Paradesulfitobacterium ferrireducens gen. nov., sp. nov., a Fe(III)-reducing bacterium from petroleum-contaminated soil and reclassification of Desulfitobacterium aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.

Author(s):  
Yanling Li ◽  
Guiqin Yang ◽  
Sijie Yao ◽  
Li Zhuang

A strictly anaerobic bacterium, strain PLL0T, was isolated from petroleum-contaminated soil sampled in Gansu Province, PR China. Cells were rods, non-motile and Gram-stain-positive. The strain grew at 25–37 °C (optimum, 30 °C) in the presence of 0–3 % (w/v) NaCl (optimum, 2 %). Strain PLL0T was able to reduce ferrihydrite, Fe(III) citrate and thiosulphate. The 16S rRNA gene analysis revealed that this strain clustered with the genus Desulfitobacterium , and showed highest similarity to Desulfitobacterium aromaticivorans UKTLT (95.4 %) followed by Desulfitobacterium chlororespirans Co23T (93.9 %). However, strains PLL0T and UKTLT showed no more than 94.0 % similarity to other species of the genus Desulfitobacterium , and formed an independent group in the phylogenetic tree. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain PLL0T and Desulfitobacterium species (except for D. aromaticivorans ) were 67.4–68.5 % and 12.6–12.7 %, respectively, which are far below the threshold for delineation of a new species. Based on ANI, dDDH, average amino acid identity, phylogenetic analysis and physiologic differences from the previously described taxa, we suggest that strain PLL0T represents a novel species of a novel genus, for which the name Paradesulfitobacterium ferrireducens gen. nov. sp. nov. is proposed. The type strain is PLL0T (=MCCC 1K05549=KCTC 25248). We also propose the reclassification of D. aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.

Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C. A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  

A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52–74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1480-1485 ◽  
Author(s):  
Heeji Hong ◽  
So-Jeong Kim ◽  
Ui-Gi Min ◽  
Yong-Jae Lee ◽  
Song-Gun Kim ◽  
...  

A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19T, was isolated from coal-contaminated soil in the Republic of Korea. IRF19T cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5–8.0 and 40 °C, while the optimum range was pH 6.5–10.0 and 20–45 °C, respectively. Strain IRF19T did not require NaCl for growth but it tolerated up to 2 % (w/v). Growth was observed with yeast extract, d-glucose, d-fructose, d-ribose, d-mannitol, d-mannose, l-serine, l-alanine and l-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19T is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2T (93.5 % similarity), Geosporobacter subterraneus VNs68T (93.2 %) and Thermotalea metallivorans B2-1T (92.3 %). The major cellular fatty acids of strain IRF19T were C14 : 0, iso-C15 : 0 and C16 : 0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19T was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19T was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19T is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19T ( = KCTC 15396T = JCM 19988T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2396-2404 ◽  
Author(s):  
Ana Faria Tomás ◽  
Dimitar Karakashev ◽  
Irini Angelidaki

An extremely thermophilic, xylanolytic, spore-forming and strictly anaerobic bacterium, strain DTU01T, was isolated from a continuously stirred tank reactor fed with xylose and household waste. Cells stained Gram-negative and were rod-shaped (0.5–2 µm in length). Spores were terminal with a diameter of approximately 0.5 µm. Optimal growth occurred at 70 °C and pH 7, with a maximum growth rate of 0.1 h−1. DNA G+C content was 34.2 mol%. Strain DTU01T could ferment arabinose, cellobiose, fructose, galactose, glucose, lactose, mannitol, mannose, melibiose, pectin, starch, sucrose, xylan, yeast extract and xylose, but not cellulose, Avicel, inositol, inulin, glycerol, rhamnose, acetate, lactate, ethanol, butanol or peptone. Ethanol was the major fermentation product and a maximum yield of 1.39 mol ethanol per mol xylose was achieved when sulfite was added to the cultivation medium. Thiosulfate, but not sulfate, nitrate or nitrite, could be used as electron acceptor. On the basis of 16S rRNA gene sequence similarity, strain DTU01T was shown to be closely related to Thermoanaerobacter mathranii A3T, Thermoanaerobacter italicus Ab9T and Thermoanaerobacter thermocopriae JT3-3T, with 98–99 % similarity. Despite this, the physiological and phylogenetic differences (DNA G+C content, substrate utilization, electron acceptors, phylogenetic distance and isolation site) allow for the proposal of strain DTU01T as a representative of a novel species within the genus Thermoanaerobacter , for which the name Thermoanaerobacter pentosaceus sp. nov. is proposed, with the type strain DTU01T ( = DSM 25963T = KCTC 4529T = VKM B-2752T = CECT 8142T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).


Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.


Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1083-1088 ◽  
Author(s):  
Kai Chen ◽  
Shu-Kun Tang ◽  
Guang-Li Wang ◽  
Guo-Xing Nie ◽  
Qin-Fen Li ◽  
...  

Bacterial strain 14-2AT, isolated from a long-term DDT-contaminated soil in China, was characterized by using a polyphasic approach to clarify its taxonomic position. Strain 14-2AT was found to be Gram-negative, aerobic, non-spore-forming, non-motile, non-flagellated and rod-shaped. The new isolate was able to grow at 4–42 °C, pH 6.0–9.0 and with 0–5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the family Sphingobacteriaceae . The 16S rRNA gene sequence of strain 14-2AT showed the highest similarity with Olivibacter oleidegradans TBF2/20.2T (99.4 %), followed by Pseudosphingobacterium domesticum DC-186T (93.8 %), Olivibacter ginsengisoli Gsoil 060T (93.6 %), Olivibacter terrae Jip13T (93.1 %), Olivibacter soli Gsoil 034T (92.8 %) and Olivibacter sitiensis AW-6T (89.6 %). The DNA–DNA hybridization value between strains 14-2AT and O. oleidegradans TBF2/20.2T was 34.45±2.11 %. Strain 14-2AT contained phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminophospholipid and phosphatidylinositol mannoside as the major polar lipids. The DNA G+C content was 41.2 mol%. MK-7 is the major isoprenoid quinone. Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH are the major fatty acids. The phenotypic and chemotaxonomic data confirmed the affiliation of strain 14-2AT to the genus Olivibacter . On the basis of the phylogenetic and phenotypic characteristics, and chemotaxonomic data, strain 14-2AT is considered to represent a novel species of the genus Olivibacter , for which the name Olivibacter jilunii sp. nov. is proposed; the type strain is 14-2AT ( = KCTC 23098T = CCTCC AB 2010105T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 442-448 ◽  
Author(s):  
Samson Viulu ◽  
Kohei Nakamura ◽  
Yurina Okada ◽  
Sakiko Saitou ◽  
Kazuhiro Takamizawa

A novel species of Fe(III)-reducing bacterium, designated strain OSK6T, belonging to the genus Geobacter , was isolated from lotus field mud in Japan. Strain OSK6T was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l−1. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6T was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6T is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6T is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6T ( = DSM 24905T = JCM 17780T).


2020 ◽  
Vol 70 (9) ◽  
pp. 4851-4858 ◽  
Author(s):  
Tiphaine Le Roy ◽  
Patrick Van der Smissen ◽  
Adrien Paquot ◽  
Nathalie Delzenne ◽  
Giulio G. Muccioli ◽  
...  

A strictly anaerobic, Gram-stain-negative, non-spore-forming, non-motile, non-pigmented bacterium, strain J115T, was isolated from human faeces. Cells of strain J115T were straight rods, generally 1.8–3.0 µm, but could be up to 18 µm long. Growth occurred below 2 % (w/v) NaCl and 2 % (v/v) bile. Strain J115T produced acid from myo-inositol but not from d-glucose, d-ribose or d-xylose. Butyric acid was the major end-product from myo-inositol. The genomic DNA G+C content was 58.92 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the closest cultivated neighbours of strain J115T were Oscillibacter ruminantium GH1T (95.4 % similarity) and Oscillibacter valericigenes Sjm18-20T (94.1 %). Strain J115T was also related to the not-yet-cultured bacterium Oscillospira guilliermondii (92–93 % similarity). Coherently with the 16S rRNA gene sequence results, the ANI scores don't have units of strain J115T to O. ruminantium GH1T and O. valericigenes Sjm18-20T were 73.37 and 73.24, respectively, while in silico estimations of DNA–DNA hybridization were both 20.4 %, with confidence intervals of 18.2–22.9 % and 18.2–22.8 %, respectively. The major fatty acids were iso-C15 : 0 (24.2 %), C18 : 0 DMA (18.4 %), anteiso-C15 : 0 (15.2 %) and C16 : 0 DMA (7.6 %). No respiratory quinone was detected. Based on phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in a new genus, Dysosmobacter welbionis gen. nov., sp. nov. The type strain of Dysosmobacter welbionis is J115T (DSM 106889T=LMG 30601T).


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 2986-2991 ◽  
Author(s):  
Xiao-Li Su ◽  
Qi Tian ◽  
Jie Zhang ◽  
Xian-Zheng Yuan ◽  
Xiao-Shuang Shi ◽  
...  

A strictly anaerobic, mesophilic, carbohydrate-fermenting, hydrogen-producing bacterium, designated strain RL-CT, was isolated from a reed swamp in China. Cells were Gram-stain-negative, catalase-negative, non-spore-forming, non-motile rods measuring 0.7–1.0 µm in width and 3.0–8.0 µm in length. The optimum temperature for growth of strain RL-CT was 37 °C (range 25–40 °C) and pH 7.0–7.5 (range pH 5.7–8.0). The strain could grow fermentatively on yeast extract, tryptone, arabinose, glucose, galactose, mannose, maltose, lactose, glycogen, pectin and starch. The main end products of glucose fermentation were acetate, H2 and CO2. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth; however, it stimulated growth slightly. Nitrate, sulfate, sulfite, thiosulfate, elemental sulfur and Fe(III) nitrilotriacetate were not reduced as terminal electron acceptors. Aesculin was hydrolysed but not gelatin. Indole and H2S were produced from yeast extract. The G+C content of the genomic DNA was 51.2 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. The most abundant polar lipid of strain RL-CT was phosphatidylethanolamine. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured Blvii28 wastewater-sludge group (http://www.arb-silva.de/) in the family Rikenellaceae of the phylum Bacteroidetes, and shared low sequence similarities with the related species Alistipes shahii WAL 8301T (81.8 %), Rikenella microfusus ATCC 29728T (81.7 %) and Anaerocella delicata WN081T (80.9 %). On the basis of these data, a novel species in a new genus of the family Rikenellaceae is proposed, Acetobacteroides hydrogenigenes gen. nov., sp. nov. The type strain of the type species is RL-CT ( = JCM 17603T = DSM 24657T = CGMCC 1.5173T).


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