title: Microbial community assembly and metabolic function during mammalian corpse decomposition.
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.
authors.affiliation: 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.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Metcalf
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Zhenjiang Zech
authors.initials: ZZ
authors.lastname: Xu
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA.
authors.forename: Sophie
authors.initials: S
authors.lastname: Weiss
authors.affiliation: 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.
authors.forename: Simon
authors.initials: S
authors.lastname: Lax
authors.affiliation: Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Will
authors.initials: W
authors.lastname: Van Treuren
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Embriette R
authors.initials: ER
authors.lastname: Hyde
authors.affiliation: 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.
authors.forename: Se Jin
authors.initials: SJ
authors.lastname: Song
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Amnon
authors.initials: A
authors.lastname: Amir
authors.affiliation: 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.
authors.forename: Peter
authors.initials: P
authors.lastname: Larsen
authors.affiliation: 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.
authors.forename: Naseer
authors.initials: N
authors.lastname: Sangwan
authors.affiliation: Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Haarmann
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Greg C
authors.initials: GC
authors.lastname: Humphrey
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Gail
authors.initials: G
authors.lastname: Ackermann
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
authors.forename: Luke R
authors.initials: LR
authors.lastname: Thompson
authors.affiliation: Nestlé Institute of Health Sciences, École Polytechnique Fédérale Lausanne, Bâtiment H, 1015 Lausanne, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Lauber
authors.affiliation: BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Bibat
authors.affiliation: BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Nicholas
authors.affiliation: BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Gebert
authors.affiliation: Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Petrosino
authors.affiliation: U.S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, USA.
authors.forename: Sasha C
authors.initials: SC
authors.lastname: Reed
authors.affiliation: 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.
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.affiliation: Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Lynne
authors.affiliation: Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA.
authors.forename: Sibyl R
authors.initials: SR
authors.lastname: Bucheli
authors.affiliation: Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA.
authors.forename: David O
authors.initials: DO
authors.lastname: Carter
authors.affiliation: 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.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000378:metabolism*; D001673:Biodegradation, Environmental; D002102:Cadaver; D017753:Ecosystem; D005658:Fungi / Q000145:classification / Q000378:metabolism*; D051379:Mice; D059013:Microbial Consortia; D058458:Nitrogen Cycle; D012987:Soil / Q000737:chemistry / Q000145:classification; D012988:Soil Microbiology
chemical_list: D012987:Soil