Limnovirga soli gen. nov., sp. nov., isolated from river sediment

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Kyung June Yim ◽  
Dong-Hyun Jung ◽  
Seok Won Jang ◽  
Sanghwa Park
Keyword(s):  
Phylogenetic Trees ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genome Analyses

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0–8.0 (optimum, pH 7.0) and 10–37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae , for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.

Paraneptunicella aestuarii gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from seawater in East China Sea

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yanzhu Zhang ◽  
Shufen He ◽  
Liufei Shi ◽  
Yang Liu ◽  
Deqiang Mao ◽  
...  
Keyword(s):  
Amino Acid Identity ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Genomic Core

An aerobic Gram-stain-negative, curved rod-shaped and non-spore-forming bacterial strain (NBU2194T) was isolated from seawater collected in an intertidal zone in Ningbo, Zhejiang Province, PR China. It was motile though a single polar flagellum and grew at 20–42 °C (optimum, 30 °C), in 0–2.0 % NaCl (0 %, w/v) and at pH 5.0–9.0 (pH 6.0–7.0). The sole respiratory quinone was ubiquinone-8. The major cellular fatty acids were C16 : 0, C16 : 1  ω7c and/or C16 : 1  ω6c. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and two unidentified aminophosphoglycolipids. A phylogenetic analysis based on 16S rRNA gene sequences and 65 genomic core genes showed that strain NBU2194T formed a distinct lineage in the family Alteromonadaceae . The genome of strain NBU2194T was 4 913 533 bp with a DNA G+C content of 43.9 mol% and coded 3895 genes, 12 rRNA genes and 47 tRNA genes. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain NBU2194T and related species of Alteromonadaceae were below the threshold limit for prokaryotic species delineation. NBU2194T could be distinguished from other genera in the family Alteromonadaceae based on phenotypic, chemotaxonomic and genomic characteristics. On the basis of the polyphasic taxonomic evidence collected in this study, strain NBU2194T is considered to represent a novel genus and species in the family Alteromonadaceae , for which the name Paraneptunicella aestuarii is proposed. The type strain is NBU2194T (=KCTC 82442T=GDMCC 1.2217T).

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Minchung Kang ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Taegun Seo
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Beach Sand ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Bacterium Strain

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11T (97.0 %), Sphingomonas edaphi DAC4T (96.8 %), Sphingomonas xanthus AE3T (96.5 %) and Sphingomonas oryziterrae YC6722T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3T grew at 7–50 °C (optimum, 30–35 °C), pH 5.0–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3T and its reference strains with publicly available genomes were 17.9–18.9 %, 72.0–75.3 % and 63.3–76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas . The type strain is sand1-3T (=KCTC 82358T=NBRC 114538T).

Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 533-539 ◽  
Author(s):  
Asif Hameed ◽  
Mariyam Shahina ◽  
Shih-Yao Lin ◽  
Wei-An Lai ◽  
You-Cheng Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Surface Seawater ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium, motile by gliding, designated strain CC-AMO-30DT, was isolated from surface seawater collected near Taichung harbour, Taiwan. Strain CC-AMO-30DT shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5 % with the type strains of the type species of the genera Joostella , Pustulibacterium and Galbibacter , respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (≥5 % of total) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was the triamine sym-homospermidine. The DNA G+C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMO-30DT represents a novel genus and species of the family Flavobacteriaceae , for which the name Robertkochia marina gen. nov., sp. nov. is proposed; the type strain of the type species Robertkochia marina is CC-AMO-30DT ( = JCM 18552T = BCRC 80469T). Emended descriptions of the genera Joostella and Galbibacter are also proposed.

scholarly journals Tabrizicola algicola sp. nov. isolated from culture of microalga Ettlia sp.

2020 ◽  
Vol 70 (12) ◽  
pp. 6133-6141 ◽  
Author(s):  
Chan-Yeong Park ◽  
Seong-Jun Chun ◽  
Chunzhi Jin ◽  
Ve Van Le ◽  
Yingshun Cui ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Major Respiratory Quinone ◽  
Bacterium Strain

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile, and rod-shaped bacterium, strain ETT8T was isolated from a chemostat culture of microalga Ettlia sp. YC001. Optimal growth was with 0–2% NaCl and at 25–37 °C on R2A medium. Phylogenetic analysis based on the 16S rRNA gene and genome sequence showed that strain ETT8T belongs to the genus Tabrizicola , with the close neighbours being T. sediminis DRYC-M-16T (98.1 %), T. alkalilacus DJCT (97.6 %), T. fusiformis SY72T (96.9 %), T. piscis K13M18T (96.8 %), and T. aquatica RCRI19T (96.5 %). The genomic comparison of strain ETT8T with type species in the genus Tabrizicola was analysed using the genome-to-genome distance calculator (GGDC), average nucleotide identity (ANI), and average amino acid identity (AAI) (values indicated ≤17.7, ≤75.4 and ≤71.9 %, respectively). The genomic DNA G+C content of strain ETT8T was 64.4 %, plus C18 : 1  ω6c and C18 : 0-iso were the major fatty acids and Q-10 the major respiratory quinone. Strain ETT8T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine aminolipid, and four unidentified lipids as the major polar lipids. Based on the chemotaxonomic, genotypic, and phenotype results, strain ETT8T was recognized as a novel species of the genus Tabrizicola for which the name Tabrizicola algicola sp. nov. is proposed. The type strain is ETT8T (=KCTC 72206T=JCM 31893T=MCC 4339T).

scholarly journals Pontibacter mangrovi sp. nov., isolated from mangrove sediment

2020 ◽  
Vol 70 (7) ◽  
pp. 4245-4249 ◽  
Author(s):  
kun-lian Mo ◽  
Ling Wang ◽  
Qing-juan Wu ◽  
Lin Ye ◽  
Xing-di Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Polar Lipids ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

A Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10–45 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0.5–9.0 % (w/v) NaCl (optimum, 2–5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).

scholarly journals Reclassification of Geobacillus galactosidasius and Geobacillus yumthangensis as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov., respectively

2020 ◽  
Vol 70 (12) ◽  
pp. 6518-6523 ◽  
Author(s):  
Ishfaq Nabi Najar ◽  
Sayak Das ◽  
Nagendra Thakur
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Whole Genome ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Genome Analyses ◽  
Type Strains

Members of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus Geobacillus was subdivided into two genera based on whole-genome approaches. The new genus, Parageobacillus , comprises five genomospecies. In this study, we recommend the reclassification of two Geobacillus species, Geobacillus galactosidasius and Geobacillus yumthangensis , into the genus Parageobacillus . We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 Geobacillus and Parageobacillus type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA–DNA hybridization) denoted that the type strains of G. galactosidasius and G. yumthangensis belong to the genus Parageobacillus . Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, recN gene sequences and core genes identified from the whole-genome analyses designated that the type strains of G. galactosidasius and G. yumthangensis belong in the genus Parageobacillus . With these findings, we consequently propose that G. galactosidasius and G. yumthangensis should be reclassified as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov.

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
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Phylogenetic Data ◽  
The Family

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).

scholarly journals Marinilabilia rubra sp. nov., isolated from a marine solar saltern

2019 ◽  
Vol 69 (4) ◽  
pp. 914-919 ◽  
Author(s):  
Rui Zhang ◽  
Shuo Wang ◽  
Chong Wang ◽  
Guang-Yu Wang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

A novel cherry-red-pigmented, Gram-stain-negative, gliding, facultatively anaerobic and rod-shaped bacterium, designated strain WTE16T, was isolated from a sediment sample taken from a marine solar saltern of Wendeng, China (36° 59′ 56.49′′ N 122° 1′ 38.84′′ E). The novel isolate was able to grow at 20–40 °C (optimum 33 °C), at pH 6.0–9.0 (optimum pH 7.0) and with 1.0–12.0 % (w/v) NaCl (optimum 3.0–5.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species is Marinilabilia salmonicolor JCM 21150T (96.0 % similarity). Average nucleotide identity, average amino acid identity, percentage of conserved proteins and digital DNA–DNA hybridization values between strain WTE16T and Marinilabilia salmonicolor JCM 21150T were 73.8 %, 73.5 %, 63.4 % and 19.5–24.2 %, respectively. The genomic DNA G+C content of strain WTE16T was 40.8 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acids included iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain WTE16T included phosphatidylethanolamine, three unidentified phospholipids and three unidentified lipids. On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics, strain WTE16T is suggested to represent a novel species of the genus Marinilabilia , for which the name Marinilabilia rubra sp. nov. is proposed. The type strain is WTE16T (=KCTC 62599T=MCCC 1H00311T).

scholarly journals Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf

2020 ◽  
Vol 70 (7) ◽  
pp. 4130-4138 ◽  
Author(s):  
Rashmi Fotedar ◽  
Matthew E. Caldwell ◽  
Krithivasan Sankaranarayanan ◽  
Aisha Al -Zeyara ◽  
Ameena Al-Malki ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Arabian Gulf ◽  
Marine Water ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Distinct Lineage

Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15–45 °C (optimum, 30 °C), at pH 5–11 (optimum, pH 6.5–8) and with 0–6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae , sharing the highest sequence similarities to the genera Alteromonas (93.7–95.4 %), Aestuariibacter (94.0–95.1 %), Agaribacter (93.3–93.7 %), Glaciecola (92.0–93.7 %), Marisendiminitalea (93.2–93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium . Major fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).

Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Wonjae Kim ◽  
Minkyung Kim ◽  
Woojun Park
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Major Respiratory Quinone ◽  
Obligate Aerobic

Strain NIBR12T (=KACC 22094T=HAMBI 3739T), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture (Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12T belongs to the genus Roseococcus , with its closest neighbours being Roseococcus suduntuyensis SHETT (98.8%), Roseococcus thiosulfatophilus RB-3T (97.7%), “Sediminicoccus rosea” R-30T (95.7 %) and Rubritepida flocculans H-8T (95.0 %). Genomic comparison of strain NIBR12T with type species in the genus Roseococcus was conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12T was 70.9 mol%. The major fatty acids of strain NIBR12T were summed feature 8 (C18 : 1  ω7c and/or C18:1 ω6c) and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12T is identified as represeting a novel species of the genus Roseococcus , for which the name Roseococcus microcysteis sp. nov. is proposed.

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