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Honeker LK, Pugliese G, Ingrisch J, Fudyma J, Gil-Loaiza J, Carpenter E, Singer E, Hildebrand G, Shi L, Hoyt DW, Chu RK, Toyoda J, Krechmer JE, Claflin MS, Ayala-Ortiz C, Freire-Zapata V, Pfannerstill EY, Daber LE, Meeran K, Dippold MA, Kreuzwieser J, Williams J, Ladd SN, Werner C, Tfaily MM, Meredith LK. Author Correction: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nat Microbiol 2024; 9:1146-1147. [PMID: 37803148 PMCID: PMC10994830 DOI: 10.1038/s41564-023-01507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Affiliation(s)
- Linnea K Honeker
- Biosphere 2, University of Arizona, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Giovanni Pugliese
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - Johannes Ingrisch
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Jane Fudyma
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | | | | | - Gina Hildebrand
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Lingling Shi
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - David W Hoyt
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason Toyoda
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jordan E Krechmer
- Aerodyne Research, Inc., Billerica, MA, USA
- Bruker Daltonics Inc., Billerica, MA, USA
| | | | | | | | - Eva Y Pfannerstill
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - L Erik Daber
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | | | - Michaela A Dippold
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Jürgen Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Jonathan Williams
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - S Nemiah Ladd
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Christiane Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Malak M Tfaily
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Laura K Meredith
- Biosphere 2, University of Arizona, Tucson, AZ, USA.
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA.
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2
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Ellenbogen JB, Borton MA, McGivern BB, Cronin DR, Hoyt DW, Freire-Zapata V, McCalley CK, Varner RK, Crill PM, Wehr RA, Chanton JP, Woodcroft BJ, Tfaily MM, Tyson GW, Rich VI, Wrighton KC. Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems 2024; 9:e0069823. [PMID: 38063415 PMCID: PMC10805028 DOI: 10.1128/msystems.00698-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/24/2023] [Indexed: 01/24/2024] Open
Abstract
While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.
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Affiliation(s)
- Jared B. Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Mikayla A. Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Bridget B. McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Dylan R. Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Carmody K. McCalley
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Ruth K. Varner
- Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, New Hampshire, USA
| | - Patrick M. Crill
- Department of Geological Sciences, Bolin Center for Climate Research, Stockholm University, Stockholm, Sweden
| | - Richard A. Wehr
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jeffrey P. Chanton
- Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, Florida, USA
| | - Ben J. Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Malak M. Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
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3
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Hildebrand GA, Honeker LK, Freire-Zapata V, Ayala-Ortiz C, Rajakaruna S, Fudyma J, Daber LE, AminiTabrizi R, Chu RL, Toyoda J, Flowers SE, Hoyt DW, Hamdan R, Gil-Loaiza J, Shi L, Dippold MA, Ladd SN, Werner C, Meredith LK, Tfaily MM. Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants. Sci Total Environ 2023; 899:165689. [PMID: 37481084 DOI: 10.1016/j.scitotenv.2023.165689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023]
Abstract
Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.
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Affiliation(s)
- Gina A Hildebrand
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA
| | - Linnea K Honeker
- BIO5 Institute, The University of Arizona, 1657 E Helen St., Tucson, AZ 85719, USA; School of Natural Resources and the Environment, University of Arizona, 1064 E Lowell St., Tucson, AZ 85721, USA
| | - Viviana Freire-Zapata
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA
| | - Christian Ayala-Ortiz
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA
| | - Sumudu Rajakaruna
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA
| | - Jane Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA; Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95816, USA
| | - L Erik Daber
- Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Roya AminiTabrizi
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA
| | - Rosalie L Chu
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Jason Toyoda
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Sarah E Flowers
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - David W Hoyt
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Rasha Hamdan
- Department of Chemistry and Biochemistry, Lebanese University, Beirut, Lebanon
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, 1064 E Lowell St., Tucson, AZ 85721, USA
| | - Lingling Shi
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Schnarrenbergstrasse 94-96, 72076 Tuebingen, Germany
| | - Michaela A Dippold
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Schnarrenbergstrasse 94-96, 72076 Tuebingen, Germany
| | - S Nemiah Ladd
- Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany; Department of Environmental Science, University of Basel, Bernoullistrasse 30/32, 4056 Basel, Switzerland
| | - Christiane Werner
- Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Laura K Meredith
- BIO5 Institute, The University of Arizona, 1657 E Helen St., Tucson, AZ 85719, USA; School of Natural Resources and the Environment, University of Arizona, 1064 E Lowell St., Tucson, AZ 85721, USA; Biosphere 2, University of Arizona, 32540 S Biosphere Rd, Oracle, AZ 85739, USA
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St., AZ 85721, USA; BIO5 Institute, The University of Arizona, 1657 E Helen St., Tucson, AZ 85719, USA; Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA.
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Honeker LK, Pugliese G, Ingrisch J, Fudyma J, Gil-Loaiza J, Carpenter E, Singer E, Hildebrand G, Shi L, Hoyt DW, Chu RK, Toyoda J, Krechmer JE, Claflin MS, Ayala-Ortiz C, Freire-Zapata V, Pfannerstill EY, Daber LE, Meeran K, Dippold MA, Kreuzwieser J, Williams J, Ladd SN, Werner C, Tfaily MM, Meredith LK. Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nat Microbiol 2023; 8:1480-1494. [PMID: 37524975 PMCID: PMC10390333 DOI: 10.1038/s41564-023-01432-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/19/2023] [Indexed: 08/02/2023]
Abstract
Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking 13C from position-specific 13C-pyruvate into CO2 and VOCs in parallel with multi-omics. During drought, efflux of 13C-enriched acetate, acetone and C4H6O2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,13C-CO2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.
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Affiliation(s)
- Linnea K Honeker
- Biosphere 2, University of Arizona, Tucson, AZ, USA
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Giovanni Pugliese
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - Johannes Ingrisch
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Jane Fudyma
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | | | | | - Gina Hildebrand
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Lingling Shi
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - David W Hoyt
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason Toyoda
- Environmental Molecular Science Laboratory (EMSL), Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jordan E Krechmer
- Aerodyne Research, Inc., Billerica, MA, USA
- Bruker Daltonics Inc., Billerica, MA, USA
| | | | | | | | - Eva Y Pfannerstill
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - L Erik Daber
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | | | - Michaela A Dippold
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Jürgen Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Jonathan Williams
- Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany
| | - S Nemiah Ladd
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Christiane Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Malak M Tfaily
- Department of Environmental Sciences, University of Arizona, Tucson, AZ, USA
| | - Laura K Meredith
- Biosphere 2, University of Arizona, Tucson, AZ, USA.
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA.
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5
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Ayala-Ortiz C, Graf-Grachet N, Freire-Zapata V, Fudyma J, Hildebrand G, AminiTabrizi R, Howard-Varona C, Corilo YE, Hess N, Duhaime MB, Sullivan MB, Tfaily MM. MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data. Microbiome 2023; 11:28. [PMID: 36803638 PMCID: PMC9936664 DOI: 10.1186/s40168-023-01476-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. RESULTS Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. CONCLUSION Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User's guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ), respectively. Video Abstract.
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Affiliation(s)
| | - Nathalia Graf-Grachet
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: Roche, Pleasanton, CA 94588 USA
| | | | - Jane Fudyma
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: University of California, Davis|Department of Plant Pathology, Davis, CA 95616-8751 USA
| | - Gina Hildebrand
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
| | - Roya AminiTabrizi
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Present address: University of Chicago Biological Sciences Division, Metabolomics Platform, Chicago, IL 60637 USA
| | - Cristina Howard-Varona
- Department of Microbiology, Ohio State University, Columbus, OH 43210 USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210 USA
| | - Yuri E. Corilo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Nancy Hess
- Present address: University of California, Davis|Department of Plant Pathology, Davis, CA 95616-8751 USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210 USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210 USA
| | - Malak M. Tfaily
- Department of Environmental, Science, University of Arizona, Tucson, AZ 85721 USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
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6
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Espindola AS, Sempertegui-Bayas D, Bravo-Padilla DF, Freire-Zapata V, Ochoa-Corona F, Cardwell KF. TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics. Viruses 2021; 13:v13071223. [PMID: 34202758 PMCID: PMC8310100 DOI: 10.3390/v13071223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/03/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.
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Affiliation(s)
- Andres S. Espindola
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Correspondence:
| | - Daniela Sempertegui-Bayas
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Danny F. Bravo-Padilla
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Viviana Freire-Zapata
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francisco Ochoa-Corona
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kitty F. Cardwell
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
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