Pseudomonas guangdongensis sp. nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4599-4605 ◽  
Author(s):  
Guiqin Yang ◽  
Luchao Han ◽  
Junlin Wen ◽  
Shungui Zhou

A Gram-negative, straight to slightly curved rod-shaped bacterium, motile with peritrichous flagella, designated SgZ-6T, was isolated from an electroactive biofilm and was characterized by means of a polyphasic approach. Growth occurred with 0–5.0 % (w/v) NaCl (optimum 1 %), at pH 6.0–10.0 (optimum pH 7.0) and at 10–42 °C (optimum 30 °C) in trypticase soya broth. Phylogenetic analyses based on the 16S rRNA and gyrB genes identified the isolate as a member of a novel species of the genus Pseudomonas . Strain SgZ-6T exhibited the highest 16S rRNA gene sequence similarity to ‘ Pseudomonas linyingensis’ CGMCC 1.10701 (97.5 %), followed by Pseudomonas sagittaria JCM 18195T (97.4 %), P. oleovorans subsp. lubricantis DSM 21016T (96.6 %), P. tuomuerensis JCM 14085T (96.5 %) and P. alcaliphila JCM 10630T (96.4 %). Strain SgZ-6T showed the highest gyrB gene sequence similarity of 93.7 % to ‘P. linyingensis’ CGMCC 1.10701 among all type strains of genus Pseudomonas . DNA–DNA pairing studies showed that strain SgZ-6T displayed 47.1 and 40.3 % relatedness to ‘P. linyingensis’ CGMCC 1.10701 and P. sagittaria JCM 18195T, respectively. The major isoprenoid quinone was ubiquinone 9 (Q-9). The whole-cell fatty acids consisted mainly of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of the genomic DNA was 68.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SgZ-6T is proposed to represent a novel species of the genus Pseudomonas , for which the name Pseudomonas guangdongensis sp. nov. is proposed. The type strain is SgZ-6T ( = CCTCC AB 2012022T = KACC 16606T). An emended description of the genus Pseudomonas is also proposed.

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1952-1957 ◽  
Author(s):  
Ji Hee Lee ◽  
Keun Sik Baik ◽  
Duwoon Kim ◽  
Chi Nam Seong

Two motile, rod-shaped and agarolytic bacterial strains, designated PSC101T and KDW4T, were isolated from seawater and gut microflora of abalone, respectively, collected from the South Sea (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive. Strains PSC101T and KDW4T showed high 16S rRNA gene sequence similarity to each other (98.6 %). Psychrosphaera saromensis SA4-48T was the nearest neighbour of strains PSC101T and KDW4T with 96.6 % and 97.0 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness among strains PSC101T, KDW4T and Psychrosphaera saromensis KCTC 23240T was less than 70 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belonged to the genus Psychrosphaera and formed a distinct phyletic line from Psychrosphaera saromensis SA4-48T. The common major cellular fatty acids of the two novel isolates were C16 : 0, C17 : 1ω8c and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). Flexirubin-type pigments were absent. The main ubiquinone was UQ-8 and the DNA G+C content of strains PSC101T and KDW4T was 49.5 and 42.5 mol%, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. On the basis of the polyphasic characterization of the two strains, it is suggested that the two isolates represent two novel species of the genus Psychrosphaera , for which the names Psychrosphaera aestuarii sp. nov. (type strain, PSC101T = KCTC 32274T = JCM 19496T) and Psychrosphaera haliotis sp. nov. (type strain, KDW4T = KCTC 22500T = JCM 16340T) are proposed. An emended description of the genus Psychrosphaera is also proposed.


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1617-1621 ◽  
Author(s):  
Shungui Zhou ◽  
Jia Tang ◽  
Dongxing Qin ◽  
Qin Lu ◽  
Guiqin Yang

A thermophilic bacterium, designated DX-1T, was isolated from the anode biofilm of a microbial fuel cell (MFC). Cells of strain DX-1T were oxidase-positive, catalase-positive and Gram-staining-negative. The strain was found to be rod-shaped and non-motile and to produce subterminal spores. The strain was able to grow with NaCl at concentrations ranging from 0 to 6 %, at temperatures of 25–60 °C (optimum 55 °C) and pH 6.0–8.0 (optimum pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DX-1T formed a cluster with Ureibacillus thermosphaericus DSM 10633T (96.9 % 16S rRNA sequence similarity), Ureibacillus composti DSM 17951T (95.8 %), Ureibacillus thermophilus DSM 17952T (95.7 %) and Ureibacillus terrenus DSM 12654T (95.3 %). The G+C content of the genomic DNA was 40.4 mol%. The major quinone was MK-7, the peptidoglycan type was l-Lys←d-Asp, and the major cellular fatty acids (>5 %) were iso-C16 : 0 and iso-C14 : 0. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phospholipids of unknown composition. Based on phenotypic characteristics, chemotaxonomic features and results of phylogenetic analyses, the strain was determined to represent a distinct novel species of the genus Ureibacillus , and the name proposed for the novel species is Ureibacillus defluvii sp. nov., with type strain DX-1T ( = CGMCC 1.12358T = KCTC 33127T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 661-666 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Deok-Chun Yang

A Gram-stain-negative, non-motile, red bacterium, designated DCY57T, was isolated from soil of a ginseng field in a mountainous region of Chungnam province in South Korea. Strain DCY57T grew with 0–1 % (w/v) NaCl and the optimum temperature for growth was 30 °C. Strain DCY57T contained MK-7 as the predominant menaquinone. The polyamine was sym-homospermidine. The major fatty acids were C16:1ω5c, iso-C15:0, anteiso-C15:0 and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids. The DNA G+C content was 58.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY57T was most closely related to members of the genus Hymenobacter . The isolate exhibited 91.7 % 16S rRNA gene sequence similarity with H. soli PB17T, 94.5 % with H. flocculans A2-50AT and 95.8 % with H. metalli A2-91T. On the basis of the evidence presented in this study, strain DCY57T represents a novel species within the genus Hymenobacter , for which the name Hymenobacter ginsengisoli sp. nov. is proposed. The type strain is DCY57T ( = KCTC 23674T = JCM 17841T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2828-2834 ◽  
Author(s):  
S. Kalyana Chakravarthy ◽  
E. V. V. Ramaprasad ◽  
E. Shobha ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two strains (JA266T and JA333) of Gram-negative, rod-shaped, phototrophic, purple non-sulfur bacteria were isolated from a freshwater fish pond and an industrial effluent. Both strains were capable of phototrophic and chemotrophic growth. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series were present as photosynthetic pigments. The major fatty acid for both strains was C18 : 1ω7c (>65 %), with minor amounts of 11-methyl C18 : 1ω7c, C16 : 0, C16 : 1ω7c and C18 : 0 also present. Both strains have the lamellar type of intracellular photosynthetic membranes. Ubiquinone-10 (Q10) and rhodoquinone-10 (RQ10) were present as primary quinone components. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were the major polar lipids, while minor amounts of amino lipids (AL1, AL2) and an unidentified lipid (L1) were common to both strains. The DNA G+C contents of strains JA266T and JA333 were 71.3 and 69.9 mol%, respectively. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains clustered with members of the genus Rhodoplanes in the class Alphaproteobacteria . Strains JA266T and JA333 had gene sequence similarity of 98.7 and 98.9 % with Rhodoplanes serenus TUT3530T, 96.4 and 96.5 % with Rhodoplanes elegans AS130T, respectively, and less than 96 % with other members of the genus Rhodoplanes . 16S rRNA gene sequence similarity between the two strains was 99.3 % and they exhibited high (84.7 %) relatedness based on DNA–DNA hybridization. Furthermore, both strains had less than 65 % DNA–DNA relatedness with the type strain R. serenus TUT3530T. On the basis of phenotypic and genotypic data, it is proposed that strain JA266T be classified as a novel species of the genus Rhodoplanes , with the species name Rhodoplanes piscinae sp. nov. The type strain of the proposed novel species is JA266T ( = JCM 14934T = KCTC 5627T), while strain JA333 ( = NBRC 107574 = KCTC 5962) is an additional strain.


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2897-2902 ◽  
Author(s):  
Ishwinder Kaur ◽  
Chandandeep Kaur ◽  
Fazlurrahman Khan ◽  
Shanmugam Mayilraj

A Gram-negative, non-motile bacterial strain that formed straight rods and straw yellow colonies, designated FCS-5T, was isolated from a marine sediment from the Arabian Sea. The isolate exhibited most of the phenotypic properties expected for a member of the genus Flavobacterium . The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C17 : 1ω9c and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c). The only isoprenoid quinone was MK-6. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA was 32.4 mol%. According to 16S rRNA gene sequence analysis, strain FCS-5T belonged to the genus Flavobacterium and exhibited 99.3 % 16S rRNA gene sequence similarity with Flavobacterium beibuense F44-8T and 90.9–94.6 % sequence similarity with other members of the genus Flavobacterium . The results of physiological and biochemical tests allowed the discrimination of the isolate from its phylogenetic relatives. Strain FCS-5T is a representative of a novel species of the genus Flavobacterium , for which the name Flavobacterium rakeshii sp. nov. is proposed. The type strain is FCS-5T ( = MTCC 10967T = JCM 17928T). An emended description of F. beibuense is also proposed.


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1610-1615 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-flagellated, gliding, rod-shaped bacterial strain, designated WT-MY15T, was isolated from wood falls in the South Sea in Korea and subjected to a polyphasic taxonomic study. Strain WT-MY15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MY15T clustered with the type strains of two Olleya species, exhibiting 16S rRNA gene sequence similarity values of 97.7–98.1 %. Strain WT-MY15T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain WT-MY15T were similar to those of Olleya aquimaris L-4T and Olleya marilimosa CIP 108537T. The DNA G+C content of strain WT-MY15T was 42.8 mol% and its mean DNA–DNA relatedness values with O. aquimaris L-4T and O. marilimosa CIP 108537T were 8.3 and 5.6 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MY15T is separate from the two recognized species of the genus Olleya . On the basis of the data presented, strain WT-MY15T is considered to represent a novel species of the genus Olleya , for which the name Olleya namhaensis sp. nov. is proposed. The type strain is WT-MY15T ( = KCTC 23673T = CCUG 61507T). An emended description of the genus Olleya is also presented.


Author(s):  
Yong Li ◽  
Shengkun Wang ◽  
Danran Bian ◽  
Shang Sun ◽  
Tengfei Ma

Two Gram-negative, aerobic, motile bacteria strains were isolated from leaf spot disease of Quercus mongolica. Strain hsmgli-8T has 99.86 % 16S rRNA gene sequence similarity to LY10J, and the highest 16S rRNA gene sequence similarity to Pseudomonas cerasi 58T (97.2 %), then Pseudomonas ficuserectae JCM 2400T (97.18 %), Pseudomonas meliae CFBP 3225T, Pseudomonas tremae CFBP 6111T and Pseudomonas congelans DSM 14939T (all 97.12 %), and less than 97.1 % similarity to other recognized species. In phylogenetic trees based on 16S rRNA gene and multilocus sequence data, the two novel strains form a separate branch, indicating that they do not belong to any Pseudomonas group and subgroup, and should belong to a novel species within the genus Pseudomonas . This assertion is also supported by the results of genome average nucleotide identity analysis. The major fatty acids are C16 : 0, C18 : 1  ω7c and/or C18 : 1  ω6c, C16 : 1  ω7c and/or C16 : 1  ω6c. Polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, aminolipid and seven uncharacterized phospholipids. The predominant respiratory quinone is Q-9. The DNA G+C content is 59.45–59.50 mol%. Based on these data, we propose that the two novel strains should be assigned as a novel species within the genus Pseudomonas . We propose that the novel strains be named Pseudomonas quercus sp. nov. The type strain is hsmgli-8T (=CFCC 15739T=LMG 31544T).


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1145-1150 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Sayaka Tsuchida ◽  
Koh Kawasumi ◽  
Hiromi Amao ◽  
...  

Strains of Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces, and three strains, ST161T, ST33 and ST37T, were investigated taxonomically. Based on phylogenetic analyses and specific phenotypic characteristics, the three strains were allocated to the genus Bacteroides . Phylogenetic analyses of their 16S rRNA gene sequences revealed that strain ST161T formed a distinct line of descent, with highest sequence similarity to strain ST33 (98.7 %) and Bacteroides oleiciplenus JCM 16102T (97.7 %). High levels of DNA–DNA relatedness (79–89 %) were found between strains ST161T and ST33, but low levels were found between strain ST161T and B. oleiciplenus JCM 16102T (33–37 %) and between strain ST33 and B. oleiciplenus JCM 16102T (33–37 %). These data clearly indicated that strains ST161T and ST33 represent a single novel species. 16S rRNA gene sequence analyses showed that strain ST37T also formed a distinct line of descent, with highest sequence similarity to Bacteroides acidifaciens JCM 10556T (96.5 %) and Bacteroides caccae JCM 9498T (95.6 %). Analysis of hsp60 gene sequences also supported these relationships. Based on phenotypic and phylogenetic characteristics, two novel species, Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., are thus proposed. The type strains of B. stercorirosoris and B. faecichinchillae are ST161T ( = JCM 17103T = CCUG 60872T) and ST37T ( = JCM 17102T = CCUG 60873T), respectively. The DNA G+C contents of strains ST161T and ST37T were 45.7 and 41.0 mol%, respectively.


2020 ◽  
Vol 70 (12) ◽  
pp. 6381-6389 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Li-Chu Chen ◽  
Che-Chia Yang ◽  
Aurelien Carlier ◽  
Wen-Ming Chen

A novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18T, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18T were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18T was 50.9 %. Strain NBD-18T was most closely related to Orrella dioscoreae LMG 29303T and Algicoccus marinus HZ20T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303T and A. marinus HZ20T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18T, O. dioscoreae LMG 29303T and A. marinus HZ20T are affiliated with the same genus. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18T represents a novel species. Thus, A. marinus HZ20T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18T represents a novel species in the genus Orrella , for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18T (=BCRC 81197T=LMG 31338T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5263-5270 ◽  
Author(s):  
Wen-Rui Cao ◽  
Lan-Zeng Zhang ◽  
Yi-Hao Hu ◽  
Ming-Yu Jiang ◽  
Ying-Jie Li

Strains J15B81-2T and J15B91T were isolated from a sediment sample collected from the South China Sea. Cells of both strains were observed to be rod-shaped, non-gliding, Gram-stain-negative, yellow-pigmented, facultatively anaerobic, catalase-positive, oxidase-negative and showing optimum growth at 30 °C. Strains J15B81-2T and J15B91T could tolerate up to 9 and 10  % (w/v) NaCl concentration and grow at pH 6.5–9.5 and 6.0–9.0, respectively. The strains shared 97.4 % 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 81.1–85.8 % ANIb and 31.5 % dDDH values calculated using whole genome sequences. Strains J15B81-2T and J15B91T shared highest 16S rRNA gene sequence similarity to Salinimicrobium xinjiangense CGMCC 1.12522T (98.4 %) and Salinimicrobium sediminis CGMCC 1.12641T (98.0 %), respectively. Among species with validly published names, S. sediminis CGMCC 1.12641T shared close genetic relatedness with strains J15B81-2T [85.1–85.3% average nucleotide identity based on blastBlast+ (ANIb) and 30.6 % digital DNA–DNA hybridization (dDDH)] and J15B91T (76.6–79.1 % ANIb and 21.5 % dDDH). The major fatty acid of strains J15B81-2T and J15B91T were identified as iso-C15 : 0 and iso-C16 : 0, respectively, and the major polar lipids of the two strains consisted of phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The strains contained MK-6 as their predominant menaquinone. The genomic G+C contents of strains J15B81-2T and J15B91T were determined to be 41.7 and 41.8 mol %, respectively. Both strains are considered to represent two novel species of the genus Salinimicrobium and the names Salinimicrobium nanhaiense sp. nov. and Salinimicrobium oceani sp. nov. are proposed for strains J15B81-2T (=KCTC 72867T=MCCC 1H00410T) and J15B91T (=KCTC 72869T=MCCC 1H00411T), respectively.


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