scholarly journals Massilia norwichensis sp. nov., isolated from an air sample

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 56-64 ◽  
Author(s):  
Ivana Orthová ◽  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
René Kaden ◽  
Hans-Jürgen Busse

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia . The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia . Major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C10 : 0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA–DNA hybridizations demonstrate that strain NS9T is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9T ( = CCUG 65457T = LMG 28164T).

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 754-759 ◽  
Author(s):  
Paulina Corral ◽  
Angela Corcelli ◽  
Antonio Ventosa

An extremely haloalkaphilic archaeon, strain T26T, belonging to the genus Halostagnicola , was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26T was closely related to Halostagnicola alkaliphila 167-74T (98.4 %), Halostagnicola larsenii XH-48T (97.5 %) and Halostagnicola kamekurae 194-10T (96.8 %). Strain T26T grew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg2+ was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26T was 60.1 mol% and DNA–DNA hybridization showed a relatedness of 19 and 17 % with Halostagnicola alkaliphila CECT 7631T and Halostagnicola larsenii CECT 7116T, respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA–DNA hybridization studies revealed that strain T26T belongs to the genus Halostagnicola , and represents a novel species for which the name Halostagnicola bangensis sp. nov. is proposed. The type strain is T26T ( = CECT 8219T = IBRC-M 10759T = JCM 18750T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1906-1911 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were Sphingobium amiense YTT, Sphingobium yanoikuyae GIFU 9882T and Sphingobium scionense WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus Sphingobium . The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus Sphingobium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus Sphingobium , for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).


2020 ◽  
Vol 70 (9) ◽  
pp. 5012-5018 ◽  
Author(s):  
Hui Zhao ◽  
Yinan Ma ◽  
Xiaogang Wu ◽  
Liqun Zhang

A Gram-stain-negative aerobic bacterium, strain 11K1T, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by using polyphasic taxonomy. The bacterial cells of strain 11K1T were rod-shaped, motile by two polar flagella and positive for oxidase and catalase. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain had the highest similarities to Pseudomonas thivervalensis DSM 13194T (99.52 %), Pseudomonas lini CFBP 5737T (99.45 %), Pseudomonas chlororaphis subsp. chlororaphi s NBRC 3904T (99.31 %), Pseudomonas kilonensis DSM 13647T (99.25 %) and Pseudomonas brassicacearum JCM11938T (99.24 %). Multilocus sequence analysis using the 16S rRNA, gyrB, rpoB and rpoD gene sequences demonstrated that strain 11K1T was a member of the Pseudomonas corrugata subgroup within the Pseudomonas fluorescens lineage, but was distant from all closely related species. The average nucleotide identity and in silico DNA–DNA hybridization values were lower than recommended thresholds of 95 and 70 %, respectively, for species delineation. The major isoprenoid quinone of strain 11K1T was ubiquinone (Q-9) and the major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and two unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain 11K1T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas viciae sp. nov. is proposed. The type strain is 11K1T (=GDMCC 1.1743T=KACC 21650T).


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3804-3809 ◽  
Author(s):  
Samantha J. Stropko ◽  
Shannon E. Pipes ◽  
Jeffrey D. Newman

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 .


2020 ◽  
Vol 70 (5) ◽  
pp. 3440-3448 ◽  
Author(s):  
Wen-Ming Chen ◽  
Tzu-Ying Chen ◽  
Che-Chia Yang ◽  
Shih-Yi Sheu

Bacterial strain TWA-58T, isolated from irrigation water in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TWA-58T formed a phylogenetic lineage in the genus Oleiharenicola of the family Opitutaceae . Strain TWA-58T was most closely related to Oleiharenicola alkalitolerans NVTT with a 96.7 % 16S rRNA gene sequence similarity. Strain TWA-58T showed 75.2 % average nucleotide identity, 70.9 % average amino acid identity and 21.0 % digital DNA–DNA hybridization identity with O. alkalitolerans NVTT. Cells were Gram-stain-negative, aerobic, motile, coccoid-shaped and formed transparent colonies. Optimal growth occurred at 25 °C, pH 6, and 0 % NaCl. The major fatty acids of strain TWA-58T were iso-C15 : 0 and anteiso-C15 : 0. The predominant hydroxy fatty acid was iso-C13 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TWA-58T was 65.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TWA-58T should be classified in a novel species of the genus Oleiharenicola , for which the name Oleiharenicola lentus sp. nov. is proposed. The type strain is TWA-58T (=BCRC 81161T=LMG 31019T=KCTC 62872T).


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1634-1639 ◽  
Author(s):  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
Takashi Itoh ◽  
...  

Two agar-degrading halophilic archaeal strains, 62ET and 197A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2–2.0 µm in diameter and stained Gram-negative. Colonies were pink-pigmented. Strain 62ET was able to grow with 24–30 % (w/v) NaCl (optimum, 27 %), at pH 6.5–8.5 (optimum, pH 7.5) and at 22–47 °C (optimum, 42 °C). The 16S rRNA gene sequences of strains 62ET and 197A were identical, and the level of DNA–DNA relatedness between them was 90 and 90 % (reciprocally). The closest relative was Halococcus saccharolyticus JCM 8878T with 99.7 % similarity in 16S rRNA orthologous gene sequences, followed by Halococcus salifodinae JCM 9578T (99.6 %), while similarities with other species of the genus Halococcus were equal to or lower than 95.1 %. The rpoB′ gene tree strongly supported that the two strains were members of the genus Halococcus . Mean DNA–DNA relatedness between strain 62ET and H. saccharolyticus JCM 8878T and H. salifodinae JCM 9578T was 46 and 44 %, respectively. The major polar lipids were archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, and sulfated diglycosyl archaeol-1. Several unidentified glycolipids were present. Based on the phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halococcus , for which the name Halococcus agarilyticus sp. nov. is proposed. The type strain is 62ET ( = JCM 19592T = KCTC 4143T).


2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1022-1030 ◽  
Author(s):  
Lei Zhang ◽  
Yuanyuan Pan ◽  
Kaibiao Wang ◽  
Xiaoxia Zhang ◽  
Cheng Zhang ◽  
...  

Strain NEAU-ST5-21T was isolated from saline and alkaline soils in Zhaodong City, Heilongjiang Province, China. It was aerobic, Gram-stain-negative, rod-shaped and motile with a polar flagellum. It produced yellow–orange colonies with a smooth surface, and grew in the presence of 0–5 % (w/v) NaCl (optimum 0 %, w/v), at temperatures of 20–40 °C (optimum 28 °C) and at pH 7–11 (optimum pH 7). Phylogenetic analyses based on the separate 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that strain NEAU-ST5-21T belongs to the genus Pseudomonas in the class Gammaproteobacteria . The most closely related species is Pseudomonas xanthomarina , whose type strain (KMM 1447T) showed gene sequence similarities of 99.0 % for 16S rRNA, 81.8 % for gyrB and 85.0 % for rpoD with strain NEAU-ST5-21T. DNA–DNA hybridization values between strain NEAU-ST5-21T and P. xanthomarina DSM 18231T, Pseudomonas kunmingensis CGMCC 1.12273T, Pseudomonas stutzeri DSM 5190T, Pseudomonas oleovorans subsp. lubricantis DSM 21016T, Pseudomomas chengduensis CGMCC 2318T, Pseudomonas alcaliphila DSM 17744T and Pseudomonas toyotomiensis DSM 26169T were 52±0 % to 25±2 %. The DNA G+C content of strain NEAU-ST5-21T was 65 mol%. The major fatty acids (>10 %) were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 1ω7c and/or C16 : 1ω6c and C16 : 0, the predominant respiratory quinone was ubiquinone 9, and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid, phosphatidylglycerol, one unknown aminolipid, one unknown lipid and a glycolipid. The proposed name is Pseudomonas zhaodongensis sp. nov., NEAU-ST5-21T ( = ACCC 06362T = DSM 27559T) being the type strain.


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1479-1484 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated WT-MW11T, was isolated from wood falls on the coast of Wando, an island of South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain WT-MW11T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0–3.0 % (w/v) NaCl. Bacteriochlorophyll a was not produced. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MW11T clustered with Pseudorhodobacter ferrugineus IAM 12616T and Pseudorhodobacter aquimaris HDW-19T, with which it exhibited 16S rRNA gene sequence similarity values of 97.9 and 95.5 %, respectively. Strain WT-MW11T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain WT-MW11T was similar to those of P. ferrugineus JCM 20687T and P. aquimaris HDW-19T. The DNA G+C content of strain WT-MW11T was 61.6 mol% and its mean DNA–DNA relatedness value with P. ferrugineus JCM 20687T was 12.3 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MW11T was distinguishable from the two recognized species of the genus Pseudorhodobacter . On the basis of the data presented, strain WT-MW11T is considered to represent a novel species of the genus Pseudorhodobacter , for which the name Pseudorhodobacter wandonensis sp. nov. is proposed. The type strain is WT-MW11T ( = KCTC 23672T = CCUG 61506T). The description of the genus Pseudorhodobacter is emended.


Author(s):  
Chao-Nan Wang ◽  
Feng-Qing Wang ◽  
Yuan Liu ◽  
Ming-Yi Wang ◽  
Zong-Jun Du

A novel Gram-stain-negative, short rod-shaped, facultatively anaerobic, non-motile, non-gliding, oxidase-positive and catalase-negative bacterium, designated ML27T, was isolated from oyster homogenate in Rushan, Weihai, PR China. Growth occurred at 20–33 °C (optimum, 30 °C), at pH 7.0–9.0 (optimum, pH 7.5–8.0) and in the presence of 1–6 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ML27T was 90.7 % similar to Suttonella ornithocola DSM 18249T, 89.2 % to Suttonella indologenes JCM 1478T and 88.2 % to Cardiobacterium hominis DSM 8339T; similarities to other species were less than 90 %. The average amino acid identity between strain ML27T, S. indologenes JCM 1478T, S. ornithocola DSM 18249T, C. hominis DSM 8339T and Dichelobacter nodosus ATCC 25549T were 46.23, 45.86, 45.54 and 45.84 %, respectively. Phylogenomic tree and phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate formed a novel family-level clade in the order Cardiobacteriales . The sole respiratory quinone was ubiquinone-7 (Q-7). The dominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 46.3 %), C16 : 0 (17.8 %) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 13.5 %). The DNA G+C content of strain ML27T was 45.6 mol%. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified lipid. Comparative analyses of 16S rRNA gene sequences, genomic distinctiveness and characterization indicated that strain ML27T represents a novel species of a new genus within a novel family of the order Cardiobacteriales , for which the name Ostreibacterium oceani gen. nov., sp. nov. is proposed. The type strain of Ostreibacterium oceani is ML27T (=MCCC 1H00372T=KCTC 72155T). In addition, a novel family, Ostreibacteriaceae fam. nov., is proposed to accommodate the genus Ostreibacterium.


2020 ◽  
Vol 70 (4) ◽  
pp. 2888-2895 ◽  
Author(s):  
Wen-Ming Chen ◽  
Tzu-Ying Chen ◽  
Soon-Wo Kwon ◽  
Shih-Yi Sheu

A novel bacterial strain, designated KMB7T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed cream colonies. Optimal growth occurred at 25 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain KMB7T is affiliated with species in the genus Aquabacterium . The 16S rRNA gene sequence similarity indicated that strain KMB7T is closely related to species within the genus Aquabacterium (95.2–97.6 % sequence similarity) and is most similar to A. fontiphilum CS-6T (97.6 %), followed by A. parvum B6T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization identity between strain KMB7T and the closely related strains were 74.6–78.0 % and 19.0–21.2 %, respectively. The major fatty acids of strain KMB7T were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C18 : 1  ω7c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unidentified phospholipids. The sole isoprenoid quinone was ubiquinone-8 (Q-8). Genomic DNA G+C content of strain KMB7T was 65.4 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KMB7T should be classified in a novel species of the genus Aquabacterium , for which the name Aquabacterium lacunae sp. nov. is proposed. The type strain is KMB7T (=BCRC 81156T=LMG 30924T=KCTC 62867T).


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