Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3994-3999 ◽  
Author(s):  
Jian-Kang Zhao ◽  
Xiao-Ming Li ◽  
Ming-Jiang Zhang ◽  
Jing-hua Jin ◽  
Cheng-Ying Jiang ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Polluted Soils ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Emended Description ◽  
Polycyclic Aromatic ◽  
Growth Ph ◽  
The 16S Rrna Gene

A novel pyrene-degrading, Gram-negative bacterium, designated strain P-4T, was isolated from a polycyclic aromatic hydrocarbon-degrading enrichment of polluted soils from a coking chemical plant. Cells of strain P-4T were non-motile rods. Strain P-4T grew at 15–45 °C (optimum, 37 °C), pH 6.0–10.0 (optimum, pH 8.5) and 0–4 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence showed that strain P-4T was related phylogenetically to members of the genus Parapedobacter , with sequence similarity of 93.7–95.1 %. The cellular fatty acids of strain P-4T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0 ), anteiso-C15 : 0, iso-C15 : 0 3-OH, C16 : 0, iso-C15 : 1 G, C16 : 0 3-OH and C17 : 0 2-OH. Cells contained menaquinone 7 as the major quinone. The polyamine of strain P-4T was homospermidine, and the main polar lipids were phosphatidylethanolamine and a sphingolipid. The G+C content of the DNA was 45.4 mol%. Strain P-4T showed a range of phenotypic characteristics that differentiated it from previously recognized Parapedobacter species, particularly its ability to use pyrene as a sole carbon source for growth and its alkaline optimal pH for growth (pH 8.5). On the basis of these results, it is concluded that strain P-4T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter pyrenivorans (type strain P-4T = NBRC 109113T = CGMCC 1.12195T) is proposed. An emended description of the genus Parapedobacter is also provided.

scholarly journals Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 36-41 ◽  
Author(s):  
Jing Hu ◽  
Qi-Qi Yang ◽  
Yi Ren ◽  
Wen-Wu Zhang ◽  
Gang Zheng ◽  
...  
Keyword(s):  
Intertidal Zone ◽  
Algal Bloom ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Emended Description ◽  
Sea Area

A novel facultatively anaerobic, Gram-stain-negative bacterium, designated strain HT7-2T, was isolated from Ulva prolifera collected from the intertidal zone of Qingdao sea area, China, during its bloom. Cells were rod-shaped (1.9–3.5×0.4–0.6 µm), non-sporulating and motile by gliding. Strain HT7-2T was able to grow at 4–50 °C (optimum 40–42 °C), pH 5.5–8.5 (optimum pH 7.0), 0–8 % (w/v) NaCl (optimum 2–3 %) and 0.5–10 % (w/v) sea salts (optimum 2.5 %). The genomic DNA G+C content was 38.8 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HT7-2T belonged to the genus Maribacter with sequence similarity values of 94.5–96.6 %, and was most closely related to Maribacter aestuarii GY20T (96.6 %). Chemotaxonomic analysis showed that the main isoprenoid quinone was MK-6 and the major fatty acids were iso-C15 : 0 and unknown equivalent chain-length 13.565. The polar lipids of strain HT7-2T consisted of one phosphatidylethanolamine, four unidentified lipids and one unidentified aminolipid. On the basis of the phenotypic, phylogenetic and chemotaxonomic characteristics, strain HT7-2T ( = CGMCC 1.12207T = JCM 18466T) is concluded to represent a novel species of the genus Maribacter , for which the name Maribacter thermophilus sp. nov. is proposed. An emended description of the genus Maribacter is also proposed.

scholarly journals Kiloniella spongiae sp. nov., isolated from a marine sponge and emended description of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 230-234 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Jung-Hyun Lee ◽  
Sang-Jin Kim ◽  
Kae Kyoung Kwon
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Emended Description ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-negative, aerobic, rod-shaped and non-motile marine bacterium, designated MEBiC09566T was isolated from a sponge collected at Uljin County in the coastal area of the East Sea (36° 55′ N, 129° 25′ E), Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC09566T showed the highest similarity with the Kiloniella laminariae LD81T (96.7 %). Growth was observed at 11–31 °C (optimum 25 °C), at pH 6.0–8.5 (optimum pH 7.0) and with 0–6 % (optimum 2.5 %) NaCl. The predominant cellular fatty acids were summed feature 8 (comprised of C18 : 1ω7c/C18 : 1ω6c) and summed feature 3 (comprised of C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content is 44.6 mol%. The major respiratory quinone is Q-9. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid were detected as major polar lipids. On the basis of this polyphasic taxonomic data, it is concluded that strain MEBiC09566T should be classified as representing a novel species in the genus Kiloniella and the name proposed is Kiloniella spongiae sp. nov. The type strain is MEBiC09566T ( = KCCM 43040T = JCM 19930T). Emended descriptions of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae are also given.

scholarly journals Oryzihumus terrae sp. nov., isolated from soil and emended description of the genus Oryzihumus

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2395-2399 ◽  
Author(s):  
Jun-Muk Lim ◽  
Soo-Jin Kim ◽  
Moriyuki Hamada ◽  
Jae-Hyung Ahn ◽  
Hang-Yeon Weon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Emended Description ◽  
Unknown Lipid

A Gram-stain-positive, aerobic, non-flagellated bacterium, designated KIS22-12T, was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. Cells were non-spore-forming cocci showing catalase-positive and oxidase-negative reactions. Growth of strain KIS22-12T was observed between 10 and 35 °C (optimum, 28–30 °C), between pH 5.0 and 9.0 (optimum, pH 7.0) and with 0–3 % (w/v) NaCl. Strain KIS22-12T contained MK-8(H4) as the predominant menaquinone, and C17 : 1ω8c, iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Strain KIS22-12T contained diphosphatidylglycerol, phosphatidylinositol, one unknown aminophospholipid, one unknown aminolipid, two unknown phospholipids and one unknown lipid. The peptidoglycan type was A1γ. The G+C content of the genomic DNA was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS22-12T formed a phyletic lineage with Oryzihumus leptocrescens KV-628T. 16S rRNA gene sequence similarity between the two strains was 96.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain KIS22-12T represents a novel species within the genus Oryzihumus , for which the name Oryzihumus terrae sp. nov. is proposed. The type strain is KIS22-12T ( = KACC 16543T = DSM 27161T = NBRC 109596T). An emended description of the genus Oryzihumus is also provided.

Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3409-3414 ◽  
Author(s):  
Naysim Lo ◽  
Hyun Mi Jin ◽  
Che Ok Jeon
Keyword(s):  
Tidal Flat ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Optimum Ph ◽  
Emended Description ◽  
Gwangyang Bay

A Gram-staining-negative, strictly aerobic bacterial strain, motile by gliding, designated GY20T, was isolated from a tidal flat at Gwangyang Bay, South Korea. Cells were moderately halophilic, catalase- and oxidase-positive rods. Growth of strain GY20T was observed at 10–30 °C (optimum, 25 °C), at pH 6.5–11.0 (optimum, pH 7.0–8.0) and in the presence of 1–5 % (w/v) NaCl (optimum, 2–3 %). MK-6 was detected as the sole isoprenoid quinone, and iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH as major fatty acids. Strain GY20T contained phosphatidylethanolamine, one unidentified glycolipid and one unidentified lipid as major polar lipids. The G+C content of the genomic DNA was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GY20T formed a tight phyletic lineage with members of the genus Maribacter . Strain GY20T was most closely related to Maribacter dokdonensis DSW-8T, with sequence similarity of 96.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain GY20T was shown to represent a novel species within the genus Maribacter , for which the name Maribacter aestuarii sp. nov. is proposed. The type strain is GY20T ( = KACC 16440T = JCM 18631T). An emended description of the genus Maribacter is also proposed.

scholarly journals Neptunomonas acidivorans sp. nov., isolated from sediment, and emended description of the genus Neptunomonas

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3650-3654 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Jung-Hyun Lee ◽  
Sang-Jin Kim ◽  
Kae Kyoung Kwon
Keyword(s):  
The Yellow Sea ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Emended Description ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-negative, aerobic, rod-shaped (1.2–1.6 µm×0.6–0.8 µm), flagellated and motile marine bacterium, designated MEBiC06243T, was isolated from a sediment collected at Daebu Island in the Yellow Sea (37° 20′ N 126° 41′ E), Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC06243T showed high similarity with Neptunomonas naphthovorans NAG-2N-126T (96.3 %). Growth was observed at 10–39 °C (optimum 29 °C), at pH 6.0–9.0 (optimum pH 7) and with 0–7 % (optimum 2.5 %) NaCl. The predominant cellular fatty acids were C10 : 0 3-OH (6.1 %), C12 : 0 (5.8 %), C16 : 0 (30.5 %), C18 : 1ω7c (21.6 %) and summed feature 3 (comprising C15 : 0 2-OH and/or C16 : 1ω7c; 30.7 %). The DNA G+C content was 41.4 mol%. The major respiratory quinone was Q-8. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified lipids, one unidentified aminophospholipid and three unidentified aminolipids were detected as major polar lipids. On the basis of this polyphasic taxonomic data, strain MEBiC06243T should be classified as a novel species of the genus Neptunomonas proposed as Neptunomonas acidivorans sp. nov. The type strain is MEBiC06243T ( = KCCM 42975T = JCM 18291T). An emended description of the genus Neptunomonas is also given.

Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 933-939 ◽  
Author(s):  
Aihua Li ◽  
Hongcan Liu ◽  
Bingda Sun ◽  
Yuguang Zhou ◽  
Yuhua Xin
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
High Altitude Lake ◽  
Nam Co Lake ◽  
The 16S Rrna Gene

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated NP180T and NR80, were isolated from water of Nam Co Lake, located in Tibet, China. Growth of strains NP180T and NR80 occurred at 4–25 °C and at pH 6.5–10.0 (optima, 15–20 °C and pH 7.5–8.5). The 16S rRNA gene sequence similarity to the phylogenetically closest related strains, Flavobacterium filum EMB 34T, F. ponti GSW-R14T and F. gelidilacus LMG 21477T, was 95.1, 94.8 and 94.6 %, respectively. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major menaquinone of the two strains was menaquinone 6 (MK-6). Phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids in both strains. The G+C contents of the genomic DNA were 34.9 and 35.1 mol%, respectively, for strains NP180T and NR80. DNA–DNA relatedness between strains NP180T and NR80 was 99 %, indicating that they belong to the same species. According to phylogenetic inference and phenotypic characteristics, a novel species, Flavobacterium lacus sp. nov., is proposed. The type strain is NP180T ( = CGMCC 1.12504T = NBRC 109715T). An emended description of Flavobacterium filum is also provided.

Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 518-521 ◽  
Author(s):  
Zhiyong Ruan ◽  
Yanwei Wang ◽  
Jinlong Song ◽  
Shenghua Jiang ◽  
Huimin Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Large Scale ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biogas Slurry ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Method Analysis ◽  
The 16S Rrna Gene

A novel facultatively anaerobic bacterium, designated strain LAM0618T, was isolated from biogas slurry samples collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM0618T were Gram-stain-positive, motile, non-spore-forming and short-rod-shaped. The optimal temperature and pH for growth were 30 °C and 7.0, respectively. The strain did not require NaCl for growth but tolerated up to 70 g NaCl l−1. The major fatty acids of strain LAM0618T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and C18 : 0. The predominant menaquinones of strain LAM0618T were menaquinone 7 (MK-7) and menaquinone 6 (MK-6). The main polar lipids of strain LAM0618T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unknown glycolipids. The genomic DNA G+C content was 41 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence revealed that strain LAM0618T was a member of the genus Kurthia , and was most closely related to ‘ Kurthia massiliensis’ DSM 24639, Kurthia zopfii DSM 20580T, Kurthia gibsonii DSM 20636T and Kurthia sibirica DSM 4747T, with 96.9, 95.7, 95.6 and 94.9 % sequence similarity, respectively. Based on its phenotypic and genotypic properties, strain LAM0618T is suggested to represent a novel species of the genus Kurthia , for which the name Kurthia huakuii sp. nov. is proposed. The type strain is LAM0618T ( = ACCC 06121T = JCM 19187T).

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).

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

Muriicola soli sp. nov., isolated from soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph ◽  
Genomic Characterization

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

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