Arenibacter amylolyticus sp. nov., an amylase-producing bacterium of the family Flavobacteriaceae isolated from marine water in India

Author(s):  
Chandni Sidhu ◽  
Mohit Kumar Saini ◽  
Naga Radha Srinivas Tanuku ◽  
Anil Kumar Pinnaka

A novel Gram-stain-negative, curved rod-shaped, 0.5–0.7 µm wide and 3.0–10.0 µm long, non-motile bacterium, designated strain AK53T, was isolated from a 5 m depth water sample collected from the Bay of Bengal, Visakhapatnam, India. Colonies on marine agar were circular, small, dark orange, shiny, smooth, translucent, flat, with an entire margin. The major fatty acids included iso-C15 : 0, iso-C15 : 0 3OH, anteiso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c and/or iso-C15 : 0-2OH). Polar lipids included phosphatidylethanolamine and five unidentified lipids. The DNA G+C content of the strain AK53T was found to be 40.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK53T was closely related to Arenibacter latericius KMM 426T and Arenibacter certesii KMM3941T (pair-wise sequence similarity of 99.17 and 98.89 %, respectively), forming a distinct branch within the genus Arenibacter and clustering with A. latericius . Strain AK53T shared average nucleotide identity (ANIb, based on blast) of 78.07 and 77.44 % with A. latericius JCM 13508T and A. certesii JCM 13507T, respectively. Based on the observed phenotypic, chemotaxonomic characteristics and phylogenetic analysis, strain AK53T is described in this study as representing a novel species in the genus Arenibacter , for which the name Arenibacter amylolyticus sp. nov. is proposed. The type strain of Arenibacter amylolyticus is AK53T (=MTCC 12004T= JCM 19206T=KCTC 62553T).

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2753-2757 ◽  
Author(s):  
Tae-Su Kim ◽  
Ji-Hye Han ◽  
Yochan Joung ◽  
Seung Bum Kim

A novel Gram-stain-positive, non-spore-forming, pale yellow, irregular rod-shaped bacterium designated strain HWE2-01T was isolated from the surface-sterilized root of horseweed (Conyza canadensis). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HWE2-01T belongs to the family Microbacteriaceae and showed sequence similarity levels of 97.1–97.7 % with species of the genus Salinibacterium , 95.9–97.6 % with species of the genus Leifsonia and 97.1 % with Homoserinimonas aerilata . The highest sequence similarity (97.7 %) was with Salinibacterium xinjiangense 0543T. The genomic DNA G+C content of the novel strain was 68.1 mol%. The predominant cellular fatty acid of strain HWE2-01T was anteiso-C15 : 0, major menaquinones were MK-10, MK-9 and MK-11, and diagnostic polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The peptidoglycan of the novel strain contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The cell-wall sugars of strain HWE2-01T were galactose, mannose and rhamnose. The murein was of the acetyl type. Based on the results of the phenotypic and phylogenetic analysis, strain HWE2-01T differed in some respects from other members of the family Microbacteriaceae . Therefore, strain HWE2-01T is proposed to represent a novel species of a new genus in the family Microbacteriaceae with the name Conyzicola lurida gen. nov., sp. nov. (type strain = HWE2-01T = KCTC 29231T = JCM 19257T).


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4115-4119 ◽  
Author(s):  
Parisa Zarparvar ◽  
Mohammad Ali Amoozegar ◽  
Mahdi Moshtaghi Nikou ◽  
Peter Schumann ◽  
Antonio Ventosa

A halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269T (95.5 %) and Marininema mesophilum SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family Thermoactinomycetaceae , for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).


Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim

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).


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

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).


Author(s):  
Zhaobin Huang ◽  
Xiaomei Wei ◽  
Qiliang Lai ◽  
Shiyong Chen ◽  
Jianjun Yuan

Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae , sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae . Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal

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).


Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.


Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Author(s):  
Yu-Wen Wang ◽  
Wen-Ting Ren ◽  
Yuan-You Xu ◽  
Xin-Qi Zhang

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4–42 °C (optimum, 35 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5). Salt was required for growth (0.5–12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1  ω7c, 11-methyl C18 : 1  ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera Maritimibacter (95.61–96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60–80 % was calculated to be 68.56–76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.


Author(s):  
Md. Amdadul Huq ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
M. Mizanur Rahman ◽  
Md Ashrafudoulla ◽  
...  

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10–40 °C, at pH 6.0–9.0 and with 0–1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria–Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae . Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae , for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).


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