Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 254-259 ◽  
Author(s):  
Amit Kumar Singh ◽  
Nidhi Garg ◽  
Pushp Lata ◽  
Roshan Kumar ◽  
Vivek Negi ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Species Cluster ◽  
Physiological Tests

An orange-pigmented bacterial strain, designated LP100T, was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100T occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9T (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100T contained MK-7 as the predominant menaquinone and sym-homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain LP100T were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100T was 58.2 mol%. The results of DNA–DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter . Therefore, strain LP100T represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100T ( = CCM8435T = MCC2027T).

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 723-728 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Fazlurrahman Khan ◽  
Miroslava Sedlackova ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Dump Site ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL01T, was isolated from hexachlorocyclohexane (HCH)-contaminated soil at Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL01T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.5 %). The DNA G+C content of strain LL01T was 66.1 mol%. The predominant respiratory pigment was ubiquinone Q-10. The polar lipid profile of strain LL01T also corresponded to those reported for other Sphingobium species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipids), supporting its identification as a member of the genus Sphingobium . Spermidine was the major polyamine observed. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain LL01T from closely related species of the genus Sphingobium . Therefore, strain LL01T represents a novel species of the genus Sphingobium , for which the name Sphingobium czechense sp. nov. is proposed (type strain LL01T = CCM 7979T = DSM 25410T).

Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 667-672 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Miroslava Sedlackova ◽  
Ales Hampl ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL02T, was isolated from hexachlorocyclohexane-contaminated soil from Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL02T occupied a distinct phylogenetic position in the genus Novosphingobium and showed the highest sequence similarity with Novosphingobium resinovorum NCIMB 8767T (98.59 %). DNA–DNA relatedness between strain LL02T and its closest phylogenetic neighbours was <70 %, which indicated that strain LL02T represented a novel species of the genus Novosphingobium . The DNA G+C content of strain LL02T was 67.72±0 mol%. The major respiratory quinone was ubiquinone Q-10. The polar lipid profile of the isolate corresponded to those reported for other members of the genus Novosphingobium (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipids), thus supporting its classification in the genus. Spermidine was the major polyamine. The major fatty acids were summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c; 40.13 %), summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 31.09 %) and C14 : 0 2-OH (23.16 %). The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain LL02T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium barchaimii sp. nov. is proposed. The type strain is LL02T ( = CCM 7980T  = DSM 25411T).

Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 309-313 ◽  
Author(s):  
Vatsala Dwivedi ◽  
Neha Niharika ◽  
Rup Lal
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Polar Lipid Profile ◽  
Dump Site ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Physiological Tests

A Gram-negative, orange-pigmented, rod-shaped, motile and aerobic bacterial strain designated DM9T was isolated from hexachlorocyclohexane (HCH)-contaminated soil (Lucknow, India) and its taxonomic position was determined using a polyphasic approach. 16S rRNA gene sequence analysis showed that the isolate belonged to the phylum Bacteroidetes and confirmed its placement in the genus Pontibacter , with sequence similarity ranging from 93.92 to 96.21 % with other members of the genus Pontibacter . The major cellular fatty acids of the novel strain were iso-C17 : 0 3-OH (6.00 %), iso-C15 : 0 (21.54 %) and summed feature 4 (comprising C17 : 1 iso I/anteiso B; 32.3 %). The polar lipid profile of strain DM9T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, two unknown aminolipids and four unknown polar lipids. Strain DM9T contained MK-7 as the predominant menaquinone and its DNA G+C content was 49.2 mol%. sym-Homospermidine was the major polyamine observed in the cell. The results obtained on the basis of phenotypic characteristics, phylogenetic analysis, biochemical and physiological tests clearly distinguished DM9T from closely related members of the genus Pontibacter . It is proposed that DM9T represents a novel species, Pontibacter lucknowensis sp. nov.; the type strain is DM9T ( = CCM 7955T = MTCC 11079T).

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).

scholarly journals Postechiella marina gen. nov., sp. nov., isolated from seawater

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1528-1535 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sun Ja Cho ◽  
Suk Min Kim ◽  
Sun Bok Lee
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-staining-negative, strictly aerobic, non-motile, yellow-pigmented bacterium, designated strain M091T, was isolated from seawater at Damupo beach in Pohang, Republic of Korea, and investigated using a polyphasic taxonomic approach. The novel strain grew optimally at 25 °C, pH 7.0–8.0, and in the presence of 3 % (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain M091T formed a lineage within the family Flavobacteriaceae that was distinct from the most closely related genera of Flaviramulus (95.1 % sequence similarity), Algibacter (94.9–93.9 %), Mariniflexile (94.8–94.2 %), Winogradskyella (94.8–93.2 %), Lacinutrix (94.7–93.8 %) and Tamlana (94.7–92.9 %). The polar lipid profile of the novel strain comprised phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and seven unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (20.5 %), iso-C17 : 0 3-OH (15.4 %), iso-C15 : 0 3-OH (12.4 %), C15 : 0 (10.9 %) and iso-C15 : 1 G (9.9 %). The genomic DNA G+C content of strain M091T was 34.4 mol% and the major respiratory quinone was MK-6. Based on phenotypic and genotypic data, strain M091T represents a new genus and novel species in the family Flavobacteriaceae , for which the name Postechiella marina gen. nov., sp. nov. is proposed. The type strain of the type species is M091T ( = KCTC 23537T = JCM 17630T).

Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3755-3761 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Euan K. James ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
Contaminated Soil ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Nitrogen Fixing ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A novel nitrogen-fixing strain, designated DQS-4T, was isolated from oil-contaminated soil in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain DQS-4T stained Gram-negative, contained poly-β-hydroxybutyrate granules and were motile rods, surrounded by a thin capsule. Cells displayed a strictly aerobic type of metabolism and fixed nitrogen microaerobically. Growth occurred at 10–45 °C (optimum, 35–40 °C), at pH 7.0–8.0 (optimum, pH 7.0) and with 0–2 % NaCl (optimum, 0.5–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DQS-4T belonged to the genus Azoarcus , and its closest neighbours were Azoarcus indigens VB32T and Azoarcus communis SWub3T, with sequence similarities of 97.4 and 96.4 %, respectively. The major cellular fatty acids of strain DQS-4T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 64.5 mol%. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The mean level of DNA–DNA relatedness between strain DQS-4T and A. indigens LMG 9092T was 27.4 %. On the basis of the genotypic and phenotypic data, strain DQS-4T represents a novel species in the genus Azoarcus , for which the name Azoarcus olearius sp. nov. is proposed. The type strain is DQS-4T ( = BCRC 80407T = KCTC 23918T = LMG 26893T).

Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2463-2471 ◽  
Author(s):  
Parag Vaishampayan ◽  
Christine Moissl-Eichinger ◽  
Rüdiger Pukall ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
New Taxon ◽  
The Novel ◽  
Clean Room ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Unique Cell ◽  
Spacecraft Assembly

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MAT and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481T, Arthrobacter luteolus ATCC BAA-272T, Arthrobacter tumbae DSM 16406T and Arthrobacter subterraneus DSM 17585T. In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod–coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis . The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MAT and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MAT and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MAT ( = NRRL B-59547T = DSM 30849T).

Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4663-4668 ◽  
Author(s):  
Ji Young Kang ◽  
Jeesun Chun ◽  
Kwang Yeop Jahng
Keyword(s):  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterium, designated strain GSR3061T, was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GSR3061T indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.7 % to Rufibacter tibetensis NRRL B-51285T, 92.4 % to Adhaeribacter terreus KACC 14257T and 91.9 % to Pontibacter korlensis KACC 15371T. Growth was observed at 15–40 °C and pH 6.5–9.5. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0, C17 : 1ω6c and iso-C16 : 1 H. Flexirubin-type pigments were absent. The DNA G+C content of strain GSR3061T was 44.9 mol% and the major quinone was MK-7. The polar lipid profile consisted mainly of phosphatidylethanolamine; three unidentified lipids, two unknown aminolipids, two unknown phospholipids, an unknown aminophospholipid and an unknown glycolipid were also present. On the basis of the evidence presented, it is concluded that strain GSR3061T represents a novel species of a new genus, for which the name Nibribacter koreensis gen. nov., sp. nov. is proposed. The type strain of Nibribacter koreensis is GSR3061T ( = KACC 16450T = JCM 17917T).

Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3040-3045 ◽  
Author(s):  
Soo-Jin Kim ◽  
Joo-Hyeon Park ◽  
Jun-Muk Lim ◽  
Jae-Hyung Ahn ◽  
Rangasamy Anandham ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Greenhouse Soil ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family Chitinophagaceae , and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2–92.6 %), Sediminibacterium (90.8–91.4 %) and Chitinophaga (89.2–91.7 %), Filimonas lacunae YT21T (91.7 %), members of the genus Segetibacter (90.2–91.6 %), Parasegetibacter luojiensis RHYL-37T (90.9 %) and Flavihumibacter petaseus T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).

Cupriavidus cauae sp. nov., isolated from blood of an immunocompromised patient

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Oh Joo Kweon ◽  
Wenting Ruan ◽  
Shehzad Abid Khan ◽  
Yong Kwan Lim ◽  
Hye Ryoun Kim ◽  
...  
Keyword(s):  
Polar Lipid ◽  
Type Species ◽  
Immunocompromised Patient ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph

A novel Gram-stain-negative, facultative aerobic and rod-shaped bacterium, designated as MKL-01T and isolated from the blood of immunocompromised patient, was genotypically and phenotypically characterized. The colonies were found to be creamy yellow and convex. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that strain MKL-01T was most closely related to Cupriavidus gilardii LMG 5886T, present within a large cluster in the genus Cupriavidus . The genome sequence of strain MKL-01T showed the highest average nucleotide identity value of 92.1 % and digital DNA–DNA hybridization value of 44.8 % with the closely related species C. gilardii LMG 5886T. The genome size of the isolate was 5 750 268 bp, with a G+C content of 67.87 mol%. The strain could grow at 10–45 °C (optimum, 37–40 °C), in the presence of 0–10 % (w/v) NaCl (optimum, 0.5%) and at pH 6.0–10.0 (optimum, pH 7.0). Strain MKL-01T was positive for catalase and negative for oxidase. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c and/or C16 : 1  ω6c/C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified polar lipid. Moreover, strain MKL-01T contained ubiquinone Q-8 as the sole respiratory quinone. Based on its molecular, phenotypic and chemotaxonomic properties, strain MKL-01T represents a novel species of the genus Cupriavidus ; the name Cupriavidus cauae sp. nov. is proposed for this strain. The type strain is MKL-01T.

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