scholarly journals Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

2016 ◽  
Vol 82 (21) ◽  
pp. 6440-6453 ◽  
Author(s):  
Yiran Dong ◽  
Robert A. Sanford ◽  
Maxim I. Boyanov ◽  
Kenneth M. Kemner ◽  
Theodore M. Flynn ◽  
...  

ABSTRACTA novel halophilic and metal-reducing bacterium,Orenia metallireducensstrain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity withOrenia marismortuibut demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genusOrenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducingShewanellaandGeobacterspecies, this organism lacks thec-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genusOrenia(orderHalanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from otherOreniaspp. support the designation of strain Z6 as a new species,Orenia metallireducenssp. nov.IMPORTANCEA novel iron-reducing species,Orenia metallireducenssp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack ofc-type cytochromes typically affiliated with iron reduction inGeobacterandShewanellaspecies, and (iii) being the only member of theHalanaerobialescapable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.

2013 ◽  
Vol 79 (13) ◽  
pp. 3974-3985 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Andreas Teske

ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.


2020 ◽  
Vol 70 (10) ◽  
pp. 5432-5438 ◽  
Author(s):  
Pawina Kanchanasin ◽  
Masahiro Yuki ◽  
Takuji Kudo ◽  
Moriya Ohkuma ◽  
Wongsakorn Phongsopitanun ◽  
...  

A novel actinomycete strain, CT2-14T, belonging to the genus Nocardia , was isolated from a soil sample collected from Phichit Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic approach. The strain grew at 15–40 °C (optimum, 28–37 °C), pH 6–11 (optimum, pH 6–8) and on an International Streptomyces Project 2 with 4 % (w/v) NaCl agar plate. Meso-diaminopimelic acid was detected in the cell-wall peptidoglycan. Ribose, arabinose and galactose were detected in its whole-cell hydrolysates. Mycolic acids were present. The strain contained C16 : 0, summed feature 3, C17 : 0 10-methyl and C18 : 1 ω9c as the major fatty acids and MK-8(H4ω-cycl) as the major menaquinone. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol mannosides. Strain CT2-14T showed the highest 16S rRNA gene similarity to Nocardia veterana JCM 11307T (98.4 %), Nocardia africana JCM 11438T (98.2 %) and Nocardia kruczakiae JCM 13032T (98.0 %). The draft genome of strain CT2-14T was 7.37 Mb with 6685 coding sequences with an average G+C content of 67.9 mol %. Based on the phylogenomic tree analysis, the strain was closely related to Nocardia niigatensis NBRC 100131T. On the basis of polyphasic and genome analyses, strain CT2-14T represented a novel species of the genus Nocardia for which the name Nocardia aurantiaca sp. nov. is proposed. The type strain is CT2-14T (=JCM 33775T=TISTR 2838T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5235-5242 ◽  
Author(s):  
Soon Dong Lee ◽  
Hanna Choe ◽  
Ji-Sun Kim ◽  
In Seop Kim

A strictly aerobic, Gram-stain-negative, non-motile, ovoid- and rod-shaped bacterium, designated strain GH1-50T, was isolated from a tidal mudflat sample collected from Dongmak seashore on Gangwha Island, Republic of Korea. The organism showed growth at 20–40 °C (optimum, 30 °C), pH 7–8 (optimum, pH 7) and 2–6  % (w/v) NaCl (optimum, 5 %). The pufLM genes were present but bacteriochlorophyll a was not detected. The major isoprenoid quinone was Q-10. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid and five unidentified lipids. The predominant cellular fatty acids were C18 : 1  ω7c, C18 : 1  ω7c 11-methyl and C18 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the isolate belonged to the family Rhodobacteraceae and was loosely associated with members of the recognized genera. The closest relative was the type strain of Pseudoruegeria marinistellae (96.8 % similarity) followed by Boseongicola aestuarii (96.4 %). Other members of the family shared 16S rRNA gene similarity values below 96.0 % to the novel isolate. The DNA G+C content calculated from the draft genome sequence was 64.0 %. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between genome sequences of strain GH1-50T and all the type strains of the recognized taxa compared were <70.0, <84.1 and <20.5 %, respectively. Based on data obtained by a polyphasic approach, strain GH1-50T (=KCTC 72224T=NBRC 113929T) represents a novel species of a new genus in the family Rhodobacteraceae , for which the name Kangsaoukella pontilimi gen. nov., sp. nov. is proposed.


2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.


2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).


2019 ◽  
Vol 69 (4) ◽  
pp. 1075-1080 ◽  
Author(s):  
Leni Sun ◽  
Yan Chen ◽  
Wei Tian ◽  
Lunguang Yao ◽  
Zhaojin Chen ◽  
...  

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).


Author(s):  
Inhyup Kim ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Minchung Kang ◽  
Yoonseop So ◽  
...  

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.


Author(s):  
Sára Szuróczki ◽  
Gorkhmaz Abbaszade ◽  
Dominika Buni ◽  
Károly Bóka ◽  
Peter Schumann ◽  
...  

Three Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped, black, facultative phototrophic bacterial strains, RG-N-1aT, DMA-N-7a and RA-N-9 were isolated from the water sample from Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Rhodobacteraceae and their closest relatives are Tabrizicola piscis K13M18T (96.32%) followed by Cypionkella psychrotolerans PAMC 27389T (96.25%). The novel bacterial strains prefer alkaline environments and grow optimally at 23–33 °C in the presence of NaCl (1–2 w/v%). Bacteriochlorophyll a was detected. Cells contained exclusively ubiquinone Q-10. The major cellular fatty acids were C18 : 1ω7c, C19 : 1iso ω5c, C18 : 0 3-OH and C18 : 1ω7c 11-methyl. The polar lipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid and four unidentified lipids. The assembled draft genome of RG-N-1aT had 33 contigs with N50 values 315 027 nt, 96× genome coverage, total length of 4 326 551 bp and a DNA G+C content of 64.9%. Genome-based calculations (genome-to-genome distance and DNA G+C percentage) and pairwise amino acid identity (AAI <73.5%) indicate that RG-N-1aT represents a novel genus. RG-N-1aT (=DSM 108317T=NCAIM B.02647T) is suggested as the type strain of a novel genus and species in the family Rhodobacteraceae , for which the name Fertoeibacter niger gen. nov., sp. nov. is proposed.


Author(s):  
Héléna Cuny ◽  
Clément Offret ◽  
Amine M. Boukerb ◽  
Leila Parizadeh ◽  
Olivier Lesouhaitier ◽  
...  

Three bacterial strains, named hOe-66T, hOe-124 and hOe-125, were isolated from the haemolymph of different specimens of the flat oyster Ostrea edulis collected in Concarneau bay (Finistère, France). These strains were characterized by a polyphasic approach, including (i) whole genome analyses with 16S rRNA gene sequence alignment and pangenome analysis, determination of the G+C content, average nucleotide identity (ANI), and in silico DNA–DNA hybridization (isDDH), and (ii) fatty acid methyl ester and other phenotypic analyses. Strains hOe-66T, hOe-124 and hOe-125 were closely related to both type strains Pseudoalteromonas rhizosphaerae RA15T and Pseudoalteromonas neustonica PAMC 28425T with less than 93.3% ANI and 52.3% isDDH values. Regarding their phenotypic traits, the three strains were Gram-negative, 1–2 µm rod-shaped, aerobic, motile and non-spore-forming bacteria. Cells grew optimally at 25 °C in 2.5% NaCl and at 7–8 pH. The most abundant fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C17:1 ω8c. The strains carried a genome average size of 4.64 Mb and a G+C content of 40.28 mol%. The genetic and phenotypic results suggested that strains hOe-66T, hOe-124 and hOe-125 belong to a new species of the genus Pseudoalteromonas . In this context, we propose the name Pseudoalteromonas ostreae sp. nov. The type strain is hOe-66T (=CECT 30303T=CIP 111911T).


Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Md. Amdadul Huq

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20–40 °C, at pH 5.0–10.0 and with 0–1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-13T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAH-13T and five closely related type strains were in the range of 73.7–85.5 % and 20.7–30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13T represents a novel species within the genus Frateuria , for which the name Frateuria flava sp. nov. is proposed, with MAH-13T (=KACC 19743T=CGMCC 1.13655T) as the type strain.


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