Investigation of catechol 2,3-dioxygenase and 16S rRNA gene diversity in hypoxic, petroleum hydrocarbon contaminated groundwater

2010 ◽  
Vol 33 (7) ◽  
pp. 398-406 ◽  
Author(s):  
András Táncsics ◽  
István Szabó ◽  
Erzsébet Baka ◽  
Sándor Szoboszlay ◽  
József Kukolya ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Petroleum Hydrocarbon ◽  
Gene Diversity ◽  
Contaminated Groundwater ◽  
Rrna Gene

scholarly journals Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2080-2091 ◽  
Author(s):  
Anne-Laure Michon ◽  
Fabien Aujoulat ◽  
Laurent Roudière ◽  
Olivier Soulier ◽  
Isabelle Zorgniotti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
Natural Populations ◽  
Variable Region ◽  
Housekeeping Gene ◽  
Single Copy ◽  
Population Based ◽  
Rrna Gene ◽  
Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

High bacterial 16S rRNA gene diversity above the atmospheric boundary layer

Aerobiologia ◽  
2012 ◽  
Vol 28 (4) ◽  
pp. 481-498 ◽  
Author(s):  
Ulla Li Zweifel ◽  
Åke Hagström ◽  
Karin Holmfeldt ◽  
Runar Thyrhaug ◽  
Camilla Geels ◽  
...  
Keyword(s):  
Boundary Layer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Atmospheric Boundary Layer ◽  
Gene Diversity ◽  
Rrna Gene ◽  
Bacterial 16S Rrna Gene

scholarly journals Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater

2010 ◽  
Vol 60 (2) ◽  
pp. 358-363 ◽  
Author(s):  
Kimberly S. Bowman ◽  
Rachael E. Dupré ◽  
Fred A. Rainey ◽  
William M. Moe
Keyword(s):  
Carbon Dioxide ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Groundwater ◽  
Rrna Gene ◽  
Positive Staining ◽  
16S Rrna Gene Sequences ◽  
Cellular Fatty Acids ◽  
Chlorinated Solvent ◽  
Acetate Butyrate

Four hydrogen-producing, aerotolerant, anaerobic bacterial strains isolated from chlorinated solvent-contaminated groundwater were characterized using a polyphasic approach. Three of the strains, designated BL-18, BL-19 and BL-20T, were found to be identical in 16S rRNA gene sequences and in phenotypic properties. Cells of these strains are Gram-positive-staining, spore-forming, motile rods with peritrichous flagella. Growth occurred at 15–40 °C, pH 5.0–10.0 and at NaCl concentrations up to 5 % (w/v). Acid was produced in fermentation of cellobiose, fructose, galactose (weak), glucose, maltose and salicin. Products of fermentation in PYG medium were acetate, butyrate, ethanol, formate, carbon dioxide and hydrogen. Dominant cellular fatty acids when grown in PYG medium were C13 : 0 iso, C16 : 0, C13 : 0 anteiso, C15 : 0 iso and C15 : 0 anteiso. The genomic DNA G+C content was 30.4 mol%. These isolates can be differentiated from their closest phylogenetic relative, the cluster I Clostridium species Clostridium frigidicarnis (97.2 % similar to the type strain in 16S rRNA gene sequence), on the basis of phenotypic and chemotaxonomic properties. The other strain characterized in this study, BL-28T, was Gram-positive-staining with spore-forming, rod-shaped cells. Growth occurred at 15–46 °C, pH 6.0–8.5 and at NaCl concentrations up to 3 % (w/v). Acid was produced from cellobiose, dextran, fructose (weak), glucose, maltose, salicin and trehalose. End products of PYG fermentation included acetate, butyrate, pyruvate, carbon dioxide and hydrogen. Dominant cellular fatty acids from cells grown in PYG medium at 30 °C were C14 : 0, C14 : 0 dimethyl aldehyde, C16 : 0 and C12 : 0. The DNA G+C content was 28.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BL-28T falls within cluster I of the genus Clostridium, but with ≤95.2 % identity with previously described species. On the basis of results presented here, strains BL-20T (=NRRL B-51348T =DSM 21757T) and BL-28T (=NRRL B-51352T =DSM 21758T) are proposed as the type strains of novel species of the genus Clostridium with the names Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., respectively.

scholarly journals Morphological Identification of Ticks and Molecular Detection of Tick-Borne Pathogens from Bare-Nosed Wombats (Vombatus Ursinus)

2020 ◽  
Author(s):  
Danielle Beard ◽  
Hayley J Stannard ◽  
Julie M Old
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Adult Male ◽  
Tick Species ◽  
Gene Diversity ◽  
Host Record ◽  
Sarcoptic Mange ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Microbial Composition

Abstract Background Ticks are obligate hematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they impact wombats affected by sarcoptic mange.Methods Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA (gDNA) was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3-V4 hypervariable region, next generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition.Results A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising Bothriocroton auruginans (n = 420), Haemaphysalis bancrofti (n = 10), H. longicornis (n = 1), Ixodes tasmani (n = 12), and I. holocyclus (n = 4). Tick infestations ranged from 1 to 73 ticks per wombat. B. auruginans was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to C. burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani.Conclusions A new host record for H. longicornis is bare-nosed wombats. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in NSW and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats is B. auruginans confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks.

scholarly journals Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 274-279 ◽  
Author(s):  
Milán Farkas ◽  
András Táncsics ◽  
Balázs Kriszt ◽  
Tibor Benedek ◽  
Erika M. Tóth ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Petroleum Hydrocarbon ◽  
Sequence Similarity ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated BucT, was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BucT formed a distinct phyletic lineage within the genus Zoogloea . Its closest relative was found to be Zoogloea caeni EMB43T (97.2 % 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7T (95.9 %), Zoogloea ramigera ATCC 19544T (95.5 %) and Zoogloea resiniphila DhA-35T (95.4 %). The level of DNA–DNA relatedness between strain BucT and Z. caeni EMB43T was 31.6 %. Cells of strain BucT are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5–35 °C (optimum 25–28 °C), and at pH 6.0–9.0 (optimum 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH, C12 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate BucT is considered to represent a novel species of the genus Zoogloea , for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is BucT ( = DSM 28387T = NCAIM B 02570T).

scholarly journals Plastid 16S rRNA Gene Diversity among Eukaryotic Picophytoplankton Sorted by Flow Cytometry from the South Pacific Ocean

PLoS ONE ◽  
2011 ◽  
Vol 6 (4) ◽  
pp. e18979 ◽  
Author(s):  
Xiao Li Shi ◽  
Cécile Lepère ◽  
David J. Scanlan ◽  
Daniel Vaulot
Keyword(s):  
Flow Cytometry ◽  
Pacific Ocean ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
South Pacific ◽  
Rrna Gene ◽  
The South ◽  
South Pacific Ocean

scholarly journals Morphological identification of ticks and molecular detection of tick-borne pathogens from bare-nosed wombats (Vombatus ursinus)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Danielle Beard ◽  
Hayley J. Stannard ◽  
Julie M. Old
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Adult Male ◽  
Tick Species ◽  
Gene Diversity ◽  
Host Record ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Haemaphysalis Longicornis ◽  
Microbial Composition

Abstract Background Ticks are obligate haematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they may impact wombats and wombat handlers. Methods Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3–V4 hypervariable region, next-generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition. Results A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising wombat tick Bothriocroton auruginans (n = 420), wallaby tick Haemaphysalis bancrofti (n = 8), bush tick Haemaphysalis longicornis (n = 3), common marsupial tick Ixodes tasmani (n = 12), and Australian paralysis tick Ixodes holocyclus (n = 4). Tick infestations ranged from one to 73 ticks per wombat. The wombat tick was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to Coxiella burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani. Conclusions A new host record for H. longicornis is the bare-nosed wombat. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in New South Wales, and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats was B. auruginans, confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks.

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