Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 821-826 ◽  
Author(s):  
José-David Flores-Félix ◽  
Lorena Carro ◽  
Encarna Velázquez ◽  
Ángel Valverde ◽  
Eugenia Cerda-Castillo ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Northern Spain ◽  
Content Type ◽  
Link Type

A strain, PEPV15T, was isolated from a nodule on Phaseolus vulgaris grown in soil in northern Spain. Phylogenetic analyses of 16S rRNA and atpD genes showed that this strain belongs to the genus Phyllobacterium . The most closely related species were, in both cases, Phyllobacterium brassicacearum , Phyllobacterium bourgognense and Phyllobacterium trifolii , the type strains of which gave sequence similarities of 98.9, 98.6 and 98.4 %, respectively, in the 16S rRNA gene and 88.1, 87.5 and 88.7 %, respectively, in the atpD gene. PEPV15T contained Q-10 as the major quinone (88 %) and low amounts of Q-9 (12 %). It differed from its closest relatives in its growth in diverse culture conditions and in the assimilation of several carbon sources. The strain was not able to produce nodules in Phaseolus vulgaris. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium for which the name Phyllobacterium endophyticum sp. nov. is proposed; the type strain is PEPV15T ( = LMG 26470T = CECT 7949T). An emended description of the genus Phyllobacterium is also provided.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Endophytic Actinobacterium

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Peng Wang ◽  
Yuxin Gao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Desert Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).

Sphingobium fontiphilum sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1906-1911 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

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).

Bizionia hallyeonensis sp. nov., isolated from seawater in an oyster farm

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 685-690 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Chul-Hyung Kang ◽  
Yong-Taek Jung ◽  
So-Jung Kang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Oyster Farm

A Gram-staining-negative, non-spore-forming, aerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain T-y7T, was isolated from seawater collected in an oyster farm in the South Sea, South Korea, and subjected to a polyphasic study. Strain T-y7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain T-y7T fell within a clade comprising Bizionia species. It formed a coherent cluster with the type strains of Bizionia algoritergicola , B. argentinensis , B. echini and B. myxarmorum , with which it exhibited 16S rRNA gene sequence similarities of 97.4–98.9 % and mean DNA–DNA relatedness values of 11–27 %. Strain T-y7T had MK-6 as its predominant menaquinone and iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH as its major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The genomic DNA G+C content was 37.1 mol%. Its phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain T-y7T does not belong to any established Bizionia species. On the basis of the data presented, strain T-y7T is considered to represent a novel species of the genus Bizionia , for which the name Bizionia hallyeonensis sp. nov. is proposed. The type strain is T-y7T ( = KCTC 23881T  = CCUG 62110T).

Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2277-2281 ◽  
Author(s):  
Eu Jin Chung ◽  
Jeong Ae Park ◽  
Prabhat Pramanik ◽  
Fehmida Bibi ◽  
Che Ok Jeon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Pythium Ultimum ◽  
Rrna Gene ◽  
Content Type ◽  
Suaeda Maritima ◽  
Link Type

A Gram-negative, aerobic, short rod-shaped bacterium, designated strain YC6898T, was isolated from the surface-sterilized root of a halophyte (Suaeda maritima) inhabiting tidal flat of Namhae Island, Korea. Strain YC6898T grew optimally at 30–37 °C and pH 6.5–7.5. The strain inhibited mycelial growth of Pythium ultimum and Phytophthora capsici. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC6898T belongs to the genus Hoeflea in the family Phyllobacteriaceae . Its closest relatives were Hoeflea alexandrii AM1V30T (96.7 % 16S rRNA gene sequence similarity), Hoeflea anabaenae WH2KT (95.7 %), Hoeflea phototrophica DFL-43T (95.5 %) and Hoeflea marina LMG 128T (94.8 %). Strain YC6898T contained Q-10 as the major ubiquinone. The major fatty acids of strain YC6898T were C18 : 1ω7c (61.1 %), C16 : 0 (11.9 %), 11-methyl C18 : 1ω7c (9.6 %) and C19 : 0 cyclo ω8c (8.0 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unknown lipids and an unknown glycolipid. The total genomic DNA G+C content was 53.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain YC6898T represents a novel species of the genus Hoeflea , for which the name Hoeflea suaedae sp. nov. is proposed. The type strain is YC6898T ( = KACC 14911T = NBRC 107700T).

Gryllotalpicola gen. nov., with descriptions of Gryllotalpicola koreensis sp. nov., Gryllotalpicola daejeonensis sp. nov. and Gryllotalpicola kribbensis sp. nov. from the gut of the African mole cricket, Gryllotalpa africana, and reclassification of Curtobacterium ginsengisoli as Gryllotalpicola ginsengisoli comb. nov.

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2363-2370 ◽  
Author(s):  
Hyangmi Kim ◽  
Doo-Sang Park ◽  
Hyun-Woo Oh ◽  
Kang Hyun Lee ◽  
Dong-Ho Chung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Mole Cricket ◽  
Link Type ◽  
The Family

Strains RU-16T, RU-28, RU-04T and PU-02T were isolated from the gut of the African mole cricket, Gryllotalpa africana. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belonged to the family Microbacteriaceae . All four strains were most closely related to Curtobacterium ginsengisoli DCY26T (below 97 % 16S rRNA gene sequence similarity). These isolates were Gram-stain-positive, motile (by gliding), rod-shaped and exhibited ivory-coloured colonies. Their chemotaxonomic properties included MK-11 as the major respiratory quinone, ornithine as the cell-wall diamino acid, acetyl as the acyl type of the peptidoglycan, cyclohexyl-C17 : 0 as the major fatty acid and phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, we propose a new genus in the family Microbacteriaceae , Gryllotalpicola gen. nov., with three novel species, Gryllotalpicola daejeonensis sp. nov. (type strain RU-04T  = KCTC 13809T  = JCM 17590T), Gryllotalpicola koreensis sp. nov. (type strain RU-16T  = KCTC 13810T  = JCM 17591T) and Gryllotalpicola kribbensis sp. nov. (type strain PU-02T  = KCTC 13808T  = JCM 17593T). Gryllotalpicola koreensis is the type species of the genus. Additionally, we propose that Curtobacterium ginsengisoli should be reclassified in the genus as Gryllotalpicola ginsengisoli comb. nov. (type strain DCY26T  = KCTC 13163T  = JCM 14773T).

Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to Methylobacterium organophilum ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus Methylobacterium , for which the names Methylobacterium haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and Methylobacterium brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.

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