Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 604-609 ◽  
Author(s):  
Liqiong Li ◽  
Hongliang Liu ◽  
Zunji Shi ◽  
Gejiao Wang
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Resistant Bacterium ◽  
Rrna Gene ◽  
Mine Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Copper Mine ◽  
Link Type ◽  
Emended Description

A Gram-negative, aerobic, copper-resistant bacterium, designated strain CU4T, was isolated from copper mine soil in Daye, China. Phylogenetic analysis based on 16S rRNA gene sequences showed highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.4 %), followed by Sphingobium francense Sp+T (97.2 %), Sphingobium japonicum UT26T (97.1 %), Sphingobium abikonense NBRC 16140T (97.0 %), Sphingobium xenophagum DSM 6383T (96.9 %) and Sphingobium yanoikuyae DSM 7462T (95.5 %). The major fatty acids (>5 %) were summed feature 7 (C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), summed feature 4 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH, and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylcholine. The genomic DNA G+C content of strain CU4T was 64.9 mol%. Comparison of DNA–DNA hybridization, phenotypic and chemotaxonomic characteristics between strain CU4T and phylogenetically related strains revealed that the new isolate represents a novel species of the genus Sphingobium , for which the name Sphingobium cupriresistens sp. nov. is proposed. The type strain is CU4T ( = KCTC 23865T = CCTCC AB 2011146T). An emended description of the genus Sphingobium is also proposed.

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.

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2607-2611 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Joon Yong Kim ◽  
Ji-Hyun Yun ◽  
Dong-Wook Hyun ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Intestinal Tract ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis ◽  
Emended Description

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33T, was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33T grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33T contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33T was most closely related to Gibbsiella quercinecans FRB 97T and Gibbsiella dentisursi NUM 1720T, with 98.7 % similarities. DNA–DNA hybridization experiments indicated less than 40.7±2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97T. The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33T represents a novel species within the genus Gibbsiella , for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33T ( = KACC 16707T = JCM 18389T). An emended description of the genus Gibbsiella is also proposed.

scholarly journals Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas

2020 ◽  
Vol 70 (4) ◽  
pp. 2657-2663 ◽  
Author(s):  
Shasha Wang ◽  
Lijing Jiang ◽  
Xuewen Liu ◽  
Suping Yang ◽  
Zongze Shao
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Elemental Sulfur ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Emended Description

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .

scholarly journals Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1790-1798 ◽  
Author(s):  
V. Venkata Ramana ◽  
S. Kalyana Chakravarthy ◽  
P. Shalem Raj ◽  
B. Vinay Kumar ◽  
E. Shobha ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rhodopseudomonas Palustris ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Geographical Regions ◽  
Emended Description ◽  
Type Strains

Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

scholarly journals Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4038-4042 ◽  
Author(s):  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Ji Hee Lee ◽  
Sang Suk Lee ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A non-motile and rod-shaped bacterium, designated strain 02SUJ3T, was isolated from freshwater collected from the Juam Reservoir (Republic of Korea). Cells were Gram-stain-negative, aerobic, oxidase-negative and catalase-positive. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The strain contained MK-7 as the major isoprenoid quinone. The main polar lipid was phosphatidylethanolamine. The DNA G+C content was 46.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 02SUJ3T forms an independent lineage within the genus Flavisolibacter with low sequence similarity to Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T (95.7 %). Phenotypic characteristics distinguished strain 02SUJ3T from members of the genus Flavisolibacter . On the basis of the evidence presented in this study, strain 02SUJ3T is considered to represent a novel species, for which the name Flavisolibacter rigui sp. nov. is proposed. The type strain is 02SUJ3T ( = JCM 17515T = KCTC 23328T). An emended description of the genus Flavisolibacter is also provided.

scholarly journals Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 562-569 ◽  
Author(s):  
Hong Cheng ◽  
Shun Zhang ◽  
Ying-Yi Huo ◽  
Xia-Wei Jiang ◽  
Xin-Qi Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Hydrolysis Of ◽  
Sequence Similarities

A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Antonio Castellano-Hinojosa ◽  
David Correa-Galeote ◽  
Martha-Helena Ramírez-Bahena ◽  
Germán Tortosa ◽  
Jesús González-López ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

scholarly journals Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3804-3809 ◽  
Author(s):  
Samantha J. Stropko ◽  
Shannon E. Pipes ◽  
Jeffrey D. Newman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Emended Description

While characterizing a related strain, it was noted that there was little difference between the 16S rRNA gene sequences of Bacillus indicus LMG 22858T and Bacillus cibi DSM 16189T. Phenotypic characterization revealed differences only in the utilization of mannose and galactose and slight variation in pigmentation. Whole genome shotgun sequencing and comparative genomics were used to calculate established phylogenomic metrics and explain phenotypic differences. The full, genome-derived 16S rRNA gene sequences were 99.74 % similar. The average nucleotide identity (ANI) of the two strains was 98.0 %, the average amino acid identity (AAI) was 98.3 %, and the estimated DNA–DNA hybridization determined by the genome–genome distance calculator was 80.3 %. These values are higher than the species thresholds for these metrics, which are 95 %, 95 % and 70 %, respectively, suggesting that these two strains should be classified as members of the same species. We propose reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and an emended description of Bacillus indicus .

scholarly journals Sneathiella chungangensis sp. nov., isolated from a marine sand, and emended description of the genus Sneathiella

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1468-1472 ◽  
Author(s):  
Chatuphon Siamphan ◽  
Hyungjin Kim ◽  
Jung-Sook Lee ◽  
Wonyong Kim
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Sand Sample ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Marine Sand ◽  
Emended Description

A Gram-stain-negative, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1294T, was isolated from a sand sample and its taxonomic position was investigated using a polyphasic approach. The strain grew optimally at pH 6.5 and 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1294T formed a lineage with member of the genus Sneathiella and exhibited similarity to Sneathiella glossodoripedis MKT133T (96.3 % similarity) and Sneathiella chinensis LMG 23452T (95.1 % similarity). Strain CAU 1294T contained Q-10 as the predominant respiratory quinone. C18 : 1ω7c, C16 : 0 and cyclo-C19 : 0ω8c were the major cellular fatty acids. The polar lipids were composed of phosphatidylethanolamine, phosphatidylmethylethanolamine and two unidentified phospholipids. The DNA G+C content was 56.6 mol%. On the basis of these results, strain CAU 1294T is considered to represent a novel species of the genus Sneathiella , for which the name Sneathiella chungangensis is proposed. The type strain is CAU 1294T ( = KCTC 32476T = CECT 8513T). An emended description of the genus Sneathiella is also proposed.

scholarly journals Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2400-2406 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Watanalai Panbangred ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

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