skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »; ; ; ; ; « less
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
U.S. Department of Justice (DOJ) - National Institute of Justice; National Institutes of Health (NIH) - National Human Genome Research Institute (NHGRI)
OSTI Identifier:
1368069
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Science
Additional Journal Information:
Journal Volume: 351; Journal Issue: 6269; Journal ID: ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English

Citation Formats

Metcalf, J. L., Xu, Z. Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E. R., Song, S. J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G. C., Ackermann, G., Thompson, L. R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M. J., Petrosino, J. F., Reed, S. C., Gilbert, J. A., Lynne, A. M., Bucheli, S. R., Carter, D. O., and Knight, R. Microbial community assembly and metabolic function during mammalian corpse decomposition. United States: N. p., 2015. Web. doi:10.1126/science.aad2646.
Metcalf, J. L., Xu, Z. Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E. R., Song, S. J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G. C., Ackermann, G., Thompson, L. R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M. J., Petrosino, J. F., Reed, S. C., Gilbert, J. A., Lynne, A. M., Bucheli, S. R., Carter, D. O., & Knight, R. Microbial community assembly and metabolic function during mammalian corpse decomposition. United States. doi:10.1126/science.aad2646.
Metcalf, J. L., Xu, Z. Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E. R., Song, S. J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G. C., Ackermann, G., Thompson, L. R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M. J., Petrosino, J. F., Reed, S. C., Gilbert, J. A., Lynne, A. M., Bucheli, S. R., Carter, D. O., and Knight, R. Thu . "Microbial community assembly and metabolic function during mammalian corpse decomposition". United States. doi:10.1126/science.aad2646.
@article{osti_1368069,
title = {Microbial community assembly and metabolic function during mammalian corpse decomposition},
author = {Metcalf, J. L. and Xu, Z. Z. and Weiss, S. and Lax, S. and Van Treuren, W. and Hyde, E. R. and Song, S. J. and Amir, A. and Larsen, P. and Sangwan, N. and Haarmann, D. and Humphrey, G. C. and Ackermann, G. and Thompson, L. R. and Lauber, C. and Bibat, A. and Nicholas, C. and Gebert, M. J. and Petrosino, J. F. and Reed, S. C. and Gilbert, J. A. and Lynne, A. M. and Bucheli, S. R. and Carter, D. O. and Knight, R.},
abstractNote = {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.},
doi = {10.1126/science.aad2646},
journal = {Science},
issn = {0036-8075},
number = 6269,
volume = 351,
place = {United States},
year = {2015},
month = {12}
}

Works referenced in this record:

Seasonal variation of postmortem microbial communities
journal, March 2015

  • Carter, David O.; Metcalf, Jessica L.; Bibat, Alexander
  • Forensic Science, Medicine, and Pathology, Vol. 11, Issue 2
  • DOI: 10.1007/s12024-015-9667-7

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014


Global biogeography of highly diverse protistan communities in soil
journal, December 2012

  • Bates, Scott T.; Clemente, Jose C.; Flores, Gilberto E.
  • The ISME Journal, Vol. 7, Issue 3
  • DOI: 10.1038/ismej.2012.147

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
journal, June 2009

  • Lauber, C. L.; Hamady, M.; Knight, R.
  • Applied and Environmental Microbiology, Vol. 75, Issue 15
  • DOI: 10.1128/AEM.00335-09

Functional metagenomic profiling of nine biomes
journal, March 2008

  • Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana
  • Nature, Vol. 452, Issue 7187
  • DOI: 10.1038/nature06810

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010

  • Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
  • DOI: 10.1073/pnas.1000080107

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

Initial insights into bacterial succession during human decomposition
journal, November 2014

  • Hyde, Embriette R.; Haarmann, Daniel P.; Petrosino, Joseph F.
  • International Journal of Legal Medicine, Vol. 129, Issue 3
  • DOI: 10.1007/s00414-014-1128-4

The role of carrion in maintaining biodiversity and ecological processes in terrestrial ecosystems
journal, September 2012


PyNAST: a flexible tool for aligning sequences to a template alignment
journal, November 2009


The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing
journal, June 2013

  • Pechal, Jennifer L.; Crippen, Tawni L.; Benbow, M. Eric
  • International Journal of Legal Medicine, Vol. 128, Issue 1
  • DOI: 10.1007/s00414-013-0872-1

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
journal, August 2013

  • Langille, Morgan G. I.; Zaneveld, Jesse; Caporaso, J. Gregory
  • Nature Biotechnology, Vol. 31, Issue 9
  • DOI: 10.1038/nbt.2676

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system
journal, October 2013

  • Metcalf, Jessica L.; Wegener Parfrey, Laura; Gonzalez, Antonio
  • eLife, Vol. 2
  • DOI: 10.7554/eLife.01104

Cadaver decomposition in terrestrial ecosystems
journal, November 2006


Computational Inference of Neural Information Flow Networks
journal, January 2006


Detritus, trophic dynamics and biodiversity: Detritus, trophic dynamics and biodiversity
journal, June 2004


Carrion decomposition and nutrient cycling in a semiarid shrub–steppe ecosystem
journal, November 2009

  • Parmenter, Robert R.; MacMahon, James A.
  • Ecological Monographs, Vol. 79, Issue 4
  • DOI: 10.1890/08-0972.1

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303