Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5 mol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5 % as well as digital DNA-DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16 : 0, C17 : 1  ω8c or C18 : 1  ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).

Nocardioides jiangxiensis sp. nov., a novel actinobacterium isolated from lakeside soil, exhibiting the biosynthesis potential of mycofactocin

A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated WY-20T, was isolated from a lakeside soil sample collected in Jiangxi Province, PR China. Growth was observed at 20-42 °C (optimum 30 °C), pH 5.0-8.0 (optimum pH 7.0) and salinity of 0-3.0% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain WY-20T belongs to the genus Nocardioides and showed the highest sequence similarity (98.1%) to N. phosphati WYH11-7T, followed by N. cavernaquae K1W22B-1T (97.8%), N. marmoriterrae JOS5-1T (97.2%) and N. jensenii NBRC 14755T (97.1%). The average nucleotide identity and digital DNA-DNA hybridization values between strains WY-20T and N. phosphati WYH11-7T were 83.5% and 26.2%, respectively. The predominant fatty acids (≥ 10% of the total fatty acids) were C18:1ω9c, C17:0, C16:0, summed feature 8 (C18:1ω7c and/or C18: 1ω6c) and C17:1ω9c. The major menaquinone was MK-8 (H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Based on phenotypic, genotypic and phylogenetic pieces of evidence, strain WY-20T represents a novel species in the genus Nocardioides, for which the name Nocardioides jiangxiensis sp. nov. is proposed. The type strain is WY-20T (= GDMCC 4.317T = KACC 23379T).

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5-97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4-97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2-77.3 % and 21.3-21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).

Nocardioides ochotonae sp. nov., Nocardioides campestrisoli sp. nov. and Nocardioides pantholopis sp. nov., isolated from the Qinghai-Tibet Plateau

Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313^T, ZJ1307, MC1495^T, Y192, 603^T and X2025) were isolated from the Qinghai-Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides, and strains ZJ1313^T and ZJ1307 were most closely related to N. solisilvae JCM 31492^T (16S rRNA gene sequence similarity, 98.0 %), MC1495^T and Y192 to N. houyundeii 78^T (98.5 %), and 603^T and X2025 to N. dokdonensis JCM 14815^T (97.6 %). The digital DNA-DNA hybridization values of strains ZJ1313^T, MC1495^T and 603^T among each other and with type strains of their closest relatives were all below the 70 % cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C_16 : 0, C_17 : 1  ω8c or C_18 : 1  ω9c. MK-8(H₄) was the predominant respiratory menaquinone and ʟʟ-2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313^T, MC1495^T and 603^T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313^T/ZJ1307, MC1495^T/Y192 and 603^T/X2025 represent three new species of genus Nocardioides, for which the names Nocardioides ochotonae sp. nov. (ZJ1313^T=GDMCC 4.177^T=KCTC 49537^T=JCM 34185^T), Nocardioides campestrisoli sp. nov. (MC1495^T=GDMCC 4.176^T=KCTC 49536^T=JCM 34307^T) and Nocardioides pantholopis sp. nov. (603^T=CGMCC 4.7510^T=DSM 106494^T) are proposed accordingly.

Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana

An actinobacterial strain, designated R-N-C8T, was isolated from the rhizosphere soil of Arabidopsis thaliana collected in Yunnan Province, south-west China. Based on the results of 16S rRNA gene sequence analysis, strain R-N-C8T had highest similarity to Nocardioides terrae CGMCC 1.7056T (96.5%), Nocardioides opuntiae KCTC 19804T (96.3%) and Nocardioides currus IB-3T (96.1%), and lower than 96.0 % similarity to other members of the genus Nocardioides . Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R-N-C8T formed an isolated branch with N. terrae CGMCC 1.7056T and N. opuntiae KCTC 19804T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, one unidentified phosphoglycolipid and four unidentified phospholipids in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, anteiso-C17 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 70.9 mol%. The orthologous average nucleotide identiy values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 77.1 and 75.1 %, respectively. DNA–DNA hybridization values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 20.7 and 19.9 % respectively. Data from phenotypic and genotypic analyses supported that strain R-N-C8T represents a new species of Nocardioides , for which the name Nocardioides nematodiphilus sp. nov. is proposed. The type strain is R-N-C8T (=CGMCC 1.18723T= KCTC 49528T).

Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099T, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to Nocardioides pelophilus KACC 19192T with 98.11 % similarity. The DNA G+C content of strain BN130099T was 68.84 mol% (draft genome sequence). The genome sequence of BN130099T displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the major respiratory quinone. The predominant fatty acid was iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099T from N. pelophilus KACC 19192T. The strain represents a novel species of the genus Nocardioides , for which we propose the name Nocardioides humilatus sp. nov. The type strain is BN130099T (=KCTC 49079T=CCTCC AB 2018135T).

Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu

A novel Gram-stain-positive, strictly anaerobic, elliptical, non-motile and non-flagellated bacterium, designed LZLJ-2^T, was isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. Growth occurred at 28-45 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.0) and with concentrations of NaCl up to 2 % (w/v; optimum, 0 %). On the basis of 16S rRNA gene sequence similarity, strain LZLJ-2^T belonged to the genus Thermophilibacter and was most closely related to Thermophilibacter mediterraneus Marseille-P3256^T (similarity 96.9 %), Olsenella gallinarum ClaCZ62^T (similarity 96.6 %) and Thermophilibacter provencensis Marseille-P2912^T (similarity 96.4 %). In addition, strain LZLJ-2^T had high similarity to the genus Olsenella, including Olsenella profusa DSM 13989^T (similarity 94.9 %), Olsenella umbonata DSM 22620^T (similarity 94.9 %), Olsenella uli ATCC 49627^T (similarity 94.22 %), Tractidigestivibacter scatoligenes DSM 28304^T (similarity 93.9 %) and Paratractidigestivibacter faecalis KCTC 15699^T (similarity 93.25 %). Comparative genome analysis showed that orthoANI values between strain LZLJ-2^T and Thermophilibacter mediterraneus Marseille-P3256^T, Olsenella gallinarum ClaCZ62^T, Thermophilibacter provencensis Marseille-P2912^T, Olsenella profusa DSM 13989^T, Olsenella umbonata DSM 22620^T, Olsenella uli ATCC 49627^T, Tractidigestivibacter scatoligenes DSM 28304^T and Paratractidigestivibacter faecalis KCTC 15699^T were 78.68, 78.99, 78.29, 73.40, 74.00, 74.30, 75.08 and 77.23 %, and the genome-to-genome distance values were respectively 22.3, 22.5, 22.4, 19.6, 20.5, 19.7, 20.5 and 21.5 %. The genomic DNA G+C content of strain LZLJ-2^T was 65.21 mol%. The predominant cellular fatty acids (>10 %) of strain LZLJ-2^T were C_18 : 1 cis 9 (33.7 %), C_14 : 0 (22.0 %) and C_18 : 1 cis 9 DMA (13.5 %). d-Glucose, sucrose, mannose, maltose, lactose (weak), salicin, glycerol (weak), cellobiose and trehalose (weak) could be used by strain LZLJ-2^T as sole carbon sources. Enzyme activity results showed positive reactions with valine arylamidase, leucine arylamidase, crystine arylamidase, acid phosphatase, alkaline phosphatase, esterase (C4) (weakly positive), naphthol-AS-BI-phosphohydrolase, α-glucosidase and β-glucosidase. The major end products of glucose fermentation were lactic acid and acetic acid. It produced skatole from indole acetic acid, and produced p-cresol from modified peptone-yeast extract medium with glucose. Based on the 16S rRNA gene trees as well as the genome core gene tree, it is suggested that Olsenella gallinarum are transferred to genus Thermophilibacter as Thermophilibacter gallinarum comb. nov. Based on phenotypic, genotypic and phylogenetic data, strain LZLJ-2^T is considered to represent a novel species of the genus Thermophilibacter, for which the name Thermophilibacter immobilis sp. nov. is proposed. The type strain is LZLJ-2^T (=KCTC 25162^T=JCM 34224^T).

Nocardioides stalactiti sp. nov., isolated from a cave stalactite surface

An aerobic, rod-shaped, Gram-stain-positive, actinobacterial strain, designated 1.0914^T, was isolated from a stalactite sample collected from a cave located in Guizhou Province, southwest PR China. Based on 16S rRNA gene sequence analysis, strain 1.0914^T shared highest similarities values with Nocardioides pelophilus CGMCC 4.7388^T (97.7 %), Nocardioides immobilis CCTCC AB 2017083^T (97.5 %) and Nocardioides silvaticus CCTCC AB 2018079^T (97.3 %) and values lower than 97.0 % to other members of the genus Nocardioides. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain 1.0914^T formed an isolated branch with N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T and N. silvaticus CCTCC AB 2018079^T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and one unidentified phospholipid in the cellular membrane. The major fatty acids were identified as iso-C_16 : 0, C_18 : 1 ω9c, C_17 : 1 ω8c and C_16 : 0. The predominant respiratory quinone was MK-8(H₄) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 71.1 mol%. The orthologous average nucleotide identiy values between N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T, N. silvaticus CCTCC 2018079^T and strain 1.0914^T were 82.3, 81.7 and 81.9 % respectively. DNA-DNA hybridization values between N. pelophilus CGMCC 4.7388^T, N. immobilis CCTCC AB 2017083^T, N. silvaticus CCTCC 2018079^T and strain 1.0914^T were 25.2, 24.6 and 24.5 % respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain 1.0914^T as representing a new species of Nocardioides, for which the name Nocardioides stalactiti sp. nov. is proposed. The type strain is 1.0914^T (=CCTCC AB 2018266^T=KCTC 49243^T).

Nocardioides antri sp. nov., Isolated from Soil in a Rock Cave

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041^T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34 ^T, N. pelophilus THG-T63^T, and N. immobilis FLL521^T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27 Mb containing 424 contigs with a DNA G + C content of 70.5 mol%. The ANI value between strain BN140044^T and its closely related species N. silvaticus S-34 ^T was 82.6%. The genome sequence of BN140041^T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C_16:0 (55.3%), C_18:1ω9c (7.7%) and iso-C_17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041^T from related the Nocardioides strains. Therefore, strain BN140041^T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041^T (= KCTC 49080 ^T = CCTCC AB 2018226 ^T).

Persicimonas caeni gen. nov., sp. nov., the Representative of a Novel Wide-Ranging Predatory Taxon in Bradymonadales

A novel bacterial strain, designated YN101^T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, China. Strain YN101^T was Gram-stain negative, facultatively anaerobic, oxidase and catalase negative bacterium with the ability to prey on other microbes. A cross-streaking culture method was utilized to analyze the predatory activity of strain YN101^T. The results showed strain YN101^T could prey on various bacteria, either Gram-stain negative or Gram-stain positive. According to the predatory assays, different species in the same genus may behave differently when attacked by strain YN101^T. The predatory behavior of strain YN101^T to four typical species was analyzed, and furthermore, predation to Algoriphagus marinus am2^T were quantitatively studied by fluorogenic quantitative PCR, and the gene copies decreased over two magnitudes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN101^T shared the greatest sequence similarity of 93.9% to Bradymonas sediminis FA350^T. The complete genome sequence of strain YN101^T was 8,047,306 bp in size and the genomic DNA G + C content was 63.8 mol%. The digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) values between strain YN101^T and B. sediminis FA350^T were 13.9 and 74.0%. The genetic features showed that the biosynthesis of many important compounds was deficient in genome of strain YN101^T, which may lead to its predation. Moreover, its genome encoded many genes affiliated with type IV pili, secretion system, membrane proteins and transduction proteins. Similar with myxobacteria and Bdellovibrio and like organisms (BALOs), these genes should play important roles in motility, adhesion or virulence to attack prey cells during predation. The predominant polar lipid profile of strain YN101^T consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified aminophospholipid (APL). The major cellular fatty acid of strain YN101^T was iso-C_17:0, and the sole respiratory quinone was MK-7. Based on the chemotaxonomic, physiological and biochemical characteristics, strain YN101^T represents a novel species of a novel genus in the family Bradymonadaceae, for which the name Persicimonas caeni gen. nov., sp. nov. is proposed. The type strain is YN101^T (=KCTC 72083^T = MCCC 1H00374^T).

Nocardioides silvaticus sp. nov., isolated from forest soil

A Gram-stain-positive, non-motile, rod-shaped bacterial strain S-34^T was isolated from forest soil. According to 16S rRNA gene sequence analysis, strain S-34^T was related to Nocardioides members and showed the highest similarities to Nocardioides thalensis NCCP-696^T (97.3 %) and Nocardioides panacisoliGsoil 346^T (97.0 %), Nocardioides litorisoli X-2^T (96.5 %) and Nocardioides immobilis FLL521^T (96.4 %). Phylogenetic trees showed that strain S-34^T fell within the cluster containing strain S-34^T and N. immobilis FLL521^T. The levels of DNA-DNA relatedness between strain S-34^T and N. thalensis CCTCC AB 2016296^T and between strain S-34^T and N. panacisoli KCTC 19470^T were 50.6 and 58.8 %, respectively. The genome orthoANI value between strain S-34^T and N. immobilis CCTCC AB 2017083^T was 82.4 %. Strain S-34^T had ll-diaminopimelic acid in the cell-wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol, four unknown phospholipids and one unknown lipid as the polar lipids, meanquinone-8(H4) as the only respiratory quinone and iso-C16 : 0, C17:1ω8c, C17:1ω6c, C17 : 0 and C17 : 0 10-methyl (tbsa) as the major fatty acids. The genome length of strain S-34^T was 4.53 Mb containing 52 contigs and with a DNA G+C content of 71.2 mol%. Strain S-34^T could be distinguished from the other Nocardioides members mainly based on the data of phylogenetic analyses, DNA-DNA hybridization, polar lipids and some biochemical differences. Therefore, strain S-34^T represents a novel species of the genus Nocardioides, for which the name Nocardioidessilvaticus sp. nov. is proposed. The type strain is S-34^T (=KCTC 49137^T=CCTCC AB 2018079^T).