scholarly journals Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Richard Kevorkian ◽  
Jordan T. Bird ◽  
Alexander Shumaker ◽  
Karen G. Lloyd
Keyword(s):  
Population Dynamics ◽  
Microbial Community ◽  
16S Rrna ◽  
Sulfate Reduction ◽  
Relative Quantification ◽  
Turnover Rates ◽  
Content Type ◽  
Sulfate Reducing ◽  
Population Turnover ◽  
Read Abundance

ABSTRACT The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for “fraction of read abundance times cells”), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community. IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for “fraction of read abundance times cells,” which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

scholarly journals Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2907-2914 ◽  
Author(s):  
Thuy T. An ◽  
Flynn W. Picardal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Optimal Growth ◽  
Coal Bed ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBMT, was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBMT were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBMT was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16–37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBMT, but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBMT grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBMT into a distinct lineage within the class Deltaproteobacteria . The closest, cultivated phylogenetic relative of strain SCBMT was Desulfarculus baarsii DSM 2075T, with only 91.7 % 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBMT represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBMT ( = DSM 28127T = JCM 19826T). Desulfocarbo is the second genus of the order Desulfarculales .

scholarly journals Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

2013 ◽  
Vol 80 (2) ◽  
pp. 757-765 ◽  
Author(s):  
Amber M. Koskey ◽  
Jenny C. Fisher ◽  
Mary F. Traudt ◽  
Ryan J. Newton ◽  
Sandra L. McLellan
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Fecal Indicator ◽  
Fecal Samples ◽  
Content Type

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcusindoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified asEnterococcusspp., 1.2% were identified asStreptococcusspp., and none were identified asC. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions ofC. marimammalium16S rRNA gene sequences (>50-fold) relative to typical mEI culturableEnterococcusspp.C. marimammaliumtherefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.

scholarly journals CHARACTERIZATION OF SULFATE REDUCING BACTERIA FROM BIOFILM SULFATE REDUCTION AND CU PRECIPITATION BIOREACTOR (BATCH CULTURE).

2018 ◽  
Vol 2 (2) ◽  
pp. 1
Author(s):  
Tyas Nyonita Punjungsari
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sulfate Reduction ◽  
Batch Culture ◽  
Microbial Community Structure ◽  
Sulfate Reducing Bacteria ◽  
Zeolite Surface ◽  
Sulfate Reducing ◽  
Reducing Bacteria

The biofilm is a microbial community structure formed on the zeolite surface in a sulfate reduction bioreactor and Cu deposition using a SRB consortium . The biofilm soluble microbial solvent is expected to have the capability in sulfate reduction and Cu deposition. Characterization of isolates is required for the optimization of pure culture . The aim of this study is to isolate and characterize the biofilm sulfate reducing bacteria in the sulfate reduction bioreactor and the precipitation of Cu in Batch Culture by a consortium of Sulfate Reducing Bacteria. The method used in this study cultivation was done by using postgate B medium, isolation was done by diluting biofilm on NaCl salt, bacteria grown on NB and postgate B media, characterization done by morphology and biochemistry. There were 3 isolates of B1 (Metylobacterium ), B3 ( Desulfucoccus ), and B2 ( Desulfobacter ). B3 ( Desulfococcus) has the best ability to reduce sulfate and Cu precipitation.Keywords : Sulfur Reducing Bacteria (SRB), Biofilm, Sulfate, Cu. Received: 26 August, 2017; Accepter: 10 September, 2017 

Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 761-765 ◽  
Author(s):  
Yuriko Higashioka ◽  
Hisaya Kojima ◽  
Miho Watanabe ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sulfate Reducing ◽  
Tidal Flat Sediment

A novel sulfate-reducing bacterium, strain S28bFT, was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bFT were rod-shaped (0.5–0.6×1.7–3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8–7.3 and the optimum temperature was 34–42 °C. Strain S28bFT used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bFT was characterized by the presence of anteiso-C15 : 0 and C16 : 0 as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class Deltaproteobacteria . Its closest relative was Desulfosarcina cetonica DSM 7267T with a 16S rRNA gene sequence similarity of 93.3 %. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bFT with 16S rRNA gene sequence similarities of 99 %, and the same physiological characteristics were shared with strain S28bFT. On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bFT ( = NBRC 107166T = DSM 23472T).

scholarly journals Diversity decoupled from sulfur isotope fractionation in a sulfate reducing microbial community

2019 ◽  
Author(s):  
Jesse Colangelo ◽  
Claus Pelikan ◽  
Craig W. Herbold ◽  
Ianina Altshuler ◽  
Alexander Loy ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Ecology ◽  
Sulfate Reduction ◽  
Isotope Fractionation ◽  
Sulfur Isotopes ◽  
List Type ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Sulfate Reduction Rates

AbstractThe extent of fractionation of sulfur isotopes by sulfate reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates <0.3 x 10−15 moles cell−1 day−1. Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38 to 45‰) net isotope fractionation (ε34Ssulfide−sulfate). Measured ε34S values could be reproduced in a mechanistic fractionation model if 1-2% of the microbial community (10-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-metabolizing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold alpha diversity value, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.Subject categoriesIntegrated genomics and post-genomics approaches in microbial ecologyMicrobial ecology and functional diversity of natural habitats

scholarly journals Linking Microbial Community Function to Phylogeny of Sulfate-Reducing Deltaproteobacteria in Marine Sediments by Combining Stable Isotope Probing with Magnetic-Bead Capture Hybridization of 16S rRNA

2009 ◽  
Vol 75 (15) ◽  
pp. 4927-4935 ◽  
Author(s):  
Tetsuro Miyatake ◽  
Barbara J. MacGregor ◽  
Henricus T. S. Boschker
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
16S Rrna ◽  
Marine Sediments ◽  
Magnetic Bead ◽  
Stable Isotope Probing ◽  
Target Range ◽  
Microbial Community Function ◽  
Sulfate Reducing ◽  
Community Function

ABSTRACT We further developed the stable isotope probing, magnetic-bead capture method to make it applicable for linking microbial community function to phylogeny at the class and family levels. The main improvements were a substantial decrease in the protocol blank and an approximately 10-fold increase in the detection limit by using a micro-elemental analyzer coupled to isotope ratio mass spectrometry to determine 13C labeling of isolated 16S rRNA. We demonstrated the method by studying substrate utilization by Desulfobacteraceae, a dominant group of complete oxidizing sulfate-reducing Deltaproteobacteria in marine sediments. Stable-isotope-labeled [13C]glucose, [13C]propionate, or [13C]acetate was fed into an anoxic intertidal sediment. We applied a nested set of three biotin-labeled oligonucleotide probes to capture Bacteria, Deltaproteobacteria, and finally Desulfobacteraceae rRNA by using hydrophobic streptavidin-coated paramagnetic beads. The target specificities of the probes were examined with pure cultures of target and nontarget species and by determining the phylogenetic composition of the captured sediment rRNA. The specificity of the final protocol was generally very good, as more than 90% of the captured 16S rRNA belonged to the target range of the probes. Our results indicated that Desulfobacteraceae were important consumers of propionate but not of glucose. However, the results for acetate utilization were less conclusive due to lower and more variable labeling levels in captured rRNA. The main advantage of the method in this study over other nucleic acid-based stable isotope probing methods is that 13C labeling can be much lower, to the extent that δ13C ratios can be studied even at their natural abundances.

Genomic variation of microbial populations on a continuous 10,000-year sediment sequence from Lake Cadagno (Piora Valley, Switzerland)

2021 ◽  
Author(s):  
Paula Catalina Rodriguez Ramirez ◽  
Jasmine Berg ◽  
Longhui Deng ◽  
Hendrik Vogel ◽  
Mark A. Lever ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reduction ◽  
Microbial Populations ◽  
Gene Copy ◽  
Sulfur Cycling ◽  
Rrna Gene ◽  
Sediment Layer ◽  
Metagenomic Sequencing ◽  
Sulfate Reducing

&lt;p&gt;Lake Cadagno is a meromictic Alpine lake located in the Piora Valley, Switzerland. In 2019, a 10,000-year (10 m)sediment sequence was collected and found to contain three main lithological units: glacial sediment deposited under oxic conditions; a Mn-rich and organic-matter-rich sediment layer deposited during the transition from an oxic late-glacial lake to the onset of anoxia, and dark, sulfidic sediments deposited during the period of euxinia to the present. This study investigates the relationships between the physical-chemical properties and microorganisms of the sediment sequenceusing genome-resolved and targeted metagenomics.&amp;#160; &amp;#160;&lt;/p&gt;&lt;p&gt;Results show that 16S rRNA gene abundance peaks in upper 1-32 cm of the sediment core (10&lt;sup&gt;8&lt;/sup&gt; copies per gram of sediment) and decreases with depth. The abundance of a marker gene for sulfate reduction, dsrB, is positively correlated to 16S rRNA gene copy numbers, decreasing with depth from approximately 10&lt;sup&gt;8&lt;/sup&gt; copies per gram of sediment in the top 30 cm to 10&lt;sup&gt;4&lt;/sup&gt; gene copies per gram of sediment at 900 cm below the sediment depth.&amp;#160; These results suggest that sulfate-reducing microbial communities in surface sediments harvest the bioavailable oxidized sulfur inorganic species. In contrast, the presence of sulfate-reducing genes in sediments with sulfate concentrations below detection may indicate the engagement of microbial populations in sulfur cycling using alternative metabolic strategies (e.g. secondary fermentation).&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Moreover, a clear differentiation between surface and deep sediment communities is observed. Sequencing of dsrB amplicons show a decrease in dsrB sequence richness with depth and sediment age. A clear transition from a surface section dominated (&gt;80% relative abundance) by Deltaproteobacteria-related dsrB sequences from well-studied groups, to a deeper section below 40 cm dominated by a group of unclassified dsrB sequences most likely related to Firmicutes or Chloroflexi is also observed. The identity of these unclassified dsrB sequences will be determined by genome-resolved metagenomic sequencing (currently in progress). Furthermore, these analyses will give information on the presence of complete sulfate-reduction pathways and/or genes related to sulfur cycling in these microbial groups. By reconstructing the genomes of sulfate reducers and other microbial populations throughout the core, we will investigate whether there are genomic changes associated with the main geochemical trends. This work will enable us to assess the influence of a changing lake with the evolution of sediment-dwelling prokaryotic populations over thousands of years.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

Desulfotomaculum defluvii sp. nov., a sulfate-reducing bacterium isolated from the subsurface environment of a landfill

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2290-2295 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
Stefan Spring ◽  
Pinnaka Anil Kumar ◽  
Shanmugam Mayilraj ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus Desulfotomaculum . Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus Desulfotomaculum . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to Desulfotomaculum aeronauticum DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus Desulfotomaculum , for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).

scholarly journals Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline

2011 ◽  
Vol 77 (19) ◽  
pp. 6908-6917 ◽  
Author(s):  
Hyung Soo Park ◽  
Indranil Chatterjee ◽  
Xiaoli Dong ◽  
Sheng-Hung Wang ◽  
Christoph W. Sensen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Sodium Bisulfite ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Iron Corrosion ◽  
Injection Point ◽  
Content Type ◽  
Sulfate Reducing

ABSTRACTPipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) ofPseudomonasnot found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereasDeltaproteobacteriaof the generaDesulfomicrobiumandDesulfocapsawere not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) ofMethanobacteriaceaearchaea but increased fractions of sulfate-reducingDesulfomicrobium(18% and 48%) and of bisulfite-disproportionatingDesulfocapsa(35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters.

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