scholarly journals Haloflavibacter putidus gen. nov., sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (6) ◽  
pp. 3740-3748 ◽  
Author(s):  
Xi Feng ◽  
Yi-Ran Wang ◽  
Qi-Hang Zou ◽  
Jin-Yu Zhang ◽  
Zong-Jun Du

A Gram-stain-negative, aerobic, gliding, rod-shaped (0.2–0.5×1.0-13.0 µm) and yellow-pigmented bacterium, designated PLHSN227T, was isolated from seawater collected near the coast of Yantai, PR China. PLHSN227T was found to grow at 15–37 °C (optimum, 28–30 °C) and pH 6.0–8.5 (optimum, 6.5–7.5) in the presence of 2–14 % (w/v) NaCl (optimum, 5.0 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that PLHSN227T represented a member of the family Flavobacteriaceae and exhibited the highest sequence similarity (94.6 %) to the type strain Salegentibacter holothuriorum NBRC 100249T. The chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included C19 : 0ω8c cyclo, iso-C15 : 0, anteiso-C15 : 0, C18 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids included phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content of PLHSN227T was 35.6 mol%. PLHSN227T showed the highest average amino acid identity value of 67.2 %, the average nucleotide identity value of 75.6 and 14.5 % digital DNA–DNA hybridization identity with Mesonia algae DSM 15361T. According to the phylogenetic data, PLHSN227T formed a distinct clade in the phylogenetic tree. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is considered that PLHSN227T represents a novel genus within the family Flavobacteriaceae , for which the name Haloflavibacter putidus gen. nov., sp. nov. is proposed. The type strain is PLHSN227T (=KCTC 72159T=MCCC 1H00371T).

2020 ◽  
Vol 70 (3) ◽  
pp. 1850-1860 ◽  
Author(s):  
Zahra Noviana ◽  
Selma Vieira ◽  
Javier Pascual ◽  
Serge Alain Tanemossu Fobofou ◽  
Manfred Rohde ◽  
...  

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913T and R5959T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C19 : 0 cyclo ω8c and C16 : 0; in addition, C18 : 1ω7c was also found as a predominant fatty acid in strain R5913T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913T and R5959T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656T, Dongia mobilis CGMCC 1.7660T, Dongia soli D78T and Dongia rigui 04SU4-PT. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae , for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913T=DSM 109816T=CECT 9472T) and Hypericibacter adhaerens sp. nov. (type strain R5959T=DSM 109817T=CECT 9620T).


Author(s):  
Lingping Zhuang ◽  
Haiyue Pang ◽  
Li Xu ◽  
Dan Chen

A novel bacterial strain, designated as HN-E44T, was isolated from marine sponge collected from Yangpu Bay, Hainan, PR China. Strain HN-E44T was Gram-stain-negative, non-motile, catalase-positive, oxidase-negative, rod-shaped and yellow-pigmented. Growth occurred at 4–37 °C (optimum, 28 °C), at pH 6–8 (pH 7) and in 0.5–14 % (w/v) NaCl (3–5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN-E44T formed an independent cluster with Marixanthomonas ophiurae JCM 14121T within the family Flavobacteriaceae and had the highest sequence similarity of 93.6 % to the closest type strain M. ophiurae JCM 14121T. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C15 : 1 G. The polar lipids comprised phosphatidylethanolamine, sphingolipid, four unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. The respiratory quinone was identified as MK-6. The genomic DNA G+C content was determined to be 40.6 mol%. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain HN-E44T and closest type strain M. ophiurae JCM 14121T were, respectively, 79.6 and 85.2 %, both of which were below thresholds for species delineation (95–96 % ANI and 95–96 % AAI), but were over thresholds for genus delineation (73.98 % ANI and 70–76 % AAI). The combined genotypic and phenotypic distinctiveness demonstrated that strain HN-E44T could be differentiated from closely related genera. Therefore, it is proposed that strain HN-E44T represents a novel species of the genus Marixanthomonas , for which the name Marixanthomonas spongiae sp. nov. is proposed, with the type strain HN-E44T (=MCCC 1K03332T=LMG 30459T).


2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3293-3300 ◽  
Author(s):  
Yi-Han Hsu ◽  
Wei-An Lai ◽  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Mariyam Shahina ◽  
...  

A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031T was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031T formed a discrete monophyletic lineage in the family Xanthomonadaceae , sharing high pairwise sequence similarity of 93.5–95.2 and 94.8 % with species of the genus Dokdonella (94.9 % similarity to the type strain of the type species) and Aquimonas voraii GPTSA 20T, respectively. The genomic DNA G+C content of strain CC-YHH031T was 68.6±0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5 % of total fatty acids) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 1ω9c, iso-C14 : 0, iso-C11 : 0 and iso-C11 : 0 3-OH. The polar lipid profile of strain CC-YHH031T included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1–2) and four unidentified phospholipids (PL1–4). Strain CC-YHH031T was distinguished particularly from the type species of the genus Dokdonella ( Dokdonella koreensis ) by the presence of major amounts of iso-C14 : 0 and summed feature 3 and minor amounts of iso-C17 : 0 and by the complete absence of anteiso-C17 : 0, the presence of PL1–3 and APL1–2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031T is proposed to represent a novel genus and species within the family Xanthomonadaceae , for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031T ( = BCRC 80273T = DSM 24163T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5479-5487 ◽  
Author(s):  
MinJi Kim ◽  
Su-Kyoung Shin ◽  
Hana Yi

Two novel bacteria, designated HYN0043T and HYN0046T, were isolated from a freshwater lake in Korea. 16S rRNA gene sequence phylogeny indicated that strain HYN0043T belongs to the genus Mucilaginibacter of the family Sphingobacteriaceae because it showed highest sequence similarity to Mucilaginibacter oryzae (98.2 %). The average nucleotide identity between strain HYN0043T and M. oryzae was 83.5 %, which is clearly below the suggested threshold for species demarcation. Strain HYN0046T was found to belong to the family Moraxellaceae and shared highest sequence similarity with Agitococcus lubricus (93.8 %). The average amino acid identity values between strain HYN0046T and representative type strains of closely related genera (Alkanindiges, Agitococcus and Acinetobacter ) were 53.1–60.7 %, implying the novelty of the isolate at the genus level. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of the two isolates. Thus, we suggest the following names to accommodate strains HYN0043T and HYN0046T: Mucilaginibacter celer sp. nov. (type strain HYN0043T=KACC 19184T=NBRC 112738T) in the family Spingobacteriaceae and phylum Bacteroidetes and Aquirhabdus parva gen. nov., sp. nov. (type strain HYN0046T=KACC 19178T=NBRC 112739T) in the family Moraxellaceae and phylum Proteobacteria .


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).


2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2624-2630 ◽  
Author(s):  
Vikram Surendra ◽  
Pant Bhawana ◽  
Korpole Suresh ◽  
T. N. R. Srinivas ◽  
Pinnaka Anil Kumar

A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia , Coenonia and Capnocytophaga , being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1639-1645 ◽  
Author(s):  
Lei Zhang ◽  
Xihui Shen ◽  
Yingbao Liu ◽  
Shiqing Li

A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10T, was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30–37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10T was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311T (90.2 % sequence similarity), Marivirga sericea LMG 13021T (89.2 %), Cesiribacter andamanensis AMV16T (89.1 %) and Marivirga tractuosa DSM 4126T (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10T should be classified as a novel species of a new genus in the family Flammeovirgaceae , for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10T ( = CCTCC AB 208222T = KCTC 23983T).


2020 ◽  
Vol 70 (3) ◽  
pp. 1496-1502 ◽  
Author(s):  
Jin Li ◽  
Yan Xu ◽  
Jiarong Feng ◽  
Mingqi Zhong ◽  
Qingyi Xie ◽  
...  

A Gram-stain-negative, aerobic, non-motile and rod-shaped marine bacterium, CW2-9T, was isolated from algae collected from Fujian Province in PR China. 16S rRNA gene sequence analysis showed that this strain was affiliated with the genus Tamlana in the family Flavobacteriaceae of the class Flavobacteriia and was very similar to the type strain Tamlana sedimentorum MCCC 1A10799T (96.3 % sequence similarity). The whole genome of strain CW2-9T comprised 3 997 513 bp with a G+C content of 34.3 mol%. The average nucleotide identity value between strain CW2-9T and T. sedimentorum MCCC 1A10799T was 73.8 %. Growth was observed from 15 to 40 °C (optimum, 30 °C), at pH from pH 5.0 to 10.0 (pH 8.0) and in the presence of 0–4 % (w/v) NaCl (0–1 %). The major fatty acids (>10 % of the total) were iso-C15 : 0, iso G-C15 : 1, iso-C17 : 0 3-OH and anteiso-C15 : 0. The predominant menaquinone was MK-6. The combined phylogenetic, physiological and chemotaxonomic data indicate that strain CW2-9T represents a novel species in the genus Tamlana , for which the name Tamlana fucoidanivorans sp. nov. is proposed. The type strain is CW2-9T (=CICC 24749T=KCTC 72389T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3323-3327 ◽  
Author(s):  
Qian Wang ◽  
Sheng-Dong Cai ◽  
Jie Liu ◽  
De-Chao Zhang

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10T, was isolated from marine sediment. Strain S1-10T grew at 4–42 °C (optimally at 30–35 °C), at pH 7.0–10 (optimally at pH 9) and in the presence of 0.5–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1bT (97.7%). The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10T was 34.6 mol%. The polar lipid profile of strain S1-10T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10T and A. viscosa CGMCC 1.11023T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10T is the representative of a novel species of the genus Aequorivita , for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10T=CGMCC 1.12579T=JCM 19789T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2T (= KCTC 62141T= NBRC 113025T) and the type strain of Aequorivita aquimaris comb. nov. is D-24T (=KCTC 42708T=DSM 101732T).


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