Shixue Zheng

Paenibacillus selenitireducens sp nov., a selenite-reducing bacterium isolated from a selenium mineral soil

A Gram-stain-positive, rod-shaped, facultatively anaerobic bacterium, designated strain ES3-24(T), was isolated from a selenium mineral soil. The isolate was endospore-forming, nitrate-reducing and motile by means of peritrichous flagella. The major menaquinone was menaquinone 7 (MK-7) and the predominant fatty acids (>5%) were anteiso-C15:0, iso-C16:0, C16:0 and anteiso-C17:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and two unknown aminophospholipids. Strain ES3-24(T) contained meso-diaminopimelic acid in the cell-wall peptidoglycan and the DNA G+C content was 49.6 mol%. According to phylogenetic analysis based on the 16S rRNA gene sequence, strain ES3-24(T) was most closely related to Paenibacillus terrigena A35(T), with 16S rRNA gene sequence identity of 98.3%, while the other members of the genus Paenibacillus had 16S rRNA gene sequence identities of less than 95.0%. DNA-DNA relatedness between strain ES3-24(T) and P. terrigena CCTCC AB206026(T) was 39.3 %. In addition, strain ES3-24(T) showed obvious differences from closely related species in major polar lipids, nitrate reduction and other physiological and biochemical characteristics. The data from our polyphasic taxonomic study reveal that strain ES3-24(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus selenitireducens sp. nov. is proposed. The type strain is ES3-24(T) ( = KCTC 33157(T) = CCTCC AB2013097(T)).

Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter.

A Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped, non-photosynthetic bacterial strain, DW2-9(T), was isolated from soil. The highest 16S rRNA gene sequence similarities were found to Rhodobacter capsulatus ATCC 11166(T) (97.1%), Rhodobacter viridis JA737(T) (96.4%), Rhodobacter maris JA276(T) (96.2%), Rhodobacter veldkampii ATCC 35703(T) (96.0%), Haematobacter massiliensis CCUG 47968(T) (96.0%), Haematobacter missouriensis CCUG 52307(T) (95.9%) and Rhodobacter aestuarii JA296(T) (95.7%). The genomic DNA G+C content was 67.2 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>5%) were C(18 : 1)ω7c, C(16 : 0), C(19 : 0) cyclo ω8c and summed feature 3 (one or more of iso-C(15 : 0) 2-OH, C(16 : 1)ω6c and C(16 : 1)ω7c). However, unlike species of the genus Rhodobacter, strain DW2-9(T) neither formed internal photosynthetic membranes nor produced photosynthetic pigments. DNA-DNA hybridization between strain DW2-9(T) and R. capsulatus JCM 21090(T) showed a relatedness of 33%. Strain DW2-9(T) contained phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid as major polar lipids, which differed from those of species of the genera Rhodobacter and Haematobacter. In addition to the differences in phylogenetic position and polar lipid types, strain DW2-9(T) could be distinguished from species of the genus Haematobacter by the cultivation conditions. On the basis of our polyphasic taxonomic analysis, strain DW2-9(T) is considered to represent a novel genus and species, for which the name Paenirhodobacter enshiensis gen. nov., sp. nov. is proposed. The type strain of Paenirhodobacter enshiensis is DW2-9(T) ( = CCTCC AB 2011145(T) = KCTC 15169(T)). Emended descriptions of the genera Rhodobacter and Haematobacter are also proposed.

Paenibacillus selenii sp. nov., isolated from selenium mineral soil.

Strain W126(T), a Gram-reaction-positive, spore-forming, rod-shaped, facultatively anaerobic bacterium, motile by means of peritrichous flagella, was isolated from selenium mineral soil in Hubei province of China. 16S rRNA gene sequence analysis demonstrated that this isolate belonged to the genus Paenibacillus, with 97.9 % sequence similarity to Paenibacillus anaericanus MH21(T), while compared with the other species of the genus Paenibacillus, the 16S rRNA gene sequence similarities were less than 96.0%. DNA-DNA hybridization between strain W126(T) and Paenibacillus anaericanus DSM 15890(T) was 24%. The major isoprenoid menaquinone was menaquinone-7. Anteiso-C(15 : 0) was the major fatty acid. The DNA G+C content was 42.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. Strain W126(T) contained A1γ-meso-diaminopimelic acid in the cell-wall peptidoglycan. The phenotypic, chemotaxonomic and genotypic data indicate that strain W126(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus selenii sp. nov. is proposed. The type strain is W126(T) ( = KCTC 33420(T) = CCTCC AB 2014003(T)).

Chitinophaga barathri sp. nov., isolated from mountain soil

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium, designated strain YLT18T, was isolated from mountain cliff soil of Enshi Grand Canyon in China. The major menaquinone was menaquinone 7 (MK-7) and the predominant fatty acids (>5 %) were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH) and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unknown aminophospholipids, two unknown aminolipids and two unknown polar lipids. The DNA G+C content was 55.4 mol%. According to phylogenetic analysis based on 16S rRNA gene sequences, strain YLT18T was related most closely to Chitinophaga niabensis JS13-10T ( = DSM 24787T) and Chitinophaga cymbidii R156-2T ( = KCTC 23738T), with similarities of 96.7 and 96.2 %, respectively. In addition, strain YLT18T showed obvious differences from the closely related species in terms of esterase (C4) activity, acid production from fructose and rhamnose, and sole carbon source utilization by arabinose and rhamnose. The results from this polyphasic taxonomic study revealed that strain YLT18T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga barathri sp. nov. is proposed. The type strain is YLT18T ( = KCTC 42472T = CCTCC AB 2015054T).

Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil

A Gram-stain-positive, strictly aerobic, non-motile and rod-shaped bacterial strain, designated YS-17T, was isolated from soil in the Lengshuijiang antimony mine, Hunan Province, China. Comparative 16S rRNA gene sequencing analysis clustered it with Flavihumibacter strains, and strain YS-17T was most closely related to Flavihumibacter cheonanensis WS16T (97.2 % similarity), Flavihumibacter petaseus T41T (96.6 %) and Flavihumibacter solisilvae 3-3T (96.5 %). The level of DNA-DNA relatedness between strain YS-17T and F. cheonanensis JCM 19322T was 35.5±0.1 % (n=2). The major respiratory quinone of strain YS-17T was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified lipids, two unidentified amino lipids and phospholipid. The major fatty acids (≥5 %) were iso-C15 : 0, iso-C15 : 1 G, unknown ECL 13.565, iso-C17 : 0 3-OH, C15 : 0, C16 : 1ω5c and anteiso-C15 : 0. The DNA G+C content was 47.8 mol%. Compared with other Flavihumibacter strains, strain YS-17T showed major biophysical and biochemical differences, with the ability to hydrolyse gelatin and to assimilate salicin and l-proline. The results demonstrated that strain YS-17T belongs to the genus Flavihumibacter and represents a novel species, for which the name Flavihumibacter stibioxidans sp. nov. is proposed. The type strain is YS-17T (=CCTCC AB 2016053T=KCTC 52205T).

Domibacillus antri sp. nov., isolated from the soil of a cave.

A Gram-reaction-positive, strictly aerobic, capsule-forming, motile and rod-shaped bacterium, designated strain XD80T, was isolated from the soil of a native cave in Lichuan, Hubei province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XD80T was most closely related to Domibacillus iocasae CCTCC AB 2015183T (98.66 % sequence similarity), followed by Domibacillus robiginosus DSM 25058T(97.83 %), Domibacillus tundrae KCTC 33549T (97.70 %), Domibacillus enclensis CCTCC AB 2011121T (97.21 %) and Domibacillus indicus DSM 28032T (96.96 %). Levels of DNA-DNA relatedness between strain XD80T and D. iocasae CCTCC AB 2015183T, D. robiginosusDSM 25058T, D. tundrae KCTC 33549T and D. enclensis CCTCC AB 2011121T were 37.4 %, 53.8 %, 53.6 % and 52.7 %, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipid and two unknown phospholipids. The predominant fatty acids (>5 %) were iso-C15 : 0 (37.3 %), anteiso-C15 : 0 (10.8 %), C16 : 0 (10.4 %), iso-C17 : 0 (10.3 %), C16 : 1ω11c (9.6 %) and anteiso-C17 : 0 (7.4 %). MK-6 (86.4 %) was the major respiratory quinone. The DNA G+C content was 46.4 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid (type A1γ). Ribose and glucose were the major whole-cell sugars. In addition, strain XD80T showed differential physiological characteristics from most members of the genus Domibacillus, encompassing hydrolysis of starch, acid production from inositol and raffinose, and production of valine arylamidase. The results of this polyphasic study indicated that strain XD80T represents a novel species of the genus Domibacillus, for which the name Domibacillus antri sp. nov. is proposed. The type strain is XD80T (=CCTCC AB 2015053T=KCTC 33636T).

Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33

ABSTRACT Pseudomonas migulae ES3-33 is a Gram-negative strain that strongly reduces Se(IV) and was isolated from a selenium mining area in Enshi, southwest China. Here we present the draft genome of this strain containing potential genes involved in selenite reduction and a large number of genes encoding resistances to copper and antibiotics.

Nocardioides litorisoli sp. nov., isolated from lakeside soil

A Gram-stain-positive, rod-shaped, non-spore-forming bacterium, designated as x-2T, was isolated from lakeside soil of Sayram in the Xinjiang Uygur Autonomous Region, PR China. On the basis of 16S rRNA gene sequences, strain x-2T belongs to the genus Nocardioides in the family Nocardioidaceae, being most closely related to Nocardioides panacisoli Gsoil 346T (97.36 % 16S rRNA gene sequence similarity). Strain x-2T was characterized chemotaxonomically and found to have ll-diaminopimelic acid in the cell-wall peptidoglycan, phosphatidylglycerol, diphosphatidylglycerol, glycolipids and another three unknown phospholipids as the major polar lipids, MK-8(H4) as the predominant menaquinone and C18 : 1ω9c, iso-C16 : 0, C17 : 1ω8c and C16 : 0 as the major fatty acids. The genomic DNA G+C content of the novel strain was 71.1 mol%. The level of DNA-DNA relatedness between strain x-2T and N. panacisoli KCTC 19470T (=Gsoil 346T) was 29.8 %. These chemotaxonomic characters support the position of strain x-2T within the genus Nocardioides. The results of physiological and biochemical tests, as well as phylogenetic analysis, suggest that strain x-2T represents a novel species of the genus Nocardioides, for which the name Nocardioides litorisoli sp. nov. is proposed. The type strain is x-2T (=KCTC 39845T=CCTCCAB 2016255T).

Hymenobacter monticola sp. nov., isolated from mountain soil.

A Gram-reaction-negative, aerobic, non-motile, red-pigmented and rod-shaped bacterium, designated XF-6RT, was isolated from mountain soil in the Sichuan province of China. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that XF-6RT belonged to the genus Hymenobacter. The greatest 16S rRNA gene sequence similarities of strain XF-6RT were with Hymenobacter soli PB17T (96.4 %) and Hymenobacter saemangeumensis GSR0100T (95.8 %). Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c and anteiso-C15 : 0 were the major fatty acids (>10 %). The only menaquinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine, four aminolipids, four phosphoaminolipids and three lipids. The DNA G+C content was 62 mol%. On the basis of the polyphasic taxonomic analysis, strain XF-6RT is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter monticola sp. nov. is proposed. The type strain is XF-6RT ( = KCTC 42733T = CCTCC AB 2015206T).

Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.

A Gram-stain-negative, light pink, non-motile, rod-shaped, aerobic bacterium, designated strain XNV015T, was isolated from soil of a vanadium mine. Phylogenetic analyses based on 16S rRNA gene sequences indicated that it belongs to the genus Pedobacter and was closely related to Pedobacter suwonensis DSM 18130T (96.93 % sequence similarity), Pedobacter alluvionis NWER-II11T (96.66 %), Pedobacter terrae DS-57T (96.54 %), Pedobacter kyungheensis KACC 16221T (96.54 %) and Pedobacter soli KACC 14939T (96.47 %). This strain clearly differed from the closely related species in terms of acid production from rhamnose and ethanol. Menaquinone-7 was the predominant respiratory quinone. The predominant fatty acids included iso-C15 : 0, C16 : 1ω5c, summed feature 3, iso-C17 : 0 3-OH and C17 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, glycolipids, lipids and aminolipids. The genomic DNA G+C content was 43.8 mol%. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strain XNV015T represents a novel species of the genus Pedobacter, for which the name Pedobacter vanadiisoli sp. nov. is proposed. The type strain is XNV015T (=CCTCC AB 2015319T=KCTC 42866T).