scholarly journals Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1926-1931 ◽  
Author(s):  
Qin-Fen Li ◽  
Li-Na Sun ◽  
Soon-Wo Kwon ◽  
Qing Chen ◽  
Jian He ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Resistant Bacterium ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Xylophilus Ampelinus

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8T, was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Xenophilus azovorans , Xenophilus aerolatus , Simplicispira metamorpha , Variovorax soli , and Xylophilus ampelinus . However, the phylogenetic tree indicated that strain YW8T formed a separate clade from Xenophilus azovorans . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain YW8T and its closest phylogenetic neighbours were below 24.2–35.5 %, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8T were C16 : 0, C 17 : 0 cyclo, C18 : 1ω7c, and summed feature 3(C16 : 1ω6c and/or C16 : 1ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA–DNA hybridization and chemotaxonomic data, strain YW8T is considered to represent a novel species of the genus Xenophilus , for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8T ( = CCTCC AB2012103T = KACC 16853T).

scholarly journals Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1264-1270 ◽  
Author(s):  
Heike Anders ◽  
Peter F. Dunfield ◽  
Kirill Lagutin ◽  
Karen M. Houghton ◽  
Jean F. Power ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Total Lipid Extract ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Heated Soil

A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373T, was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2–0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373T was shown to belong to the family Chitinophagaceae (class Sphingobacteriia ) of the phylum Bacteroidetes , with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034T, having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373T grew at 35–63 °C with an optimum temperature of 60 °C, and at pH 5.5–8.7 with an optimum growth pH of 7.3–7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1–0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow–orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373T from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373T ( = ICMP 20041T = DSM 27268T).

scholarly journals Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1271-1276 ◽  
Author(s):  
Guosheng Luo ◽  
Zunji Shi ◽  
Hui Wang ◽  
Gejiao Wang
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Resistant Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Major Respiratory Quinone

A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to Skermanella aerolata 5416T-32T (97.3 %), Skermanella parooensis ACM 2042T (95.8 %) and Skermanella xinjiangensis 10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and S. aerolata KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus Skermanella , for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.

scholarly journals Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1659-1665 ◽  
Author(s):  
Guosheng Luo ◽  
Zunji Shi ◽  
Gejiao Wang
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Resistant Bacterium ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Subsurface Soil ◽  
Iron Mine

A Gram-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain ZS79T, was isolated from subsurface soil of an iron mine in China. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ZS79T clustered closely with strains of five Lysobacter species, with 96.9, 96.1, 96.0, 95.8 and 95.3 % sequence similarities to Lysobacter concretionis Ko07T, L. daejeonensis GH1-9T, L. defluvii IMMIB APB-9T, L. spongiicola KMM 329T and L. ruishenii CTN-1T, respectively. The major cellular fatty acids were iso-C15 : 0 (28.6 %), iso-C17 : 1ω9c (19.9 %), iso-C16 : 0 (13.6 %), iso-C11 : 0 (12.6 %) and iso-C11 : 0 3-OH (12.4 %). The genomic DNA G+C content was 70.7 mol% and the major respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unknown phospholipid. On the basis of morphological and physiological/biochemical characteristics, phylogenetic position and chemotaxonomic data, this strain is considered to represent a novel species of the genus Lysobacter , for which the name Lysobacter arseniciresistens sp. nov. is proposed; the type strain is ZS79T ( = CGMCC 1.10752T = KCTC 23365T).

scholarly journals Arachidicoccus soli sp. nov., a bacterium isolated from soil

2020 ◽  
Author(s):  
Shin Ae Lee ◽  
Tae-Wan Kim ◽  
Mee-Kyung Sang ◽  
Jaekyeong Song ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10–33 °C, pH 6.0–7.5 and with 0–4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA–DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus . The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus , for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).

Bacillus thermocopriae sp. nov., isolated from a compost

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3024-3029 ◽  
Author(s):  
Luchao Han ◽  
Guiqin Yang ◽  
Xuemei Zhou ◽  
Dehui Yang ◽  
Pei Hu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Hybridization Experiment ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph

A Gram-reaction-positive, facultatively anaerobic, motile, endospore-forming, rod-shaped strain, designated SgZ-7T, was isolated from a windrow compost pile and was characterized by means of a polyphasic approach. Growth occurred with 0–3 % (w/v) NaCl (optimum 1 %), at pH 6.0–10.0 (optimum pH 7.2) and at 40–60 °C (optimum 50 °C). The main respiratory quinone was MK-7. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 46.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain SgZ-7T should be assigned to the genus Bacillus and was related most closely to Bacillus drentensis LMG 21831T (sequence similarity 97.2 %). The result of the DNA–DNA hybridization experiment revealed a low relatedness (27.2 %) between the isolate and B. drentensis LMG 21831T. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain SgZ-7T represents a novel species, for which the name Bacillus thermocopriae sp. nov. is proposed. The type strain is SgZ-7T ( = CCTCC AB 2012030T = KACC 16700T).

Faecalibacter bovis sp. nov., isolated from cow faeces

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Fuxiang Li ◽  
Wenhua Zhao ◽  
Qionghua Hong ◽  
Qingyong Shao ◽  
Jianling Song ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
West China ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, non-spore-forming, yellow-pigmented, aerobic, pleomorphic rod-shaped bacterium, designated ZY171143T, was isolated from faeces of a cow with diarrhoea in Wenshan, Yunnan Province, south-west China and its taxonomic position was studied. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZY171143T belonged to the family Weeksellaceae and was most closely related to the only species of the genus Faecalibacter , Faecalibacter macacae CCTCC AB 2016016T with a sequence similarity of 97.8 %. The genomic OrthoANI and digital DNA–DNA hybridization values between the strain and F. macacae CCTCC AB 2016016T were 86.2 and 30.5 %, respectively. The genomic G+C content was 31.1 mol%. The predominant fatty acids (>5 %) were C15 : 0 iso, C17 : 0 iso 3OH, C16 : 0, C16 : 1 ω5c and summed feature 3 (C16 : 1 ω7c and/or 16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, triacylglycerol and sulfonolipid. The sole respiratory quinone was MK-6. These chemotaxonomic characterizations also revealed that strain ZY171143T was a member of the genus Faecalibacter . Based on the phenotypic, chemotaxonomic and genotypic data, strain ZY171143T represents a novel species within the genus Faecalibacter , for which the name Faecalibacter bovis sp. nov. is proposed. The type strain is ZY171143T (=CGMCC 1.13663T=KCTC 62642T).

scholarly journals Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2133-2139 ◽  
Author(s):  
S. Shivaji ◽  
P. Vishnu Vardhan Reddy ◽  
S. S. S. Nageshwara Rao ◽  
Zareena Begum ◽  
Poorna Manasa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Type Species ◽  
Unsaturated Fatty Acids ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense , Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA–DNA hybridization with Cyclobacterium amurskyense KCTC 12363T and Cyclobacterium marinum DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.

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

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1622-1627 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Saline Lake ◽  
Qaidam Basin ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative bacterium, strain TS-T86T, 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-T86T 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-T86T 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-T86T was associated with the genus Belliella , and showed the highest sequence similarity to Belliella baltica BA134T (98.5 %) and then to Belliella kenyensis No.164T (95.7 %) and Belliella pelovolcani CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to Belliella baltica DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus Belliella , for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).

Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Qin Ma ◽  
Rui-Feng Lei ◽  
Yu-Qian Li ◽  
Dilireba Abudourousuli ◽  
Zulihumaer Rouzi ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Pr China ◽  
Genome Analyses ◽  
Wall Characteristic

A bacterial strain, designated YZGR15T, was isolated from the root of an annual halophyte Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, north-west PR China. Cells of the isolate were Gram-stain-positive, facultatively anaerobic, irregular rods. Growth occurred at 4–42 °C (optimum, 30–37 °C), at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0–9 % (w/v) NaCl (optimum, 2–5 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain YZGR15T showed the highest sequence similarity to Sanguibacter keddieii (98.27 %), Sanguibacter antarcticus (98.20 %) and Sanguibacter inulinus (98.06 %). Results of genome analyses of strain YZGR15T indicated that the genome size was 3.16 Mb, with a genomic DNA G+C content of 71.9 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between strain YZGR15Tand three type strains were in the range of 76.5–77.8 % and 20.0–22.2 %, respectively. Analysis of the cellular component of strain YZGR15T revealed that the primary fatty acids were anteiso-C15 : 0, C16 : 0, C14 : 0 and iso-C16 : 0 and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. The cell-wall characteristic amino acids were glutamic acid, alanine and an unknown amino acid. The whole-cell sugars for the strain were mannose, ribose, rhamnose, glucose and an unidentified sugar. The predominant respiratory quinone was MK-9(H4). Based on the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain YZGR15T represents a novel species of the genus Sanguibacter , for which the name Sanguibacter suaedae sp. nov. is proposed. The type strain is YZGR15T (=CGMCC 1.18691T=KCTC 49659T)

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3823-3828 ◽  
Author(s):  
Chokchai Kittiwongwattana ◽  
Chitti Thawai
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Low Levels ◽  
Sequence Similarity Analysis ◽  
Ph Range

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

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