98.3 % similarity. Phylogenetic analyses based on 16S rRNA gene sequence and phylogenomic analysis based on core proteomes alignment revealed that strain CMS6Z-2T belonged to the genus Phycicoccus and formed a robust cluster with Phycicoccus endophyticus IP6SC6T within the genus Phycicoccus. The average nucleotide identity value and estimated digital DNA-DNA hybridization value between strain CMS6Z-2T and the type strain of Phycicoccus endophyticus were 81.5 and 23.9 %, respectively. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain CMS6Z-2T represents a novel species of the genus Phycicoccus, for which the name Phycicoccus flavus sp. nov. is proposed. The type strain is CMS6Z-2T (=KCTC 49240T=CGMCC4.7549T).

Brachybacterium halotolerans sp. nov., a halotolerant, endophytic actinomycete isolated from branch of Bruguiera gymnoirhiza.

A novel, aerobic, moderately halophilic Gram-positive actinomycete, strain MASK1Z-5T was isolated from a surface-sterilized branch of Bruguiera gymnoirhiza in Shankou Mangrove Nature Reserve, Guangxi, China. The taxonomic position of the strain was investigated using a polyphasic approach. Strain MASK1Z-5T tolerated up to 20% (w/v) NaCl (optimum 0-7%), and grew at pH 5.0-12.0 (optimum pH 7.0-8.0), 20-37 °C (optimum 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MASK1Z-5T belonged to the genus Brachybacterium, and showed the highest 16S rRNA gene sequence similarity of 98.0% to B. endophyticum M1HQ-2T. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. MK-7 was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and three unidentified lipids. The major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The DNA G + C content was calculated to be 71.8 mol% based on the whole genome sequence. The estimated values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) based on whole genome sequences between strain MASK1Z-5T and B. endophyticum M1HQ-2T were 81.8% and 25.0%, respectively. The phenotypic, chemotaxonomic and genotypic properties clearly indicated that strain MASK1Z-5T represents a novel species within the genus Brachybacterium, for which the name Brachybacterium halotolerans sp. nov. is proposed. The type strain is MASK1Z-5T (= CGMCC1.18660T = JCM 34339T).

Nocardioides acrostichi sp. nov., a novel endophytic actinobacterium isolated from leaf of Acrostichum aureum.

A short-rod-shaped, non-spore-forming endophytic actinobacterium, was isolated from a surface-sterilized leaf of Acrostichum aureum in Fangchenggang, Guangxi Zhuang Autonomous Region, China, designated strain CBS4Y-1T and examined by a polyphasic approach to determine its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate mycelia and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain CBS4Y-1T grew optimally with 0-1.0% (w/v) NaCl at 30 °C, pH 7.0-8.0. Comparative analysis of 16S rRNA genes showed that strain CBS4Y-1T shared the highest 16S rRNA gene sequence similarities with Nocardioides marinus CL-DD14T (96.7%) and Nocardioides terrae BX5-10T (96.7%). Phylogenetic analyses based on 16S rRNA gene sequence and phylogenomic analysis based on core proteomes alignment revealed that strain CBS4Y-1T belonged to the genus Nocardioides and formed a distinct cluster within the genus Nocardioides. The DNA G + C content of strain CBS4Y-1T was 71.1 mol%. The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. Phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI) were detected in the polar lipid extracts. The major fatty acids were iso-C16:0, C18:1ω9c and iso-C17:0. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain CBS4Y-1T represents a novel species of the genus Nocardioides, for which the name Nocardioides acrostichi sp. nov. is proposed. The type strain is CBS4Y-1T (= KCTC 49238T = CGMCC 4.7548T).

Auraticoccus cholistanensis sp. nov., an actinomycete isolated from soil of the Cholistan Desert, and emended description of the genus Auraticoccus.

A Gram-stain-positive, aerobic, non-motile and non-spore-forming actinobacterium, designated as F435T, was isolated from soil sample collected from the Cholistan Desert, Pakistan. The taxonomic position of the strain was established by using a polyphasic taxonomic approach. The cells were coccoid-shaped and found in single or arrangement of pairs. The novel strain grew at 15‒37 °C (optimum, 25‒30 °C), pH 7‒11 (optimum, pH 7-8) and in the presence of 0‒8% (w/v) NaCl (optimum, 0 %). Results of blast analysis based on 16S rRNA gene sequences showed that Auraticoccus monumenti MON 2.2T was its closest relative with 97.4 % similarity followed by Desertihabitans aurantiacus CPCC 204711T (95.2 %). In phylogenetic trees, strain F435T formed a robust cluster with the only member of the genus Auraticoccus. The peptidoglycan isomer present in the cell wall was ll-diaminopimelic acid. The major fatty acid was determined to be anteiso-C15 : 0. Characteristic polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinone was MK-9(H4). The genomic G+C content was calculated as 73.5 mol%. The digital DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) values between strain F435T and A. monumenti MON 2.2T were 24.6 and 81.8 %, respectively. Based on the results of phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain F435T represents a novel specie of the genus Auraticoccus, for which the name Auraticoccus cholistanensis sp. nov. is proposed. The type strain is F435T (=JCM 33648T=CGMCC 1.17443T). The description of the genus Auraticoccus has also been emended.

Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil.

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5T grew at 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5T formed a distinct lineage within the genus Nocardioides and had the highest similarity to Nocardioides albidus THG-S11.7T (97.30 %), followed by Nocardioides kongjuensis A2-4T (97.22 %), Nocardioides nitrophenolicus NSP 41T (97.15 %) and Nocardioides caeni MN8T (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed ll-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H4) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0 and 10-methyl C18 : 0. The genome length of strain 21Sc5-5T was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5T represents a novel species of the genus Nocardioides, for which the name Nocardioides vastitatis sp. nov. is proposed. The type strain is 21Sc5-5T (=JCM 33365T=CGMCC 4.7608T).

Glycomyces buryatensis sp. nov., an actinobacterium isolated from steppe soil.

A novel actinobacterial strain, designated 18T, was isolated from a steppe soil sample collected in Buryatia, Russia and subjected to polyphasic taxonomic characterization. The strain was aerobic and Gram-stain-positive. The 16S rRNA gene sequence of strain 18T exhibited highest similarity to Glycomyces paridis CPCC 204357T (97.2 %). Results of phylogenetic analysis showed that strain 18T formed a distinct branch clearly affiliated to the genus Glycomyces. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the cell-wall diamino acid. The whole-cell sugar profile was found to contain galactose, glucose, ribose and xylose. MK-10(H4) and MK-11(H4) were the predominant menaquinones. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and four unidentified polar lipids. The major fatty acids identified were anteiso-C15 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain 18T was 68.0 mol% (draft genome sequence). Based on its phylogenetic, phenotypic and chemotaxonomic features, strain 18T was considered to represent a novel species of the genus Glycomyces, for which the name Glycomyces buryatensis sp. nov. is proposed. The type strain of Glycomyces buryatensis is 18T (=JCM 33362T=CGMCC 4.7610T).

Desertihabitans brevis sp. nov., an actinobacterium isolated from sand of the Taklamakan desert, and emended description of the genus Desertihabitans.

A novel actinobacterium, designated strain 16Sb5-5T, was isolated from a sand sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Cells of the isolate were Gram-staining-positive, aerobic, non-motile and short-rod shaped. Strain 16Sb5-5T grew optimally at 37 °C, pH 7.0 and with 0‒2 % (w/v) NaCl. The cell-wall peptidoglycan was of the A3γ type and contained alanine, glycine, glutamic acid and ll-diaminopimelic acid (ll-DAP). Ribose, arabinose and glucose were detected in the whole-cell hydrolysates. The predominant menaquinone was MK-9(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, three unidentified glycolipids and three unidentified lipids. The major whole-cell fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 16Sb5-5T was closely related to Desertihabitans aurantiacus CPCC 204711T (99.8 % similarity) and formed a robust clade with D. aurantiacus in the phylogenetic trees. In silico genomic comparisons showed that strain 16Sb5-5T exhibited ANI values of 94.8-94.9 % and GGDC value of 59.5 % to D. aurantiacus CPCC 204711T. The genomic G+C content was 73.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, strain 16Sb5-5T could be distinguishable from its closest phylogenetic relative and represents a novel species of the genus Desertihabitans, for which the name Desertihabitans brevis sp. nov. is proposed. The type strain is 16Sb5-5T (=KCTC 49116T=CGMCC 1.16553T). The description of the genus Desertihabitans has also been emended.

Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella.

Two novel strains, designated 11W25H-1T and 8H24J-4-2T, were isolated from surface-sterilized plant tissues collected from the Taklamakan Desert in the Xinjiang Uygur Autonomous Region, China. The strains were characterized by a polyphasic approach in order to clarify their taxonomic positions. They were Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped. The 16S rRNA gene sequences of the strains showed highest similarities with Labedella gwakjiensis KCTC 19176T (99.2% and 98.9%, respectively) and Labedella endophytica CPCC 203961T (98.9% and 99.0%, respectively). The sequence similarity between strains 11W25H-1T and 8H24J-4-2T was 99.4%. Phylogenetic analyses based on 16S rRNA gene sequences and single-copy phylogenetic marker genes (pMGs) showed that the two strains belonged to the genus Labedella and formed a separate cluster from the closest species L. gwakjiensis KCTC 19176T and L. endophytica CPCC 203961T. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly separated the strains from each other and from the other species of the genus Labedella with values below the thresholds for species delineation. The two strains showed chemotaxonomic characteristics and phenotypic properties in agreement with the description of the genus Labedella and also confirmed the differentiation from the closest species. The data demonstrated that strains 11W25H-1T and 8H24J-4-2T represented two novel species of the genus Labedella, for which the names Labedella phragmitis sp. nov. (type strain 11W25H-1T=JCM 33144T=CGMCC 1.16700T) and Labedella populi sp. nov. (type strain 8H24J-4-2T=JCM 33143T=CGMCC 1.16697T) are proposed.

Aeromicrobium endophyticum sp. nov., an endophytic actinobacterium isolated from reed (Phragmites australis).

A Gram-staining-positive, motile and short-rod-shaped actinobacterium designated 9W16Y-2T was isolated from surface-sterilized leaves of reed (Phragmites australis) collected from Taklamakan Desert in Xinjiang Uygur Autonomous Region, China. Colonies were pale greenish yellow, circular, smooth, and convex. The 16S rRNA gene sequence of strain 9W16Y-2T exhibited highest sequence similarities with Aeromicrobium camelliae CGMCC 1.12942T (99.0%) and Aeromicrobium erythreum NRRL B-3381T (97.2%). Phylogenetic analyses based on 16S rRNA gene sequences and single-copy phylogenetic marker genes (pMGs) showed that strain 9W16Y-2T belonged to the genus Aeromicrobium and formed a monophyletic clade with Aeromicrobium camelliae CGMCC 1.12942T. Furthermore, average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) clearly separated strain 9W16Y-2T from the other species of the genus Aeromicrobium with values below the thresholds for species delineation. The G+C content of the genomic DNA is 68.9 mol%. The diagnostic diamino acid of the cell-wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinone was MK-9(H4). The major fatty acids (> 10% of the total fatty acids) were C18:0 10-methyl (TBSA) (28.2%), C16:0 (21.0%), C16:0 2-OH (20.8%) and C18:1ω9c (12.8%). The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenic, phenotypic and chemotaxonomic features, strain 9W16Y-2T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium endophyticum sp. nov. is proposed. The type strain is 9W16Y-2T (= CGMCC 1.13876T = JCM 33141T).

Kocuria soli sp. nov., an actinobacterium isolated from soil.

A Gram-stain-positive, aerobic, coccoid-shaped, non-spore-forming actinobacterial strain, designated M5W7-7T, was isolated from a hot spring soil sample collected from Anshan, Liaoning province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M5W7-7T clustered closely with species of the genus Kocuria, and showed the highest sequence similarity of 97.1 % to Kocuria subflava YIM 13062T. Strain M5W7-7T grew at 10-37 °C (optimum, 37 °C), pH6.0-11.0 (pH 6.0-7.0) and in the presence of 0-7 % (w/v) NaCl (0 %). Substrate mycelia and aerial mycelia were not formed, and diffusible pigments were not observed on any media tested. Strain M5W7-7T contained MK-6(H2) and MK-7(H2) as the dominant menaquinones. The polar lipid profile of strain M5W7-7T contained diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The predominant whole-cell sugars were galactose and glucose. The predominant fatty acid was anteiso-C15 : 0. The DNA G+C content of strain M5W7-7T was 67.0 mol%. On the basis of phylogenetic relationships, phenotypic characterization and chemotaxonomic analyses, strain M5W7-7T represents a novel species of the genus Kocuria, for which the name Kocuriasoli sp. nov. is proposed. The type strain is M5W7-7T (=KCTC 49195T =CGMCC 1.13744T).