Glaciimonas singularis sp. nov., isolated from a uranium mine wastewater treatment plant

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2344-2350 ◽  
Author(s):  
Ana Paula Chung ◽  
Igor Tiago ◽  
M. Fernanda Nobre ◽  
António Veríssimo ◽  
Paula V. Morais

A bacterial strain, A2-57T, recovered from a water sample collected in a uranium mine was taxonomically studied in detail. This strain was a Gram-reaction-negative, rod-shaped bacterium that grew optimally at 25 °C and at pH 6.0–7.0 and had a DNA G+C content of 55.0 mol%. Ubiquinone 8 (UQ-8) was the predominant respiratory quinone and the major fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or ω7c and/or C15 : 0 iso 2-OH) and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A2-57T belonged to the family Oxalobacteraceae and formed a distinct branch with Glaciimonas immobilis Cr9-30T. Strain A2-57T shared approximately 97.3 % 16S rRNA sequence similarity with G. immobilis Cr9-30T and also showed high sequence similarity with members of the genera Herbaspirillum (96.3–97.0 %) and Collimonas (96.2–97.0 %). Although phylogenetically closely related to the type strain of G. immobilis , the low level of DNA–DNA hybridization between the two strains (21.6 %) and several physiological and biochemical properties indicated that the novel strain could be clearly distinguished from G. immobilis LMG 25547T. Therefore, it is concluded that strain A2-57T represents a novel species of the genus Glaciimonas , for which the name Glaciimonas singularis sp. nov. is proposed. The type strain is A2-57T ( = CIP 110539T = LMG 27070T).

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).


Author(s):  
Selma Vieira ◽  
Katharina J. Huber ◽  
Meina Neumann-Schaal ◽  
Alicia Geppert ◽  
Manja Luckner ◽  
...  

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1  ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1488-1494 ◽  
Author(s):  
Daichi Fujii ◽  
Fumiko Nagai ◽  
Yohei Watanabe ◽  
Yukio Shirasawa

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus Flavobacterium . In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of Flavobacterium caeni and Flavobacterium terrigena , with 16S rRNA gene sequence similarity values of 94.9 % and 96.2 %, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15 : 1 G (14.4 %), iso-C16 : 0 (13.2 %), C15 : 0 (12.9 %), iso-C15 : 0 (12.9 %) and iso-C17 : 0 3-OH (11.5 %). Those of strain YIT 12746T were iso-C15 : 0 (21.5 %), iso-C16 : 0 (13.3 %), C15 : 0 (12.0 %) and iso-C15 : 1 G (11.9 %). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium , for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T = JCM 19141T = DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T = JCM 19142T = DSM 27078T) are proposed. Emended descriptions of Flavobacterium caeni and Flavobacterium terrigena are also proposed.


2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2865-2871 ◽  
Author(s):  
Chul-Hyung Kang ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-spore-forming, strictly aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, designated SMS-12T, was isolated from marine sand in a firth on the western coast of South Korea. Strain SMS-12T grew optimally at 25 °C, at pH 7.0–7.5 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SMS-12T fell within the clade comprising species of the genus Mucilaginibacter , forming a coherent cluster with the type strain of Mucilaginibacter lappiensis , with which it exhibited the highest 16S rRNA gene sequence similarity value of 97.5 %. Levels of sequence similarity to the type strains of the other species of the genus Mucilaginibacter and the other species used in the phylogenetic analysis were 93.3–96.4 % and <91.5 %, respectively. Strain SMS-12T contained MK-7 as the predominant menaquinone, and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified aminophospholipid; sphingolipids were present. The DNA G+C content was 41.8 mol% and the mean DNA–DNA relatedness with M. lappiensis KACC 14978T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SMS-12T is separate from other species of the genus Mucilaginibacter . On the basis of the data presented, strain SMS-12T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter sabulilitoris sp. nov. is proposed. The type strain is SMS-12T ( = KCTC 32111T = CCUG 62214T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2234-2238 ◽  
Author(s):  
Ahyoung Choi ◽  
Jang-Cheon Cho

Gram-negative strains, motile by a single polar flagellum, non-pigmented and with a curved rod-shaped morphology, designated IMCC1826T and IMCC1883, were isolated from a surface seawater sample from the Yellow Sea. The two strains shared 99.9 % 16S rRNA gene sequence similarity and showed 92 % DNA–DNA relatedness, suggesting that they belonged to the same genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were related most closely to the type strain of Thalassolituus oleivorans with a sequence similarity of 96.4 % and formed a robust phyletic lineage with T. oleivorans . DNA–DNA relatedness between the two strains and T. oleivorans DSM 14913T was 8.7–11.6 %. A putative alkane hydroxylase (alkB) gene was detected in strain IMCC1826T by PCR, but the amino acid sequence of the gene was distantly related to that of the AlkB homologue of T. oleivorans DSM 14913T. As expected from the presence of the alkB gene, the new strains utilized n-tetradecane and n-hexadecane as a carbon source. The DNA G+C content was 54.6–56.0 mol% and the main isoprenoid quinone detected was Q-9. Polar lipids of strain IMCC1826T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and amino-group-containing lipids. On the basis of taxonomic data obtained in this study, strains IMCC1826T and IMCC1883 represent a novel species of the genus Thalassolituus , for which the name Thalassolituus marinus sp. nov. is proposed, with IMCC1826T ( = KCTC 23084T = NBRC 107590T) as the type strain.


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1359-1364 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, ovoid or rod-shaped bacterial strain, designated L-6T, was isolated from seawater of Baekdo harbour of the East Sea in Korea and its taxonomic position was investigated by using a polyphasic study. Strain L-6T grew optimally at 30 °C, at pH 7.5–8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain L-6T formed a cluster with the type strain of Celeribacter neptunius at a bootstrap resampling value of 100 %. Strain L-6T exhibited 16S rRNA gene sequence similarity values of 97.7 % to C. neptunius H 14T and of less than 96.2 % to the type strains of other species used in the phylogenetic analysis. The G+C content of the chromosomal DNA of strain L-6T was 60.9 mol%. The predominant ubiquinone found in strain L-6T and C. neptunius CIP 109922T was ubiquinone-10 (Q-10). The predominant fatty acid of strain L-6T and C. neptunius CIP 109922T was C18 : 1ω7c. The major polar lipids of strain L-6T were phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The mean level of DNA–DNA relatedness between strain L-6T and C. neptunius CIP 109922T was 17 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain L-6T is distinguishable from C. neptunius . On the basis of the data presented, strain L-6T is considered to represent a novel species of the genus Celeribacter , for which the name Celeribacter baekdonensis sp. nov. is proposed. The type strain is L-6T ( = KCTC 23497T  = CCUG 60799T).


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).


Author(s):  
Juan Zhou ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.


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