Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

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.


2019 ◽  
Vol 69 (4) ◽  
pp. 1001-1008 ◽  
Author(s):  
Yuanyuan Tian ◽  
Chuanyu Han ◽  
Jiangmeihui Hu ◽  
Junwei Zhao ◽  
Chen Zhang ◽  
...  

A novel actinomycete, designated strain NEAU-TCZ24T, was isolated from soil and characterized using a polyphasic approach. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Cellulomonas and formed a stable clade with its closest relatives Cellulomonas terrae JCM 14899T (98.4 % 16S rRNA gene sequence similarity), Cellulomonas xylanilytica JCM 14281T (97.9 %) and Cellulomonas humilata JCM 11945T (97.7 %). The major menaquinones were identified as MK-9(H4) and MK-8(H4). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositolmannoside, a ninhydrin-positiveglycolipid, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15 : 0, C18 : 1ω9c, C16 : 0 and anteiso-C17 : 0. Moreover, morphological and chemotaxonomic properties of NEAU-TCZ24T also confirmed the affiliation of the isolate to the genus Cellulomonas . However, multilocus sequence analysis based on five other house-keeping genes (gyrB, rpoB, recA, relA and atpD), DNA–DNA relatedness, physiological and biochemical data indicated that NEAU-TCZ24T could be distinguished from its closest relatives. Therefore, it is proposed that NEAU-TCZ24T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas rhizosphaerae sp. nov. is proposed. The type strain is NEAU-TCZ24T (=CCTCC AA 2018042T=JCM 32383T).


Author(s):  
Ji Young Choi ◽  
Seung-Hyeon Choi ◽  
Jam-Eon Park ◽  
Ji-Sun Kim ◽  
Jiyoung Lee ◽  
...  

An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces of a 2-week-old piglet raised at the National Institute of Animal Science in Wanju, Republic of Korea. Growth of strain AGMB03916T occurred at 30–45 °C (optimum, 37 °C), at pH 6–9 (optimum, pH 8) and in the presence of 0.5–1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence analyses, strain AGMB03916T was closely related to two validly published species of the genus Phocaeicola , Phocaeicola plebeius and Phocaeicola coprocola . The 16S rRNA gene sequence similarity of strain AGMB03916T compared to P. plebeius M12T (=KCTC 5793T) and P. coprocola M16T (=KCTC 5443T) were 96.3 and 95.0 %, respectively. The genomic DNA G+C content of strain AGMB03916T was 46.4 mol%. The average nucleotide identity values between strain AGMB03916T and the reference strains were 74.9–78.5 %. Cells were able to utilize d-glucose, lactose, sucrose, maltose, salicin, aesculin hydrolysis, cellobiose and raffinose. The major end product of metabolism was acetate. The major cellular fatty acids (>10 %) of the isolate were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, C16 : 0 3-OH and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA). On the basis of the genotypic, biochemical, chemotaxonomic, phenotypic and phylogenetic data, strain AGMB03916T represents a novel species of the genus Phocaeicola , for which the name Phocaeicola faecicola sp. nov. is proposed. The type strain is AGMB03916T (=KCTC 25014T=GDMCC 1.2574T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4006-4011 ◽  
Author(s):  
Yirang Cho ◽  
Hyunwoo Chung ◽  
Gwang Il Jang ◽  
Dong Han Choi ◽  
Jae Hoon Noh ◽  
...  

A Gram-staining-negative, non-motile, spore-forming, rod-shaped, marine bacterial strain, CL-KR2T, was isolated from tropical seawater near Kosrae, an island in the Federated States of Micronesia. Analysis of the 16S rRNA gene sequence of strain CL-KR2T revealed a clear affiliation with the genus Gracilimonas . Based on phylogenetic analysis, strain CL-KR2T showed the closest phylogenetic relationship to Gracilimonas tropica CL-CB462T, with 16S rRNA gene sequence similarity of 96.6 %. DNA–DNA relatedness between strain CL-KR2T and G. tropica CL-CB462T was 6.7 % (reciprocal 9.5 %). Strain CL-KR2T grew in the presence of 1–20 % sea salts and the optimal salt concentration was 3.5–5 %. The temperature and pH optima for growth were 35 °C and pH 7.5. The major cellular fatty acids (≥10.0 %) of strain CL-KR2T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 1ω9c and the only isoprenoid quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, two unidentified glycolipids and two unidentified lipids. The genomic DNA G+C content of strain CL-KR2T was 43.2 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain CL-KR2T could be distinguished from the only member of the genus Gracilimonas with a validly published name. Thus, strain CL-KR2T should be assigned to a novel species in the genus Gracilimonas , for which the name Gracilimonas rosea sp. nov. is proposed. The type strain is CL-KR2T ( = KCCM 90206T = JCM 18898T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 212-218 ◽  
Author(s):  
Mustafa Camas ◽  
Anil Sazak ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk ◽  
Demet Cetin ◽  
...  

A novel actinomycete, strain A4036T, was isolated from a soil sample collected from the Jabi district in Abuja, Nigeria. The taxonomic position of strain A4036T was established using a combination of genotypic and phenotypic analyses. The organism formed extensively branched substrate and aerial hyphae that generated spiral chains of spores with warty surfaces. The cell wall contained meso-diaminopimelic acid and the cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, two unidentified phospholipids and four unknown glucosamine-containing phospholipids. The major cellular fatty acids were iso-C16 : 0 2-OH, iso-C16 : 0 and 10-methyl C17 : 0. On the basis of 16S rRNA gene sequence similarity studies, strain A4036T grouped in the genus Nonomuraea , being most closely related to Nonomuraea angiospora IFO 13155T (99.05 %), Nonomuraea candida HMC10T (98.78 %), Nonomuraea kuesteri GW 14-1925T (98.49 %), Nonomuraea endophytica YIM 65601T (98.42 %), Nonomuraea maheshkhaliensis 16-5-14T (98.40 %), Nonomuraea turkmeniaca DSM 43926T (98.38 %), Nonomuraea helvata IFO 14681T (98.29 %), Nonomuraea rubra DSM 43768T (98.10 %) and Nonomuraea salmonea DSM 43678T (98.06 %). Levels of 16S rRNA gene sequence similarity to the type strains of other species of the genus Nonomuraea were <98 %. Despite the high 16S rRNA gene sequence similarities, DNA–DNA relatedness values and phenotypic data demonstrated that strain A4036T was clearly distinguished from all closely related species of the genus Nonomuraea . Thus, this isolate is considered to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea jabiensis sp. nov. is proposed. The type strain is A4036T ( = DSM 45507T = KCTC 19870T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 208-211 ◽  
Author(s):  
Lourdes Martínez-Aguilar ◽  
Jesús Caballero-Mellado ◽  
Paulina Estrada-de los Santos

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T  = DSM 15562T  = CIP 108892T).


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1724-1728 ◽  
Author(s):  
Peter Kämpfer ◽  
Marie T. Poppel ◽  
Gottfried Wilharm ◽  
Stefanie P. Glaeser ◽  
Hans-Jürgen Busse

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain 280T) isolated from a chicken was studied for its taxonomic allocation. 16S rRNA gene sequence analyses clearly allocated the isolate in the genus Paenochrobactrum group with a 16S rRNA gene sequence similarity of 98.8 % to the currently recognized species, Paenochrobactrum gallinarii and Paenochrobactrum glaciei . This allocation was confirmed by the fatty acid data (major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c) and a polyamine pattern with the major compound putrescine and relatively high amounts of spermidine. Also, the polar lipid profile with phosphatidylethanolamine, phosphatiylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and the genus-specific ‘stretched aminolipid’ was well in line with the description of the genus Paenochrobactrum . The quinone system consisted predominantly of ubiquinone Q-10 with traces of Q-9 and Q-11. DNA–DNA hybridization of strain 280T with Paenochrobactrum gallinarii Sa25T and Paenochrobactrum glaciei KMM 3858T showed relatedness values of 38.8 % (reciprocal 20.2 %) and 30.2 % (reciprocal 29.8 %), respectively. These results in combination with differentiating physiological and biochemical data clearly showed that strain 280T merits species status. We propose the name Paenochrobactrum pullorum sp. nov. to accommodate this strain with the type strain 280T ( = LMG 28095T = CIP 110700T).


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 945-951 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod- or coccoid-shaped bacterial strain, designated HD-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HD-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HD-22T fell within the clade comprising species of the genus Jannaschia , clustering with the type strains of Jannaschia helgolandensis , Jannaschia donghaensis and Jannaschia rubra , with which it exhibited highest 16S rRNA gene sequence similarity (97.6–98.2 %). Levels of 16S rRNA gene sequence similarity between strain HD-22T and the type strains of the other species of the genus Jannaschia were in the range 94.4–97.5 %. The DNA G+C content was 64.6 mol% and mean DNA–DNA relatedness values between strain HD-22T and the type strains of J. helgolandensis , J. donghaensis and J. rubra were 42.1, 40.1 and 27.0 %, respectively. Strain HD-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain HD-22T is distinguishable from recognized species of the genus Jannaschia . On the basis of the data presented, strain HD-22T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia faecimaris sp. nov. is proposed. The type strain is HD-22T ( = KCTC 32179T = CCUG 63415T).


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 979-983 ◽  
Author(s):  
Long Jin ◽  
Hyung-Gwan Lee ◽  
Song-Gun Kim ◽  
Keun Chul Lee ◽  
Chi-Yong Ahn ◽  
...  

A taxonomic study using a polyphasic approach was performed on a Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain PB156T, isolated from grass soil. Comparative 16S rRNA gene sequence studies showed that the isolate was clearly affiliated with the phylum Bacteroidetes , and most closely related to Hymenobacter soli PB17T, Hymenobacter antarcticus VUG-A42aaT and Hymenobacter glaciei VUG-A130T, showing 96.4, 96.2 and 95.9 % 16S rRNA gene sequence similarity, respectively, while all other species of the genus shared only 89.3–95.2 % similarity. The main polyamine present was sym-homospermidine. The predominant menaquinone was MK-7. The major fatty acids were C15 : 0 iso, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c/t), C16 : 1ω5c and C15 : 0 anteiso. The G+C content of the genomic DNA of strain PB156T was 61.7 mol%. The combined genotypic and phenotypic data supported the conclusion that strain PB156T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter ruber sp. nov. is proposed. The type strain is PB156T ( = KCTC 32477T = JCM 19433T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1880-1884 ◽  
Author(s):  
Nithyanand Paramasivam ◽  
Eitan Ben-Dov ◽  
Luba Arotsker ◽  
Ariel Kushmaro

A marine bacterial strain, designated MD2T, was isolated from the damaged tissue of a hydrocoral, Millepora dichotoma, collected from the coral reef in the northern Red Sea, Gulf of Eilat, Israel. Strain MD2T was Gram-reaction-negative, rod-shaped and motile, and formed small, creamy and opaque colonies, 1–2 mm in diameter, after 3 days incubation on Marine agar at 30°C. The novel strain grew well in nutrient broth at 1.5–6 % NaCl and at 20–37°C. The major cellular fatty acids were iso-C17 : 1ω9c, iso-C17 : 0, C18 : 1ω7c and C17 : 1ω6c. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified lipid, two unidentified phospholipids, two unidentified glycolipids and two unidentified aminolipids. Ubiquinone Q-10 was the only respiratory lipoquinone. The DNA G+C content was 60.3 mol%. Analysis of the 16S rRNA gene sequence placed the organism in the α-subclass of the Proteobacteria with a sequence divergence of about 9 % from any species with a validly published name. The highest 16S rRNA gene sequence similarity (approximately 91 %) was notably with type strains of members of the genus Kordiimonas , Kordiimonas aestuarii 101-1T , Kordiimonas lacus S3-22T and Kordiimonas gwangyangensis GW14-5T. On the basis of genotypic, chemotaxonomic and phenotypic distinctness, strain MD2T represents a novel species in a new genus of the class Alphaproteobacteria , for which the name Eilatimonas milleporae gen. nov., sp. nov. is proposed. The type strain of the type species is MD2T ( = LMG 26586T = DSM 25217T).


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