scholarly journals Vallitalea guaymasensis gen. nov., sp. nov., isolated from marine sediment

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3019-3023 ◽  
Author(s):  
Raja Lakhal ◽  
Nathalie Pradel ◽  
Anne Postec ◽  
Moktar Hamdi ◽  
Bernard Ollivier ◽  
...  

A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic, halophilic, Gram-stain-negative bacterium, was isolated from sediments of Guaymas Basin. The strain, designated Ra1766G1T, grew at 20–40 °C (optimum, 30–35 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). It required 0.5–7.5 % NaCl (optimum, 2–3 %) for growth. Sulfate, thiosulfate, elemental sulfur, sulfite, fumarate, nitrate and nitrite were not used as terminal electron acceptors. Strain Ra1766G1T used cellobiose, glucose, mannose, maltose, arabinose, raffinose, galactose, ribose, sucrose, pyruvate and xylose as electron donors. The main fermentation product from glucose metabolism was acetate. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso DMA-C15 : 0 and C16 : 0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, iso-DMA-C15 : 0 glycolipids and phospholipids. The G+C content of the genomic DNA was 31.2 mol%. The closest phylogenetic relatives of strain Ra1766G1T were Natranaerovirga pectinivora AP3T (92.4 % 16S rRNA gene sequence similarity), Natranaerovirga hydrolytica APP2T(90.2 %) and Defluviitalea saccharophila 6LT2T (88.9 %). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766G1T represents a novel species of a new genus for which the name Vallitalea guaymasensis is proposed. The type strain of the type species is Ra1766G1T ( = DSM 24848T = JCM17997T).

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 469-474 ◽  
Author(s):  
Ying Liu ◽  
Liang-Zi Liu ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Fang-Jun Qi ◽  
...  

A Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1T, was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1T were non-flagellated short rods, 0.3–0.5 µm wide and 0.5–1.0 µm long. Growth was observed at 15–30 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 2–3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1T contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10 %) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2 %), C16 : 1ω7c/C16 : 1ω6c (14.3 %), iso-C15 : 0 3-OH (13.5 %) and iso-C15 : 1 G (10.8 %). 16S rRNA gene sequence analyses indicated that strain D1T belonged to the family Flavobacteriaceae and showed closest phylogenetic relationship to the genus Lutibacter , with highest sequence similarity to Lutibacter aestuarii MA-My1T (92.2 %). The DNA G+C content of strain D1T was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1T was considered to represent a novel species in a new genus of the family Flavobacteriaceae , for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1T ( = CGMCC 1.12162T = JCM 18494T).


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1307-1313 ◽  
Author(s):  
Heng-Lin Cui ◽  
Xin Yang ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
Pei-Jin Zhou ◽  
...  

Two halophilic archaea, strains TBN53T and CSW2.24.4T, were characterized to elucidate their taxonomic status. Strain TBN53T was isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China, whereas strain CSW2.24.4T was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53T was able to grow at 25–55 °C (optimum 45 °C), with 1.4–5.1 M NaCl (optimum 2.6–3.9 M NaCl), with 0–1.0 M MgCl2 (optimum 0–0.1 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0), whereas strain CSW2.24.4T was able to grow at 25–45 °C (optimum 37 °C), with 2.6–5.1 M NaCl (optimum 3.4 M NaCl), with 0.01–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53T and 12 % (w/v) for strain CSW2.24.4T. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53T and CSW2.24.4T showed 94.1 % similarity to each other and were closely related to Halobellus clavatus TNN18T (95.0 and 94.7 % similarity, respectively). Levels of rpoB′ gene sequence similarity between strains TBN53T and CSW2.24.4T, and between these strains and Halobellus clavatus TNN18T were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53T and CSW2.24.4T were 69.2 and 67.0 mol%, respectively. The level of DNA–DNA relatedness between strain TBN53T and strain CSW2.24.4T was 25 %, and these two strains showed low levels of DNA–DNA relatedness with Halobellus clavatus TNN18T (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus Halobellus are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53T = CGMCC 1.10331T = JCM 16811T) and Halobellus salinus sp. nov. (type strain CSW2.24.4T = DSM 18730T = CGMCC 1.10710T = JCM 14359T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4691-4697 ◽  
Author(s):  
Mi-Jeong Park ◽  
Teddy Namirimu ◽  
Sung-Hyun Yang ◽  
Kae Kyoung Kwon

Strain MEBiC09520T, which was isolated from a tidal sediment in Incheon, Korea, is a pale yellow, rod-shaped bacterium, cells of which are 0.4–0.5 µm in width and 1.5–2 µm in length. Strain MEBiC09520T shared 95.17 and 92.57% 16S rRNA gene sequence similarity with Emcibacter nanhaiensis and E. congregatus , respectively. It grew optimally at pH 6.0, at 55 °C and with 2.5–3.5% (w/v) NaCl. Its polar lipid components included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), an unidentified phospholipid (PL), three unidentified aminolipids (ALs) and two unidentified lipids (L). The fatty acids C16:0, C19:0 cyclo ω8c, C14:0 2-OH and summed feature 8 (C18:1ω7c and/or C18:1ω6c) were predominantly present in its cell wall. Strain MEBiC09520T was thermophilic, while E. nanhaiensis and E. congregatus were mesophilic. Although E. nanhaiensis showed no nitrate reduction activity, MEBiC09520T and E. congregatus showed a positive reaction. These strains differed in carbohydrate utilization. In particular, E. congregatus was able to thrive on various carbohydrate substrates as compared to the other strains. The average nucleotide identity value was 69.92% between strain MEBiC09520T and E. congregatus ZYLT, 70.38% between E. congregatus ZYLT and E. nanhaiensis HTCJW17T, and 72.83% between strain MEBiC09520 and E. nanhaiensis HTCJW17T. Considering these differences, strain MEBiC09520T (=KCCM 43320T=MCCC 1K03920T) is suggested to represent and novel species of a new genus, Luteithermobacter gelatinilyticus gen. nov., sp. nov., and E. congregatus should be reclassified as Paremcibacter congregatus gen. nov., comb. nov.


Author(s):  
Regina Rettenmaier ◽  
Nils Thieme ◽  
Johanna Streubel ◽  
Luca Di Bello ◽  
Marie-Louise Kowollik ◽  
...  

Strain MD1T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7–8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1T are C14:0 DMA and C16:0. Strain MD1T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1T are Mobilitalea sibirica P3M-3T and Anaerotaenia torta FH052T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae , for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1T=DSM 110715T=JCM 39125T) is proposed.


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 907-914 ◽  
Author(s):  
Itay Amir ◽  
Philippe Bouvet ◽  
Christine Legeay ◽  
Uri Gophna ◽  
Abraham Weinberger

A catalase-positive, rod-shaped, non-proteolytic, non-motile, anaerobic bacterial strain, designated B086562T, was isolated from a blood culture of an 84-year-old male patient in Israel. According to 16S rRNA gene sequence phylogeny, this strain has no known close relatives among recognized bacteria but should be placed within the family Lachnospiraceae . The most closely related recognized bacteria were from the ‘ Clostridium clostridioforme group’: C. clostridioforme (92.4 %) and Clostridium bolteae (92.3 %). The isolate produced butyrate, lactate, acetate and succinate as major metabolic end products. The major fatty acids were C16 : 0 and C18 : 1 cis 9 DMA and the DNA G+C content was 46.0 mol%. On the basis of the phenotypic properties and phylogenetic distinctiveness, the blood isolate represents a novel species of a new genus in the family Lachnospiraceae , for which the name Eisenbergiella tayi gen. nov., sp. nov. is proposed. The type strain of Eisenbergiella tayi is B086562T ( = LMG 27400T = DSM 26961T = ATCC BAA-2558T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4052-4057 ◽  
Author(s):  
Soo-Jin Kim ◽  
Ji-Young Moon ◽  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
Hang-Yeon Weon ◽  
...  

A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4T, was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10–37 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0). It can tolerate up to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1–97.0 % with species of the genus Leifsonia , 95.7–96.7 % with species of the genus Herbiconiux , 95.1–96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and Homoserinimonas aerilata . The highest sequence similarities (97.0 %) were with Leifsonia aquatica JCM 1368T, Leifsonia poae VKM Ac-1401T and Leifsonia psychrotolerans LI1T. The peptidoglycan type determined for strain 5GHs34-4T was B2γ with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain 5GHs34-4T differed in some respects from those of members of the family Microbacteriaceae . Therefore, strain 5GHs34-4T is considered to represent a novel species of a new genus in the family Microbacteriaceae , for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4T ( = KACC 15523T = NBRC 108754T).


2020 ◽  
Vol 70 (7) ◽  
pp. 4298-4304 ◽  
Author(s):  
Yeon Bee Kim ◽  
Joon Yong Kim ◽  
Hye Seon Song ◽  
Changsu Lee ◽  
Juseok Kim ◽  
...  

A novel, facultatively anaerobic actinobacterium, designated strain CBA3103T, was isolated from sediment of the Geum River in South Korea. Phylogenetic analysis indicated that strain CBA3103T is most closely related to Raineyella antarctica LZ-22T (98.47 % 16S rRNA gene sequence similarity). The genome of strain CBA3103T was 3 649 865 bp with a DNA G+C content of 69.6 mol%. The average nucleotide identity value between strain CBA3103T and R. antarctica LZ-22T was 79.22 %. Cells of strain CBA3103T were Gram-positive, rod-shaped, 0.6–0.9 µm wide and 1.4–2.4 µm long. Growth occurred at 15–40 °C (optimum, 35 °C), at pH 6.0–7.0 (optimum, pH 7.0) and with 0–2 % NaCl (w/v) (optimum, 0–1 %, w/v). The major cellular fatty acids in strain CBA3103T were anteiso-C15 : 0, anteiso-C15 : 1 A and iso-C14 : 0. The major respiratory quinone was menaquinone-9(H4). The polar lipids of strain CBA3103T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified glycolipids and three unidentified phospholipids. Based on the genotypic, phenotypic and chemotaxonomic analyses, strain CBA3103T represents a novel species of the genus Raineyella , for which the name Raineyella fluvialis sp. nov. (type strain CBA3103T=KACC 21446T=DSM 110288T) is proposed.


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.


2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).


Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).


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