scholarly journals Anaerobic Oxidation of Arsenite Linked to Chlorate Reduction

2010 ◽  
Vol 76 (20) ◽  
pp. 6804-6811 ◽  
Author(s):  
Wenjie Sun ◽  
Reyes Sierra-Alvarez ◽  
Lily Milner ◽  
Jim A. Field
Keyword(s):  
Organic Carbon ◽  
16S Rrna ◽  
Molar Ratio ◽  
Gene Clone ◽  
Rrna Gene ◽  
Microbial Oxidation ◽  
Anaerobic Conditions ◽  
Low Concentrations ◽  
Pure Cultures ◽  
Low Levels

ABSTRACT Microorganisms play a significant role in the speciation and mobility of arsenic in the environment. In this study, the oxidation of arsenite [As(III)] to arsenate [As(V)] linked to chlorate (ClO3 −) reduction was shown to be catalyzed by sludge samples, enrichment cultures (ECs), and pure cultures incubated under anaerobic conditions. No activity was observed in treatments lacking inoculum or with heat-killed sludge, or in controls lacking ClO3 −. The As(III) oxidation was linked to the complete reduction of ClO3 − to Cl−, and the molar ratio of As(V) formed to ClO3 − consumed approached the theoretical value of 3:1 assuming the e − equivalents from As(III) were used to completely reduce ClO3 −. In keeping with O2 as a putative intermediate of ClO3 − reduction, the ECs could also oxidize As(III) to As(V) with O2 at low concentrations. Low levels of organic carbon were essential in heterotrophic ECs but not in autotrophic ECs. 16S rRNA gene clone libraries indicated that the ECs were dominated by clones of Rhodocyclaceae (including Dechloromonas, Azospira, and Azonexus phylotypes) and Stenotrophomonas under autotrophic conditions. Additional phylotypes (Alicycliphilus, Agrobacterium, and Pseudoxanthomonas) were identified in heterotrophic ECs. Two isolated autotrophic pure cultures, Dechloromonas sp. strain ECC1-pb1 and Azospira sp. strain ECC1-pb2, were able to grow by linking the oxidation of As(III) to As(V) with the reduction of ClO3 −. The presence of the arsenite oxidase subunit A (aroA) gene was demonstrated with PCR in the ECs and pure cultures. This study demonstrates that ClO3 − is an alternative electron acceptor to support the microbial oxidation of As(III).

scholarly journals Bifidobacterium stercoris sp. nov., isolated from human faeces

2010 ◽  
Vol 60 (12) ◽  
pp. 2823-2827 ◽  
Author(s):  
Min-Soo Kim ◽  
Seong Woon Roh ◽  
Jin-Woo Bae
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Molar Ratio ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Human Faeces ◽  
Negative Results ◽  
Low Levels

Strain Eg1T, an anaerobic, Gram-stain-positive, non-motile and non-spore-forming bacterium, was isolated from human faeces. The optimal temperature for growth was 37 °C and tests for oxidase and catalase activities gave negative results. Fructose-6-phosphate phosphoketolase activity was detected. Acid was produced during fermentation of several substrates, including glucose. The end products of glucose fermentation were acetic acid and lactic acid, which were produced in a molar ratio of 1.76 : 1 (approximately 3 : 2). The G+C content was 57.8 mol%. Comparative analysis of 16S rRNA gene sequences showed that strain Eg1T was closely related to Bifidobacterium adolescentis YIT 4011T (98.36 % 16S rRNA gene sequence similarity) and Bifidobacterium ruminantium JCM 8222T (97.93 %) and analysis of hsp60 sequences showed that strain Eg1T was closely related to B. adolescentis JCM 1275T (99.35 % hsp60 sequence similarity) and B. ruminantium JCM 8222T (92.13 %). However, despite these degrees of similarity being high enough for strain Eg1T to be included at the same species level as B. adolescentis and B. ruminantium (96.5–100 % for the genus Bifidobacterium), the isolate could be distinguished from B. adolescentis KCTC 3216T and B. ruminantium KCTC 3425T by low levels of DNA–DNA relatedness (41 and 17 %, respectively). Based on phenotypic, genotypic and phylogenetic analyses, we propose that strain Eg1T is classified in a novel species, Bifidobacterium stercoris sp. nov. The type strain is Eg1T (=KCTC 5756T =JCM 15918T).

scholarly journals Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis

2014 ◽  
Vol 48 (8) ◽  
pp. 717-728 ◽  
Author(s):  
M. N. Zakaria ◽  
T. Takeshita ◽  
Y. Shibata ◽  
H. Maeda ◽  
N. Wada ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Apical Periodontitis ◽  
Gene Clone ◽  
Rrna Gene ◽  
Clone Library Analysis

scholarly journals Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil

2011 ◽  
Vol 61 (11) ◽  
pp. 2626-2631 ◽  
Author(s):  
K. S. Inglett ◽  
H. S. Bae ◽  
H. C. Aldrich ◽  
K. Hatfield ◽  
A. V. Ogram
Keyword(s):  
Contaminated Soil ◽  
Clostridium Beijerinckii ◽  
Rrna Gene ◽  
Acid Fermentation ◽  
Mixed Acid ◽  
Morphological Studies ◽  
Group I ◽  
Low Concentrations ◽  
Low Levels ◽  
Sequence Similarities

A Cr(VI)-resistant, Gram-positive, spore-forming, obligate anaerobe, designated GCAF-1T, was isolated from chromium-contaminated soil by its ability to reduce Cr(VI) in low concentrations. Mixed acid fermentation during growth on glucose resulted in accumulation of acetate, butyrate, formate and lactate. Morphological studies indicated the presence of peritrichous flagella, pili and an S-layer. The major cellular fatty acids (>5 %) were C16 : 0, C14 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), C18 : 1ω7c, C16 : 1ω9c, summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B) and C18 : 1ω9c. The DNA G+C content of strain GCAF-1T was 30.7 mol%. Phylogenetic interference indicated that strain GCAF-1T clustered with group I of the genus Clostridium. Of strains within this cluster, strain GCAF-1T shared the highest 16S rRNA gene sequence similarities (98.1–98.9 %) with Clostridium beijerinckii DSM 791T, C. saccharobutylicum NCP 262T, C. saccharoperbutylacetonicum N1-4T, C. puniceum DSM 2619T and C. roseum DSM 51T. However, strain GCAF-1T could be clearly distinguished from its closest phylogenetic neighbours by low levels of DNA–DNA relatedness (<50 %) and some phenotypic features. Based on the evidence presented here, strain GCAF-1T ( = DSM 23318T  = KCTC 5935T) represents a novel species of the genus Clostridium, for which the name Clostridium chromiireducens sp. nov. is proposed.

scholarly journals Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore

2010 ◽  
Vol 60 (12) ◽  
pp. 2719-2723 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sung-Ran Moon ◽  
Young-Hyun Park ◽  
Jung-Ho Kim ◽  
Hoon Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Crude Oil ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Low Levels

A novel Gram-negative, aerobic, motile, short rod-shaped bacterium, designated MS-3T, was isolated from a crude oil-contaminated seashore in Taean, Korea. Strain MS-3T grew at 4–30 °C, at pH 6.0–9.5 and with 0–5 % NaCl and was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MS-3T was most similar to Pseudomonas marincola KMM 3042T (97.9 % 16S rRNA gene sequence similarity), P. cuatrocienegasensis 1NT (97.8 %), P. borbori R-20821T (97.3 %) and P. lundensis ATCC 49968T (97.1 %). Relatively low levels of DNA–DNA relatedness were found between strain MS-3T and P. cuatrocienegasensis LMG 24676T (57.2 %), P. borbori LMG 23199T (39.7 %), P. marincola KMM 3042T (32.2 %) and P. lundensis KACC 10832T (32.1 %), which support the classification of strain MS-3T within a novel species of the genus Pseudomonas. The G+C content of the genomic DNA of strain MS-3T was 57.6 mol% and the major isoprenoid quinone was Q-9. Strain MS-3T contained summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 38.0 %), C16 : 0 (24.4 %), C18 : 1 ω7c (12.8 %), C12 : 0 (9.6 %) and C10 : 0 3-OH (4.9 %) as the major cellular fatty acids. On the basis of the phenotypic, genotypic and phylogenetic data, strain MS-3T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas taeanensis sp. nov. is proposed. The type strain is MS-3T (=KCTC 22612T =KACC 14032T =JCM 16046T =NBRL 105641T).

Insights into Bacterial Community Structure of a Commercial Copper Bioheapleaching Plant: Growth of Heterotrophic Bacteria in the System

2013 ◽  
Vol 825 ◽  
pp. 50-53 ◽  
Author(s):  
Xing Yu Liu ◽  
Bo Wei Chen ◽  
Jian Kang Wen
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Heterotrophic Bacteria ◽  
Outer Part ◽  
Gene Clone ◽  
Rrna Gene ◽  
Liquid Samples ◽  
Lower Depth

The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.

scholarly journals Detection of Low-Level Cardinium and Wolbachia Infections in Culicoides

2015 ◽  
Vol 81 (18) ◽  
pp. 6177-6188 ◽  
Author(s):  
Peter T. Mee ◽  
Andrew R. Weeks ◽  
Peter J. Walker ◽  
Ary A. Hoffmann ◽  
Jean-Bernard Duchemin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Conventional Pcr ◽  
Content Type ◽  
Low Level ◽  
The United Kingdom ◽  
Geographical Regions ◽  
Movement Screening ◽  
Low Levels

ABSTRACTBacterial endosymbionts have been identified as potentially useful biological control agents for a range of invertebrate vectors of disease. Previous studies ofCulicoides(Diptera: Ceratopogonidae) species using conventional PCR assays have provided evidence ofWolbachia(1/33) andCardinium(8/33) infections. Here, we screened 20 species ofCulicoidesforWolbachiaandCardinium, utilizing a combination of conventional PCR and more sensitive quantitative PCR (qPCR) assays. Low levels ofCardiniumDNA were detected in females of all but one of theCulicoidesspecies screened, and low levels ofWolbachiawere detected in females of 9 of the 20Culicoidesspecies. Sequence analysis based on partial 16S rRNA gene andgyrBsequences identified “CandidatusCardinium hertigii” from group C, which has previously been identified inCulicoidesfrom Japan, Israel, and the United Kingdom.Wolbachiastrains detected in this study showed 98 to 99% sequence identity toWolbachiapreviously detected fromCulicoidesbased on the 16S rRNA gene, whereas a strain with a novelwspsequence was identified inCulicoidesnarrabeenensis. Cardiniumisolates grouped to geographical regions independent of the hostCulicoidesspecies, suggesting possible geographical barriers toCardiniummovement. Screening also identifiedAsaiabacteria inCulicoides. These findings point to a diversity of low-level endosymbiont infections inCulicoides, providing candidates for further characterization and highlighting the widespread occurrence of these endosymbionts in this insect group.

Enrichment and Isolation of Acidophilic Microorganisms from Sediments of Gold Mine Waste Leachate

2015 ◽  
Vol 1130 ◽  
pp. 581-584
Author(s):  
Aleksander Bulaev ◽  
Nikolay V. Pimenov ◽  
Denis A. Ivasenko ◽  
Olga V. Karnachuk
Keyword(s):  
Biochemical Characterization ◽  
Mine Drainage ◽  
Mine Waste ◽  
Sulfur Oxidation ◽  
16S Rrna Gene Sequencing ◽  
West Siberia ◽  
Rrna Gene ◽  
Anaerobic Conditions ◽  
Pure Cultures ◽  
Set Up

Microorganisms living in acidic environments associated with various types of mining wastes can be used for bioremediation of acid mine drainage (AMD) and related waste streams. We studied microbial diversity of the acidic sediments of a leachate puddle at the basement of a waste rock pile from gold mining in abandoned gold deposit in Martiga (Kemerovo region, West Siberia, Russia). The enrichments were established from four sediment samples with a pH ranging from 2.29 to 6.16. The enrichments cultures were set up at aerobic and anaerobic conditions. Pure cultures of bacteria involved in iron and sulfur oxidation were isolated. The isolated iron- and sulfur-oxidizing cultures were affiliated with Acidithiobacillus and Acidocella genera as was revealed by 16S rRNA gene sequencing. Strains of Desulfosporosinus-like spore-forming bacteria were isolated under anaerobic conditions. The pure culture isolates physiological and biochemical characterization is underway, which will provide new knowledge of AMD formation and natural processes of metal attenuation. The strains can also be prospective agents for use in bioleaching and bioremediation processes.

scholarly journals Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques

2005 ◽  
Vol 71 (4) ◽  
pp. 2162-2169 ◽  
Author(s):  
Hideyuki Tamaki ◽  
Yuji Sekiguchi ◽  
Satoshi Hanada ◽  
Kazunori Nakamura ◽  
Nakao Nomura ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Clone Library ◽  
Eutrophic Lake ◽  
Freshwater Sediment ◽  
Gene Clone ◽  
Rrna Gene ◽  
Shallow Eutrophic Lake

ABSTRACT Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

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