scholarly journals Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

2017 ◽  
Author(s):  
Taylor K Dunivin ◽  
Justine Miller ◽  
Ashley Shade
Keyword(s):  
Coal Seam ◽  
Arsenic Exposure ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Resistant Bacteria ◽  
Rare Biosphere ◽  
Genes Encoding ◽  
Arsenic Resistant Bacteria

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic arsenic resistant bacteria spanning six genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRG). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRG provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate’s performance given arsenic exposure in situ. Our results suggest that considering taxonomically-linked tolerance and potential for resistance transferability from the rare biosphere will inform strategies for microbiological management and remediation of environmental As and contribute to a larger consideration of As-exposed microbial ecology.

scholarly journals Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

2017 ◽  
Author(s):  
Taylor K Dunivin ◽  
Justine Miller ◽  
Ashley Shade
Keyword(s):  
Coal Seam ◽  
Arsenic Exposure ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Resistant Bacteria ◽  
Rare Biosphere ◽  
Genes Encoding ◽  
Arsenic Resistant Bacteria

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic arsenic resistant bacteria spanning six genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRG). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRG provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate’s performance given arsenic exposure in situ. Our results suggest that considering taxonomically-linked tolerance and potential for resistance transferability from the rare biosphere will inform strategies for microbiological management and remediation of environmental As and contribute to a larger consideration of As-exposed microbial ecology.

scholarly journals Revealing microbial species diversity using sequence capture by hybridization

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Sophie Marre ◽  
Cyrielle Gasc ◽  
Camille Forest ◽  
Yacine Lebbaoui ◽  
Pascale Mosoni ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Human Gut ◽  
Content Type ◽  
Innovative Strategy ◽  
Human Gut Microbiota ◽  
Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination

2018 ◽  
Vol 64 (5) ◽  
pp. 305-316 ◽  
Author(s):  
Fengqiu An ◽  
Zhan Diao ◽  
Jialong Lv
Keyword(s):  
Heavy Metal ◽  
Physicochemical Properties ◽  
Agricultural Soils ◽  
Microbial Community Composition ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Resistant Bacteria ◽  
Available Phosphorus ◽  
Highly Correlated

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

scholarly journals Characterization of Blood Culture Isolates ofStreptococcus dysgalactiae subsp. equisimilisPossessing Lancefield's Group A Antigen

1999 ◽  
Vol 37 (12) ◽  
pp. 4194-4197 ◽  
Author(s):  
Claudia M. Brandt ◽  
Gerhard Haase ◽  
Norbert Schnitzler ◽  
Reinhard Zbinden ◽  
Rudolf Lütticken
Keyword(s):  
Blood Culture ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Virulence Determinants ◽  
Streptococcus Dysgalactiae ◽  
Genes Encoding ◽  
Group A ◽  
Biochemical Identification ◽  
Species Assignment

For three human blood culture isolates of beta-hemolytic streptococci with Lancefield's serogroup A antigen, phylogenetic analysis of the 16S rRNA genes confirmed biochemical identification asStreptococcus dysgalactiae subsp. equisimilis. Genes encoding M or M-like proteins, which are considered to be major virulence determinants in streptococci, were detected in all of these strains. Our data clearly demonstrate that for beta-hemolytic streptococci, the species assignment should not be based on the results of serogrouping alone.

scholarly journals Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

2006 ◽  
Vol 72 (9) ◽  
pp. 5957-5962 ◽  
Author(s):  
Ellen Kandeler ◽  
Kathrin Deiglmayr ◽  
Dagmar Tscherko ◽  
David Bru ◽  
Laurent Philippot
Keyword(s):  
16S Rrna ◽  
Primary Succession ◽  
Early Stage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Glacier Foreland ◽  
Copy Numbers ◽  
Genes Encoding ◽  
Target Molecules ◽  
Denitrification Genes

ABSTRACT Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 � 105 to 8.9 � 105 copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 � 103 to 2.6 � 104, 7.4 � 102 to 1.4 � 103, 2.5 � 102 to 6.4 � 103, and 1.2 � 103 to 5.5 � 103, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.

Anaerocolumna chitinilytica sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Atsuko Ueki ◽  
Akio Tonouchi ◽  
Nobuo Kaku ◽  
Katsuji Ueki
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Fermentation Products ◽  
Content Type ◽  
Soil Disinfestation ◽  
Link Type ◽  
The Family ◽  
Genes Encoding

An obligately anaerobic bacterial strain (CTTWT) belonging to the family Lachnospiraceae within the class Clostridia was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan. Strain CTTWT decomposed cell biomass and cell-wall preparations of an ascomycete plant pathogen, Fusarium oxysporum f. sp. spinaciae. The strain produced acetate, ethanol, H2 and CO2 as fermentation products from the utilized substrates. The major cellular fatty acids of the strain were C16 : 1 ω7c dimethylacetal (DMA), C16 : 0 DMA and C18 : 1 ω7c DMA. The closely related species of strain CTTWT based on the 16S rRNA gene sequences were species in the genus Anaerocolumna with sequence similarities of 95.2–97.6 %. Results of genome analyses of strain CTTWT indicated that the genome size of the strain was 5.62 Mb and the genomic DNA G+C content was 38.3 mol%. Six 16S rRNA genes with five different sequences from each other were found in the genome. Strain CTTWT had genes encoding chitinase, xylanase, cellulase, β-glucosidase and nitrogenase as characteristic genes in the genome. Homologous genes encoding these proteins were found in the genomes of the related Anaerocolumna species, but the genomic and phenotypic properties of strain CTTWT were distinct from them. Based on the phylogenetic, genomic and phenotypic analyses, the name Anaerocolumna chitinilytica sp. nov., in the family Lachnospiraceae is proposed for strain CTTWT (=NBRC 112102T=DSM 110036T).

scholarly journals Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance

2011 ◽  
Vol 78 (5) ◽  
pp. 1361-1369 ◽  
Author(s):  
Johanna Sjöstedt ◽  
Per Koch-Schmidt ◽  
Mikael Pontarp ◽  
Björn Canbäck ◽  
Anders Tunlid ◽  
...  
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Ecosystem Processes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Physiological Tolerance ◽  
Rare Biosphere ◽  
The Baltic ◽  
The Impact ◽  
Bacterioplankton Communities

ABSTRACTA bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml−1) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

scholarly journals Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Emily A. Kraus ◽  
Daniel Nothaft ◽  
Blake W. Stamps ◽  
Kaitlin R. Rempfert ◽  
Eric T. Ellison ◽  
...  
Keyword(s):  
Low Temperature ◽  
16S Rrna ◽  
Microbial Activity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Metagenomic Sequencing ◽  
Production Of Hydrogen ◽  
Genes Encoding ◽  
Subsurface Waters

ABSTRACT Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization. IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4. Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth’s history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4. These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.

scholarly journals Antibiotic Susceptibility and Sequence Type Distribution of Ureaplasma Species Isolated from Genital Samples in Switzerland

2015 ◽  
Vol 59 (10) ◽  
pp. 6026-6031 ◽  
Author(s):  
Sarah C. Schneider ◽  
Regula Tinguely ◽  
Sara Droz ◽  
Markus Hilty ◽  
Valentina Donà ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Ureaplasma Urealyticum ◽  
Mycoplasma Hominis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Content Type ◽  
Ureaplasma Parvum ◽  
Genes Encoding ◽  
Antimicrobial Susceptibility Tests

ABSTRACTAntibiotic resistance inUreaplasma urealyticum/Ureaplasma parvumandMycoplasma hominisis an issue of increasing importance. However, data regarding the susceptibility and, more importantly, the clonality of these organisms are limited. We analyzed 140 genital samples obtained in Bern, Switzerland, in 2014. Identification and antimicrobial susceptibility tests were performed by using the Mycoplasma IST 2 kit and sequencing of 16S rRNA genes. MICs for ciprofloxacin and azithromycin were obtained in broth microdilution assays. Clonality was analyzed with PCR-based subtyping and multilocus sequence typing (MLST), whereas quinolone resistance and macrolide resistance were studied by sequencinggyrA, gyrB,parC, andparEgenes, as well as 23S rRNA genes and genes encoding L4/L22 ribosomal proteins. A total of 103 samples were confirmed as positive forU. urealyticum/U. parvum, whereas 21 were positive for bothU. urealyticum/U. parvumandM. hominis. According to the IST 2 kit, the rates of nonsusceptibility were highest for ciprofloxacin (19.4%) and ofloxacin (9.7%), whereas low rates were observed for clarithromycin (4.9%), erythromycin (1.9%), and azithromycin (1%). However, inconsistent results between microdilution and IST 2 kit assays were recorded. Various sequence types (STs) observed previously in China (ST1, ST2, ST4, ST9, ST22, and ST47), as well as eight novel lineages, were detected. Only some quinolone-resistant isolates had amino acid substitutions in ParC (Ser83Leu inU. parvumof serovar 6) and ParE (Val417Thr inU. parvumof serovar 1 and the novel Thr417Val substitution inU. urealyticum). Isolates with mutations in 23S rRNA or substitutions in L4/L22 were not detected. This is the first study analyzing the susceptibility ofU. urealyticum/U. parvumisolates in Switzerland and the clonality outside China. Resistance rates were low compared to those in other countries. We hypothesize that some hyperepidemic STs spread worldwide via sexual intercourse. Large combined microbiological and clinical studies should address this important issue.

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