Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4202-4206 ◽  
Author(s):  
Hiroaki Minegishi ◽  
Yuto Yamauchi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Solar Salt ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Nitrate And Nitrite ◽  
The 16S Rrna Gene ◽  
Moderately Acidophilic

Two halophilic moderately acidophilic archaeal strains, MH1-136-2T and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2T was pink pigmented, while MH1-370-1 was orange–red pigmented. Strain MH1-136-2T was able to grow at 9–30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5–6.2 (optimum, pH 5.2–5.5) and at 18–55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12–30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2–6.0 (optimum, pH 5.2–5.5) and 20–50 °C (optimum, 45 °C). Strain MH1-136-2T required at least 1 mM Mg2+, while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2T and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3T with 98.3 % similarity. The level of DNA–DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2T and Halarchaeum acidiphilum MH1-52-1T, Halarchaeum salinum MH1-34-1T and Halarchaeum rubridurum MH1-16-3T was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2T ( = JCM 16331T = CECT 7573T) isolated from solar salt produced in Japan.

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink–red pigmented, while four other strains were orange–pink pigmented. Strain MH1-16-3T was able to grow at 9–30 % (w/v) NaCl [with optimum at 18 % (w/v) NaCl], at pH 4.5–6.8 (optimum, pH 5.5) and at 20–50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1–2 nt differences) to 100 % similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1T and Halarchaeum salinum MH1-34-1T with 97.7 % similarity. The DNA G+C contents of the six strains were 63.2–63.7 mol%. Levels of DNA–DNA relatedness amongst the six strains were 79–86 %, while those between MH1-16-3T and H. acidiphilum MH1-52-1T and H. salinum MH1-34-1T were both 43 and 45 % (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3T ( = JCM 16108T = CECT 7535T).

Halarchaeum salinum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1138-1142 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Hirokazu Shimoshige ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Three halophilic archaeal strains, MH1-34-1T, MH1-16-1 and MH1-224-5 were isolated from commercial salt samples produced from seawater in Indonesia, the Philippines and Japan, respectively. Cells of the three strains were pleomorphic and stained Gram-negative. Strain MH1-34-1T was orange–red pigmented, while MH1-16-1 and MH1-224-5 were pink-pigmented. Strain MH1-34-1T was able to grow at 12–30 % (w/v) NaCl (with optimum at 18 % NaCl, w/v) at pH 4.5–7.2 (optimum, pH 5.2–5.5) and at 15–45 °C (optimum, 42 °C). Strains MH1-16-1 and MH1-224-5 grew in slightly different ranges. These strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of strains MH1-34-1T, MH1-16-1 and MH1-224-5 were almost identical (99.8–99.9 % similarities), and the closest relative was Halarchaeum acidiphilum MH-1-52-1T with 98.4 % similarities. The DNA G+C contents of MH1-34-1T, MH1-16-1 and MH1-224-5 were 59.3, 60.8 and 61.0 mol%, respectively. The level of DNA–DNA relatedness amongst the three strains was 90–91 %, while that between each of the three strains and Halarchaeum acidiphilum MH1-52-1T was 51–55 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum , for which the name Halarchaeum salinum sp. nov. is proposed. The type strain is MH1-34-1T ( = JCM 16330T = CECT 7574T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

Microbacterium karelineae sp. nov. isolated from a halophyte plant in the Taklamakan desert

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Qi-hui Zhu ◽  
Cai-ling Yang ◽  
Xiao-xia Luo ◽  
Li-li Zhang ◽  
Zhan-feng Xia
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
West China ◽  
Content Type ◽  
Taklamakan Desert ◽  
North West ◽  
Link Type ◽  
Diamino Acid ◽  
The 16S Rrna Gene

A bacterial strain, designated TRM 80801T, was isolated from the Karelinea in Taklamakan desert, Xinjiang Uygur Autonomous Region, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain TRM 80801T grew at 4–50 °C, with optimum growth at 28 °C, and grew at pH 6.0–11.0 and 1–15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM 80801T within the genus Microbacterium with the highest similarities to Microbacterium suaedae YZYP 306T (98.97 %) and Microbacterium indicum BBH6T (98.17 %), respectively. The DNA G+C content of TRM 80801T is 69.38 mol%. The cell-wall peptidoglycan contained the amino acids ornithine, glutamic acid, glycine and alanine, the diagnostic diamino acid was ornithine. The acyl type of the peptidoglycan was glycolyl. Whole-cell sugars were ribose, mannose, glucose, rhamnose and galactose. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol. The whole-genome average nucleotide identity (ANI) value between strain TRM 80801T and Microbacterium suaedae YZYP 306T is 70.2 %. On the basis of the evidence presented in this study, strain TRM 80801T is representative of a novel species in the genus Microbacterium , for which the name Microbacterium karelineae sp. nov. is proposed. The type strain is TRM 80801T (=CCTCC AB 2019248T=KCTC 49357T).

Flavobacterium franklandianum sp. nov. and Flavobacterium gawalongense sp. nov., isolated from glaciers on the Tibetan Plateau

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Qing Liu ◽  
Hong-Can Liu ◽  
Lei-Lei Yang ◽  
Yu-Hua Xin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Research ◽  
Pr China ◽  
The 16S Rrna Gene

The genus Flavobacterium (family Flavobacteriaceae ) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium . None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium . Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95–96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).

Terriglobus tenax sp. nov., an exopolysaccharide-producing acidobacterium isolated from rhizosphere soil of a medicinal plant

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 431-437 ◽  
Author(s):  
Kyung-Sook Whang ◽  
Jae-Chan Lee ◽  
Hae-Ran Lee ◽  
Song-Ih Han ◽  
Sang-Ho Chung
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Optimum Ph ◽  
Type Strains

An exopolysaccharide-producing bacterium, designated strain DRP 35T, was isolated from the rhizosphere soil of a medicinal herb, Angelica sinensis, at Geumsan in Korea. Cells were Gram-staining-negative, non-motile, catalase-positive and oxidase-negative short rods. The isolate grew aerobically from 15 to 45 °C (optimum 30 °C), pH 3.5–7.0 (optimum pH 5.0) and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain DRP 35T belongs to the genus Terriglobus in the phylum Acidobacteria with a sequence similarity of 97.2 % and 97.0 % to Terriglobus saanensis SP1PR4T and Terriglobus roseus KBS63T, respectively. The genomic DNA G+C content was 62.1 mol%. DNA–DNA relatedness between strain DRP 35T and the type strains of the other species of the genus Terriglobus , T. saanensis SP1PR4T and T. roseus KBS63T, were 24.6 and 17.2 %, respectively. The predominant menaquinone was MK-8. Major fatty acids were iso-C15 : 0, C16 : 1ω7c and C16 : 0. The polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and unknown phospholipids. On the basis of polyphasic analysis from this study, strain DRP 35T represents a novel species of the genus Terriglobus for which the name Terriglobus tenax sp. nov. is proposed. The type strain is DRP 35T ( = KACC 16474T = NBRC 109677T).

Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3404-3408 ◽  
Author(s):  
Atsuko Matsumoto ◽  
Hiroaki Kasai ◽  
Yoshihide Matsuo ◽  
Yoshikazu Shizuri ◽  
Natsuko Ichikawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Seashore Sand ◽  
The 16S Rrna Gene

Bacterial strains YM16-303T and YM16-304T were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303T and YM16-304T were most similar to that of Ilumatobacter fluminis YM22-133T, and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter . Ilumatobacter fluminis YM22-133T and strains YM16-303T and YM16-304T should be classified as distinct species in the genus Ilumatobacter , however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303T = NBRC 109120T = KCTC 29139T) and Ilumatobacter coccineum sp. nov. (type strain YM16-304T = NBRC 103263T = KCTC 29153T), are proposed. The order Acidimicrobiales , which contains the genus Ilumatobacter , currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303T and YM16-304T clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133T, suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales .

scholarly journals Kiloniella spongiae sp. nov., isolated from a marine sponge and emended description of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 230-234 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Jung-Hyun Lee ◽  
Sang-Jin Kim ◽  
Kae Kyoung Kwon
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Emended Description ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-negative, aerobic, rod-shaped and non-motile marine bacterium, designated MEBiC09566T was isolated from a sponge collected at Uljin County in the coastal area of the East Sea (36° 55′ N, 129° 25′ E), Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC09566T showed the highest similarity with the Kiloniella laminariae LD81T (96.7 %). Growth was observed at 11–31 °C (optimum 25 °C), at pH 6.0–8.5 (optimum pH 7.0) and with 0–6 % (optimum 2.5 %) NaCl. The predominant cellular fatty acids were summed feature 8 (comprised of C18 : 1ω7c/C18 : 1ω6c) and summed feature 3 (comprised of C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content is 44.6 mol%. The major respiratory quinone is Q-9. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid were detected as major polar lipids. On the basis of this polyphasic taxonomic data, it is concluded that strain MEBiC09566T should be classified as representing a novel species in the genus Kiloniella and the name proposed is Kiloniella spongiae sp. nov. The type strain is MEBiC09566T ( = KCCM 43040T = JCM 19930T). Emended descriptions of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae are also given.

scholarly journals Reyranella graminifolii sp. nov., isolated from bamboo (Phyllostachys bambusoides) litter

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2503-2507 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Phyllostachys Bambusoides ◽  
Sequence Similarities

A novel strain designated Wo-34T was isolated from bamboo (Phyllostachys bambusoides) litter. Cells were Gram-stain-negative, non-motile, catalase-negative and oxidase-positive rods. The isolate grew aerobically at 15–35 °C (optimum 28 °C), pH 4.0–9.0 (optimum pH 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum 0.1 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Wo-34T belonged to the genus Reyranella with the sequence similarities of 97.9 % and 97.3 % to the other species of the genus Reyranella , Reyranella massiliensis 521T and Reyranella soli KIS14-15T, respectively. The predominant ubiquinone was Q-10. Major fatty acids were C18 : 1ω7c, C18 : 1 2-OH and C19 : 0 cyclo ω8c. The polar lipids contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipid, unidentified phospholipids and unknown lipids. DNA–DNA relatedness values between strain Wo-34T and R. massiliensis DSM 23428T and R. soli KACC 13034T were 35 % and 29 %, respectively. On the basis of polyphasic analysis from this study, strain Wo-34T represents a novel species of the genus Reyranella for which the name Reyranella graminifolii sp. nov. is proposed. The type strain is Wo-34T ( = KACC 17605T = NBRC 109813T).

Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1859-1865 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Dana Vejmelkova ◽  
Sebastian Lücker ◽  
Galina M. Streshinskaya ◽  
W. Irene C. Rijpstra ◽  
...  
Keyword(s):  
Energy Source ◽  
Type Species ◽  
Membrane Lipids ◽  
Phylogenetic Analyses ◽  
Ammonium Bicarbonate ◽  
Wall Structure ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).

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