scholarly journals Identification of Anaerobic Selenate-Respiring Bacteria from Aquatic Sediments

2007 ◽  
Vol 73 (11) ◽  
pp. 3519-3527 ◽  
Author(s):  
Priya Narasingarao ◽  
Max M. Häggblom
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Anaerobic Respiration ◽  
Pseudomonas Stutzeri ◽  
Elemental Selenium ◽  
Rrna Gene ◽  
Terminal Electron Acceptor ◽  
Isolation And Characterization ◽  
Anaerobic Biotransformation ◽  
Gene Similarity

ABSTRACT The diversity population of microorganisms with the capability to use selenate as a terminal electron acceptor, reducing it to selenite and elemental selenium by the process known as dissimilatory selenate reduction, is largely unknown. The overall objective of this study was to gain an in-depth understanding of anaerobic biotransformation of selenium in the environment, particularly anaerobic respiration, and to characterize the microorganisms catalyzing this process. Here, we demonstrate the isolation and characterization of four novel anaerobic dissimilatory selenate-respiring bacteria enriched from a variety of sources, including sediments from three different water bodies in Chennai, India, and a tidal estuary in New Jersey. Strains S5 and S7 from India, strain KM from the Meadowlands, NJ, and strain pn1, categorized as a laboratory contaminant, were all phylogenetically distinct, belonging to various phyla in the bacterial domain. The 16S rRNA gene sequence shows that strain S5 constitutes a new genus belonging to Chrysiogenetes, while strain S7 belongs to the Deferribacteres, with greater than 98% 16S rRNA gene similarity to Geovibrio ferrireducens. Strain KM is related to Malonomonas rubra, Pelobacter acidigallici, and Desulfuromusa spp., with 96 to 97% 16S rRNA gene similarity. Strain pn1 is 99% similar to Pseudomonas stutzeri. Strains S5, S7, and KM are obligately anaerobic selenate-respiring microorganisms, while strain pn1 is facultatively anaerobic. Besides respiring selenate, all these strains also respire nitrate.

scholarly journals Isolation and Characterization of “Dehalococcoides” sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene

2009 ◽  
Vol 75 (18) ◽  
pp. 5910-5918 ◽  
Author(s):  
Dan Cheng ◽  
Jianzhong He
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Anaerobic Respiration ◽  
Rrna Gene ◽  
Reductive Dehalogenase ◽  
Isolation And Characterization ◽  
Dehalococcoides Ethenogenes ◽  
Pure Cultures ◽  
Microbial Group ◽  
Rdase Genes

ABSTRACT In an attempt to understand the microorganisms involved in the generation of trans-1,2-dichloroethene (trans-DCE), pure-culture “Dehalococcoides” sp. strain MB was isolated from environmental sediments. In contrast to currently known tetrachloroethene (PCE)- or trichloroethene (TCE)-dechlorinating pure cultures, which generate cis-DCE as the predominant product, Dehalococcoides sp. strain MB reductively dechlorinates PCE to trans-DCE and cis-DCE at a ratio of 7.3 (±0.4):1. It utilizes H2 as the sole electron donor and PCE or TCE as the electron acceptor during anaerobic respiration. Strain MB is a disc-shaped, nonmotile bacterium. Under an atomic force microscope, the cells appear singly or in pairs and are 1.0 μm in diameter and ∼150 nm in depth. The purity was confirmed by culture-based approaches and 16S rRNA gene-based analysis and was corroborated further by putative reductive dehalogenase (RDase) gene-based, quantitative real-time PCR. Although strain MB shares 100% 16S rRNA gene sequence identity with Dehalococcoides ethenogenes strain 195, these two strains possess different dechlorinating pathways. Microarray analysis revealed that 10 putative RDase genes present in strain 195 were also detected in strain MB. Successful cultivation of strain MB indicates that the biotic process could contribute significantly to the generation of trans-DCE in chloroethene-contaminated sites. It also enhances our understanding of the evolution of this unusual microbial group, Dehalococcoides species.

scholarly journals Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community

2005 ◽  
Vol 71 (10) ◽  
pp. 5908-5919 ◽  
Author(s):  
Frederic Gich ◽  
Karin Schubert ◽  
Alke Bruns ◽  
Herbert Hoffelner ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Light Harvesting Complexes ◽  
Probable Number ◽  
Bacterioplankton Community ◽  
Isolation And Characterization

ABSTRACT High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α-Proteobacteria, β-Proteobacteria, Actinobacteria, Firmicutes, or Flavobacteria-Cytophaga lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α-Proteobacteria 16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of Sandaracinobacter sibiricus, the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll a bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.

scholarly journals Halomonas rifensis sp. nov., an exopolysaccharide-producing, halophilic bacterium isolated from a solar saltern

2011 ◽  
Vol 61 (11) ◽  
pp. 2600-2605 ◽  
Author(s):  
Hakima Amjres ◽  
Victoria Béjar ◽  
Emilia Quesada ◽  
Jamal Abrini ◽  
Inmaculada Llamas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Halophilic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
Terminal Electron Acceptor ◽  
Moderately Halophilic Bacterium

A polyphasic taxonomic study was conducted on strain HK31T, a moderately halophilic bacterium isolated from a solar saltern in Chefchaouen, Morocco. The strain was a Gram-reaction-negative, oxidase-positive rod, which was motile by means of peritrichous flagella. The strain required NaCl for growth and grew in salt concentrations (mixture of sea salts) of 0.5–20 % (w/v) (optimum 5–7.5 %, w/v), at 25–45 °C (optimum 32 °C) and at pH 5–10 (optimum pH 6–9). Strain HK31T did not produce acids from sugars and its metabolism was respiratory, using oxygen as terminal electron acceptor. The strain was positive for the accumulation of poly-β-hydroxyalkanoate granules and formed mucoid colonies due to the excretion of an exopolysaccharide. The DNA G+C content was 61.5 mol%. 16S rRNA gene sequence analysis indicated that it belonged to the genus Halomonas in the class Gammaproteobacteria. The most phylogenetically related species was Halomonas anticariensis, with which strain HK31T showed a 16S rRNA gene sequence similarity of 96.48 %. Its major fatty acids were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c , C16 : 1ω7c/iso-C15 : 0 2-OH and C12 : 0 3-OH and the predominant respiratory lipoquinone was ubiquinone with nine isoprene units (Q-9). Based on the evidence provided in this study, strain HK31T ( = CECT 7698T  = LMG 25695T) represents a novel species of the genus Halomonas, for which the name Halomonas rifensis is proposed.

scholarly journals Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake

2010 ◽  
Vol 60 (2) ◽  
pp. 349-352 ◽  
Author(s):  
Tong-Wei Guan ◽  
Jing Xiao ◽  
Ke Zhao ◽  
Xiao-Xia Luo ◽  
Xiao-Ping Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Salt Lake ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Terminal Electron Acceptor

A novel bacterium, TRM 0175T, belonging to the genus Halomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0–20 % (optimum at 10–13 %), at 15–50 °C (optimum at 37 °C) and at pH 6.0–9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced from d-ribose, d- and l-arabinose, d-xylose, d-galactose, d-mannose, l-rhamnose, cellobiose, maltose, trehalose and d- and l-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1 ω7c and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175T with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas anticariensis; 16S rRNA gene sequence similarity between H. anticariensis FP35T and strain TRM 0175T was 95.3 %. Phenotypically, some characteristics of TRM 0175T differed from those of H. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175T represents a novel species of the genus Halomonas, for which the name Halomonas xinjiangensis sp. nov. is proposed; the type strain is TRM 0175T (=CCTCC AB 208329T =KCTC 22608T).

scholarly journals Leisingera nanhaiensis sp. nov., isolated from marine sediment

2010 ◽  
Vol 60 (2) ◽  
pp. 275-280 ◽  
Author(s):  
Fengqin Sun ◽  
Baojiang Wang ◽  
Xiupian Liu ◽  
Qiliang Lai ◽  
Yaping Du ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Phenotypic Properties ◽  
Gram Staining ◽  
Distinct Cluster ◽  
Bacterium Strain ◽  
Gene Similarity

An aerobic, Gram-staining-negative, motile, rod-shaped bacterium, strain NH52FT, was isolated from a sandy sediment sample taken from the South China Sea. On M2 agar medium (a complex medium), colonies were beige in colour. The isolate showed highest 16S rRNA gene sequence similarities to members of the genera Leisingera (96.7 % similarity), Phaeobacter (95.4–96.0 %) and Marinovum (94.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52FT formed a distinct cluster with Leisingera methylohalidivorans MB2T and Leisingera aquimarina LMG 24366T. Optimal growth was observed at pH 7.0-8.5 and 25 °C and the new isolate required the presence of 1–4 % (w/v) NaCl. The major fatty acids were C18 : 1 ω7c, C16 : 0 2-OH, C10 : 0 3-OH, C12 : 0 3-OH, C16 : 0 and 11-methyl C18 : 1 ω7c. The DNA G+C content was 60.5 mol%. The phylogenetic and chemotaxonomic characteristics of strain NH52FT were similar to those of the genus Leisingera. However, the differences in phenotypic properties and the 16S rRNA gene similarity values demonstrated that the new isolate differed from recognized species of the genus Leisingera. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Leisingera, for which the name Leisingera nanhaiensis sp. nov. is proposed. The type strain is NH52FT (=LMG 24841T=CCTCC AB 208316T=MCCC 1A04178T).

Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to Methylobacterium organophilum ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus Methylobacterium , for which the names Methylobacterium haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and Methylobacterium brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.

scholarly journals Denitrobaculum tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp

2020 ◽  
Vol 70 (5) ◽  
pp. 3335-3339 ◽  
Author(s):  
Guanghua Wang ◽  
Dahao Tang ◽  
Guangyu Li ◽  
Shuailiang Xu ◽  
Ge Dang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Coralline Algae ◽  
Global Alignment ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

A Gram-stain-negative, non-spore-forming, aerobic, motile, curved rod-shaped bacterium, designed strain R148T was isolated from a coralline algae Tricleocarpa sp. collected from Weizhou island, PR China. The optimal growth of R148T occurred at 25 °C, pH 8–9 in the presence of 0.5 % (w/v) NaCl on the basis of amended marine broth 2216. The genomic DNA G+C content was 59.5 mol%. The only detected respiratory quinone was Q-10. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and three unidentified ninhydrin-positive lipids. The major cellular fatty acids were C18 : 1ω7c, C16 : 1ω7c, C19 : 0cyclo 9, 10 DMA and C18 : 0. The results of 16S rRNA gene-based global alignment indicated that the closest neighbour of strain R148T was Pelagibius litoralis DSM 21314T (93.1 % similarity), the second is Limibacillus halophilus KCTC 42420T (92.2 %). The results of phylogenetic analysis indicated that R148T forms a distinct branch in the robust clade of R148T and P. litoralis DSM 21314T, while the taxonomic position of this clade in the family Rhodospirillaceae is ambiguous among phylogenetic approaches. The low 16S rRNA gene similarity and distinct polar lipid and cellular fatty acid profile could readily distinguish R148T from closely related type strains. So R148T is suggested to represent a novel species in a novel genus, for which the name Denitrobaculum tricleocarpae gen. nov., sp. nov. is proposed. The type strain is R148T (=MCCC 1K03781T=KCTC 72137T).

scholarly journals Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai–Tibet Plateau

2020 ◽  
Vol 70 (4) ◽  
pp. 2204-2210 ◽  
Author(s):  
Zhi Tian ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Ji Pu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity ◽  
Qinghai Tibet Plateau ◽  
Tibetan Antelope

Two Gram-stain-positive, catalase-positive and oxidase-negative, aerobic, non-motile, cellobiose-utilizing, short-rod-shaped strains (Z28T and Z29) were isolated from faeces of Tibetan antelope (Pantholops hodgsonii) collected on the Qinghai–Tibet Plateau. Strain Z28T shared 98.1, 98.0, 97.8 and 97.4 % 16S rRNA gene similarity, 24.1, 22.8, 23.2 and 26.3 % digital DNA–DNA hybridization relatedness and 80.8, 80.0, 80.7 and 80.9 % average nucleotide identity values with Cellulomonas oligotrophica DSM 24482T, Cellulomonas flavigena DSM 20109T, Cellulomonas iranensis DSM 14785T and Cellulomonas terrae JCM 14899T, respectively. Results from further phylogenetic analyses based on the 16S rRNA gene and 148 core genes indicated that strains Z28T and Z29 were closest to C. oligotrophica DSM 24482T and C. flavigena DSM 20109T, but clearly separated from the currently recognized species of the genus Cellulomonas . The genomic DNA G+C content of strain Z28T was 75.3 mol%. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A, C16 : 0 and anteiso-C17 : 0. Ribose and mannose were detected as the whole-cell sugars. The major respiratory quinone was MK-9(H4) and ornithine was the diamino acid of the cell wall. The polar lipids present in strain Z28T were phosphatidylethanolamine, five phospholipids, two aminophospholipids, aminolipid and three unidentified lipids. Comparison of phenotypic and phylogenetic features between the two strains and the related organisms revealed that Z28T and Z29 represent a novel species of the genus Cellulomonas , for which the name Cellulomonas shaoxiangyii sp. nov. is proposed. The type strain is Z28T (=CGMCC 1.16477T=DSM 106200T).

scholarly journals Isolation and Characterization of Endophytic Bacteria from Tembelekan (Lantana camara L.) as Antibacterial Compounds Producer

2015 ◽  
Vol 2 (2) ◽  
pp. 86-98
Author(s):  
Dina Dyah Saputri ◽  
Maria Bintang ◽  
Fachriyan H Pasaribu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Endophytic Bacteria ◽  
Pathogenic Bacteria ◽  
Lantana Camara ◽  
Rrna Gene ◽  
Antibacterial Compounds ◽  
Isolation And Characterization ◽  
Ms Analysis

Endophytic bacteria are microorganisms that live in the internal tissues of plants and have symbiotic mutualism with their host plants. Endophytic bacteria may produce secondary metabolites that can be developed for medical, agricultural, and industrial purposes. Lantana camara is a medicinal plant that has therapeutic potential to treat a variety of diseases such as fever, tuberculosis, rheumatism, asthma, and skin disease. The purpose of this study was to isolate and characterize endophytic bacteria from Lantana camara which has potential to produce antibacterial compounds. The method of this research include isolation of endophytic bacteria of Lantana camara. Antibacterial activity assay was done against four types of pathogenic bacteria i.e. Bacillus cereus, Escherichia coli, Staphylococcus aureus, and Salmonella enteritidis. Characterization of endophytic bacteria was by 16S rRNA gene analysis and identification of antibacterial compounds by GC-MS analysis. Isolation of endophytic bacteria from Lantana camara resulted in BT22 as a potential isolate. Analysis of 16S rRNA gene showed that the BT22 isolate was similar to Bacillus amyloliquefaciens YB-1402 with 99% identity. The results of GC-MS analysis showed some antibacterial compounds such as: Cyclohexanone, 2-[2-(1,3-dithiolan-2-yl)propyl]-6-methyl-3-(1-methylethyl), Octadecane (CAS) n-Octadecane and Tetracosane (CAS) n-Tetracosane.

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