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Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nat Microbiol 2024; 9:595-613. [PMID: 38347104 PMCID: PMC10914610 DOI: 10.1038/s41564-023-01580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/28/2023] [Accepted: 12/08/2023] [Indexed: 03/07/2024]
Abstract
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.
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Affiliation(s)
- Zachary M Burcham
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Animal Sciences, Auburn University, Auburn, AL, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
- Institute for Systems Genetics, New York Grossman School of Medicine, New York University, New York, NY, USA
- Department of Computer Science, New York University, New York, NY, USA
| | - Anru R Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Alexandra Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Heather L Deel
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhenjiang Zech Xu
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Victoria Nieciecki
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Greg C Humphry
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Melissa Connor
- Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, CO, USA
| | - Derek Boyd
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Department of Social, Cultural, and Justice Studies, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jake Smith
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Mid-America College of Funeral Service, Jeffersonville, IN, USA
| | - Jenna M S Watson
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Giovanna Vidoli
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Dawnie Steadman
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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Manter DK, Hamm AK, Deel HL. Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing. J Microbiol Methods 2023:106740. [PMID: 37301376 DOI: 10.1016/j.mimet.2023.106740] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.
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Affiliation(s)
- Daniel K Manter
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA.
| | - Alison K Hamm
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA
| | - Heather L Deel
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA
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Burcham ZM, Weitzel MA, Hodges LD, Deel HL, Metcalf JL. A pilot study characterizing gravesoil bacterial communities a decade after swine decomposition. Forensic Sci Int 2021; 323:110782. [PMID: 33894685 DOI: 10.1016/j.forsciint.2021.110782] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Vertebrate decomposition leads to an efflux of fluids rich with biochemicals and microbes from the carcass into the surrounding soil affecting the endogenous soil bacterial community. These perturbations are detectable in soils associated with carcasses (gravesoil) and influence soil bacterial ecology for years after the decomposition event, but it is unknown for how long. Measuring these impacts over extended timescales is critical to expanding vertebrate decomposition's role in the ecosystem and may provide useful information to forensic science. Using 16S rRNA gene amplicon data, this study surveyed bacterial composition in terrestrial soils associated with surface-exposed swine decomposition for 10 years after carcass placement. This pilot study utilizes the increased statistical power associated with repeated measure/within-subjects sampling to analyze bacterial diversity trends over time. Our results demonstrate that the soil bacterial diversity was significantly impacted by decomposition, with this impact being localized to the area underneath the carcass. Bacterial community dissimilarity was greatest 12 months postmortem before beginning recovery. Additionally, random forest regressions were utilized to determine 10 important genera for distinguishing decomposition timepoints, an important component of forensic investigations. Of these 10 genera, four were further analyzed for their significant relative abundance shifts underneath the carcass. This pilot study helps expand the current knowledge of long-term effects of carcass decomposition on soil bacterial communities, and is the first to our knowledge to characterize these communities temporally from placement through a decade of decomposition.
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Affiliation(s)
- Zachary M Burcham
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80525, USA.
| | - Misty A Weitzel
- Criminal Justice Department, Western Oregon University, Monmouth, OR 97361, USA.
| | - Larry D Hodges
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
| | - Heather L Deel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80525, USA.
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80525, USA.
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