Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1089-1095 ◽  
Author(s):  
Markus Haber ◽  
Sigal Shefer ◽  
Assunta Giordano ◽  
Pierangelo Orlando ◽  
Agata Gambacorta ◽  
...  

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

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):  
Rui Yin ◽  
Yan-Jun Yi ◽  
Zhuo Chen ◽  
Guan-Jun Chen ◽  
Yan-Xia Zhou ◽  
...  

A Gram-stain-negative, aerobic, yellow, non-motile, rod-shaped and alginate-degrading bacterium, designated Dm15T, was isolated from marine alga collected in Weihai, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Dm15T represents a distinct line of the family Flavobacteriaceae . Strain Dm15T had the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Arcticiflavibacter luteus (96.7 %) and 93.7–96.4 % sequence similarity to other phylogenetic neighbours ( Bizionia paragorgiae , Winogradskyella thalassocola , Ichthyenterobacterium magnum , Psychroserpens burtonensis and Arcticiflavibacter luteus ) in the family Flavobacteriaceae . The novel isolate was able to grow at 10–40 °C (optimum, 30–33 °C), pH 7.0–9.0 (optimum, pH 7.0–7.5) and with 0.5–6.0 % NaCl (optimum 2.0–3.0 %, w/v). It could grow at 40 °C, and degrade alginate and cellulose, which were different from the neighbour genera. The draft genome consisted of 3395 genes with a total length of 3 798 431 bp and 34.1mol% G+C content. Especially, there were some specific genes coding for cellulase and alginate lyase, which provided a basis for the above phenotypic characteristics. The strain's genome sequence showed 71.1–80.2 % average amino acid identity values and 71.8–77.7 % average nucleotide identity values compared to the type strains of related genera within the family Flavobacteriaceae . It shared digital DNA–DNA hybridization identity of 19.8 and 20.9 % with I. magnum and A. luteus , respectively. The sole menaquinone was MK-6. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The polar lipids included six unidentified polar lipids, four unidentified aminolipids and phosphatidylethanolamine. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain Dm15T represents a novel species of a new genus in the family Flavobacteriaceae , phylum Bacteroidetes , for which the name Flavihalobacter algicola gen. nov., sp. nov. is proposed. The type strain is Dm15T (KCTC 42256T=CICC 23815T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 268-273 ◽  
Author(s):  
Malka Halpern ◽  
Svetlana Fridman ◽  
Yana Aizenberg-Gershtein ◽  
Ido Izhaki

Pseudomonas flectens Johnson 1956, a plant-pathogenic bacterium on the pods of the French bean, is no longer considered to be a member of the genus Pseudomonas sensu stricto. A polyphasic approach that included examination of phenotypic properties and phylogenetic analyses based on 16S rRNA, rpoB and atpD gene sequences supported the transfer of Pseudomonas flectens Johnson 1956 to a new genus in the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Two strains of Phaseolibacter flectens were studied (ATCC 12775T and LMG 2186); the strains shared 99.8 % sequence similarity in their 16S rRNA genes and the housekeeping gene sequences were identical. Strains of Phaseolibacter flectens shared 96.6 % or less 16S rRNA gene sequence similarity with members of different genera in the family Enterobacteriaceae and only 84.7 % sequence similarity with Pseudomonas aeruginosa LMG 1242T, demonstrating that they are not related to the genus Pseudomonas . As Phaseolibacter flectens formed an independent phyletic lineage in all of the phylogenetic analyses, it could not be affiliated to any of the recognized genera within the family Enterobacteriaceae and therefore was assigned to a new genus. Cells were Gram-negative, straight rods, motile by means of one or two polar flagella, fermentative, facultative anaerobes, oxidase-negative and catalase-positive. Growth occurred in the presence of 0–60 % sucrose. The DNA G+C content of the type strain was 44.3 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, Pseudomonas flectens Johnson 1956 is transferred to the novel genus Phaseolibacter gen. nov. as Phaseolibacter flectens gen. nov., comb. nov. The type strain of Phaseolibacter flectens is ATCC 12775T  = CFBP 3281T  = ICMP 745T  = LMG 2187T  = NCPPB 539T.


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1158-1164 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Duck-Chul Oh

A Gram-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, yellow-pigmented rod, designated A11T, was isolated from a marine sponge, Halichondria oshoro, collected on the coastline of Jeju Island, Republic of Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A11T was a member of the family Flavobacteriaceae . Its closest relatives were members of the genera Muricauda , Flagellimonas and Croceitalea (94.4–94.8 % 16S rRNA gene sequence similarity). The only polar lipid detected in strain A11T was phosphatidylethanolamine. The dominant fatty acids were iso-C15 : 0 (30.4 %), iso-C15 : 1 G (26.7 %), iso-C17 : 0 3-OH (12.4 %) and iso-C15 : 0 3-OH (7.3 %). The DNA G+C content of strain A11T was 41.7 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A11T represents a novel genus and species within the family Flavobacteriaceae , for which the name Spongiibacterium flavum gen. nov., sp. nov. is proposed. The type strain of the type species is A11T ( = KCTC 22665T = DSM 22638T). Emended descriptions of the genera Croceitalea and Flagellimonas are also given.


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2009-2016 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Jhen-Ci Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen

A bacterial strain, designated Npb-03T, was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10–37 °C (optimum, 30–35 °C), at pH 6.0–8.0 (optimum, pH 6.0–7.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03T forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria , most closely related to the genera Aquaspirillum , Laribacter , Leeia and Microvirgula , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the genotypic and phenotypic data, strain Npb-03T represents a novel genus and species of the family Neisseriaceae , for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03T ( = BCRC 80376T = LMG 26668T = KCTC 23712T).


2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1570-1575 ◽  
Author(s):  
Chao Zhao ◽  
Zhaoming Gao ◽  
Qiwei Qin ◽  
Fuying Li ◽  
Lingwei Ruan

A taxonomic study was carried out on strain P1T, which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5–2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22–44 °C (optimum, 35–40 °C) and pH range 5.5–8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5 % (w/v) (optimum, 0.5 %). Strain P1T utilized hydrogen, succinate, l-malate, citrate, oxalate, dl-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H2 and CO2. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1T formed a distinct evolutionary lineage within the family Desulfovibrionaceae . Strain P1T was most closely related to members of the genera Desulfovibrio (92.0–94.3 % 16S rRNA gene sequence similarity), Desulfocurvus (91.1 %), Bilophila (87.9 %) and Lawsonia (86.0 %) of the family Desulfovibrionaceae . The DNA G+C content of strain P1T was 64.5 mol% and the major cellular fatty acids were iso-C15 : 0 (18.8 %), anteiso-C15 : 0 (5.0 %), C16 : 0 (14.2 %) and iso-C17 : 1ω9c (24.4 %). The predominant menaquinone was MK-7 (97 %). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1T represents a novel species of a new genus, for which the name Desulfobaculum xiamenensis gen. nov., sp. nov. is proposed. The type strain of Desulfobaculum xiamenensis is P1T ( = CGMCC 1.5166T = DSM 24233T).


Author(s):  
Chih-Horng Kuo ◽  
Pin-Yun Huang ◽  
Shih-Yi Sheu ◽  
Der-Shyan Sheu ◽  
Li-Cheng Jheng ◽  
...  

A novel bacterial strain, designated IPMB12T, isolated from the gut of the superworm Zophobas morio in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, facultatively anaerobic, non-motile, coccoid or rod-shaped and formed translucent colonies. Optimal growth occurred at 25–37 °C, pH 9–10, and with 0–2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain IPMB12T is affiliated with genus in the the family Orbaceae in the class Gammaproteobacteria . Strain IPMB12T was most closely related to Gilliamella mensalis LMG 29880T with a 94.6 % 16S rRNA gene sequence similarity. Strain IPMB12T showed less than 71.6 % average nucleotide identity, less than 71.5 % average amino acid identity and less than 21.2 % digital DNA–DNA hybridization identity compared to the strains of related genera within the family Orbaceae . The major fatty acids of strain IPMB12T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized phosphoaminoglycolipid and one uncharacterized aminophospholipid. The major isoprenoid quinone was Q-8. Genomic DNA G+C content of strain IPMB12T was 39.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain IPMB12T represents a novel species of a new genus in the family Orbaceae , for which the name Zophobihabitans entericus gen. nov., sp. nov. is proposed. The type strain is IPMB12T (=BCRC 80908T =LMG 32079T=KCTC 82347T=KACC 22323T).


2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4425-4431 ◽  
Author(s):  
Shaoxing Chen ◽  
Yao Xu ◽  
Siqi Sun ◽  
Jingwen Liu ◽  
Feilong Chen

A halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).


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).


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