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Leontidou K, Abad-Recio IL, Rubel V, Filker S, Däumer M, Thielen A, Lanzén A, Stoeck T. Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection. Environ Microbiol 2023; 25:3484-3501. [PMID: 37974518 DOI: 10.1111/1462-2920.16530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.
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Affiliation(s)
- Kleopatra Leontidou
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Ion L Abad-Recio
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
| | - Verena Rubel
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Sabine Filker
- Molecular Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Martin Däumer
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Alexander Thielen
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Anders Lanzén
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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van Grinsven S, Sinninghe Damsté JS, Abdala Asbun A, Engelmann JC, Harrison J, Villanueva L. Methane oxidation in anoxic lake water stimulated by nitrate and sulfate addition. Environ Microbiol 2020; 22:766-782. [PMID: 31814267 PMCID: PMC7027835 DOI: 10.1111/1462-2920.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 11/21/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022]
Abstract
Methanotrophic bacteria play a key role in limiting methane emissions from lakes. It is generally assumed that methanotrophic bacteria are mostly active at the oxic-anoxic transition zone in stratified lakes, where they use oxygen to oxidize methane. Here, we describe a methanotroph of the genera Methylobacter that is performing high-rate (up to 72 μM day-1 ) methane oxidation in the anoxic hypolimnion of the temperate Lacamas Lake (Washington, USA), stimulated by both nitrate and sulfate addition. Oxic and anoxic incubations both showed active methane oxidation by a Methylobacter species, with anoxic rates being threefold higher. In anoxic incubations, Methylobacter cell numbers increased almost two orders of magnitude within 3 days, suggesting that this specific Methylobacter species is a facultative anaerobe with a rapid response capability. Genomic analysis revealed adaptations to oxygen-limitation as well as pathways for mixed-acid fermentation and H2 production. The denitrification pathway was incomplete, lacking the genes narG/napA and nosZ, allowing only for methane oxidation coupled to nitrite-reduction. Our data suggest that Methylobacter can be an important driver of the conversion of methane in oxygen-limited lake systems and potentially use alternative electron acceptors or fermentation to remain active under oxygen-depleted conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Julia C. Engelmann
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - John Harrison
- Washington State University Vancouver, School of the EnvironmentVancouverWA98686USA
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
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An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis. Appl Microbiol Biotechnol 2019; 104:751-763. [PMID: 31820070 DOI: 10.1007/s00253-019-10232-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
Abstract
Smokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constituents. Previous studies looked primarily at bacterial constituents and had not differentiated between viable vs nonviable organisms, so in this study, we sought to use a dual metatranscriptomic and metagenomic analysis to see if differences exist. Using high-throughput sequencing, we observed that there were differences in taxonomic abundances between the metagenome and metatranscriptome, and in the metatranscriptome, we also observed an abundance of plant virus RNA not previously reported in DNA-only studies. We also found in the product tested, that there were no viable bacteria capable of metabolizing nitrate to nitrite. Therefore, the product tested would not be likely to increase TSNAs during shelf storage. We tested only a single product to date using the strategy presented here, but succeeded in demonstrating the value of using of these methods in tobacco products. These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product.
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Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Zhang Y, Kitajima M, Whittle AJ, Liu WT. Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. Front Microbiol 2017; 8:2036. [PMID: 29097994 PMCID: PMC5654357 DOI: 10.3389/fmicb.2017.02036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022] Open
Abstract
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs.
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Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Andrew J Whittle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Zhang Y, Oh S, Liu WT. Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective. Environ Microbiol 2017; 19:3163-3174. [PMID: 28654183 DOI: 10.1111/1462-2920.13800] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/30/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
While microbes are known to be present at different stages of a drinking water system, their potential functions and ability to grow in such systems are poorly understood. In this study, we demonstrated that treatment and distribution processes could be viewed as ecological disturbances exhibited over space on the microbiome continuum in a groundwater-derived system. Results from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system were intense as the community diversity was substantially reduced during the treatment steps. Specifically, syntrophs and methanogens dominant in raw water (RW) disappeared after water abstraction, accompanied by a substantial decrease in both the abundance and number of functional genes related to methanogenesis. The softening effluent was dominated by an Exiguobacterium-related population, likely due to its ability to use the phosphotransferase system (PTS) as regulatory machinery to control the energy conditions of the cell. After disinfection and entering the distribution system, community-level functionality remained relatively stable, whereas the community structure differed from those taken in the treatment steps. The diversity and high abundance of some eukaryotic groups in the system suggested that predation could be a disturbance to the bacterial microbiome, which could further drive the diversification of the bacterial community.
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Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL, 61810, USA
| | - Seungdae Oh
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL, 61810, USA
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Bonifay V, Wawrik B, Sunner J, Snodgrass EC, Aydin E, Duncan KE, Callaghan AV, Oldham A, Liengen T, Beech I. Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion. Front Microbiol 2017; 8:99. [PMID: 28197141 PMCID: PMC5281625 DOI: 10.3389/fmicb.2017.00099] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes. Metabolites were analyzed by comparison with standards indicative of aerobic and anaerobic hydrocarbon metabolism and by comparison to predicted masses for KEGG metabolites. Microbial community structure was analyzed via 16S rRNA gene qPCR, sequencing of 16S PCR products, and MySeq Illumina shotgun sequencing of community DNA. Metagenomic data were used to reconstruct the full length 16S rRNA genes and genomes of dominant microorganisms. Sequence data were also interrogated via KEGG annotation and for the presence of genes related to terminal electron accepting (TEA) processes as well as aerobic and anaerobic hydrocarbon degradation. Significant and distinct differences were observed when comparing the ‘high corrosion’ (HC) and the ‘low corrosion’ (LC) pipeline systems, especially with respect to the TEA utilization potential. The HC samples were dominated by sulfate-reducing bacteria (SRB) and archaea known for their ability to utilize simple carbon substrates, whereas LC samples were dominated by pseudomonads with the genetic potential for denitrification and aerobic hydrocarbon degradation. The frequency of aerobic hydrocarbon degradation genes was low in the HC system, and anaerobic hydrocarbon degradation genes were not detected in either pipeline. This is in contrast with metabolite analysis, which demonstrated the presence of several succinic acids in HC samples that are diagnostic of anaerobic hydrocarbon metabolism. Identifiable aerobic metabolites were confined to the LC samples, consistent with the metagenomic data. Overall, these data suggest that corrosion management might benefit from a more refined understanding of microbial community resilience in the face of disturbances such as nitrate treatment or pigging, which frequently prove insufficient to alter community structure toward a stable, less-corrosive assemblage.
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Affiliation(s)
- Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jan Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
| | - Emily C Snodgrass
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Egemen Aydin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Athenia Oldham
- Department of Biology, University of Texas of the Permian Basin, Odessa TX, USA
| | - Turid Liengen
- Research Centre Porsgrunn, Statoil ASA, Herøya Industripark Porsgrunn, Norway
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
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