Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 442-448 ◽  
Author(s):  
Samson Viulu ◽  
Kohei Nakamura ◽  
Yurina Okada ◽  
Sakiko Saitou ◽  
Kazuhiro Takamizawa
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Physiological Tests ◽  
Straight Rod

A novel species of Fe(III)-reducing bacterium, designated strain OSK6T, belonging to the genus Geobacter , was isolated from lotus field mud in Japan. Strain OSK6T was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l−1. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6T was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6T is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6T is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6T ( = DSM 24905T = JCM 17780T).

Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3868-3872 ◽  
Author(s):  
Jung Moon Hwang ◽  
Eu Jin Chung ◽  
Jeong Ae Park ◽  
Jae Heon Jeong ◽  
Che Ok Jeon ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Ubiquinone 10

A novel bacterial strain, YC6899T, was isolated from the root of Suaedae maritima growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899T grew optimally at a salinity of 2–4 %, at 25–37 °C and at pH 6.5–8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899T was closely related to Amorphus orientalis YIM D10T (96.1 % similarity) and Amorphus coralli RS.Sph.026T (95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899T were C19 : 0 cyclo ω8c and C18 : 1ω7c. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899T contained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899T represents a novel species within the genus Amorphus , for which the name Amorphus suaedae sp. nov. is proposed. The type strain is YC6899T ( = KACC 14912T = NBRC 107845T).

scholarly journals Mucilaginibacter aquaedulcis sp. nov., isolated from fresh water

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 698-703 ◽  
Author(s):  
Yochan Joung ◽  
Heeyoung Kang ◽  
Beom-Il Lee ◽  
Haneul Kim ◽  
Kiseong Joh ◽  
...  
Keyword(s):  
Fresh Water ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
The Republic

An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain PGW1-R01T, was isolated from fresh water from the Yeongju in the Republic of Korea. The strain grew optimally at 30 °C and at pH 6-8 on R2A agar. The major cellular fatty acids were summed feature 3 [comprising C16 : 1ω7c and/or C16 : 1ω6c (50.2 %) and iso-C15 : 0 (24.8 %)]. The major respiratory quinone was MK-7. The G+C contents were 39.4 mol% and the predominant respiratory quinone was MK-7. Based on 16S rRNA gene phylogeny, the strain belongs to the genus Mucilaginibacter . The strain PGW1-R01T was closely related to ‘ Mucilaginibacter ginsenosidivorax’ (96.6 % sequence similarity), Mucilaginibacter lappiensis (96.4 %) and Mucilaginibacter flavus (96.4 %). On the basis of the evidence presented in this study, strain PGW1-R01T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter http://dx.doi.org/10.1601/nm.11437 aquaedulcis sp. nov., is proposed. The type strain is PGW1-R01T( = KCTC 23942T = CECT 8102T).

scholarly journals Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 845-850 ◽  
Author(s):  
Xiao-Mei Ye ◽  
Cui-Wei Chu ◽  
Chao Shi ◽  
Jian-Chun Zhu ◽  
Qin He ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Major Respiratory Quinone

Strain BUT-8T, a Gram-stain-negative, non-motile and rod-shaped aerobic bacterium, was isolated from the activated sludge of a herbicide-manufacturing wastewater treatment facility. Comparative 16S rRNA gene sequence analysis revealed that strain BUT-8T clustered with species of the genus Lysobacter and was closely related to Lysobacter ruishenii DSM 22393T (98.3 %) and Lysobacter daejeonensis KACC 11406T (98.7 %). The DNA G+C content of the genomic DNA was 70.6 mol%. The major respiratory quinone was ubiquinone-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 010-methyl). The DNA–DNA relatedness between strain BUT-8T and its closest phylogenetic neighbours was below 70 %. Phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain BUT-8T belongs to the genus Lysobacter and represents a novel species for which the name Lysobacter caeni sp. nov. is proposed. The type strain is BUT-8T ( = CCTCC AB 2013087T = KACC 17141T).

scholarly journals Arachidicoccus soli sp. nov., a bacterium isolated from soil

2020 ◽  
Author(s):  
Shin Ae Lee ◽  
Tae-Wan Kim ◽  
Mee-Kyung Sang ◽  
Jaekyeong Song ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10–33 °C, pH 6.0–7.5 and with 0–4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA–DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus . The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus , for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).

Idiomarina indica sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2497-2500 ◽  
Author(s):  
Lei Song ◽  
Fei Ren ◽  
Ying Huang ◽  
Xin Dai ◽  
Yuguang Zhou
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Major Respiratory Quinone ◽  
The Indian Ocean

Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SW104T and X07, were isolated from a seawater sample collected from the Indian Ocean. The strains grew at a temperature range of 12–50 °C (optimum, 35–37 °C), and at pH 6.0–9.0 (optimum pH 7.0–7.5). The predominant cellular fatty acids of strain SW104T were iso-C15 : 0 (41.2 %), iso-C17 : 1ω9c (15.2 %) and iso-C17 : 0 (11.1 %). The major respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C contents of strains SW104T and X07 were 49.8 and 49.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Idiomarina , showing the highest similarity with Idiomarina taiwanensis PIT1T and Idiomarina maritima 908087T (96.1 and 95.9 %, respectively). On the basis of phenotypic, genotypic and phylogenetic characteristics, it is proposed that strains SW104T and X07 should be described as representatives of a novel species of the genus Idiomarina , for which the name Idiomarina indica sp. nov. is proposed. The type strain is SW104T ( = CGMCC 1.10824T = JCM 18138T).

scholarly journals Pseudogulbenkiania gefcensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 187-191 ◽  
Author(s):  
Dong-Geol Lee ◽  
Dong-Moon Im ◽  
HeeCheol Kang ◽  
Pyeong Yun ◽  
Sun-Ki Park ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies ◽  
Major Respiratory Quinone ◽  
Rrna Gene Sequencing

A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16T were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5T. Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5T (95.9 % similarity), Paludibacterium yongneupense 5YN8-15T (95.2 % similarity), Gulbenkiania mobilis E4FC31-5T (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1T (93.9 % similarity). The isolate was able to grow at 25–40 °C, 0.3–2 % NaCl and pH 5.5–7. The DNA G+C content was 65.9±1.0 mol%. The predominant fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16:0. Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania . The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16T ( = KCCM 90100T = JCM 17850T).

scholarly journals Raineyella fluvialis sp. nov., an actinobacterium isolated from freshwater sediment

2020 ◽  
Vol 70 (7) ◽  
pp. 4298-4304 ◽  
Author(s):  
Yeon Bee Kim ◽  
Joon Yong Kim ◽  
Hye Seon Song ◽  
Changsu Lee ◽  
Juseok Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Major Respiratory Quinone

A novel, facultatively anaerobic actinobacterium, designated strain CBA3103T, was isolated from sediment of the Geum River in South Korea. Phylogenetic analysis indicated that strain CBA3103T is most closely related to Raineyella antarctica LZ-22T (98.47 % 16S rRNA gene sequence similarity). The genome of strain CBA3103T was 3 649 865 bp with a DNA G+C content of 69.6 mol%. The average nucleotide identity value between strain CBA3103T and R. antarctica LZ-22T was 79.22 %. Cells of strain CBA3103T were Gram-positive, rod-shaped, 0.6–0.9 µm wide and 1.4–2.4 µm long. Growth occurred at 15–40 °C (optimum, 35 °C), at pH 6.0–7.0 (optimum, pH 7.0) and with 0–2 % NaCl (w/v) (optimum, 0–1 %, w/v). The major cellular fatty acids in strain CBA3103T were anteiso-C15 : 0, anteiso-C15 : 1 A and iso-C14 : 0. The major respiratory quinone was menaquinone-9(H4). The polar lipids of strain CBA3103T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified glycolipids and three unidentified phospholipids. Based on the genotypic, phenotypic and chemotaxonomic analyses, strain CBA3103T represents a novel species of the genus Raineyella , for which the name Raineyella fluvialis sp. nov. (type strain CBA3103T=KACC 21446T=DSM 110288T) is proposed.

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense , Flavobacterium saliperosum and Flavobacterium suncheonense

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 886-892 ◽  
Author(s):  
Kun Dong ◽  
Fang Chen ◽  
Yan Du ◽  
Gejiao Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
The City

A Gram-negative, strictly aerobic, yellow-pigmented rod, designated DK69T, was isolated from soil collected from the waste liquid treatment facility of Bafeng Pharmaceutical Company in the city of Enshi, Hubei Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain DK69T in the genus Flavobacterium of the family Flavobacteriaceae . The highest 16S rRNA gene sequence similarities were found with Flavobacterium cauense R2A-7T (96.9 %), Flavobacterium saliperosum AS 1.3801T (96.3 %) and Flavobacterium suncheonense GH29-5T (95.7 %). The major fatty acids (≥5 %) were iso-C15 : 0, iso-C17 : 1ω9c, C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 34.4 mol%. Strain DK69T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium enshiense sp. nov. is proposed. The type strain is DK69T ( = CCTCC AB 2011144T  = KCTC 23775T). Emended descriptions of the genus Flavobacterium and Flavobacterium cauense , Flavobacterium saliperosum and Flavobacterium suncheonense are also proposed.

Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Total Dna ◽  
Physiological Tests

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).

Sign in / Sign up

Export Citation Format

Share Document