Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Gui Zhang ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Genomic Sequence ◽  
Phosphatidyl Inositol ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Content Range

Four mesophilic and Gram-stain-positive strains (zg-686T/zg-691 and HY186T/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus Gordonia according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4–68.3 mol% and low DNA relatedness (19.2–27.6 %) with all available genomes in the genus Gordonia . Strains zg-686T/zg-691 and HY186T/HY189 had C18 : 1ω9c, C18 : 0 10-methyl, C16 : 1 ω7c/C16 : 1ω6c and C16 : 0 as major cellular fatty acids. The polar lipids detected in strains zg-686T and HY186T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H2) (10.8 %) and MK9(H2) (89.2 %) for strain zg-686T, and MK6 (7.7 %), MK8(H2) (8.4 %), MK8(H4) (3.1 %) and MK9(H2) (80.8 %) for strain HY186T. Optimal growth conditions were pH 7.0, 35–37 °C and 0.5–1.5 % NaCl (w/v) for strains pair zg-686T/zg-691, and pH 7.0, 28 °C and 1.5 % (w/v) NaCl for strains pair HY186T/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus Gordonia , for which the names Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov. are proposed. The type strains are zg-686T (=GDMCC 1.1715T =JCM 33890T) and HY186T (=CGMCC 4.7607T =JCM 33466T), respectively.

scholarly journals Carboxydocella manganica sp. nov., a thermophilic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium from a Kamchatka hot spring

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 890-894 ◽  
Author(s):  
G. B. Slobodkina ◽  
A. N. Panteleeva ◽  
T. G. Sokolova ◽  
E. A. Bonch-Osmolovskaya ◽  
A. I. Slobodkin
Keyword(s):  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Kamchatka Peninsula ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Bacterium Strain

A thermophilic, anaerobic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium (strain SLM 61T) was isolated from a terrestrial hot spring on the Kamchatka peninsula. The cells were straight rods, 0.5–0.6 µm in diameter and 1.0–6.0 µm long, and exhibited tumbling motility by means of peritrichous flagellation. The strain grew at 26–70 °C, with an optimum at 58–60 °C, and at pH 5.5–8.0, with an optimum at pH 6.5. Growth of SLM 61T was observed at 0–2.0 % (w/v) NaCl, with an optimum at 0.5 % (w/v). The generation time under optimal growth conditions was 40 min. Strain SLM 61T grew and reduced Mn(IV), Fe(III) or nitrate with a number of organic acids and complex proteinaceous compounds as electron donors. It was capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor, Fe(III) but not Mn(IV) or nitrate as an electron acceptor and CO2 as a carbon source. It also was able to ferment pyruvate, yeast extract, glucose, fructose, sucrose and maltose. The G+C content of DNA of strain SLM 61T was 50.9 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Carboxydocella thermautotrophica 41T (96.9 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Carboxydocella manganica sp. nov. is proposed. The type strain is SLM 61T ( = DSM 23132T  = VKM B-2609T). C. manganica is the first described representative of the genus Carboxydocella that possesses the ability to reduce metals and does not utilize CO.

scholarly journals Marinicella rhabdoformis sp. nov., isolated from coastal sediment

2020 ◽  
Vol 70 (5) ◽  
pp. 3528-3533 ◽  
Author(s):  
Yan-lin Zhong ◽  
Xun-Ke Sun ◽  
Jian-Gang Hui ◽  
Hui-ling Teng ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539T, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5–8.0 and in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539T formed a robust clade with members of the genus Marinicella and was closely related to Marinicella litoralis JCM 16154T, Marinicella sediminis F2T and Marinicella pacifica sw153T with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA–DNA hybridization values between strain 3539T and M. litoralis JCM 16154T were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539T was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). The polar lipids of strain 3539T consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539T is considered to represent a novel species within the genus Marinicella in he family Alcanivoracaceae , for which the name Marinicella rhabdoformis sp. nov. is proposed. The type strain of the new species is 3539T (=KCTC 72414T=MCCC 1H00388T).

scholarly journals Noviherbaspirillum aerium sp. nov., isolated from air

2020 ◽  
Vol 70 (12) ◽  
pp. 6390-6395 ◽  
Author(s):  
Han Xue ◽  
Chun-gen Piao ◽  
Ying-hua Lin ◽  
Dan-ran Bian ◽  
Yong Li
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-stain-negative, strictly aerobic, non-spore-forming, rod-shaped, motile with polar flagella and pale-orange bacterium, designated strain 122213-3T, was isolated from air, collected at the foot of the Xiangshan Mountain, located in Beijing, PR China. Optimal growth occurred at 28 °C, at pH 7 and in the presence of 0–1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 122213-3T clustered with species of the genus Noviherbaspirillum and formed a distinct sublineage, showing highest similarities to Noviherbaspirillum malthae CC-AFH3T (96.88 %), Noviherbaspirillum massiliense JC206T (95.78 %) and Noviherbaspirillum aurantiacum SUEMI08T (95.78 %). The predominant cellular fatty acids were summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c), summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The predominant quinone was ubiquinone 8 (Q-8). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid and two unidentified polar lipids. The polyamine pattern showed the presence of putrescine as the major polyamine, with minor amounts of 2-hydroxyputrescine. The DNA G+C content was 60.1 mol%. The phylogenetic analysis and physiological and biochemical data showed that strain 122213-3T should be classified as representing a novel species in the genus Noviherbaspirillum , for which the name Noviherbaspirillum aerium sp. nov. is proposed. The type strain of N. aerium is 122213-3T (=CFCC 14286T=LMG 30131T).

Thermosipho ferrireducens sp.nov., an anaerobic thermophilic iron(III)-reducing bacterium isolated from a deep-sea hydrothermal sulfide deposits

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yao Chen ◽  
Yang He ◽  
Zongze Shao ◽  
Xiqiu Han ◽  
Danling Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Carlsberg Ridge

A thermophilic, anaerobic, iron-reducing bacterium strain JL129W03T (=KCTC 15905T=MCCC 1A14213T) was isolated from a sulfide sample collected from the Daxi hydrothermal field (60.5° E, 6.4° N, 2919 m depth) on the Carlsberg Ridge, northwest Indian Ocean. Cells grew at 55–75 °C(optimum, 70 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and at NaCl concentrations of 1.5–4.5 % (w/v; optimum 3.0 %). Under optimal growth conditions, the generation time was around 85 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, carbohydrates, organic acids and one amino acid. It was anaerobic and facultatively dependent on elemental sulphur and various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulphate, thiosulfate or nitrate. The G+C content of its genomic DNA was 34.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that its closest relative was Thermosipho atlanticus DV1140T with 95.81 % 16S rRNA sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Thermosipho , for which the name Thermosipho ferrireducens sp. nov. is proposed. The type strain is strain JL129W03T (=KCTC 15905T;=MCCC 1A14213T).

Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai–Tibet Plateau

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yanpeng Cheng ◽  
Yifan Jiao ◽  
Sihui Zhang ◽  
Jing Yang ◽  
Shan Lu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Tibet Plateau ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Qinghai Tibet Plateau

In the present study, four bacterial strains, two (S-713 T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531 T and 1598) from leaves of dandelion collected on the Qinghai–Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713 T /406 and S-531 T /1598 form two independent branches belonging to the genus Nocardioides , and are closest to Nocardioides lianchengensis , Nocardioides dokdonensis , Nocardioides salarius , Nocardioides marinisabuli , Nocardioides psychrotolerans and Nocardioides szechwanensis . Although sharing MK8-(H 4 ) as their major isoprenoid quinone, strains S-713 T and S-531 T contained C 18 : 1  ω 9 c (24.64 and 16.34 %) and iso-C 16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713 T and S-531 T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides , for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713 T (=JCM 33698 T =CGMCC 4.7660 T ) and S-531 T (=JCM 33468 T =CGMCC 4.7659 T ) as the respective type strains.

scholarly journals Falsirhodobacter deserti sp. nov., isolated from sandy soil

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 650-655 ◽  
Author(s):  
Lin Wang ◽  
Zhengfu Zhou ◽  
Gang Wu ◽  
Ming Chen ◽  
Min Lin ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Enrichment Culture ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Close Relationship ◽  
Pr China

A Gram-stain-negative, non-motile, heterotrophic, rod-shaped bacterium, designated strain W402T, was isolated from an enrichment culture of a Tamarix ramosissima rhizosphere soil sample from the Xinjiang desert in the PR China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to a species of the genus Falsirhodobacter , having a close relationship to Falsirhodobacter halotolerans JA744T (97 % similarity). However, DNA–DNA relatedness between W402T and F. halotolerans JA744T was 43.2±1.2 %. Strain W402T grew in 0–10 % (w/v) NaCl. The temperature and pH ranges for growth were 10–40 °C and pH 5.5–10.0, respectively. Optimal growth occurred at 1–3 % (w/v) NaCl, 30 °C and pH 7.0. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.4 %), C18 : 0 (9.8 %) and 11-methyl C18 : 1ω7c (8.2 %). The major quinone of strain W402T was Q-10. Phosphatidylethanolamine was predominant in the polar lipid profile. The DNA G+C content of strain W402T was 67.3 mol%. Taken together, these results confirm that W402T represents a novel species of the genus Falsirhodobacter , for which the name Falsirhodobacter deserti sp. nov. is proposed. The type strain is W402T ( = ACCC 05851T = KCTC 32408T).

scholarly journals Mesohalobacter halotolerans gen. nov., sp. nov., isolated from a marine solar saltern

2020 ◽  
Vol 70 (6) ◽  
pp. 3588-3596 ◽  
Author(s):  
Xi Feng ◽  
Jin-Yu Zhang ◽  
Jin Sang ◽  
Da-Shuai Mu ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-stain-negative, non-motile, fine rod or short filament shaped, jacinth pigmented bacterium, designated strain WDS2C27T, was isolated from a marine solar saltern in Wendeng, Weihai, PR China (37°31′5″ N, 122°1′47″ E). Growth of WDS2C27T occurred at 20–42 °C (optimum 37 °C) and pH 6.5–8.5 (optimal pH 7.0–8.0). Optimal growth occurred in modified marine broth containing 6 % (w/v) NaCl. The major polar lipids in WDS2C27T were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The major respiratory quinone of WDS2C27T was MK-6. The dominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 35.0 mol%. The nucleotide sequence of the 16S rRNA gene indicated that the most closely related strain was Psychroflexus planctonicus X15M-8T (92.0 % over 1452 bp). WDS2C27T showed 60.7 % average amino acid identity, 55.6 % percentage of conserved proteins, 75.0 % average nucleotide identity and 13.1 % digital DNA–DNA hybridization identity with the type species of the genus Psychroflexus , Psychroflexus torquis ATCC 700755T. The phenotypic and genotypic properties and phylogenetic inference indicated that WDS2C27T could be assigned to a novel species within a novel genus, for which the name Mesohalobacter halotolerans gen. nov., sp. nov. is proposed. Strain WDS2C27T (=MCCC 1H00133T=KCTC 52044T) is the type strain.

scholarly journals Mucilaginibacter glaciei sp. nov. and Mucilaginibacter pankratovii sp. nov., isolated from a glacier on the Tibetan Plateau

2020 ◽  
Author(s):  
Lei-Lei Yang ◽  
Yu Pang ◽  
Hong-Can Liu ◽  
Yu-Hua Xin ◽  
Qing Liu
Keyword(s):  
Tibetan Plateau ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
The Tibetan Plateau ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Pr China

Two Gram-stain-negative, aerobic, rod-shaped, non-motile, bacterial strains, designated as ZB1P21T and ZT4R22T, were isolated from ice and cryoconite samples collected from Zepu glacier on the Tibetan Plateau, PR China. The phylogenetic analysis of 16S rRNA gene showed that the two strains belong to the genus Mucilaginibacter . Strain ZB1P21T showed the highest similarity to Mucilaginibacter rigui WPCB133T (97.35 %), while strain ZT4R22T showed the highest similarity to Mucilaginibacter gilvus F01003T (99.11 %). The average nucleotide identity values between the two novel strains and their closest relatives were 79.42 and 85.72 % respectively. The two novel strains contained MK-7 as the major menaquinone, and summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15:0, iso-C17 : 03-OH and C16 : 1  ω5c as the major fatty acids. The major polar lipid of the two novel strains were phosphatidylethanolamine. Based on these data, we propose two novel species, Mucilaginibacter glaciei sp. nov. (ZB1P21T=CGMCC 1.23981T=NBRC 113932T) and Mucilaginibacter pankratovii sp. nov. (ZT4R22T=CGMCC 1.23487T=NBRC 113931T).

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Xue Zhang ◽  
Lida Zhang ◽  
XiaoYan Yu ◽  
Jing Zhang ◽  
Yanjie Jiao ◽  
...  
Keyword(s):  
Type Species ◽  
Cow Dung ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Pr China ◽  
Taxonomic Characterization ◽  
Reference Strains

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia , with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1  ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia , for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).

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