scholarly journals Chitinophaga tropicalis sp. nov., isolated from forest soil

2020 ◽  
Vol 70 (6) ◽  
pp. 3859-3864 ◽  
Author(s):  
Xian-Jiao Zhang ◽  
Guang-Da Feng ◽  
Qing Yao ◽  
Jun Zhang ◽  
Le Thi Bich Phuong ◽  
...  
Keyword(s):  
Forest Soil ◽  
Dna Hybridization ◽  
National Park ◽  
Type Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Cat Tien National Park ◽  
Type Strains

A novel bacterial strain, designated ysch24T, was isolated from a forest soil sample collected from the Cat Tien National Park, southern Vietnam. Cells were Gram-stain-negative, aerobic, gliding, filamentous or rod-shaped. The results of 16S rRNA gene analyses revealed that strain ysch24T belongs to the genus Chitinophaga , and was most closely related to Chitinophaga silvisoli GDMCC 1.1411T (97.4 %), followed by Chitinophaga oryziterrae JCM 16595T (97.3 %) and Chitinophaga sancti NBRC 15057T (96.9 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain ysch24T and closely related type strains were 72.0–74.0 % and 19.1–19.4 %, respectively. Major fatty acids were iso-C15 : 0, C16 : 1  ω5c and iso-C17 : 0 3-OH and the predominant respiratory quinone was menaquinone 7. Polar lipids consisted of phosphatidylethanolamine, four unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. The genomic DNA G+C content was 45.6 mol%. The study clearly showed that strain ysch24T should represent a novel species of the genus Chitinophaga , for which the name Chitinophaga tropicalis sp. nov. is proposed. The type strain is ysch24T (=GDMCC 1.1355T=KACC 21527T).

scholarly journals Zoogloea dura sp. nov., a N2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera

2020 ◽  
Vol 70 (10) ◽  
pp. 5312-5318 ◽  
Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Type Strains ◽  
Zoogloea Ramigera

A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14T, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28–35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14T formed a lineage within the genus Zoogloea . The closest members were Zoogloea resiniphila ATCC 70068T (98.6 % sequence similarity), Zoogloea caeni EMB43T (98.2 %), Zoogloea oryzae A-7T (97.7 %), Zoogloea ramigera IAM 12136T (96.9 %) and Zoogloea oleivorans BucT (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16  : 1 ω7c) and C16 : 0. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain G-4-1-14T and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14T represents a novel species in the genus Zoogloea , for which the name Zoogloea dura sp. nov. is proposed. The type strain is G-4-1-14T (=KACC 21618T=NBRC 114358T). In addition, we propose emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera .

scholarly journals Pseudomonas helmanticensis sp. nov., isolated from forest soil

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2338-2345 ◽  
Author(s):  
Martha-Helena Ramírez-Bahena ◽  
Maria José Cuesta ◽  
José David Flores-Félix ◽  
Rebeca Mulas ◽  
Raúl Rivas ◽  
...  
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phosphate Solubilizing Bacteria ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Phylogenetic Affiliation ◽  
Type Strains

A bacterial strain, OHA11T, was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11T shared 99.1 % similarity with respect to Pseudomonas baetica a390T, and 98.9 % similarity with the type strains of Pseudomonas jessenii , Pseudomonas moorei , Pseudomonas umsongensis , Pseudomonas mohnii and Pseudomonas koreensis . The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus Pseudomonas and showed similarities lower than 95 % in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The strain was oxidase-, catalase- and urease-positive, positive for arginine dihydrolase but negative for nitrate reduction, β-galactosidase production and aesculin hydrolysis. It was able to grow at 31 °C and at pH 11. The DNA G+C content was 58.1 mol%. DNA–DNA hybridization results showed values lower than 49 % relatedness with respect to the type strains of the seven closest related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strain OHA11T to a novel species of the genus Pseudomonas , for which the name Pseudomonas helmanticensis sp. nov. is proposed. The type strain is OHA11T ( = LMG 28168T = CECT 8548T).

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%.

Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Su Jung ◽  
Byung Hee Chun ◽  
Hyung Min Kim ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27T and SE-s28T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25–30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28T produced flexirubin-type pigments, but strain SE-s27T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27T contained iso-C15 : 1 and iso-C15 : 1G, whereas SE-s28T contained iso-C15 : 0 and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH. The DNA G+C contents of strains SE-s27T and SE-s28T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27T and SE-s28T formed respective distinct phylogenetic lineages within the genus Flavobacterium . Strains SE-s27T and SE-s28T were most closely related to Flavobacterium macrobrachii an-8T and Flavobacterium piscinae ICH-30T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27T and SE-s28T represent novel species of the genus Flavobacterium , for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27T (=KACC 18802T=JCM 31544T) and SE-s28T (=KACC 18803T=JCM 31545T), respectively.

Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Yan Gao ◽  
Guangyu Li ◽  
Chen Fang ◽  
Zongze Shao ◽  
Yue-Hong Wu ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Overlying Water ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, rod-shaped and aerobic bacterial strain, named Ery12T, was isolated from the overlying water of the Lau Basin in the Southwest Pacific Ocean. Strain Ery12T showed high 16S rRNA gene sequences similarity to Tsuneonella flava MS1-4T (99.9 %), T. mangrovi MCCC 1K03311T (98.1 %), Altererythrobacter ishigakiensis NBRC 107699T (97.3 %) and exhibited ≤97.0 % sequence similarity with other type strains of species with validly published names. Growth was observed in media with 0–10.0 % NaCl (optimum 0–1.0 %, w/v), pH 5.0–9.5 (optimum 6.0–7.0) and 10–42 °C (optimum 30–37 °C). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acid was summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The major polar lipids were sphingoglycolipid, phosphatidyglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified glycolipids, one unidentified aminoglycolipid and one unidentified lipid. The DNA G+C content was 60.8 %. The ANI and in silico DDH values between strain Ery12T and the type strains of its closely related species were 71.0- 91.8 % and 19.5- 44.6 %, respectively. According to the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain Ery12T represents a novel species of the genus Tsuneonella , for which the name Tsuneonella suprasediminis is proposed. The type strain is Ery12T (=CGMCC 1.16500 T=MCCC 1A04421T=KCTC 62388T). We further propose to reclassify Altererythrobacter rhizovicinus and Altererythrobacter spongiae as Pelagerythrobacter rhizovicinus comb. nov. and Altericroceibacterium spongiae comb. nov., respectively.

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.

Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4081-4086 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Xiu Chen ◽  
Xiao-Mei Zhang ◽  
Xiao-Yang Zhi ◽  
Ji-Cheng Yao ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Cell Protein ◽  
Rrna Gene ◽  
Good Growth ◽  
Sand Sample ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Two novel isolates of rapidly growing, Gram-stain-positive, non-chromogenic species of the genus Mycobacterium , strain YIM M13028T from a sediment sample collected from the South China Sea (19° 30.261′ N 111° 0.247′ E) at a depth of 42 m and strain YIM 121001T from a coastal zone sand sample collected in Dubai, United Arab Emirates, were obtained in our laboratory. Their taxonomic positions were determined by a polyphasic approach. Good growth of the two strains was observed at 28 °C and pH 7.0 with 0–2 % NaCl on tryptic soy agar medium. Both strains formed round orange–red colonies, strain YIM M13028T had a rough surface, while YIM 121001T was smooth. Cellular fatty acids, whole-cell protein profiles and TLC analysis of their mycolic acids show significant differences from reference stains. Phenotypic characteristics and multilocus sequence analysis (MLSA) of 16S rRNA gene, hsp65, rpoB and 16S–23S internal transcribed spacer (ITS) sequences indicated that both strains YIM M13028T and YIM 121001T belong to the genus Mycobacterium . DNA–DNA hybridization values revealed a low relatedness (<70 %) of the two isolates with the type strains Mycobacterium neoaurum DSM 44074T and Mycobacterium hodleri DSM 44183T. The low DNA–DNA hybridization values (40.4±3.5 %) between strains YIM M13028T and YIM 121001T and phenotypic distinctiveness indicated that the two strains were representatives of different novel species of the genus Mycobacterium . The names proposed for these novel species are Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., and the type strains are YIM M13028T ( = DSM 45643T = KCTC 19999T) and YIM 121001T ( = DSM 45768T = JCM 18538T), respectively.

scholarly journals Description of Kribbella italica sp. nov., isolated from a Roman catacomb

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 491-496 ◽  
Author(s):  
Gareth J. Everest ◽  
Sarah M. Curtis ◽  
Filomena De Leo ◽  
Clara Urzì ◽  
Paul R. Meyers
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).

Lysinibacillus manganicus sp. nov., isolated from manganese mining soil

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3568-3573 ◽  
Author(s):  
Hongliang Liu ◽  
Yumei Song ◽  
Fang Chen ◽  
Shixue Zheng ◽  
Gejiao Wang
Keyword(s):  
Cell Wall ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Mining Soil ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were Lysinibacillus massiliensis CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), L. xylanilyticus XDB9T (96.7 %), L. sinduriensis JCM 15800T (96.2 %), L. odysseyi NBRC 100172T (95.9 %) and L. boronitolerans NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of L. massiliensis and L. sinduriensis were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).

scholarly journals Novosphingobium silvae sp. nov., isolated from subtropical forest soil

2020 ◽  
Vol 70 (4) ◽  
pp. 2901-2906 ◽  
Author(s):  
Guang-Da Feng ◽  
Wendi Chen ◽  
Jun Zhang ◽  
Yong-Hong Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Subtropical Forest ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A novel bacterial strain, designated FGD1T, was isolated from subtropical forest soil of the Nanling National Forest Park located in Guangdong Province, P.R. China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FGD1T was most closely related to Novosphingobium lindaniclasticum DSM 25049T (98.8 %), followed by N. barchaimii DSM 25411T (98.7 %), N. guangzhouense DSM 32207T (98.2 %), N. panipatense DSM 22890T (98.1 %) and other species of Novosphingobium (<98 %). The draft genome sequence was 4.58 Mb in length with a G+C content of 65.1 mol%. The calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain FGD1T and closely related type strains were 77.7‒79.6 % and 21.7–22.9 %, respectively. Major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C14 : 0 2-OH and C16 : 0. The predominant respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and lipid. The polyphasic taxonomic results indicated that strain FGD1T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium silvae sp. nov. is proposed. The type strain is FGD1T (=GDMCC 1.1761T=KACC 21283T).

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