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Furuta K, Byrne J, Luat K, Cheung C, Carter DO, Tipton L, Perrault Uptmor KA. Volatile organic compounds produced during postmortem processes can be linked via chromatographic profiles to individual postmortem bacterial species. J Chromatogr A 2024; 1728:465017. [PMID: 38797136 DOI: 10.1016/j.chroma.2024.465017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Decomposition odor is produced during postmortem mammalian tissue breakdown by bacteria, insects, and intrinsic chemical processes. Past research has not thoroughly investigated which volatile organic compounds (VOCs) can be linked directly to individual bacterial species on decomposing remains. The purpose of this study was to profile the VOCs produced over time by individual species of bacteria using comprehensive two-dimensional gas chromatography (GC×GC) to expand our foundational knowledge of what each bacterial species contributes to decomposition odor. Five different species of bacteria (Bacillus subtilis, Ignatzschineria indica, Ignatzschineria ureiclastica, Curtobacterium luteum, and Vagococcus lutrae) were cultured on standard nutrient agar individually and monitored daily using solid phase microextraction arrow (SPME Arrow) and GC×GC in combination with quadrupole mass spectrometry (qMS) and flame ionization detection (FID). The GC×GC-qMS/FID approach was used to generate rich VOC profiles that represented the bacterial species' metabolic VOC production longitudinally. The data obtained from the chromatographic output was used to compare with a prior study using one-dimensional GC-qMS, and also between each of the five species to investigate the extent of overlap between species. No single VOC could be found in all five bacterial species investigated, and there was little overlap in the profile between species. To further visualize these differences, chromatographic peak data was investigated using two different ordination strategies, principal component analysis (PCA) and principal coordinate analysis (PCoA). The two ordination strategies were compared with each other using a Procrustes analysis. This was performed to understand differences in ordination strategies between the separation science community and chemical ecological community. Overall, ordination strategies were found to produce similar results, as evidenced by the correlation of PCA and PCoA in the Procrustes analysis. All analysis strategies yielded distinct VOC profiles for each species. Further study of additional species will support understanding of the holistic view of decomposition odor from a chemical ecology perspective, and further support our understanding of the production of decomposition odor that culminates from such a complex environment.
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Affiliation(s)
- Kyle Furuta
- Laboratory of Forensic and Bioanalytical Chemistry, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States
| | - Julianne Byrne
- Laboratory of Forensic and Bioanalytical Chemistry, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States
| | - Kawailani Luat
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States
| | - Cynthia Cheung
- Laboratory of Forensic and Bioanalytical Chemistry, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States
| | - David O Carter
- Laboratory of Forensic Taphonomy, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States
| | - Laura Tipton
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States; Departments of Biology and Mathematics & Statistics, James Madison University, United States
| | - Katelynn A Perrault Uptmor
- Laboratory of Forensic and Bioanalytical Chemistry, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, United States; Nontargeted Separations Laboratory, Department of Chemistry, William & Mary, United States.
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Cláudia-Ferreira A, Barbosa DJ, Saegeman V, Fernández-Rodríguez A, Dinis-Oliveira RJ, Freitas AR. The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms 2023; 11:2509. [PMID: 37894167 PMCID: PMC10608847 DOI: 10.3390/microorganisms11102509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.
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Affiliation(s)
- Ana Cláudia-Ferreira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
| | - Daniel José Barbosa
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Veroniek Saegeman
- Department of Infection Control and Prevention, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Amparo Fernández-Rodríguez
- Microbiology Laboratory, Biology Service, Institute of Toxicology and Forensic Sciences, 28232 Madrid, Spain;
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Miguel M, Kim SH, Lee SS, Cho YI. Composition and functional diversity of bacterial communities during swine carcass decomposition. Anim Biosci 2023; 36:1453-1464. [PMID: 37402447 PMCID: PMC10472150 DOI: 10.5713/ab.23.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/08/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVE This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. METHODS The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. RESULTS A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. CONCLUSION This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.
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Affiliation(s)
- Michelle Miguel
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922,
Korea
| | - Seon-Ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922,
Korea
| | - Sang-Suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922,
Korea
| | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922,
Korea
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Mason AR, Taylor LS, DeBruyn JM. Microbial ecology of vertebrate decomposition in terrestrial ecosystems. FEMS Microbiol Ecol 2023; 99:6985004. [PMID: 36631293 DOI: 10.1093/femsec/fiad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.
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Affiliation(s)
- Allison R Mason
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Lois S Taylor
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
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Wang Z, Zhang F, Wang L, Yuan H, Guan D, Zhao R. Advances in artificial intelligence-based microbiome for PMI estimation. Front Microbiol 2022; 13:1034051. [PMID: 36267183 PMCID: PMC9577360 DOI: 10.3389/fmicb.2022.1034051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Postmortem interval (PMI) estimation has always been a major challenge in forensic science. Conventional methods for predicting PMI are based on postmortem phenomena, metabolite or biochemical changes, and insect succession. Because postmortem microbial succession follows a certain temporal regularity, the microbiome has been shown to be a potentially effective tool for PMI estimation in the last decade. Recently, artificial intelligence (AI) technologies shed new lights on forensic medicine through analyzing big data, establishing prediction models, assisting in decision-making, etc. With the application of next-generation sequencing (NGS) and AI techniques, it is possible for forensic practitioners to improve the dataset of microbial communities and obtain detailed information on the inventory of specific ecosystems, quantifications of community diversity, descriptions of their ecological function, and even their application in legal medicine. This review describes the postmortem succession of the microbiome in cadavers and their surroundings, and summarizes the application, advantages, problems, and future strategies of AI-based microbiome analysis for PMI estimation.
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Affiliation(s)
- Ziwei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Linlin Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Huiya Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Dawei Guan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
- *Correspondence: Dawei Guan,
| | - Rui Zhao
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
- Rui Zhao,
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von Hoermann C, Weithmann S, Sikorski J, Nevo O, Szpila K, Grzywacz A, Grunwald JE, Reckel F, Overmann J, Steiger S, Ayasse M. Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220555. [PMID: 36061525 PMCID: PMC9428529 DOI: 10.1098/rsos.220555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.
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Affiliation(s)
- Christian von Hoermann
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany
| | - Sandra Weithmann
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Omer Nevo
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Krzysztof Szpila
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Torun, Poland
| | - Andrzej Grzywacz
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Torun, Poland
| | - Jan-Eric Grunwald
- Bavarian State Criminal Police Office, SG 204, Microtraces/Biology, 80636 Munich, Germany
| | - Frank Reckel
- Bavarian State Criminal Police Office, SG 204, Microtraces/Biology, 80636 Munich, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Sandra Steiger
- Department of Evolutionary Animal Ecology, University of Bayreuth, Bayreuth, Germany
| | - Manfred Ayasse
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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7
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Dmitrijs F, Guo J, Huang Y, Liu Y, Fang X, Jiang K, Zha L, Cai J, Fu X. Bacterial Succession in Microbial Biofilm as a Potential Indicator for Postmortem Submersion Interval Estimation. Front Microbiol 2022; 13:951707. [PMID: 35942315 PMCID: PMC9356301 DOI: 10.3389/fmicb.2022.951707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteria acts as the main decomposer during the process of biodegradation by microbial communities in the ecosystem. Numerous studies have revealed the bacterial succession patterns during carcass decomposition in the terrestrial setting. The machine learning algorithm-generated models based on such temporal succession patterns have been developed for the postmortem interval (PMI) estimation. However, the bacterial succession that occurs on decomposing carcasses in the aquatic environment is poorly understood. In the forensic practice, the postmortem submersion interval (PMSI), which approximately equals to the PMI in most of the common drowning cases, has long been problematic to determine. In the present study, bacterial successions in the epinecrotic biofilm samples collected from the decomposing swine cadavers submerged in water were analyzed by sequencing the variable region 4 (V4) of 16S rDNA. The succession patterns between the repeated experimental settings were repeatable. Using the machine learning algorithm for establishing random forest (RF) models, the microbial community succession patterns in the epinecrotic biofilm samples taken during the 56-day winter trial and 21-day summer trial were determined to be used as the PMSI predictors with the mean absolute error (MAE) of 17.87 ± 2.48 ADD (≈1.3 day) and 20.59 ± 4.89 ADD (≈0.7 day), respectively. Significant differences were observed between the seasons and between the substrates. The data presented in this research suggested that the influences of the environmental factors and the aquatic bacterioplankton on succession patterns of the biofilm bacteria were of great significance. The related mechanisms of such influence need to be further studied and clarified in depth to consider epinecrotic biofilm as a reliable predictor in the forensic investigations.
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Affiliation(s)
- Finkelbergs Dmitrijs
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Juanjuan Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Department of Vascular Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yecao Huang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yafei Liu
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xinyue Fang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Kankan Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Jifeng Cai
| | - Xiaoliang Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoliang Fu
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8
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Khalikov AA, Kildyushov EM, Kuznetsov KO, Rahmatullina GR. [Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem]. Sud Med Ekspert 2022; 65:49-53. [PMID: 35613449 DOI: 10.17116/sudmed20226503149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of the review is to summarize and update the data of modern studies devoted to determining the post-mortem interval (PMI) with the use of microorganisms, as well as disclosing prospects for further study in the presented direction. Estimating the time elapsed since death based on the postmortem microbiome has great potential for accurate determination of PMI, but all methods currently used have their limitations. The dynamics of changes in microbial communities due to the influence of many external and internal factors significantly complicates the process of interpreting the results. The change of microbial communities in the human corpse has shown promising results for the assessment of PMI, but to date there is no evidence of the repeatability of such a continuity in various geographic and ecological conditions. The question of conducting new, large-scale studies, taking in all the factors that could affect the posthumous microbiome, is becoming urgent.
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Affiliation(s)
| | - E M Kildyushov
- Pirogov Russian National Research Medical University, Moscow, Russia
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9
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Diverse Effects of Climate, Land Use, and Insects on Dung and Carrion Decomposition. Ecosystems 2022. [DOI: 10.1007/s10021-022-00764-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractLand-use intensification and climate change threaten ecosystem functions. A fundamental, yet often overlooked, function is decomposition of necromass. The direct and indirect anthropogenic effects on decomposition, however, are poorly understood. We measured decomposition of two contrasting types of necromass, rat carrion and bison dung, on 179 study sites in Central Europe across an elevational climate gradient of 168–1122 m a.s.l. and within both local and regional land uses. Local land-use types included forest, grassland, arable fields, and settlements and were embedded in three regional land-use types (near-natural, agricultural, and urban). The effects of insects on decomposition were quantified by experimental exclusion, while controlling for removal by vertebrates. We used generalized additive mixed models to evaluate dung weight loss and carrion decay rate along elevation and across regional and local land-use types. We observed a unimodal relationship of dung decomposition with elevation, where greatest weight loss occurred between 600 and 700 m, but no effects of local temperature, land use, or insects. In contrast to dung, carrion decomposition was continuously faster with both increasing elevation and local temperature. Carrion reached the final decomposition stage six days earlier when insect access was allowed, and this did not depend on land-use effect. Our experiment identified different major drivers of decomposition on each necromass form. The results show that dung and carrion decomposition are rather robust to local and regional land use, but future climate change and decline of insects could alter decomposition processes and the self-regulation of ecosystems.
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10
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Hilal MG, Zhou R, Yu Q, Wang Y, Feng T, Li X, Li H. Successions of rare and abundant microbial subcommunities during fish carcass decomposition in a microcosm under the influence of variable factors. FEMS Microbiol Lett 2022; 369:6554547. [DOI: 10.1093/femsle/fnac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/08/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Animal carcasses are hotspots of ecological activity. The study of the role of microbes in carcass decomposition has been exclusively focused on microbes with higher abundance. The comparative study of abundant and rare subcommunities associated with decomposition needs in-depth exploration. The current experiment has been conducted on the decomposition of a fish carcass in a microcosm. We conducted 16S rRNA gene sequencing of the microbial communities. The correlation of the physicochemical properties of tap and Yellow river water with the microbial communities was evaluated. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were found to be the dominant phyla in both abundant and rare subcommunities. Among bacteria, the Acidobacteria, Planctomycetes, and Cyanobacteria were found only in the rare subcommunity. In both subcommunities, the abundance of Proteobacteria was found to increase over time, and that of Firmicutes to decrease. The rare subcommunity shows higher alpha diversity than the abundant one. The variation in the abundant subcommunity was influenced by time and water type, and that in the rare subcommunity was influenced by pH and water type. These results have implications for future research on the ecological role of rare and abundant subcommunities in the decomposition of carcasses in the aquatic ecosystem.
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Affiliation(s)
- Mian Gul Hilal
- MOE, Key laboratory of Cell activities and stress adaptations, School of life science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Rui Zhou
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiangkai Li
- MOE, Key laboratory of Cell activities and stress adaptations, School of life science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Huan Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
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11
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Dawson BM, Wallman JF, Barton PS. How does mass loss compare with total body score when assessing decomposition of human and pig cadavers? Forensic Sci Med Pathol 2022; 18:343-351. [PMID: 35543928 PMCID: PMC9587095 DOI: 10.1007/s12024-022-00481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Providing accurate and reliable measures of decomposition is paramount for forensic research where decomposition progress is used to estimate time of death. Mass loss is routinely used as a direct measure of biomass decomposition in ecological studies, yet few studies have analysed mass loss in a forensic context on human cadavers to determine its usefulness for modelling the decomposition process. Mass loss was examined in decomposing human and pig cadavers, and compared with other common decomposition metrics, such as total body score (TBS). One summer and one winter field decomposition experiment was conducted using human and pig cadavers, as pigs are often used as proxies for human cadavers in forensic research. The two measures of decomposition revealed two contrasting patterns of decomposition on pigs and humans, particularly in winter where TBS stabilised at similar values, but mass loss differed greatly. Mass loss was found to be faster in pigs than humans during early decomposition. Pigs lost 75% of their mass in winter, while humans lost less than 50%; however, in summer, both lost around 80% of their mass. TBS displayed similar patterns in both experiments, with TBS increasing more rapidly in pigs compared with humans but both eventually reaching similar TBS values in late decomposition. Measuring mass loss can provide additional information about decomposition progress that is missed if using TBS only. Key differences in decomposition progress between cadaver types were also observed, suggesting caution when extrapolating data from pigs to humans for forensic research and decomposition modelling.
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Affiliation(s)
- Blake M. Dawson
- grid.1007.60000 0004 0486 528XCentre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW Australia
| | - James F. Wallman
- grid.1007.60000 0004 0486 528XCentre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW Australia ,grid.117476.20000 0004 1936 7611Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
| | - Philip S. Barton
- grid.1040.50000 0001 1091 4859Future Regions Research Centre, Federation University Australia, Mount Helen, VIC, Australia
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12
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Miguel MA, Kim SH, Lee SS, Cho YI. Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses. Animals (Basel) 2021; 11:2937. [PMID: 34679958 PMCID: PMC8532636 DOI: 10.3390/ani11102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.
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Affiliation(s)
| | | | | | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.A.M.); (S.-H.K.); (S.-S.L.)
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13
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Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere 2021; 6:e0045521. [PMID: 34259562 PMCID: PMC8386422 DOI: 10.1128/msphere.00455-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bones of decomposing vertebrates are colonized by a succession of diverse microbial communities. If this succession is similar across individuals, microbes may provide clues about the postmortem interval (PMI) during forensic investigations in which human skeletal remains are discovered. Here, we characterize the human bone microbial decomposer community to determine whether microbial succession is a marker for PMI. Six human donor subjects were placed outdoors to decompose on the soil surface at the Southeast Texas Applied Forensic Science facility. To also assess the effect of seasons, three decedents were placed each in the spring and summer. Once ribs were exposed through natural decomposition, a rib was collected from each body for eight time points at 3 weeks apart. We discovered a core bone decomposer microbiome dominated by taxa in the phylum Proteobacteria and evidence that these bone-invading microbes are likely sourced from the surrounding decomposition environment, including skin of the cadaver and soils. Additionally, we found significant overall differences in bone microbial community composition between seasons. Finally, we used the microbial community data to develop random forest models that predict PMI with an accuracy of approximately ±34 days over a 1- to 9-month time frame of decomposition. Typically, anthropologists provide PMI estimates based on qualitative information, giving PMI errors ranging from several months to years. Previous work has focused on only the characterization of the bone microbiome decomposer community, and this is the first known data-driven, quantitative PMI estimate of terrestrially decomposed human skeletal remains using microbial abundance information. IMPORTANCE Microbes are known to facilitate vertebrate decomposition, and they can do so in a repeatable, predictable manner. The succession of microbes in the skin and associated soil can be used to predict time since death during the first few weeks of decomposition. However, when remains are discovered after months or years, often the only evidence are skeletal remains. To determine if microbial succession in bone would be useful for estimating time since death after several months, human subjects were placed to decompose in the spring and summer seasons. Ribs were collected after 1 to 9 months of decomposition, and the bone microbial communities were characterized. Analysis revealed a core bone decomposer microbial community with some differences in microbial assembly occurring between seasons. These data provided time since death estimates of approximately ±34 days over 9 months. This may provide forensic investigators with a tool for estimating time since death of skeletal remains, for which there are few current methods.
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Affiliation(s)
- Heather Deel
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra L. Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer Kiely
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | | | - David O. Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, USA
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, Hawaii, USA
| | - Aaron Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- 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, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Jessica L. Metcalf
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
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14
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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15
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Trumbo ST, Sikes DS. Resource concealment and the evolution of parental care in burying beetles. J Zool (1987) 2021. [DOI: 10.1111/jzo.12916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. T. Trumbo
- Department of Ecology and Evolutionary Biology University of Connecticut Waterbury CT USA
| | - D. S. Sikes
- Department of Biology and Wildlife University of Alaska Museum University of Alaska Fairbanks Fairbanks AK USA
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16
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Newsome TM, Barton B, Buck JC, DeBruyn J, Spencer E, Ripple WJ, Barton PS. Monitoring the dead as an ecosystem indicator. Ecol Evol 2021; 11:5844-5856. [PMID: 34141188 PMCID: PMC8207411 DOI: 10.1002/ece3.7542] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Dead animal biomass (carrion) is present in all terrestrial ecosystems, and its consumption, decomposition, and dispersal can have measurable effects on vertebrates, invertebrates, microbes, parasites, plants, and soil. But despite the number of studies examining the influence of carrion on food webs, there has been no attempt to identify how general ecological processes around carrion might be used as an ecosystem indicator. We suggest that knowledge of scavenging and decomposition rates, scavenger diversity, abundance, and behavior around carrion, along with assessments of vegetation, soil, microbe, and parasite presence, can be used individually or in combination to understand food web dynamics. Monitoring carrion could also assist comparisons of ecosystem processes among terrestrial landscapes and biomes. Although there is outstanding research needed to fully integrate carrion ecology and monitoring into ecosystem management, we see great potential in using carrion as an ecosystem indicator of an intact and functional food web.
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Affiliation(s)
- Thomas M. Newsome
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
| | - Brandon Barton
- Department of Biological SciencesMississippi State UniversityMississippi StateMSUSA
| | - Julia C. Buck
- Biology and Marine BiologyUniversity of North Carolina WilmingtonWilmingtonNCUSA
| | - Jennifer DeBruyn
- Biosystems Engineering and Soil ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Emma Spencer
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
| | - William J. Ripple
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| | - Philip S. Barton
- School of ScienceFederation University AustraliaMt HelenVICAustralia
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17
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Bisker C, Taylor G, Carney H, Ralebitso-Senior TK. A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.605817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introducing animal carbon-source to soil initiates biochemical and microbial processes that lead to its decomposition and recycling, which subsequently cause successional shifts in soil microbial community. To investigate the use of soil microbial community to inform criminal investigation, this study was designed to mimic clandestine graves. It compared the decomposition of stillborn piglets (Sus scrofa domesticus), as human analogues, to oak (Quercus robur) leaf litter and soil-only controls outdoors for 720 days. Environmental and edaphic parameters were monitored and showed soil microbial community alignment with temperature seasonality, which highlighted the importance of this abiotic factor. Denaturing gradient gel electrophoresis (DGGE) data were used to calculate Hill numbers and diversity indices of the bacterial 16S rRNA community did not distinguish mammalian- from plant-based decomposition consistently during the first or second year of the study. In contrast, the fungal 18S rRNA community allowed clear differentiation between different treatments (beta diversity) throughout the 720-day experiment and suggested the moment of the decomposing mammalian skin rupture. 16S rRNA-based NGS facilitated the identification of e.g., Pirellulaceae, Acidobacteria ii1-15_order and Candidatus xiphinematobacter as Year 2 bacterial markers of gravesoil at family, order and species taxonomic levels, respectively, and confirmed the similarity of the calculated Hill diversity metrics with those derived from DGGE profiling. Parallel soil elemental composition was measured by portable X-ray Fluorescence where calcium profiles for the piglet-associated soils were distinct from those without carrion. Also, soil calcium content and PMI correlated positively during the first year then negatively during the second. This study is one of the first to apply a multidisciplinary approach based on molecular and physicochemical analytical techniques to assess decomposition. It highlights the recognised potential of using soil microbial community in forensic investigations and provides a proof-of-concept for the application of a combined molecular and elemental approach to further understand the dynamics of decomposition. In addition, it sets the scene for further research in different conditions based on Hill numbers metrics instead of the classic ecological indices for soil necrobiome richness, diversity and evenness.
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18
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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] [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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19
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Trumbo ST, Philbrick PKB, Stökl J, Steiger S. Burying Beetle Parents Adaptively Manipulate Information Broadcast from a Microbial Community. Am Nat 2021; 197:366-378. [PMID: 33625971 DOI: 10.1086/712602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractMicrobial volatiles provide essential information for animals, which compete to detect, respond to, and perhaps control this information. Burying beetle parents have the opportunity to influence microbially derived semiochemicals, because they monopolize a small carcass for their family, repairing feeding holes and applying exudates that alter the microbial community. To study adaptive manipulation of microbial cues, we integrated mechanistic and functional approaches. We contrasted gas chromatography-mass spectrometry (GC-MS) volatile profiles from carcasses that were or were not prepared by a resident pair of Nicrophorus orbicollis. Methyl thiocyanate (MeSCN), the primary attractant for burying beetles seeking a fresh carcass, was reduced 20-fold by carcass preparation, while dimethyl trisulfide (DMTS), which deters breeding beetles, was increased 20-fold. These results suggest that parental care serves to make previously public information more private (crypsis, MeSCN) and to disinform rivals with a deterrent (DMTS). Functional tests in the field demonstrated that carcass preparation reduced discovery and use by congeners (threefold) as well as by dipteran rivals. Because microbes and their chemicals influence nearly every aspect of animal ecology, animal manipulation of microbial cues may be as widespread as manipulation of their own signals.
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20
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DeBruyn JM, Hoeland KM, Taylor LS, Stevens JD, Moats MA, Bandopadhyay S, Dearth SP, Castro HF, Hewitt KK, Campagna SR, Dautartas AM, Vidoli GM, Mundorff AZ, Steadman DW. Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles. Front Microbiol 2021; 11:608856. [PMID: 33519758 PMCID: PMC7838218 DOI: 10.3389/fmicb.2020.608856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Vertebrate decomposition processes have important ecological implications and, in the case of human decomposition, forensic applications. Animals, especially domestic pigs (Sus scrofa), are frequently used as human analogs in forensic decomposition studies. However, recent research shows that humans and pigs do not necessarily decompose in the same manner, with differences in decomposition rates, patterns, and scavenging. The objective of our study was to extend these observations and determine if human and pig decomposition in terrestrial settings have different local impacts on soil biogeochemistry and microbial activity. In two seasonal trials (summer and winter), we simultaneously placed replicate human donors and pig carcasses on the soil surface and allowed them to decompose. In both human and pig decomposition-impacted soils, we observed elevated microbial respiration, protease activity, and ammonium, indicative of enhanced microbial ammonification and limited nitrification in soil during soft tissue decomposition. Soil respiration was comparable between summer and winter, indicating similar microbial activity; however, the magnitude of the pulse of decomposition products was greater in the summer. Using untargeted metabolomics and lipidomics approaches, we identified 38 metabolites and 54 lipids that were elevated in both human and pig decomposition-impacted soils. The most frequently detected metabolites were anthranilate, creatine, 5-hydroxyindoleacetic acid, taurine, xanthine, N-acetylglutamine, acetyllysine, and sedoheptulose 1/7-phosphate; the most frequently detected lipids were phosphatidylethanolamine and monogalactosyldiacylglycerol. Decomposition soils were also significantly enriched in metabolites belonging to amino acid metabolic pathways and the TCA cycle. Comparing humans and pigs, we noted several differences in soil biogeochemical responses. Soils under humans decreased in pH as decomposition progressed, while under pigs, soil pH increased. Additionally, under pigs we observed significantly higher ammonium and protease activities compared to humans. We identified several metabolites that were elevated in human decomposition soil compared to pig decomposition soil, including 2-oxo-4-methylthiobutanoate, sn-glycerol 3-phosphate, and tryptophan, suggesting different decomposition chemistries and timing between the two species. Together, our work shows that human and pig decomposition differ in terms of their impacts on soil biogeochemistry and microbial decomposer activities, adding to our understanding of decomposition ecology and informing the use of non-human models in forensic research.
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Affiliation(s)
- Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Katharina M Hoeland
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lois S Taylor
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jessica D Stevens
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michelle A Moats
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sreejata Bandopadhyay
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Stephen P Dearth
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Hector F Castro
- Biological and Small Molecule Mass Spectrometry Core, Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kaitlin K Hewitt
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R Campagna
- Biological and Small Molecule Mass Spectrometry Core, Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Angela M Dautartas
- Department of Anthropology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Giovanna M Vidoli
- Department of Anthropology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Amy Z Mundorff
- Department of Anthropology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Dawnie W Steadman
- Department of Anthropology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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21
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Harrison L, Kooienga E, Speights C, Tomberlin J, Lashley M, Barton B, Jordan H. Microbial succession from a subsequent secondary death event following mass mortality. BMC Microbiol 2020; 20:309. [PMID: 33050884 PMCID: PMC7557037 DOI: 10.1186/s12866-020-01969-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/08/2020] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Each death event can be characterized by its associated microbes - a living community of bacteria composed of carcass, soil, and insect-introduced bacterial species - a necrobiome. With the possibility for close succession of these death events, it may be beneficial to characterize how the magnitude of an initial death event may impact the decomposition and necrobiomes of subsequent death events in close proximity. In this paper we hope to characterize the microbial communities associated with a proximate subsequent death event, and distinguish any changes within those communities based on the magnitude of an initial death event and the biomass of preexisting carcass (es) undergoing decomposition. For this experiment, 6 feral swine carcasses in containers were placed in the vicinity of preexisting and ongoing carcass decomposition at sites of three different scales of decomposing carcass biomass. Swab samples were collected from the skin and eye sockets of the container pigs and subjected to 16 s rRNA sequencing and OTU assignment. RESULTS PERMANOVA analysis of the bacterial taxa showed that there was no significant difference in the bacterial communities based on initial mortality event biomass size, but we did see a change in the bacterial communities over time, and slight differences between the skin and ocular cavity communities. Even without soil input, necrobiome communities can change rapidly. Further characterization of the bacterial necrobiome included utilization of the Random Forest algorithm to identify the most important predictors for time of decomposition. Sample sets were also scanned for notable human and swine-associated pathogens. CONCLUSIONS The applications from this study are many, ranging from establishing the environmental impacts of mass mortality events to understanding the importance of scavenger, and scavenger microbial community input on decomposition.
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Affiliation(s)
- Lindsay Harrison
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Emilia Kooienga
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Cori Speights
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Jeffery Tomberlin
- Department of Entomology, Texas A&M University, Minnie Bell Heep Center, Suite 412, College Station, TX, 77843, USA
| | - Marcus Lashley
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Box 9680, Mississippi State, MS, 39762, USA
| | - Brandon Barton
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Heather Jordan
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA.
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22
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Trumbo ST, Steiger S. Finding a fresh carcass: bacterially derived volatiles and burying beetle search success. CHEMOECOLOGY 2020. [DOI: 10.1007/s00049-020-00318-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Salerian AJ. Response to letter to the editor by Drs Jaloux, Amatore, Macagno, Moranda and Casanova. Burns 2020; 47:256. [PMID: 33303265 DOI: 10.1016/j.burns.2020.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/07/2020] [Indexed: 11/25/2022]
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24
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Junkins EN, Speck M, Carter DO. The microbiology, pH, and oxidation reduction potential of larval masses in decomposing carcasses on Oahu, Hawaii. J Forensic Leg Med 2019; 67:37-48. [DOI: 10.1016/j.jflm.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/02/2019] [Accepted: 08/08/2019] [Indexed: 01/08/2023]
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25
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Fungal succession during mammalian cadaver decomposition and potential forensic implications. Sci Rep 2019; 9:12907. [PMID: 31501472 PMCID: PMC6733900 DOI: 10.1038/s41598-019-49361-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/24/2019] [Indexed: 02/02/2023] Open
Abstract
The necrobiome is the postmortem community that includes bacteria, fungi, arthropods, and other cadaver-associated organisms. It has been suggested as biological evidence for forensic investigation. Fungi form distinctive mildew spots in colonizing decomposing bodies, converting them into moldy cadavers. However, the postmortem fungal community consists of more than these visible species. Characterizing the succession pattern of the fungal community during decomposition is valuable not only for understanding the ecosystem composition of the cadaver decomposition islands but also for contributing to forensic investigations. In the present study, the fungal composition of pig cadavers and succession patterns during decomposition were investigated with high-throughput sequencing. The succession patterns were easier to discern in outdoor cadavers, compared with those that were placed indoors. The metabarcoding approach revealed trends linking particular fungal taxa with specific postmortem intervals (PMIs). Dominant species increased notably in cadavers and soil. Furthermore, the succession of the soil community was driven by the cadaver decomposition. Significant mycoflora differences were observed between environmental and cadaveric soil. The results obtained suggested that postputrefaction mycoflora have considerable potential for PMI estimation, particularly in cases that involve heavily decomposed bodies. In addition, the diversity of fungal communities revealed by the metabarcoding approach allowed us to discriminate the sites of cadaver decomposition, implying that postputrefaction mycoflora may be helpful in identifying the environment in which a cadaver has been placed, or the original location from which a cadaver has been moved. Our results provide an important step towards developing fungal evidence for use in forensic science and add to the growing body of work on postmortem microbial communities.
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Cernosek T, Eckert KE, Carter DO, Perrault KA. Volatile Organic Compound Profiling from Postmortem Microbes using Gas Chromatography-Mass Spectrometry. J Forensic Sci 2019; 65:134-143. [PMID: 31479524 DOI: 10.1111/1556-4029.14173] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/29/2022]
Abstract
Volatile organic compounds (VOCs) are by-products of cadaveric decomposition and are responsible for the odor associated with decomposing remains. The direct link between VOC production and individual postmortem microbes has not been well characterized experimentally. The purpose of this study was to profile VOCs released from three postmortem bacterial isolates (Bacillus subtilis, Ignatzschineria indica, I. ureiclastica) using solid-phase microextraction arrow (SPME Arrow) and gas chromatography-mass spectrometry (GC-MS). Species were inoculated in headspace vials on Standard Nutrient Agar and monitored over 5 days at 24°C. Each species exhibited a different VOC profile that included common decomposition VOCs. VOCs exhibited upward or downward temporal trends over time. Ignatzschineria indica produced a large amount of dimethyldisulfide. Other compounds of interest included alcohols, aldehydes, aromatics, and ketones. This provides foundational data to link decomposition odor with specific postmortem microbes to improve understanding of underlying mechanisms for decomposition VOC production.
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Affiliation(s)
- Terezie Cernosek
- Laboratory of Forensic and Bioanalytical Chemistry, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, HI
| | - Kevin E Eckert
- Laboratory of Forensic and Bioanalytical Chemistry, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, HI
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, HI
| | - Katelynn A Perrault
- Laboratory of Forensic and Bioanalytical Chemistry, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, HI
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Barton PS, Evans MJ, Foster CN, Pechal JL, Bump JK, Quaggiotto MM, Benbow ME. Towards Quantifying Carrion Biomass in Ecosystems. Trends Ecol Evol 2019; 34:950-961. [PMID: 31256926 DOI: 10.1016/j.tree.2019.06.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/13/2019] [Accepted: 06/04/2019] [Indexed: 11/25/2022]
Abstract
The decomposition of animal biomass (carrion) contributes to the recycling of energy and nutrients through ecosystems. Whereas the role of plant decomposition in ecosystems is broadly recognised, the significance of carrion to ecosystem functioning remains poorly understood. Quantitative data on carrion biomass are lacking and there is no clear pathway towards improved knowledge in this area. Here, we present a framework to show how quantities derived from individual carcasses can be scaled up using population metrics, allowing for comparisons among ecosystems and other forms of biomass. Our framework facilitates the generation of new data that is critical to building a quantitative understanding of the contribution of carrion to trophic processes and ecosystem stocks and flows.
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Affiliation(s)
- Philip S Barton
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, 2601, Australia.
| | - Maldwyn J Evans
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Claire N Foster
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Joseph K Bump
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - M-Martina Quaggiotto
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G12 8QQ, UK
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI 48824, USA
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Burcham ZM, Cowick CA, Baugher CN, Pechal JL, Schmidt CJ, Rosch JW, Benbow ME, Jordan HR. Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition. J Forensic Sci 2019; 64:1707-1719. [DOI: 10.1111/1556-4029.14083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Zachary M. Burcham
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Caitlyn A. Cowick
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Courtney N. Baugher
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Jennifer L. Pechal
- Department of Entomology Michigan State University 288 Farm Ln #243 East Lansing MI 48824
| | - Carl J. Schmidt
- Department of Pathology University of Michigan Medical Science Unit I, 1301 Catherine St Ann Arbor MI 48109
| | - Jason W. Rosch
- Department of Infectious Disease St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105
| | - M. Eric Benbow
- Department of Entomology Michigan State University 288 Farm Ln #243 East Lansing MI 48824
- Department of Osteopathic Medical Specialties Michigan State University West Fee Hall, 909 Fee Road East Lansing MI 48824
| | - Heather R. Jordan
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
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Metcalf JL. Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption. Forensic Sci Int Genet 2019; 38:211-218. [DOI: 10.1016/j.fsigen.2018.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/30/2022]
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Keenan SW, Emmons AL, Taylor LS, Phillips G, Mason AR, Mundorff AZ, Bernard EC, Davoren J, DeBruyn JM. Spatial impacts of a multi-individual grave on microbial and microfaunal communities and soil biogeochemistry. PLoS One 2018; 13:e0208845. [PMID: 30540836 PMCID: PMC6291161 DOI: 10.1371/journal.pone.0208845] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/25/2018] [Indexed: 12/24/2022] Open
Abstract
Decomposing vertebrates, including humans, result in pronounced changes in surrounding soil biogeochemistry, particularly nitrogen (N) and carbon (C) availability, and alter soil micro- and macrofauna. However, the impacts of subsurface human decomposition, where oxygen becomes limited and microbial biomass is generally lower, are far less understood. The goals of this study were to evaluate the impact of human decomposition in a multi-individual, shallow (~70 cm depth) grave on soil biogeochemistry and soil microbial and nematode communities. Three individuals were interred and allowed to decay for four years. Soils were collected from two depths (0‒5 and 30‒35 cm) along linear transects radiating from the grave as well as from within and below (85‒90 cm depth) the grave during excavation to assess how decomposition affects soil properties. Along radiating surface transects, several extracellular enzymes rates and nematode richness increased with increasing distance from the grave, and likely reflect physical site disruption due to grave excavation and infill. There was no evidence of carcass-sourced C and N lateral migration from the grave, at least at 30‒35 cm depth. Within the grave, soils exhibited significant N-enrichment (e.g., ammonium, dissolved organic N), elevated electrical conductivity, and elevated respiration rates with depth. Soil biogeochemistry within the grave, particularly in the middle (30‒35 cm) and base (70‒75 cm depth), was significantly altered by human decomposition. Mean microbial gene abundances changed with depth in the grave, demonstrating increased microbial presence in response to ongoing decomposition. Human-associated Bacteroides were only detected at the base of the grave where anoxic conditions prevailed. Nematode community abundance and richness were reduced at 70‒75 cm and not detectable below 85‒90 cm. Further, we identified certain Plectus spp. as potential indicators of enrichment due to decomposition. Here we demonstrate that human decomposition influences soil biogeochemistry, microbes, and microfauna up to four years after burial.
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Affiliation(s)
- Sarah W. Keenan
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (SWK); (JMD)
| | - Alexandra L. Emmons
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Lois S. Taylor
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Gary Phillips
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Allison R. Mason
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Amy Z. Mundorff
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ernest C. Bernard
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jon Davoren
- Bode Cellmark Forensics, Lorton, Virginia, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (SWK); (JMD)
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Benbow ME, Barton PS, Ulyshen MD, Beasley JC, DeVault TL, Strickland MS, Tomberlin JK, Jordan HR, Pechal JL. Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1331] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- M. Eric Benbow
- Department of Entomology; Michigan State University; East Lansing Michigan 48824 USA
- Department of Osteopathic Medical Specialties; Michigan State University; East Lansing Michigan 48824 USA
- Ecology, Evolutionary Biology and Behavior Program; Michigan State University; East Lansing Michigan 48824 USA
| | - Philip S. Barton
- Fenner School of Environment and Society; Australian National University; Canberra Australian Capital Territory 2601 Australia
| | | | - James C. Beasley
- Savannah River Ecology Laboratory and Warnell School of Forestry and Natural Resources; University of Georgia; Aiken South Carolina 29802 USA
| | - Travis L. DeVault
- U.S. Department of Agriculture; National Wildlife Research Center; Sandusky Ohio 44870 USA
| | | | | | - Heather R. Jordan
- Department of Biological Sciences; Mississippi State University; Mississippi Mississippi 39762 USA
| | - Jennifer L. Pechal
- Department of Entomology; Michigan State University; East Lansing Michigan 48824 USA
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Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Detecting eukaryotic microbiota with single-cell sensitivity in human tissue. MICROBIOME 2018; 6:151. [PMID: 30172254 PMCID: PMC6119588 DOI: 10.1186/s40168-018-0529-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Fetal growth restriction, pre-eclampsia, and pre-term birth are major adverse pregnancy outcomes. These complications are considerable contributors to fetal/maternal morbidity and mortality worldwide. A significant proportion of these cases are thought to be due to dysfunction of the placenta. However, the underlying mechanisms of placental dysfunction are unclear. The aim of the present study was to investigate whether adverse pregnancy outcomes are associated with evidence of placental eukaryotic infection. RESULTS We modified the 18S Illumina Amplicon Protocol of the Earth Microbiome Project and made it capable of detecting just a single spiked-in genome copy of Plasmodium falciparum, Saccharomyces cerevisiae, or Toxoplasma gondii among more than 70,000 human cells. Using this method, we were unable to detect eukaryotic pathogens in placental biopsies in instances of adverse pregnancy outcome (n = 199) or in healthy controls (n = 99). CONCLUSIONS Eukaryotic infection of the placenta is not an underlying cause of the aforementioned pregnancy complications. Possible clinical applications for this non-targeted, yet extremely sensitive, eukaryotic screening method are manifest.
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Affiliation(s)
- Susanne Lager
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition. Forensic Sci Int 2018; 288:53-58. [DOI: 10.1016/j.forsciint.2018.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 02/23/2018] [Accepted: 04/07/2018] [Indexed: 12/19/2022]
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35
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Temporal dynamics of microbiota before and after host death. ISME JOURNAL 2018; 12:2076-2085. [PMID: 29867210 PMCID: PMC6052066 DOI: 10.1038/s41396-018-0157-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/24/2018] [Accepted: 05/01/2018] [Indexed: 02/07/2023]
Abstract
The habitats that animals, humans and plants provide for microbial communities are inevitably transient, changing drastically when these hosts die. Because microbes associated with living hosts are ensured prime access to the deceased host’s organic matter, it is feasible that opportunistic, adaptable lifestyles are widespread among host-associated microbes. Here we investigate the temporal dynamics of microbiota by starving to death a host—the planktonic Crustacean Daphnia magna—and tracking the changes in its microbial community as it approaches death, dies and decomposes. Along with obligate host-associated microbes that vanished after the host’s death and decomposers that appeared after the host’s death, we also detected microbes with opportunistic lifestyles, seemingly capable of exploiting the host even before its death. We suggest that the period around host death plays an important role for host–microbiota ecology and for the evolution of hosts and their microbes.
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36
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Nawrocki EM, Bradshaw M, Johnson EA. Botulinum neurotoxin-encoding plasmids can be conjugatively transferred to diverse clostridial strains. Sci Rep 2018; 8:3100. [PMID: 29449580 PMCID: PMC5814558 DOI: 10.1038/s41598-018-21342-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Most Group I Clostridium botulinum strains harbor botulinum neurotoxin (bont) genes on their chromosome, while some carry these genes (including bont/a, bont/b, and bont/f) on large plasmids. Prior work in our laboratory demonstrated that Group I BoNT plasmids were mobilized to C. botulinum recipient strains containing the Tn916 transposon. Here, we show that Tn916 is nonessential for plasmid transfer. Relying on an auxotrophic donor phenotype and a plasmid-borne selectable marker, we observed the transfer of pCLJ, a 270 kb plasmid harboring two bont genes, from its host strain to various clostridia. Transfer frequency was greatest to other Group I C. botulinum strains, but the plasmid was also transferred into traditionally nontoxigenic species, namely C. sporogenes and C. butyricum. Expression and toxicity of BoNT/A4 was confirmed in transconjugants by immunoblot and mouse bioassay. These data indicate that conjugation within the genus Clostridium can occur across physiological Groups of C. botulinum, supporting horizontal gene transfer via bont-bearing plasmids. The transfer of plasmids possessing bont genes to resistant Clostridium spp. such as C. sporogenes could impact biological safety for animals and humans. These plasmids may play an environmental role in initiating death in vertebrates, leading to decomposition and nutrient recycling of animal biomass.
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Affiliation(s)
- Erin M Nawrocki
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marite Bradshaw
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric A Johnson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Singh B, Minick KJ, Strickland MS, Wickings KG, Crippen TL, Tarone AM, Benbow ME, Sufrin N, Tomberlin JK, Pechal JL. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function. Front Microbiol 2018; 8:2616. [PMID: 29354106 PMCID: PMC5758501 DOI: 10.3389/fmicb.2017.02616] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/14/2017] [Indexed: 01/06/2023] Open
Abstract
As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.
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Affiliation(s)
- Baneshwar Singh
- Department of Forensic Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Kevan J. Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Michael S. Strickland
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, United States
| | - Kyle G. Wickings
- Department of Entomology, Cornell University, Geneva, NY, United States
| | - Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - M. Eric Benbow
- Department of Entomology and Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, United States
| | - Ness Sufrin
- Bode Cellmark Forensics, Lorton, VA, United States
| | - Jeffery K. Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Jennifer L. Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, United States
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Belk AD, Deel HL, Burcham ZM, Knight R, Carter DO, Metcalf JL. Animal models for understanding microbial decomposition of human remains. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Mbareche H, Veillette M, Bonifait L, Dubuis ME, Benard Y, Marchand G, Bilodeau GJ, Duchaine C. A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 601-602:1306-1314. [PMID: 28605849 DOI: 10.1016/j.scitotenv.2017.05.235] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/19/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
Composting is used all over the world to transform different types of organic matter through the actions of complex microbial communities. Moving and handling composting material may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects among compost industry workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in compost as well as in the aerosols emitted through composting activities. The aim of this study was to analyze the fungal diversity of both organic matter and aerosols present in facilities that process domestic compost and facilities that process pig carcasses. This was accomplished using a next generation sequencing approach that targets the ITS1 genomic region. Multivariate analyses revealed differences in the fungal community present in samples coming from compost treating both raw materials. Furthermore, results show that the compost type affects the fungal diversity of aerosols emitted. Although 8 classes were evenly distributed in all samples, Eurotiomycetes were more dominant in carcass compost while Sordariomycetes were dominant in domestic compost. A large diversity profile was observed in bioaerosols from both compost types showing the presence of a number of pathogenic fungi newly identified in bioaerosols emitted from composting plants. Members of the family Herpotrichiellaceae and Gymnoascaceae which have been shown to cause human diseases were detected in compost and air samples. Moreover, some fungi were identified in higher proportion in air compared to compost. This is the first study to identify a high level of fungal diversity in bioaerosols present in composting plants suggesting a potential exposure risk for workers. This study suggests the need for creating guidelines that address human exposure to bioaerosols. The implementation of technical and organizational measure should be a top priority. However, skin and respiratory protection for compost workers could be used to reduce the exposure as a second resort.
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Affiliation(s)
- Hamza Mbareche
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Qc, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Laval university, Quebec City, Qc, Canada
| | - Marc Veillette
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Qc, Canada
| | - Laetitia Bonifait
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Qc, Canada
| | - Marie-Eve Dubuis
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Qc, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Laval university, Quebec City, Qc, Canada
| | - Yves Benard
- Centre de Recherche Industrielle du Québec (CRIQ), Quebec City, Qc, Canada
| | - Geneviève Marchand
- Institut de Recherche Robert-Sauvé en Santé et en Sécurité du travail (IRSST), Montreal, Qc, Canada
| | - Guillaume J Bilodeau
- Pathogen Identification Research Lab, Canadian Food Inspection Agency (CFIA), Ottawa, Canada
| | - Caroline Duchaine
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Qc, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Laval university, Quebec City, Qc, Canada.
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40
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Handke J, Procopio N, Buckley M, van der Meer D, Williams G, Carr M, Williams A. Successive bacterial colonisation of pork and its implications for forensic investigations. Forensic Sci Int 2017; 281:1-8. [PMID: 29080415 DOI: 10.1016/j.forsciint.2017.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 10/11/2017] [Indexed: 11/26/2022]
Abstract
AIMS Bacteria are considered one of the major driving forces of the mammalian decomposition process and have only recently been recognised as forensic tools. At this point, little is known about their potential use as 'post-mortem clocks'. This study aimed to establish the proof of concept for using bacterial identification as post-mortem interval (PMI) indicators, using a multi-omics approach. METHODS AND RESULTS Pieces of pork were placed in the University's outdoor facility and surface swabs were taken at regular intervals up to 60 days. Terminal restriction fragment length polymorphism (T-RFLP) of the 16S rDNA was used to identify bacterial taxa. It succeeded in detecting two out of three key contributors involved in decomposition and represents the first study to reveal Vibrionaceae as abundant on decomposing pork. However, a high fraction of present bacterial taxa could not be identified by T-RFLP. Proteomic analyses were also performed at selected time points, and they partially succeeded in the identification of precise strains, subspecies and species of bacteria that colonized the body after different PMIs. CONCLUSION T-RFLP is incapable of reliably and fully identifying bacterial taxa, whereas proteomics could help in the identification of specific strains of bacteria. Nevertheless, microbial identification by next generation sequencing might be used as PMI clock in future investigations and in conjunction with information provided by forensic entomologists. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this work represents the first attempt to find a cheaper and easily accessible, culture-independent alternative to high-throughput techniques to establish a 'microbial clock', in combination with proteomic strategies to address this issue.
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Affiliation(s)
- Jessica Handke
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK; Institute for Interdisciplinary Studies, University of Amsterdam, P.O. Box 19268, 1000 GG Amsterdam, Netherlands.
| | - Noemi Procopio
- Manchester Institute of Biotechnology, 131 Princess Street, University of Manchester, Manchester M1 7DN, UK.
| | - Michael Buckley
- Manchester Institute of Biotechnology, 131 Princess Street, University of Manchester, Manchester M1 7DN, UK.
| | - Dieudonne van der Meer
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Graham Williams
- School of Law, Forensics and Policing, Staffordshire University, Stoke-on-Trent, Staffordshire ST4 2DE, UK.
| | - Martin Carr
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Anna Williams
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
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Valseth K, Nesbø CL, Easterday WR, Turner WC, Olsen JS, Stenseth NC, Haverkamp THA. Temporal dynamics in microbial soil communities at anthrax carcass sites. BMC Microbiol 2017; 17:206. [PMID: 28950879 PMCID: PMC5615460 DOI: 10.1186/s12866-017-1111-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. RESULTS The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. CONCLUSION Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.
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Affiliation(s)
- Karoline Valseth
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, The Kristine Bonnevie Building, UiO, campus Blindern, Blindern, Oslo, Norway.,Norwegian Defence Research Establishment, Kjeller, Norway
| | - Camilla L Nesbø
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, The Kristine Bonnevie Building, UiO, campus Blindern, Blindern, Oslo, Norway.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - W Ryan Easterday
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, The Kristine Bonnevie Building, UiO, campus Blindern, Blindern, Oslo, Norway
| | - Wendy C Turner
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Jaran S Olsen
- Norwegian Defence Research Establishment, Kjeller, Norway
| | - Nils Chr Stenseth
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, The Kristine Bonnevie Building, UiO, campus Blindern, Blindern, Oslo, Norway
| | - Thomas H A Haverkamp
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, The Kristine Bonnevie Building, UiO, campus Blindern, Blindern, Oslo, Norway.
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Rózsa L, Apari P, Sulyok M, Tappe D, Bodó I, Hardi R, Müller V. The evolutionary logic of sepsis. INFECTION GENETICS AND EVOLUTION 2017; 55:135-141. [PMID: 28899789 DOI: 10.1016/j.meegid.2017.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/23/2022]
Abstract
The recently proposed Microbiome Mutiny Hypothesis posits that members of the human microbiome obtain information about the host individuals' health status and, when host survival is compromised, switch to an intensive exploitation strategy to maximize residual transmission. In animals and humans, sepsis is an acute systemic reaction to microbes invading the normally sterile body compartments. When induced by formerly mutualistic or neutral microbes, possibly in response to declining host health, sepsis appears to fit the 'microbiome mutiny' scenario except for its apparent failure to enhance transmission of the causative organisms. We propose that the ability of certain species of the microbiome to induce sepsis is not a fortuitous side effect of within-host replication, but rather it might, in some cases, be the result of their adaptive evolution. Whenever host health declines, inducing sepsis can be adaptive for those members of the healthy human microbiome that are capable of colonizing the future cadaver and spread by cadaver-borne transmission. We hypothesize that such microbes might exhibit switches along the 'mutualist - lethal pathogen - decomposer - mutualist again' scenario, implicating a previously unsuspected, surprising level of phenotypic plasticity. This hypothesis predicts that those species of the healthy microbiome that are recurring causative agents of sepsis can participate in the decomposition of cadavers, and can be transmitted as soil-borne or water-borne infections. Furthermore, in individual sepsis cases, the same microbial clones that dominate the systemic infection that precipitates sepsis, should also be present in high concentration during decomposition following death: this prediction is testable by molecular fingerprinting in experimentally induced animal models. Sepsis is a leading cause of human death worldwide. If further research confirms that some cases of sepsis indeed involve the 'mutiny' (facultative phenotypic switching) of normal members of the microbiome, then new strategies could be devised to prevent or treat sepsis by interfering with this process.
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Affiliation(s)
- Lajos Rózsa
- MTA-ELTE-MTM Ecology Research Group, Budapest, Pázmány P. s. 1/C, H-1117, Hungary; Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary.
| | - Péter Apari
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Mihály Sulyok
- Institute of Tropical Medicine, Eberhard Karls University, Tübingen, Germany
| | | | - Imre Bodó
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Richárd Hardi
- St. Raphael Ophthalmological Center, Ophthalmological Ambulance, Mbuji Mayi, Democratic Republic of Congo
| | - Viktor Müller
- Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary; Institute of Biology, Eötvös Loránd University, Budapest, Hungary; Parmenides Center for the Conceptual Foundations of Science, Pullach, Munich, Germany.
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Postmortem microbial communities in burial soil layers of skeletonized humans. J Forensic Leg Med 2017; 49:43-49. [DOI: 10.1016/j.jflm.2017.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/17/2017] [Accepted: 05/01/2017] [Indexed: 11/21/2022]
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Emmons AL, DeBruyn JM, Mundorff AZ, Cobaugh KL, Cabana GS. The persistence of human DNA in soil following surface decomposition. Sci Justice 2017; 57:341-348. [PMID: 28889863 DOI: 10.1016/j.scijus.2017.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/06/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023]
Abstract
Though recent decades have seen a marked increase in research concerning the impact of human decomposition on the grave soil environment, the fate of human DNA in grave soil has been relatively understudied. With the purpose of supplementing the growing body of literature in forensic soil taphonomy, this study assessed the relative persistence of human DNA in soil over the course of decomposition. Endpoint PCR was used to assess the presence or absence of human nuclear and mitochondrial DNA, while qPCR was used to evaluate the quantity of human DNA recovered from the soil beneath four cadavers at the University of Tennessee's Anthropology Research Facility (ARF). Human nuclear DNA from the soil was largely unrecoverable, while human mitochondrial DNA was detectable in the soil throughout all decomposition stages. Mitochondrial DNA copy abundances were not significantly different between decomposition stages and were not significantly correlated to soil edaphic parameters tested. There was, however, a significant positive correlation between mitochondrial DNA copy abundances and the human associated bacteria, Bacteroides, as estimated by 16S rRNA gene abundances. These results show that human mitochondrial DNA can persist in grave soil and be consistently detected throughout decomposition.
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Affiliation(s)
- Alexandra L Emmons
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
| | - Jennifer M DeBruyn
- Dept. of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Drive, Knoxville, TN 37996-4531, United States.
| | - Amy Z Mundorff
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
| | - Kelly L Cobaugh
- Dept. of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Drive, Knoxville, TN 37996-4531, United States.
| | - Graciela S Cabana
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
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Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00672-16. [PMID: 27469950 PMCID: PMC4966454 DOI: 10.1128/genomea.00672-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We announce a draft genome sequence of a Proteus mirabilis strain derived from Lucilia sericata salivary glands. This strain is demonstrated to attract and induce oviposition by L. sericata, a common blow fly important to medicine, agriculture, and forensics. The genome sequence will help dissect interkingdom communication between the species.
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Finley SJ, Pechal JL, Benbow ME, Robertson BK, Javan GT. Microbial Signatures of Cadaver Gravesoil During Decomposition. MICROBIAL ECOLOGY 2016; 71:524-529. [PMID: 26748499 DOI: 10.1007/s00248-015-0725-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.
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Affiliation(s)
- Sheree J Finley
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - B K Robertson
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Gulnaz T Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, 915 S. Jackson St., Hatch Hall Building Room 251, Montgomery, AL, 36104, USA.
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Javan GT, Finley SJ, Abidin Z, Mulle JG. The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death. Front Microbiol 2016; 7:225. [PMID: 26941736 PMCID: PMC4764706 DOI: 10.3389/fmicb.2016.00225] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
Abstract
Death is a universal phenomenon; however, is there "life after death?" This topic has been investigated for centuries but still there are gray areas that have yet to be elucidated. Forensic microbiologists are developing new applications to investigate the dynamic and coordinated changes in microbial activity that occur when a human host dies. There is currently a paucity of explorations of the thanatomicrobiome (thanatos-, Greek for death) and epinecrotic communities (microbial communities residing in and/or moving on the surface of decomposing remains). Ongoing studies can help clarify the structure and function of these postmortem microbiomes. Human microbiome studies have revealed that 75-90% of cells in the body prior to death are microbial. Upon death, putrefaction occurs and is a complicated process encompassing chemical degradation and autolysis of cells. Decomposition also involves the release of contents of the intestines due to enzymes under the effects of abiotic and biotic factors. These factors likely have predictable effects on postmortem microbial communities and can be leveraged for forensic studies. This mini review provides a critical examination of emerging research relating to thanatomicrobiome and epinecrotic communities, how each is studied, and possible strategies of stochastic processes.
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Affiliation(s)
- Gulnaz T. Javan
- Forensic Science Program, Physical Sciences Department, Alabama State UniversityMontgomery, AL, USA
| | - Sheree J. Finley
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State UniversityMontgomery, AL, USA
| | - Zain Abidin
- Forensic Science Program, Physical Sciences Department, Alabama State UniversityMontgomery, AL, USA
| | - Jennifer G. Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory UniversityAtlanta, GA, USA
- Department of Human Genetics, School of Medicine, Emory UniversityAtlanta, GA, USA
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Olakanye AO, Thompson T, Ralebitso-Senior TK. Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition. Sci Justice 2015; 55:402-7. [DOI: 10.1016/j.scijus.2015.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/21/2015] [Accepted: 07/06/2015] [Indexed: 11/16/2022]
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50
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Chun LP, Miguel MJ, Junkins EN, Forbes SL, Carter DO. An initial investigation into the ecology of culturable aerobic postmortem bacteria. Sci Justice 2015; 55:394-401. [DOI: 10.1016/j.scijus.2015.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/17/2015] [Accepted: 07/22/2015] [Indexed: 01/13/2023]
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