scholarly journals Distribution of Dehalococcoides 16S rRNA and Dehalogenase Genes in Contaminated Sites

2017 ◽  
Vol 7 (2) ◽  
pp. 37 ◽  
Author(s):  
Miho Yoshikawa ◽  
Mio Takeuchi ◽  
Ming Zhang
Keyword(s):  
Spatial Distribution ◽  
16S Rrna ◽  
Contaminated Sites ◽  
Rrna Gene ◽  
Sediment Depth ◽  
Sediment Samples ◽  
Reductive Dehalogenase ◽  
Chlorinated Ethylenes ◽  
Reductive Dehalogenase Genes ◽  
Geological Formations

Understanding the spatial distribution of Dehalococcoides and its reductive dehalogenase genes in sediment is important for bioremediation of sites contaminated with chlorinated ethylenes. A total of 56 sediment samples were collected from four contaminated sites in Japan, and quantified copies of Dehalococcoides 16S rRNA and reductive dehalogenase genes: tceA, bvcA, and vcrA, as well as chlorinated ethylenes. Dehalococcoides was detected from 22 sediment samples with various geological formations, textures and saturation conditions. The detected Dehalococcoides 16S rRNA gene ranged from 6.4 × 102 to 2.5 × 107 copies g−1. In the 22 samples, the dehalogenase genes: tceA, bvcA, and vcrA were contained 1.4 × 103 to 1.6 × 104, 1.0 × 103 to 2.0 × 105, and     2.7 × 102 to 8.5 × 105 copies g−1, respectively. Statistical analysis revealed that the distribution of dehalogenase genes depends on site and depth, but not existence of vinyl chloride. To estimate potential for bioremediation of contaminated sites, quantification of dehalogenase genes according to sediment depth is important and thus recommended.

scholarly journals Discrimination of Multiple Dehalococcoides Strains in a Trichloroethene Enrichment by Quantification of Their Reductive Dehalogenase Genes

2006 ◽  
Vol 72 (9) ◽  
pp. 5877-5883 ◽  
Author(s):  
Victor F. Holmes ◽  
Jianzhong He ◽  
Patrick K. H. Lee ◽  
Lisa Alvarez-Cohen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequence Matching ◽  
Relative Copy Number ◽  
Reductive Dehalogenase ◽  
Copy Numbers ◽  
Reductase Gene ◽  
Reductive Dehalogenase Genes

ABSTRACT While many anaerobic microbial communities are capable of reductively dechlorinating tetrachloroethene (PCE) and trichloroethene (TCE) to dichloroethene (DCE), vinyl chloride (VC), and finally ethene, the accumulation of the highly toxic intermediates, cis-DCE (cDCE) and VC, presents a challenge for bioremediation processes. Members of the genus Dehalococcoides are apparently solely responsible for dechlorination beyond DCE, but isolates of Dehalococcoides each metabolize only a subset of PCE dechlorination intermediates and the interactions among distinct Dehalococcoides strains that result in complete dechlorination are not well understood. Here we apply quantitative PCR to 16S rRNA and reductase gene sequences to discriminate and track Dehalococcoides strains in a TCE enrichment derived from soil taken from the Alameda Naval Air Station (ANAS) using a four-gene plasmid standard. This standard increased experimental accuracy such that 16S rRNA and summed reductase gene copy numbers matched to within 10%. The ANAS culture was found to contain only a single Dehalococcoides 16S rRNA gene sequence, matching that of D. ethenogenes 195, but both the vcrA and tceA reductive dehalogenase genes. Quantities of these two genes in the enrichment summed to the quantity of the Dehalococcoides 16S rRNA gene. Further, between ANAS subcultures enriched on TCE, cDCE, or VC, the relative copy number of the two dehalogenases shifted 14-fold, indicating that the genes are present in two different Dehalococcoides strains. Comparison of cell yields in VC-, cDCE-, and TCE-enriched subcultures suggests that the tceA-containing strain is responsible for nearly all of the TCE and cDCE metabolism in ANAS, whereas the vcrA-containing strain is responsible for all of the VC metabolism.

scholarly journals Penapisan dan Identifikasi Bakteri Penghasil Agarase dari Sampel Sedimen Laut Bara Caddi, Sulawesi Selatan

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Dewi Seswita Zilda ◽  
Gintung Patantis ◽  
Mada Triandala Sibero ◽  
Yusro Nuri Fawzya
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Marine Bacteria ◽  
Solid Medium ◽  
Rrna Gene ◽  
Clear Zone ◽  
Sediment Samples ◽  
South Sulawesi ◽  
The 16S Rrna Gene

Agarase adalah enzim yang mampu menghidrolisis agar menjadi oligoagar yang sudah banyak diaplikasikan dalam industri kesehatan dan kosmetik. Bakteri laut merupakan mikroba yang paling banyak dilaporkan sebagai sumber untuk isolasi bakteri penghasil agarase. Penelitian ini bertujuan untuk melakukan penapisan, isolasi, dan identifikasi bakteri penghasil agarase dari sedimen laut. Sampel sedimen diambil dari pantai Pulau Bara Caddi, Sulawesi Selatan. Penapisan dilakukan menggunakan media air laut yang ditambahkan tripton 0,5%, ekstrak ragi 0,1%, dan agar 2%. Identifikasi dilakukan dengan amplifikasi gen 16S rRNA. Sebanyak 45 isolat berhasil dimurnikan, 16 diantaranya merupakan bakteri penghasil agarase. Pola zona bening yang terbentuk terlihat berbeda-beda, hal ini diduga disebabkan oleh perbedaan jenis agarase yang dihasilkan oleh masing-masing isolat. Hasil penelitian menunjukkan bahwa terdapat 4 genera bakteri yang memiliki kemiripan yang tinggi dengan 16 isolat bakteri penghasil agarase yang terdapat pada sampel sedimen yaitu Vibrio, Alteromonas, Salinivibrio, dan Marinobacter. Vibrio merupakan genus yang paling dominan diikuti oleh Alteromonas dan hanya satu isolat yang menunjukkan kesamaan dengan Salinivibrio dan Marinobacter. ABSTRACTAgarase is an enzyme that hydrolyze agar into agaro oligosaccharide which have been applied in health and cosmetic industries. Marine bacteria are the most widely reported microbes as a source for isolation of agarase-producing bacteria. This work was aimed to screen, isolate, and identify the agarase-producing bacteria from marine sediment. The sediment samples were collected from the sea around Bara Caddi Island, South Sulawesi. The screening of agarase-producing bacteria was carried out using seawater media containing 0.5% tryptone, 0.1 % yeast extract with 2 % agar. The identification of the bacteria obtained was carried out by amplification of the 16S rRNA gene. A total of 45 isolates were successfully purified, 16 of which were agarase-producing bacteria. The clear zone formed on solid medium by some isolates showed different pattern which may be caused by the type of agarase produced by each isolate. The results showed that there were 4 genera of bacteria which similar to the 16 isolates agarase-producing bacteria found in sediment samples i.e. Vibrio, Alteromonas, Salinivibrio, and Marinobacter. Vibrio is the most dominant genus followed by Alteromonas and only one isolate showed similarity to Salinivibrio and Marinobacter.

scholarly journals Bacterial Diversity of Water and Sediment Samples from Gull Point State Park (West Okoboji, Iowa) Determined Using 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (33) ◽  
Author(s):  
John A. Kyndt
Keyword(s):  
16S Rrna ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Great Lakes Region ◽  
Primary State ◽  
Microbial Composition ◽  
The West ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Water And Sediment Samples

Gull Point State Park is located on a peninsula on the west shore of West Okoboji Lake (Iowa, USA). It is the primary state park in the Iowa Great Lakes region. Sediment and water samples from three locations at the Gull Point pond were analyzed for their microbial composition.

Phylogenetic Differentiation of Two Closely RelatedNitrosomonas spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake

1999 ◽  
Vol 65 (11) ◽  
pp. 4855-4862 ◽  
Author(s):  
Corinne B. Whitby ◽  
Jon R. Saunders ◽  
Juana Rodriguez ◽  
Roger W. Pickup ◽  
Alan McCarthy
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Freshwater Lake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Relative Distribution ◽  
Sediment Samples ◽  
Oligonucleotide Hybridization

ABSTRACT The population of ammonia-oxidizing bacteria in a temperate oligotrophic freshwater lake was analyzed by recovering 16S ribosomal DNA (rDNA) from lakewater and sediment samples taken throughout a seasonal cycle. Nitrosospira and Nitrosomonas16S rRNA genes were amplified in a nested PCR, and the identity of the products was confirmed by oligonucleotide hybridization.Nitrosospira DNA was readily identified in all samples, and nitrosomonad DNA of the Nitrosomonas europaea-Nitrosomonas eutropha lineage was also directly detected, but during the summer months only. Phylogenetic delineation with partial (345 bp) 16S rRNA gene sequences of clones obtained from sediments confirmed the fidelity of the amplified nitrosomonad DNA and identified two sequence clusters closely related to either N. europaea or N. eutropha that were equated with the littoral and profundal sediment sites, respectively. Determination of 701-bp sequences for 16S rDNA clones representing each cluster confirmed this delineation. A PCR-restriction fragment length polymorphism (RFLP) system was developed that enabled identification of clones containing N. europaea and N. eutropha 16S rDNA sequences, including subclasses therein. It proved possible to analyze 16S rDNA amplified directly from sediment samples to determine the relative abundance of each species compared with that of the other. N. europaea and N. eutropha are very closely related, and direct evidence for their presence in lake systems is limited. The correlation of each species with a distinct spatial location in sediment is an unusual example of niche adaptation by two genotypically similar bacteria. Their occurrence and relative distribution can now be routinely monitored in relation to environmental variation by the application of PCR-RFLP analysis.

scholarly journals Layered Structure of Bacterial and Archaeal Communities and Their In Situ Activities in Anaerobic Granules

2007 ◽  
Vol 73 (22) ◽  
pp. 7300-7307 ◽  
Author(s):  
Hisashi Satoh ◽  
Yuki Miura ◽  
Ikuo Tsushima ◽  
Satoshi Okabe
Keyword(s):  
Spatial Distribution ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Layered Structure ◽  
Effective Diffusion ◽  
Middle Layer ◽  
Molecular Techniques ◽  
Rrna Gene

ABSTRACT The microbial community structure and spatial distribution of microorganisms and their in situ activities in anaerobic granules were investigated by 16S rRNA gene-based molecular techniques and microsensors for CH4, H2, pH, and the oxidation-reduction potential (ORP). The 16S rRNA gene-cloning analysis revealed that the clones related to the phyla Alphaproteobacteria (detection frequency, 51%), Firmicutes (20%), Chloroflexi (9%), and Betaproteobacteria (8%) dominated the bacterial clone library, and the predominant clones in the archaeal clone library were affiliated with Methanosaeta (73%). In situ hybridization with oligonucleotide probes at the phylum level revealed that these microorganisms were numerically abundant in the granule. A layered structure of microorganisms was found in the granule, where Chloroflexi and Betaproteobacteria were present in the outer shell of the granule, Firmicutes were found in the middle layer, and aceticlastic Archaea were restricted to the inner layer. Microsensor measurements for CH4, H2, pH, and ORP revealed that acid and H2 production occurred in the upper part of the granule, below which H2 consumption and CH4 production were detected. Direct comparison of the in situ activity distribution with the spatial distribution of the microorganisms implied that Chloroflexi contributed to the degradation of complex organic compounds in the outermost layer, H2 was produced mainly by Firmicutes in the middle layer, and Methanosaeta produced CH4 in the inner layer. We determined the effective diffusion coefficient for H2 in the anaerobic granules to be 2.66 × 10−5 cm2 s−1, which was 57% in water.

scholarly journals Distribution of Biosurfactant-Producing Bacteria in Undisturbed and Contaminated Arid Southwestern Soils

2003 ◽  
Vol 69 (6) ◽  
pp. 3280-3287 ◽  
Author(s):  
Adria A. Bodour ◽  
Kevin P. Drees ◽  
Raina M. Maier
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Relationships ◽  
Biosurfactant Production ◽  
Contaminated Sites ◽  
Soil Conditions ◽  
Rrna Gene ◽  
Surfactant Mixtures ◽  
Mineral Salts ◽  
The 16S Rrna Gene

ABSTRACT Biosurfactants are a unique class of compounds that have been shown to have a variety of potential applications in the remediation of organic- and metal-contaminated sites, in the enhanced transport of bacteria, in enhanced oil recovery, as cosmetic additives, and in biological control. However, little is known about the distribution of biosurfactant-producing bacteria in the environment. The goal of this study was to determine how common culturable surfactant-producing bacteria are in undisturbed and contaminated sites. A series of 20 contaminated (i.e., with metals and/or hydrocarbons) and undisturbed soils were collected and plated on R2A agar. The 1,305 colonies obtained were screened for biosurfactant production in mineral salts medium containing 2% glucose. Forty-five of the isolates were positive for biosurfactant production, representing most of the soils tested. The 45 isolates were grouped by using repetitive extragenic palindromic (REP)-PCR analysis, which yielded 16 unique isolates. Phylogenetic relationships were determined by comparing the 16S rRNA gene sequence of each unique isolate with known sequences, revealing one new biosurfactant-producing microbe, a Flavobacterium sp. Sequencing results indicated only 10 unique isolates (in comparison to the REP analysis, which indicated 16 unique isolates). Surface tension results demonstrated that isolates that were similar according to sequence analysis but unique according to REP analysis in fact produced different surfactant mixtures under identical growth conditions. These results suggest that the 16S rRNA gene database commonly used for determining phylogenetic relationships may miss diversity in microbial products (e.g., biosurfactants and antibiotics) that are made by closely related isolates. In summary, biosurfactant-producing microorganisms were found in most soils even by using a relatively limited screening assay. Distribution was dependent on soil conditions, with gram-positive biosurfactant-producing isolates tending to be from heavy metal-contaminated or uncontaminated soils and gram-negative isolates tending to be from hydrocarbon-contaminated or cocontaminated soils.

scholarly journals Quantitative PCR Confirms Purity of Strain GT, a Novel Trichloroethene-to-Ethene-Respiring Dehalococcoides Isolate

2006 ◽  
Vol 72 (3) ◽  
pp. 1980-1987 ◽  
Author(s):  
Youlboong Sung ◽  
Kirsti M. Ritalahti ◽  
Robert P. Apkarian ◽  
Frank E. Löffler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Gene Sequence ◽  
Threshold Concentration ◽  
Rrna Gene ◽  
Contaminated Aquifer ◽  
Reductive Dehalogenase ◽  
Copy Numbers ◽  
Inorganic Chloride

ABSTRACT A novel Dehalococcoides isolate capable of metabolic trichloroethene (TCE)-to-ethene reductive dechlorination was obtained from contaminated aquifer material. Growth studies and 16S rRNA gene-targeted analyses suggested culture purity; however, the careful quantitative analysis of Dehalococcoides 16S rRNA gene and chloroethene reductive dehalogenase gene (i.e., vcrA, tceA, and bvcA) copy numbers revealed that the culture consisted of multiple, distinct Dehalococcoides organisms. Subsequent transfers, along with quantitative PCR monitoring, yielded isolate GT, possessing only vcrA. These findings suggest that commonly used qualitative 16S rRNA gene-based procedures are insufficient to verify purity of Dehalococcoides cultures. Phylogenetic analysis revealed that strain GT is affiliated with the Pinellas group of the Dehalococcoides cluster and shares 100% 16S rRNA gene sequence identity with two other Dehalococcoides isolates, strain FL2 and strain CBDB1. The new isolate is distinct, as it respires the priority pollutants TCE, cis-1,2-dichloroethene (cis-DCE), 1,1-dichloroethene (1,1-DCE), and vinyl chloride (VC), thereby producing innocuous ethene and inorganic chloride. Strain GT dechlorinated TCE, cis-DCE, 1,1-DCE, and VC to ethene at rates up to 40, 41, 62, and 127 μmol liter−1 day−1, respectively, but failed to dechlorinate PCE. Hydrogen was the required electron donor, which was depleted to a consumption threshold concentration of 0.76 ± 0.13 nM with VC as the electron acceptor. In contrast to the known TCE dechlorinating isolates, strain GT dechlorinated TCE to ethene with very little formation of chlorinated intermediates, suggesting that this type of organism avoids the commonly observed accumulation of cis-DCE and VC during TCE-to-ethene dechlorination.

scholarly journals Distribution of Microbial Community Structure in Sediment from the Suyeong River and Bay of Busan, Republic of Korea, Determined by 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Ilwon Jeong ◽  
Junho Lee ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Sediment Samples

Here, we report a 16S rRNA gene amplicon sequence analysis presenting the microbial community in sediments from the Suyeong River and Suyeong Bay, Republic of Korea. The dominant phyla in all sediment samples were Proteobacteria (39.69 to 53.62%) and Bacteroidetes (29.78 to 33.89%).

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 Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column

2008 ◽  
Vol 74 (18) ◽  
pp. 5695-5703 ◽  
Author(s):  
Sebastian Behrens ◽  
Mohammad F. Azizian ◽  
Paul J. McMurdie ◽  
Andrew Sabalowsky ◽  
Mark E. Dolan ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Reductive Dehalogenation ◽  
Gene Copy ◽  
Rrna Gene ◽  
Reductive Dehalogenase ◽  
Gene Copies ◽  
Donor And Acceptor ◽  
Rdase Genes

ABSTRACT We investigated the distribution and activity of chloroethene-degrading microorganisms and associated functional genes during reductive dehalogenation of tetrachloroethene to ethene in a laboratory continuous-flow column. Using real-time PCR, we quantified “Dehalococcoides” species 16S rRNA and chloroethene-reductive dehalogenase (RDase) genes (pceA, tceA, vcrA, and bvcA) in nucleic acid extracts from different sections of the column. Dehalococcoides 16S rRNA gene copies were highest at the inflow port [(3.6 ± 0.6) × 106 (mean ± standard deviation) per gram soil] where the electron donor and acceptor were introduced into the column. The highest transcript numbers for tceA, vcrA, and bvcA were detected 5 to 10 cm from the column inflow. bvcA was the most highly expressed of all RDase genes and the only vinyl chloride reductase-encoding transcript detectable close to the column outflow. Interestingly, no expression of pceA was detected in the column, despite the presence of the genes in the microbial community throughout the column. By comparing the 16S rRNA gene copy numbers to the sum of all four RDase genes, we found that 50% of the Dehalococcoides population in the first part of the column did not contain either one of the known chloroethene RDase genes. Analysis of 16S rRNA gene clone libraries from both ends of the flow column revealed a microbial community dominated by members of Firmicutes and Actinobacteria. Higher clone sequence diversity was observed near the column outflow. The results presented have implications for our understanding of the ecophysiology of reductively dehalogenating Dehalococcoides spp. and their role in bioremediation of chloroethenes.

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