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International Journal of Systematic and Evolutionary Microbiology

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https://www.readbyqxmd.com/read/29792590/altererythrobacter-flavus-sp-nov-isolated-from-mangrove-sediment
#1
Hui Ma, Hao Ren, Lingfeng Huang, Yuanrong Luo
A Gram-negative, aerobic, non-motile, rod-shaped bacterium, designated MS1-4T , was isolated from mangrove sediment of the Jiulong River Estuary, Fujian Province, China. The isolate formed yellow colonies on ZB 2216E agar. Optimal growth was observed at pH 6.0, at 34 °C and in the presence of 4 % (w/v) NaCl. Strain MS1-4T shared highest 16S rRNA gene sequence similarity of 97.7 % with Altererythrobacter mangrovi C9-11T , followed by Altererythrobacter ishigakiensis JPCCMB0017T (97.2 %). Phylogenetic analysis indicated that strain MS1-4T formed a clade with A...
May 24, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29792589/using-average-nucleotide-identity-to-improve-taxonomic-assignments-in-prokaryotic-genomes-at-the-ncbi
#2
Stacy Ciufo, Sivakumar Kannan, Shobha Sharma, Azat Badretdin, Karen Clark, Seán Turner, Slava Brover, Conrad L Schoch, Avi Kimchi, Michael DiCuccio
Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to their taxonomic identity. We present the methods used to make such comparisons, the current status of GenBank verifications, and recent developments in confirming species assignments in new genome submissions.
May 24, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29792588/candida-kantuleensis-sp-nov-a-d-xylose-fermenting-yeast-species-isolated-from-peat-in-a-tropical-peat-swamp-forest
#3
Sukanya Nitiyon, Pannida Khunnamwong, Noppon Lertwattanasakul, Savitree Limtong
Three strains (DMKU-XE11T , DMKU-XE15 and DMKU-XE20) representing a single novel anamorphic and d-xylose-fermenting yeast species were obtained from three peat samples collected from Khan Thulee peat swamp forest in Surat Thani province, Thailand. The strains differed from each other by one to two nucleotide substitutions in the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and zero to one nucleotide substitution in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the three strains represented a single Candida species that was distinct from the other related species in the Lodderomyces/Candida albicans clade...
May 24, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29790846/salipaludibacillus-halalkaliphilus-sp-nov-a-moderately-haloalkaliphilic-bacterium-from-a-coastal-marine-wetland
#4
Mohammad Ali Amoozegar, Azadeh Shahinpei, Somaye Makzum, Shokufeh Rafieyan, Mahdi Moshtaghi Nikou, Cathrin Spröer, Antonio Ventosa
A Gram-stain-positive, endospore-forming rod-shaped non-motile, moderately halophilic and alkaliphilic bacterium, strain GASy1T , was isolated from a water sample from Gomishan, a marine wetland in Iran. GASy1T required at least 0.5 % (w/v) NaCl for growth and was able to grow at NaCl concentrations of up to 15 % (w/v), with optimum growth occurring at 5 % (w/v) NaCl. The optimum pH and temperature for growth were pH 8.5-9.0 and 30 °C, respectively, while it was able to grow over a pH range and a temperature range of 7...
May 23, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29786499/scheffersomyces-stambukii-f-a-sp-nov-a-d-xylose-fermenting-species-isolated-from-rotting-wood
#5
Mariana R Lopes, Thiago M Batista, Glória R Franco, Lucas R Ribeiro, Ana R O Santos, Carolina Furtado, Rennan G Moreira, Aristóteles Goes-Neto, Marcos J S Vital, Luiz H Rosa, Marc-André Lachance, Carlos A Rosa
Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade...
May 22, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29786497/massilia-armeniaca-sp-nov-isolated-from-desert-soil
#6
Mengnan Ren, Xiaoyan Li, Yueqi Zhang, Yu Jin, Siqi Li, Haidong Huang
A Gram-stain-negative, aerobic, motile and rod-shaped bacterium, strain ZMN-3T , was isolated from desert soil sample collected from Ongniod Qi, Inner Mongolia, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZMN-3T was affiliated with the genus Massilia and showed the highest similarity to Massilia humi THG S6-8T (98.9 %) and Massilia buxea A9T (98.2 %). In partial gyrB and lepA sequences, the highest similarity of strain ZMN-3T and M. humi THG S6-8T were 95.9 and 96.8 %, respectively...
May 22, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781802/zobellella-maritima-sp-nov-a-polycyclic-aromatic-hydrocarbon-degrading-bacterium-isolated-from-beach-sediment
#7
Dong Wan Lee, Hanbyul Lee, Bong-Oh Kwon, Jong Seong Khim, Un Hyuk Yim, Hongjae Park, Byeonghyeok Park, In-Geol Choi, Beom Seok Kim, Jae-Jin Kim
A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain 102-Py4T , was isolated from Sinduri beach sediment in Taean, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. The isolate grew optimally with 1-3 % (w/v) NaCl, but NaCl is not an absolute requirement for growth. 16S rRNA gene sequence analysis revealed that strain 102-Py4T clustered together with Zobellella aerophila and fell within the clade formed by recognized species of the genus Zobellella. Its closest phylogenetic neighbours were Z...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781801/methanonatronarchaeum-thermophilum-gen-nov-sp-nov-and-candidatus-methanohalarchaeum-thermophilum-extremely-halo-natrono-philic-methyl-reducing-methanogens-from-hypersaline-lakes-comprising-a-new-euryarchaeal-class-methanonatronarchaeia-classis-nov
#8
Dimitry Y Sorokin, Alexander Y Merkel, Ben Abbas, Kira S Makarova, W Irene C Rijpstra, M Koenen, Jaap S Sinninghe Damsté, Erwin A Galinski, Eugene V Koonin, Mark C M van Loosdrecht
Methanogenic enrichments from hypersaline lakes at moderate thermophilic conditions have resulted in the cultivation of an unknown deep lineage of euryarchaeota related to the class Halobacteria. Eleven soda lake isolates and three salt lake enrichment cultures were methyl-reducing methanogens that utilize C1 methylated compounds as electron acceptors and H2 or formate as electron donors, but they were unable to grow on either substrates alone or to form methane from acetate. They are extreme halophiles, growing optimally at 4 M total Na+ and the first representatives of methanogens employing the 'salt-in' osmoprotective mechanism...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781798/zhouia-spongiae-sp-nov-isolated-from-a-marine-sponge
#9
Lingping Zhuang, Binbin Lin, Fei Qin, Lianzhong Luo
A taxonomic study was carried out on strain HN-Y44T , which was isolated from sponge collected from Yangpu Bay, Hainan, China. Cells of strain HN-Y44T were Gram-stain-negative, non-motile, rod-shaped, yellow-pigmented and grew at 10-40 °C (optimum, 28 °C), at pH 6-10 (optimum, 7-8) and in 0-8 % (w/v) NaCl (optimum, 2-5 %). This isolate was positive for nitrate reduction, denitrification, oxidase, catalase and aesculin hydrolysis, but negative for indole production and urease. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN-Y44T belongs to the genus Zhouia and is clearly distinct from the other described species of this genus, Zhouia amylolytica, with a 16S rRNA gene sequence similarity of 96...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781796/starmerella-reginensis-f-a-sp-nov-and-starmerella-kourouensis-f-a-sp-nov-isolated-from-flowers-in-french-guiana
#10
Tiemele Laurent Simon Amoikon, Cécile Grondin, Théodore N'Dédé Djéni, Noémie Jacques, Serge Casaregola
Analysis of yeasts isolated from various biotopes in French Guiana led to the identification of two strains isolated from flowers and designated CLIB 1634T and CLIB 1707T . Comparison of the D1/D2 domain of the large subunit (LSU D1/D2) rRNA gene sequences of CLIB 1634T and CLIB 1707T to those in the GenBank database revealed that these strains belong to the Starmerella clade. Strain CLIB 1634T was shown to diverge from the closely related Starmerella apicola type strain CBS 2868T with a sequence divergence of 1...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781795/marinicella-sediminis-sp-nov-isolated-from-marine-sediment
#11
Xiao-Qun Wang, Chang-Ming Li, Christopher A Dunlap, Alejandro P Rooney, Zong-Jun Du
A novel heterotrophic, Gram-stain-negative, aerobic, rod-shaped, pale yellow, non-motile and non-spore-forming bacterium, designated strain F2T , was isolated from marine sediment collected from the Weihai coast, Shandong Province, PR China. Optimal growth occurred at 33 °C (range, 10-37 °C), with 3.0-4.0 % (w/v) NaCl (1.0-8.0 %) and at pH 7.5-8.0 (pH 6.5-9.0). Q-8 was the sole respiratory quinone. The major polar lipids of strain F2T were phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and two unidentified polar lipids...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29775177/novosphingobium-arvoryzae-sp-nov-isolated-from-a-flooded-rice-field
#12
Shih-Yi Sheu, Cheng-Wen Huang, Jhen-Ci Chen, Zih-Han Chen, Wen-Ming Chen
A bacterial strain, designated Jyi-02T , was isolated from a flooded rice field in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain Jyi-02T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellowish orange coloured colonies. Growth occurred at 10-40 °C (optimum, 20 °C) and pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-1.0 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain Jyi-02T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C14 : 0 2-OH...
May 18, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29775176/chitinophaga-varians-sp-nov-isolated-from-forest-soil
#13
Ying-Ying Lv, Xian-Jiao Zhang, An-Zhang Li, Wei-Ling Zou, Guang-da Feng, Hong-Hui Zhu
A Gram-stain-negative, aerobic, non-motile bacterium, designated strain 10-7W-9003T , was isolated from the forest soil of Limushan National Forest Park, south-east China (19° 10' 42″ N, 109° 44' 45″ E). Strain 10-7W-9003T showed a shape change during the course of culture from long filamentous cells (5-10×0.4-0.5 µm) at 5-36 h, to rod shaped (1.0-1.5×0.5-0.7 µm) with inoculation after 2 days. It grew optimally at 28-30 °C and pH 6.5-7.5. On the basis of 16S rRNA gene sequence analysis, it belongs to the genus Chitinophaga and is most closely related to Chitinophaga eiseniae KACC 13774T and Chitinophaga qingshengii JCM 30026T , with 16S rRNA gene sequences similarities of 98...
May 18, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29767618/hymenobacter-pedocola-sp-nov-a-novel-bacterium-isolated-from-soil
#14
Soo-Jeong Lim, Leonid N Ten, Byung-Oh Kim, In-Kyu Kang, Hee-Young Jung
Strain S12-2-1T was isolated from a soil sample collected in the Gyeongsangnam-do province of the Republic of Korea. The isolate is a Gram-stain-negative, aerobic, short, rod-shaped bacterium, and its colonies are red to pink in colour. Analysis of the 16S rRNA gene identified strain S12-2-1T as a member of the genus Hymenobacter in the family Cytophagaceae, with high levels of 16S rRNA gene sequence similarity to Hymenobacter arizonensis OR362-8T (97.7 %), Hymenobacter sedentarius DG5BT (97.4 %) and Hymenobacter humi DG31AT (97...
May 16, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29767617/mangrovicoccus-ximenensis-gen-nov-sp-nov-isolated-from-mangrove-forest-sediment
#15
Zhiliang Yu, Yang Cao, Guoqiang Zhou, Jianhua Yin, Juanping Qiu
A Gram-strain-negative, coccoid bacterium, lacking bacteriochlorophyll, designated strain T1lg56T , was isolated from a sediment sample collected from Ximen island mangrove forest, Zhejiang province, China. Cells were halotolerant, and catalase- and oxidase-positive. Growth was observed at 18-42 °C (optimum, 35 °C), at pH 6.0-9.5 (optimum, pH 6.5) and in the presence of 0-15 % (w/v) NaCl (optimum, 2-5 %). The major cellular fatty acids were C18 : 1ω7c and C16 : 0. The polar lipid profile of strain T1lg56T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified lipids...
May 16, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29762105/kandeliimicrobium-roseum-gen-nov-sp-nov-a-new-member-of-the-family-rhodobacteraceae-isolated-from-mangrove-rhizosphere-soil
#16
Kai-Ling Wang, Zhi-Man Song, Cu-Huang Rong, Ling-Yun Hao, Qi-Liang Lai, Shuang-Fei Li, Ying Xu
A Gram-stain-negative, non-flagellated, short rod-shaped bacterium, designated XY-R6T , was isolated from the rhizosphere soil of a mangrove plant, Kandelia candel (L.) Druce, in Mai Po Nature Reserve, Hong Kong. Growth of strain XY-R6T was observed at pH 5.0-9.5 (optimum 6.5-8.0), between 8 and 42 °C (optimum 28-34 °C), and in the presence of 0-9.5 % (w/v) NaCl (optimum 1-4 %). The predominant isoprenoid quinone was ubiquinone-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (55...
May 15, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29757129/qingshengfania-soli-zhang-et-al-2015-is-a-later-heterotypic-synonym-of-pseudochelatococcus-lubricantis-k%C3%A3-mpfer-et-al-2015
#17
Peter Kämpfer, Stefanie P Glaeser, Marco Gräber, Andreas Rabenstein, Jan Kuever
Qingshengfania soli DSM 103870T was compared with Pseudochelatococcus lubricantis MPA 1113T to clarify the taxonomic relationship of both species because of their high phylogenetic relationship. 16S rRNA gene sequence comparisons demonstrated that these species share 100  % sequence similarity. Investigation of fatty acid patterns, substrate utilization, and matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) profiles displayed no striking differences between the type strains of both species...
May 14, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29757127/sulfurovum-denitrificans-sp-nov-an-obligately-chemolithoautotrophic-sulfur-oxidizing-epsilonproteobacterium-isolated-from-a-hydrothermal-field
#18
Koji Mori, Kaoru Yamaguchi, Satoshi Hanada
A novel marine sulfur-oxidizing bacterium, designated strain eps51T , was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. This bacterium was Gram-staining-negative, non-motile and rod-shaped. Strain eps51T grew chemolithoautotrophically, by sulfur-oxidizing respiration with elemental sulfur and thiosulfate as electron donors and used only carbon dioxide as a carbon source. Oxygen and nitrate were used as its electron acceptors...
May 14, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29749925/pelagibacterium-montanilacus-sp-nov-an-alkaliphilic-bacterium-isolated-from-lake-cuochuolong-on-the-tibetan-plateau
#19
Huibin Lu, Peng Xing, Dorji Phurbu, Qian Tang, Qinglong Wu
A Gram-stain negative, alkaliphilic and halotolerant bacterium, designated CCL18T , was isolated from Lake Cuochuolong on the Tibetan Plateau. The strain was aerobic, short rod-shaped, catalase- and oxidase-positive, and motile by means of several polar flagella. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain CCL18T belongs to the genus Pelagibacterium, with its two closest neighbours being Pelagibacterium halotolerans B2T (96.6 %, 16S rRNA gene sequence similarity) and Pelagibacterium luteolum 1_C16_27T (96...
May 11, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29749924/chitinophaga-caeni-sp-nov-isolated-from-activated-sludge
#20
Decai Jin, Xiao Kong, Jie Wang, Jiajun Sun, Xiangyang Yu, Xuliang Zhuang, Ye Deng, Zhihui Bai
A novel Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, strictly aerobic bacterium, designated strain 13T , was isolated from an activated sludge wastewater treatment plant in Beijing, China. 16S rRNA gene sequence analysis placed this organism within the genus Chitinophaga of the class Bacteroidetes, with Chitinophaga skermanii CC-SG1B (92.4 % gene sequence similarity) and Chitinophaga rupis CS5-B1 (91.2 %) as its closest relatives. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate was ribose...
May 11, 2018: International Journal of Systematic and Evolutionary Microbiology
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