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Pérez V, Liu Y, Hengst MB, Weyrich LS. A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples. Microorganisms 2022; 10:microorganisms10081623. [PMID: 36014039 PMCID: PMC9414430 DOI: 10.3390/microorganisms10081623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.
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Affiliation(s)
- Vilma Pérez
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence:
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Martha B. Hengst
- Laboratorio de Ecología Molecular y Microbiología Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1270300, Chile
| | - Laura S. Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA 16802, USA
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Messan KS, Jones RM, Doherty SJ, Foley K, Douglas TA, Barbato RA. The role of changing temperature in microbial metabolic processes during permafrost thaw. PLoS One 2020; 15:e0232169. [PMID: 32353013 PMCID: PMC7192436 DOI: 10.1371/journal.pone.0232169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Approximately one fourth of the Earth's Northern Hemisphere is underlain by permafrost, earth materials (soil, organic matter, or bedrock), that has been continuously frozen for at least two consecutive years. Numerous studies point to evidence of accelerated climate warming in the Arctic and sub-Arctic where permafrost is located. Changes to permafrost biochemical processes may critically impact ecosystem processes at the landscape scale. Here, we sought to understand how the permafrost metabolome responds to thaw and how this response differs based on location (i.e. chronosequence of permafrost formation constituting diverse permafrost types). We analyzed metabolites from microbial cells originating from Alaskan permafrost. Overall, permafrost thaw induced a shift in microbial metabolic processes. Of note were the dissimilarities in biochemical structure between frozen and thawed samples. The thawed permafrost metabolomes from different locations were highly similar. In the intact permafrost, several metabolites with antagonist properties were identified, illustrating the competitive survival strategy required to survive a frozen state. Interestingly, the intensity of these antagonistic metabolites decreased with warmer temperature, indicating a shift in ecological strategies in thawed permafrost. These findings illustrate the impact of change in temperature and spatial variability as permafrost undergoes thaw, knowledge that will become crucial for predicting permafrost biogeochemical dynamics as the Arctic and Antarctic landscapes continue to warm.
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Affiliation(s)
- Komi S. Messan
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Robert M. Jones
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Stacey J. Doherty
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Karen Foley
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
| | - Thomas A. Douglas
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Fairbanks, Alaska, United States of America
| | - Robyn A. Barbato
- US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of America
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Karl JP, Barbato RA, Doherty LA, Gautam A, Glaven SM, Kokoska RJ, Leary D, Mickol RL, Perisin MA, Hoisington AJ, Van Opstal EJ, Varaljay V, Kelley-Loughnane N, Mauzy CA, Goodson MS, Soares JW. Meeting report of the third annual Tri-Service Microbiome Consortium symposium. ENVIRONMENTAL MICROBIOME 2020; 15:12. [PMID: 32835172 PMCID: PMC7356122 DOI: 10.1186/s40793-020-00359-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 05/05/2023]
Abstract
The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations and to facilitate resource, material and information sharing among consortium members. The 2019 annual symposium was held 22-24 October 2019 at Wright-Patterson Air Force Base in Dayton, OH. Presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) human microbiomes; 2) transitioning products into Warfighter solutions; 3) environmental microbiomes; 4) engineering microbiomes; and 5) microbiome simulation and characterization. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 3rd annual TSMC symposium.
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Affiliation(s)
- J. Philip Karl
- Military Nutrition Division, United States Army Research Institute of Environmental Medicine, Natick, MA USA
| | - Robyn A. Barbato
- United States Army Cold Regions Research and Engineering Laboratory, Hanover, NH USA
| | - Laurel A. Doherty
- Soldier Performance Optimization Directorate, United States Army Combat Capabilities Development Command Soldier Center, Natick, MA USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC USA
| | - Robert J. Kokoska
- Physical Sciences Directorate, United States Army Research Laboratory – United States Army Research Office, Research Triangle Park, Durham, NC USA
| | - Dagmar Leary
- Center for Biomolecular Science & Engineering, United States Naval Research Laboratory, Washington, DC USA
| | | | - Matthew A. Perisin
- Biotechnology Branch, United States Army Combat Capabilities Development Command-Army Research Laboratory, Adelphi, MD USA
| | - Andrew J. Hoisington
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, Dayton, OH USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO USA
- Department of Physical Medicine & Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Edward J. Van Opstal
- Human Systems Directorate, Office of the Underscretary of Defense for Research & Engineering, Washington, DC USA
| | - Vanessa Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Camilla A. Mauzy
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Michael S. Goodson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Jason W. Soares
- Soldier Performance Optimization Directorate, United States Army Combat Capabilities Development Command Soldier Center, Natick, MA USA
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Potential microbial contamination during sampling of permafrost soil assessed by tracers. Sci Rep 2017; 7:43338. [PMID: 28230151 PMCID: PMC5322388 DOI: 10.1038/srep43338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/25/2017] [Indexed: 11/08/2022] Open
Abstract
Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.
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