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Gilmour CC, Soren AB, Gionfriddo CM, Podar M, Wall JD, Brown SD, Michener JK, Urriza MSG, Elias DA. Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 33570484 DOI: 10.1099/ijsem.0.004697] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sulfate-reducing, mercury-methylating strain ND132T was isolated from the brackish anaerobic bottom sediments of Chesapeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132T has been widely used as a model strain to study the process and to determine the genetic basis of Hg methylation. Originally called Desulfovibrio desulfuricans ND132T on the basis of an early partial 16S rRNA sequence, the strain has never been formally described. Phylogenetic and physiological traits place this strain within the genus Pseudodesulfovibrio, in the recently reclassified phylum Desulfobacterota (formerly Deltaproteobacteria). ND132T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1T and Pseudodesulfovibrio indicus J2T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1T and ND132T, and 84 % similarity between ND132T and P. indicus J2T. These cut-off scores <95 %, along with a multi-gene phylogenetic analysis of members of the family Desulfovibrionacea, and differences in physiology indicate that all three strains represent separate species. The Gram-stain-negative cells are vibrio-shaped, motile and not sporulated. ND132T is a salt-tolerant mesophile with optimal growth in the laboratory at 32 °C, 2 % salinity, and pH 7.8. The DNA G+C content of the genomic DNA is 65.2 %. It is an incomplete oxidizer of short chain fatty acids, using lactate, pyruvate and fumarate with sulfate or sulfite as the terminal electron acceptors. ND132T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c and anteiso-C17 : 0. We propose the classification of strain ND132T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.
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Affiliation(s)
| | | | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Steven D Brown
- Present address: LanzaTech, Skokie, Illinois, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Christensen GA, Gionfriddo CM, King AJ, Moberly JG, Miller CL, Somenahally AC, Callister SJ, Brewer H, Podar M, Brown SD, Palumbo AV, Brandt CC, Wymore AM, Brooks SC, Hwang C, Fields MW, Wall JD, Gilmour CC, Elias DA. Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8649-8663. [PMID: 31260289 DOI: 10.1021/acs.est.8b06389] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Methylmercury (MeHg) is a bioaccumulative toxic contaminant in many ecosystems, but factors governing its production are poorly understood. Recent work has shown that the anaerobic microbial conversion of mercury (Hg) to MeHg requires the Hg-methylation genes hgcAB and that these genes can be used as biomarkers in PCR-based estimators of Hg-methylator abundance. In an effort to determine reliable methods for assessing hgcA abundance and diversity and linking them to MeHg concentrations, multiple approaches were compared including metagenomic shotgun sequencing, 16S rRNA gene pyrosequencing and cloning/sequencing hgcAB gene products. Hg-methylator abundance was also determined by quantitative hgcA qPCR amplification and metaproteomics for comparison to the above measurements. Samples from eight sites were examined covering a range of total Hg (HgT; 0.03-14 mg kg-1 dry wt. soil) and MeHg (0.05-27 μg kg-1 dry wt. soil) concentrations. In the metagenome and amplicon sequencing of hgcAB diversity, the Deltaproteobacteria were the dominant Hg-methylators while Firmicutes and methanogenic Archaea were typically ∼50% less abundant. This was consistent with metaproteomics estimates where the Deltaproteobacteria were steadily higher. The 16S rRNA gene pyrosequencing did not have sufficient resolution to identify hgcAB+ species. Metagenomic and hgcAB results were similar for Hg-methylator diversity and clade-specific qPCR-based approaches for hgcA are only appropriate when comparing the abundance of a particular clade across various samples. Weak correlations between Hg-methylating bacteria and soil Hg concentrations were observed for similar environmental samples, but overall total Hg and MeHg concentrations poorly correlated with Hg-cycling genes.
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Affiliation(s)
- Geoff A Christensen
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Caitlin M Gionfriddo
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Andrew J King
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - James G Moberly
- College of Engineering , University of Idaho , Moscow , Idaho 83844 , United States
| | - Carrie L Miller
- School of Theoretical and Applied Science , Ramapo College of New Jersey , Mahwah , New Jersey 07430 , United States
| | - Anil C Somenahally
- Department of Soil and Crop Sciences , Texas A&M University , Overton , Texas 77843-2474 , United States
| | - Stephen J Callister
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Heather Brewer
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Mircea Podar
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Steven D Brown
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Anthony V Palumbo
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Craig C Brandt
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Ann M Wymore
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
| | - Scott C Brooks
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Chiachi Hwang
- Center for Biofilm Engineering , Montana State University , Bozeman , Montana 59717 , United States
| | - Matthew W Fields
- Department of Microbiology and Immunology , Montana State University , Bozeman , Montana 59717 , United States
- Center for Biofilm Engineering , Montana State University , Bozeman , Montana 59717 , United States
| | - Judy D Wall
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Cynthia C Gilmour
- Smithsonian Environmental Research Center , Edgewater , Maryland 21037 , United States
| | - Dwayne A Elias
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831-6342 , United States
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Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. PLoS One 2018; 13:e0194663. [PMID: 29558522 PMCID: PMC5860781 DOI: 10.1371/journal.pone.0194663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/07/2018] [Indexed: 02/01/2023] Open
Abstract
Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.
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Affiliation(s)
- Geoff A. Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - JiWon Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Allison M. Veach
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer J. Mosher
- Marshall University, Biological Sciences, Huntington, West Virginia, United States of America
| | - Ann M. Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Jizhong Zhou
- University of Oklahoma, Norman, Oklahoma, United States of America
| | - Terry C. Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- University of Tennessee, Knoxville, Tennessee, United States of America
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- University of California at Berkeley, Berkeley, California, United States of America
| | - Dwayne A. Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments. Appl Environ Microbiol 2018; 84:AEM.01049-17. [PMID: 29150503 PMCID: PMC5772229 DOI: 10.1128/aem.01049-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/28/2017] [Indexed: 01/08/2023] Open
Abstract
Neurotoxic methylmercury (MeHg) is produced by anaerobic Bacteria and Archaea possessing the genes hgcAB, but it is unknown how organic substrate and electron acceptor availability impacts the distribution and abundance of these organisms. We evaluated the impact of organic substrate amendments on mercury (Hg) methylation rates, microbial community structure, and the distribution of hgcAB+ microbes with sediments. Sediment slurries were amended with short-chain fatty acids, alcohols, or a polysaccharide. Minimal increases in MeHg were observed following lactate, ethanol, and methanol amendments, while a significant decrease (∼70%) was observed with cellobiose incubations. Postincubation, microbial diversity was assessed via 16S rRNA amplicon sequencing. The presence of hgcAB+ organisms was assessed with a broad-range degenerate PCR primer set for both genes, while the presence of microbes in each of the three dominant clades of methylators (Deltaproteobacteria, Firmicutes, and methanogenic Archaea) was measured with clade-specific degenerate hgcA quantitative PCR (qPCR) primer sets. The predominant microorganisms in unamended sediments consisted of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria Clade-specific qPCR identified hgcA+Deltaproteobacteria and Archaea in all sites but failed to detect hgcA+Firmicutes Cellobiose shifted the communities in all samples to ∼90% non-hgcAB-containing Firmicutes (mainly Bacillus spp. and Clostridium spp.). These results suggest that either expression of hgcAB is downregulated or, more likely given the lack of 16S rRNA gene presence after cellobiose incubation, Hg-methylating organisms are largely outcompeted by cellobiose degraders or degradation products of cellobiose. These results represent a step toward understanding and exploring simple methodologies for controlling MeHg production in the environment.IMPORTANCE Methylmercury (MeHg) is a neurotoxin produced by microorganisms that bioacummulates in the food web and poses a serious health risk to humans. Currently, the impact that organic substrate or electron acceptor availability has on the mercury (Hg)-methylating microorganisms is unclear. To study this, we set up microcosm experiments exposed to different organic substrates and electron acceptors and assayed for Hg methylation rates, for microbial community structure, and for distribution of Hg methylators. The sediment and groundwater was collected from East Fork Poplar Creek in Oak Ridge, TN. Amendment with cellobiose (a lignocellulosic degradation by-product) led to a drastic decrease in the Hg methylation rate compared to that in an unamended control, with an associated shift in the microbial community to mostly nonmethylating Firmicutes This, along with previous Hg-methylating microorganism identification methods, will be important for identifying strategies to control MeHg production and inform future remediation strategies.
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Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment. Appl Environ Microbiol 2016; 82:6068-78. [PMID: 27422835 PMCID: PMC5038027 DOI: 10.1128/aem.01271-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/08/2016] [Indexed: 01/07/2023] Open
Abstract
Two genes, hgcA and hgcB, are essential for microbial mercury (Hg) methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability, and biogeochemistry, are critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea genomes. A distinct PCR product at the expected size was confirmed for all hgcAB+ strains tested via Sanger sequencing. Additionally, we developed clade-specific degenerate quantitative PCR (qPCR) primers that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88%, and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes, and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. The resulting data will be essential in developing accurate and robust predictive models of Hg methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB. IMPORTANCE The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microorganisms. The recent discovery of the Hg-methylating gene pair, hgcA and hgcB, has allowed us to design and optimize molecular probes against these genes within the genomic DNA for microorganisms known to methylate Hg. The protocols designed in this study allow for both qualitative and quantitative assessments of pure-culture or environmental samples. With these protocols in hand, we can begin to study the distribution of Hg-methylating organisms in nature via a cultivation-independent strategy.
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Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, Lee J, Chen F, Dangl JL, Tringe SG. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 2015; 6:771. [PMID: 26300854 PMCID: PMC4523815 DOI: 10.3389/fmicb.2015.00771] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/14/2015] [Indexed: 12/24/2022] Open
Abstract
Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data produced with different protocols can be meaningfully compared, is often unknown. Here we compare results obtained using three different amplification primer sets (targeting V4, V6–V8, and V7–V8) and two sequencing technologies (454 pyrosequencing and Illumina MiSeq) using DNA from a mock community containing a known number of species as well as complex environmental samples whose PCR-independent profiles were estimated using shotgun sequencing. We find that paired-end MiSeq reads produce higher quality data and enabled the use of more aggressive quality control parameters over 454, resulting in a higher retention rate of high quality reads for downstream data analysis. While primer choice considerably influences quantitative abundance estimations, sequencing platform has relatively minor effects when matched primers are used. Beta diversity metrics are surprisingly robust to both primer and sequencing platform biases.
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Affiliation(s)
- Julien Tremblay
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA ; National Research Council Canada Montreal, QC, Canada
| | - Kanwar Singh
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Alison Fern
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Edward S Kirton
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Shaomei He
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Janey Lee
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Feng Chen
- Illumina, Inc. San Francisco, CA, USA
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics and Molecular Biology, Department of Microbiology and Immunology, Carolina Center for Genome Sciences, University of North Carolina Chapel Hill, NC, USA
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7
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Eastman AW, Yuan ZC. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing. Front Microbiol 2015; 5:769. [PMID: 25653642 PMCID: PMC4301005 DOI: 10.3389/fmicb.2014.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/16/2014] [Indexed: 01/10/2023] Open
Abstract
Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects.
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Affiliation(s)
- Alexander W Eastman
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Government of Canada London, ON, Canada ; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario London, ON, Canada
| | - Ze-Chun Yuan
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Government of Canada London, ON, Canada ; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario London, ON, Canada
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Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD. Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. ACTA ACUST UNITED AC 2014; 30:2709-16. [PMID: 24930142 PMCID: PMC4173024 DOI: 10.1093/bioinformatics/btu391] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. RESULTS Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as an additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies. AVAILABILITY AND IMPLEMENTATION All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License. CONTACT brownsd@ornl.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M Klingeman
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miriam L Land
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Christopher W Schadt
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mitchel J Doktycz
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dale A Pelletier
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Jeukens J, Boyle B, Kukavica-Ibrulj I, Ouellet MM, Aaron SD, Charette SJ, Fothergill JL, Tucker NP, Winstanley C, Levesque RC. Comparative genomics of isolates of a Pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients. PLoS One 2014; 9:e87611. [PMID: 24505294 PMCID: PMC3914812 DOI: 10.1371/journal.pone.0087611] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/23/2013] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas aeruginosa is the main cause of fatal chronic lung infections among individuals suffering from cystic fibrosis (CF). During the past 15 years, particularly aggressive strains transmitted among CF patients have been identified, initially in Europe and more recently in Canada. The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the United Kingdom and Canada representing different virulence characteristics in order to: (1) associate comparative genomics results with virulence factor variability and (2) identify genomic and/or phenotypic divergence between the two geographical locations. We performed phenotypic characterization of pyoverdine, pyocyanin, motility, biofilm formation, and proteolytic activity. We also assessed the degree of virulence using the Dictyostelium discoideum amoeba model. Comparative genomics analysis revealed at least one large deletion (40-50 kb) in 6 out of the 7 isolates compared to the reference genome of LESB58. These deletions correspond to prophages, which are known to increase the competitiveness of LESB58 in chronic lung infection. We also identified 308 non-synonymous polymorphisms, of which 28 were associated with virulence determinants and 52 with regulatory proteins. At the phenotypic level, isolates showed extensive variability in production of pyocyanin, pyoverdine, proteases and biofilm as well as in swimming motility, while being predominantly avirulent in the amoeba model. Isolates from the two continents were phylogenetically and phenotypically undistinguishable. Most regulatory mutations were isolate-specific and 29% of them were predicted to have high functional impact. Therefore, polymorphism in regulatory genes is likely to be an important basis for phenotypic diversity among LES isolates, which in turn might contribute to this strain's adaptability to varying conditions in the CF lung.
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Affiliation(s)
- Julie Jeukens
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
| | - Brian Boyle
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
| | - Irena Kukavica-Ibrulj
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
| | - Myriam M. Ouellet
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Shawn D. Aaron
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Steve J. Charette
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Joanne L. Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Roger C. Levesque
- Institute for integrative and systems biology (IBIS), University Laval, Quebec City, Quebec, Canada
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10
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Jeukens J, Boyle B, Tucker NP, Levesque RC. Strategy for genome sequencing analysis and assembly for comparative genomics of Pseudomonas genomes. Methods Mol Biol 2014; 1149:565-577. [PMID: 24818933 DOI: 10.1007/978-1-4939-0473-0_43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bacterial genome sequencing has developed rapidly in the last decade and has become a primary method for analyzing the genomic basis of differences in phenotype between strains as well as being a valuable tool for public health epidemiology. This chapter provides a comprehensive workflow for bacterial genome sequencing from experimental design to data suitable for comparative genomics analysis, while mainly focusing on the challenges associated with genome assembly. This approach was successfully applied to 19 Pseudomonas aeruginosa genomes from phenotypically distinct strains.
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Affiliation(s)
- Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 av. de la médecine, Québec, QC, Canada, G1V 0A6,
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Abstract
Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence.
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