Microbial community assembly and metabolic function during mammalian corpse decomposition

Jessica L Metcalf; Zhenjiang Zech Xu; Sophie Weiss; Simon Lax; Will Van Treuren; Embriette R Hyde; Se Jin Song; Amnon Amir; Peter Larsen; Naseer Sangwan; Daniel Haarmann; Greg C Humphrey; Gail Ackermann; Luke R Thompson; Christian Lauber; Alexander Bibat; Catherine Nicholas; Matthew J Gebert; Joseph F Petrosino; Sasha C Reed; Jack A Gilbert; Aaron M Lynne; Sibyl R Bucheli; David O Carter; Rob Knight

doi:10.1126/science.aad2646

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science. 2016 Jan 8;351(6269):158-62. doi: 10.1126/science.aad2646. Epub 2015 Dec 10.

Authors

Jessica L Metcalf¹, Zhenjiang Zech Xu², Sophie Weiss³, Simon Lax⁴, Will Van Treuren⁵, Embriette R Hyde², Se Jin Song⁶, Amnon Amir², Peter Larsen⁷, Naseer Sangwan⁸, Daniel Haarmann⁹, Greg C Humphrey², Gail Ackermann², Luke R Thompson², Christian Lauber¹⁰, Alexander Bibat¹¹, Catherine Nicholas¹¹, Matthew J Gebert¹¹, Joseph F Petrosino¹², Sasha C Reed¹³, Jack A Gilbert¹⁴, Aaron M Lynne⁹, Sibyl R Bucheli⁹, David O Carter¹⁵, Rob Knight¹⁶

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA. robknight@ucsd.edu jessica.metcalf@colorado.edu.
² Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
³ Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA.
⁴ Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA.
⁵ Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
⁶ Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
⁷ Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA.
⁸ Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA.
⁹ Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA.
¹⁰ Nestlé Institute of Health Sciences, École Polytechnique Fédérale Lausanne, Bâtiment H, 1015 Lausanne, Switzerland.
¹¹ BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
¹² Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
¹³ U.S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, USA.
¹⁴ Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA. Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA.
¹⁵ Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA.
¹⁶ Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA. Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92037, USA. robknight@ucsd.edu jessica.metcalf@colorado.edu.

PMID: 26657285
DOI: 10.1126/science.aad2646

Abstract

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Bacteria / classification
Bacteria / metabolism*
Biodegradation, Environmental
Cadaver*
Ecosystem
Fungi / classification
Fungi / metabolism*
Mice
Microbial Consortia*
Nitrogen Cycle
Soil / chemistry
Soil / classification
Soil Microbiology*

Substances

Soil

Abstract

Publication types

MeSH terms

Substances

Grants and funding