scholarly journals Description of Comamonas serinivorans sp. nov., isolated from wheat straw compost

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4141-4146 ◽  
Author(s):  
Daochen Zhu ◽  
Changxiao Xie ◽  
Ying Huang ◽  
Jianzhong Sun ◽  
Weimin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Rrna Gene ◽  
Comamonas Testosteroni ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Type Strains

A Gram-stain-negative bacterium, designated SP-35T, was isolated from compost and was subjected to a taxonomic study. This isolate was short-rod-shaped and non-spore-forming. Phylogenetic analysis based on 16S rRNA sequence comparison indicated the isolate was related to the genus Comamonas . 16S rRNA gene sequence analysis showed that its closest neighbours were the type strains Comamonas odontotermitis Dant 3-8T (96.8 % similarity), Comamonas testosteroni DSM 50244T (96.5 %), Comamonas guangdongensis CY01T (95.9 %) and Comamonas composti YY287T (95.6 %). Using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics we could clearly distinguish strain SP-35T from type strains of the genus Comamonas . The genomic DNA G+C content of strain SP-35T was 63.1 mol%. The predominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidlyglycerol. Differences in phenotypic and phylogenetic characteristics support the classification of strain SP-35T as a representative of a novel species in the genus Comamonas , for which the name Comamonas serinivorans sp. nov. is proposed. The type strain is SP-35T ( = DSM 26136T = JCM 18194T).

Luteimonas huabeiensis sp. nov., isolated from stratum water

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3352-3357 ◽  
Author(s):  
Gang Wu ◽  
Yang Liu ◽  
Qing Li ◽  
Huijing Du ◽  
Jing You ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Taxonomic Approach ◽  
Type Strains ◽  
Physiological And Biochemical

A yellow-coloured bacterial strain, designated HB2T, isolated from stratum water was investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a member of the genus Luteimonas , its three closest neighbours being Luteimonas aquatica BCRC 17731T (97.5 % similarity), Luteimonas marina JCM 12488T (97.3 %) and Luteimonas aestuarii DSM 19680T (96.9 %). Strain HB2T could clearly be distinguished from these type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain HB2T represents a novel species of the genus Luteimonas , for which the name Luteimonas huabeiensis sp. nov. is proposed. The type strain is HB2T ( = DSM 26429T = CICC 11005sT).

Brevibacillus nitrificans sp. nov., a nitrifying bacterium isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2121-2126 ◽  
Author(s):  
Fumihiko Takebe ◽  
Kikue Hirota ◽  
Yoshinobu Nodasaka ◽  
Isao Yumoto
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sewage Treatment ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Brevibacillus Choshinensis ◽  
Type Strains

A heterotrophic nitrifying bacterium, designated strain DA2T, was isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks. Cells of strain DA2T were Gram-positive, facultatively anaerobic, sporulating rods that were motile by means of peritrichous flagella; they were able to grow at pH 5–8. The major isoprenoid quinone of strain DA2T was menaquinone-7 (MK-7) and its cellular fatty acid profile consisted mainly of iso-C15 : 0 (18.6 %) and anteiso-C15 : 0 (69.1 %). The DNA G+C content was 54.1 mol%. 16S rRNA gene sequence phylogeny suggested that strain DA2T is a member of the genus Brevibacillus , with highest sequence similarities (in parentheses) to the type strains of Brevibacillus choshinensis (99.7 %), B. formosus (99.4 %), B. brevis (99.4 %), B. agri (99.0 %), B. reuszeri (98.8 %), B. parabrevis (98.7 %), B. centrosporus (98.6 %), B. limnophilus (97.4 %), B. panacihumi (97.3 %) and B. invocatus (97.3 %). DNA–DNA hybridization showed less than 60 % relatedness between strain DA2T and type strains of the most closely related species given above. Given the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA sequence and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Brevibacillus nitrificans is proposed; the type strain of this species is DA2T ( = JCM 15774T = NCIMB 14531T).

scholarly journals Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3862-3866 ◽  
Author(s):  
Shi Peng ◽  
Dong Dan Hong ◽  
Yang Bing Xin ◽  
Li Ming Jun ◽  
Wei Ge Hong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to Sphingobacterium nematocida CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus Sphingobacterium . Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

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
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

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).

scholarly journals Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1348-1353 ◽  
Author(s):  
Hui-xian Wu ◽  
Pok Yui Lai ◽  
On On Lee ◽  
Xiao-jian Zhou ◽  
Li Miao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248T, was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248T fell within the genus Erythrobacter . Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3 % (with Erythrobacter gangjinensis ) to 98.2 % (with Erythrobacter citreus ). However, levels of DNA–DNA relatedness between strain UST081027-248T and the type strains of closely related species were below 70 %. Optimal growth of the isolate occurred in the presence of 2.0 % NaCl, at pH 8.0–9.0 and at 28–36 °C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C15 : 0 2-OH. The genomic DNA G+C content of strain UST081027-248T was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248T ( = JCM 17468T = NRRL 59511T).

scholarly journals Pseudoalteromonas caenipelagi sp. nov., isolated from a tidal flat

2020 ◽  
Vol 70 (12) ◽  
pp. 6301-6306
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1  ω7c and/or C16 : 1  ω6c, C16 : 0 and C18 : 1  ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Peng Wang ◽  
Yuxin Gao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .

Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1132-1137 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Soon-Wo Kwon ◽  
Jian He ◽  
Shun-Gui Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Type Species ◽  
Amide Bond ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A facultatively anaerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-reaction-negative, coccoid to short rod-shaped strain, designated FLN-7T, was isolated from activated sludge of a wastewater biotreatment facility. The strain was able to hydrolyse amide pesticides (e.g. diflubenzuron, propanil, chlorpropham and dimethoate) through amide bond cleavage. Strain FLN-7T grew at 4–42 °C (optimum 28 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–5.0 % (w/v) NaCl (optimum 1.0 %). The major respiratory quinone was ubiquinone-10. The major cellular fatty acid was C18 : 1ω7c. The genomic DNA G+C content of strain FLN-7T was 66.4±0.5 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FLN-7T was a member of the genus Paracoccus and showed highest 16S rRNA gene sequence similarities with Paracoccus aminovorans JCM 7685T (99.2 %), P. denitrificans DSM 413T (97.8 %), P. yeei CDC G1212T (97.3 %) and P. thiocyanatus THI 011T (97.1 %). Strain FLN-7T showed low DNA–DNA relatedness with P. aminovorans KACC 12261T (36.5±3.4 %), P. denitrificans KACC 12251T (30.5±2.6 %), P. yeei CCUG 46822T (26.2±2.4 %) and P. thiocyanatus KACC 13901T (15.5±0.9 %). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain FLN-7T was clearly distinguished from all recognized species of the genus Paracoccus and should be classified in a novel species, for which the name Paracoccus huijuniae sp. nov. is proposed. The type strain is FLN-7T ( = KACC 16242T  = ACCC 05690T).

scholarly journals Chryseobacterium gallinarum sp. nov., isolated from a chicken, and Chryseobacterium contaminans sp. nov., isolated as a contaminant from a rhizosphere sample

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1419-1427 ◽  
Author(s):  
Peter Kämpfer ◽  
Marie T. Poppel ◽  
Gottfried Wilharm ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Rhizosphere Sample ◽  
Sequence Similarities

Two yellow-pigmented bacterial strains (100T and C26T), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus Chryseobacterium showed the highest sequence similarities of strains 100T and C26T to the type strains of Chryseobacterium joostei (respectively 97.5 and 98.2 %), C. viscerum (96.6, 97.8 %), C. gleum (97.1, 97.7 %), C. arthrosphaerae (97.3%, 97.7 %), C. indologenes (97.2, 97.7 %), C. tructae (96.6, 97.6 %), C. jejuense (97.0, 97.6 %) and C. oncorhynchi (96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus Chryseobacterium were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA–DNA hybridizations between the two strains and between the novel strains and the type strains of C. joostei , C. indologenes , C. jejuense , C. tructae and C. viscerum resulted in relatedness values clearly below 70 %. These DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100T and C26T represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100T = LMG 27808T = CCM 8493T) and Chryseobacterium contaminans sp. nov. (type strain C26T = LMG 27810T = CCM 8492T) are proposed.

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