Carcass mass has little influence on the structure of gravesoil microbial communities

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.

Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation

Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum Firmicutes and Bacteroidota were the most abundant in both the winter and summer pig rectum. However, Proteobacteria became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0-8Dvs. WPG 16-40D, p < 0.0001; WPS 0-16Dvs. WPS 24-40D, p = 0.003; SPG 0D vs. SPG 8-40D, p = 0.0005; and SPS 0D vs. SPS 8-40D, p = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus Vagococcus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI.

Microbial ecology of vertebrate decomposition in terrestrial ecosystems

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.

Application of artificial intelligence and machine learning technology for the prediction of postmortem interval: A systematic review of preclinical and clinical studies

BACKGROUND /PURPOSE

Establishing an accurate postmortem interval (PMI) is exceptionally crucial in forensic investigation. Artificial intelligence (AI) and Machine learning (ML) models are widely employed in forensic practice. ML is a part of AI, both terms are highly associated and sometimes used interchangeably. This systematic review aims to evaluate the application and performance of AI technology for the prediction of PMI.

METHODS

Systematic literature search across different electronic databases using PubMed/Google Scholar/EMBASE/Scopus/CINAHL/Web of Science/Cochrane library was conducted from inception to 3 December 2021 for preclinical and clinical studies reported ML models for PMI estimation.

RESULTS

We identified 18 studies (12 preclinical and 06 clinical) that met the inclusion criteria in the qualitative analysis. Most of the studies employed supervised learning (N = 15), and others employed unsupervised learning (N = 3). Due to the heterogeneity of the samples, quantitative analysis was not performed.

CONCLUSION

In this systematic review, we discussed the performance of AI-based automated systems in PMI estimation. ML models have demonstrated accuracy and precision and the ability to overcome human errors and bias. However, the research is limited, conducted in primarily small, selected human populations. In addition, we suggest further research in larger population-based studies is needed to fully understand the extent of integrated ML models.

Successions of rare and abundant microbial subcommunities during fish carcass decomposition in a microcosm under the influence of variable factors

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.

Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses

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.

A pilot study characterizing gravesoil bacterial communities a decade after swine decomposition

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.

Microbiome in Death and Beyond: Current Vistas and Future Trends

Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.

Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model

Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH₃-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH₃-N, NO₃-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.

Soil nematode functional diversity, successional patterns, and indicator taxa associated with vertebrate decomposition hotspots

Decomposition of vertebrate remains is a dynamic process that creates localized soil enrichment zones. A growing body of literature has documented effects of vertebrate decomposition on soil pH, electrical conductivity, oxygen levels, nitrogen and carbon speciation, microbial biomass, and microbial successional patterns. However, relatively few studies have examined the microfaunal members of the soil food web that function as secondary consumers, specifically nematodes. Nematodes are often used as indicators of enrichment in other systems, and initial observations from vertebrate decomposition zones have indicated there is an effect on nematode communities. Our goal was to catalog decomposition-induced nematode succession and changes to alpha, beta, and functional diversity, and identify potential indicator taxa associated with decomposition progression. Six adult beaver (Castor canadensis) carcasses were allowed to decompose in a forest ecosystem for one year. During this period soil temperature, moisture, and electrical conductivity were monitored. Soils samples were taken at two depths in order to assess nematode community dynamics: 30-cm cores and 1-cm interface samples. Nematode abundance, alpha, beta, and functional diversity all responded to soil enrichment at the onset of active decay, and impacts persisted through skeletonization. After one year, nematode abundances and alpha diversity had recovered to original levels, however both community membership and functional diversity remained significantly altered. We identified seven indicator taxa that marked major transitions in decomposition progression. Enrichment of Rhabditidae (B1) and Diplogasteridae (B1) coupled with depletion in Filenchus (F2) characterized active and advanced decay prior to skeletonization in both cores and interface soils. Enrichment of Acrobeloides (B2), Aphelenchoides (F2), Tylencholaimidae (F4) and Seinura (P2) occurred during a narrow period in mid-skeletonization (day 153). Our study has revealed soil nematode successional patterns during vertebrate decomposition and has identified organisms that may function as indicator taxa for certain periods during decomposition.

Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver

Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin microbiomes change prior to autopsy and, if so, whether these changes interfere with linking objects to decedents. The current study included microbiomes from 16 scenes of death in the City and County of Honolulu and tested whether objects at the scenes can be linked to individual decedents. Postmortem skin microbiomes were stable during repeated sampling up to 60 h postmortem and were similar to microbiomes of an antemortem population. Objects could be traced to decedents approximately 75% of the time, with smoking pipes and medical devices being especially accurate (100% match), house and car keys being poor (0%), and other objects like phones intermediate (~80%). These results show that microbes from objects at death scenes can be matched to individual decedents, opening up a new method of establishing associations and identifications.

Temporal dynamics of microbiota before and after host death

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.

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models

Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is uncertain. The postmortem interval can lead to the identification of the deceased and the validation of witness statements and suspect alibis. Recent research has demonstrated that microbes provide an accurate clock that starts at death and relies on ecological change in the microbial communities that normally inhabit a body and its surrounding environment. Here, we explore how to build the most robust Random Forest regression models for prediction of PMI by testing models built on different sample types (gravesoil, skin of the torso, skin of the head), gene markers (16S ribosomal RNA (rRNA), 18S rRNA, internal transcribed spacer regions (ITS)), and taxonomic levels (sequence variants, species, genus, etc.). We also tested whether particular suites of indicator microbes were informative across different datasets. Generally, results indicate that the most accurate models for predicting PMI were built using gravesoil and skin data using the 16S rRNA genetic marker at the taxonomic level of phyla. Additionally, several phyla consistently contributed highly to model accuracy and may be candidate indicators of PMI.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

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.

Mass mortality events and the role of necrophagous invertebrates

Scale is important in understanding and applying concepts in ecology. Historically, the mechanisms regulating necrophagous arthropod community structure have been well explored on a single vertebrate carcass. However, practically nothing is known of whether such findings can be extrapolated to cases where large numbers of carcasses have been introduced into an ecosystem at a single time point. With the increasing incidences of mass mortality events (MMEs), understanding how scale effects community assembly of necrophagous insects and the resulting bottom-up or top-down effects on the impacted ecosystem are of utmost importance. Unfortunately, MMEs are unpredictable, making their study nearly impossible within a robust experimental framework. The objectives of this paper are to provide a brief overview of what is known with regards to ecological responses to carrion, opine on the ramifications of MMEs on local communities, and provide a brief overview of knowledge gaps, avenues for future research, and a potential study systems for rigorous MME experiments.

Temporal dynamics in microbial soil communities at anthrax carcass sites

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.

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure

We investigated the impacts of leachates from a swine carcass burial site and a cow manure heap on the geochemical and microbiological properties of agricultural water samples, including leachate, groundwater from monitoring wells and background wells, and stream water. The leachate from the livestock burial site showed extremely high electrical conductivity, turbidity, and major ion concentrations, but low redox potential and dissolved oxygen levels. The groundwater in the monitoring wells adjacent to both sites showed severe contamination from the leachate, as indicated by the increases in EC, turbidity, Cl^-, and SO₄^2-. Bacteria from the phylum Firmicutes and Bacteriodetes and Archaea from the phylum Euryarchaeota were the major phyla in both the leachates and manure heap. However, the class- or genus-level components of these phyla differed markedly between the leachate and manure heap samples. The relative abundance of Firmicutes decreased from 35% to 0.3~13.9% in the monitoring wells and background wells at both sites. The Firmicutes in these wells was unlikely to have originated from the transportation of leachate to the surrounding environment because Firmicutes genera differed drastically between the leachate and monitoring wells. Meanwhile, sulfate-reducing bacteria (SRB) from the livestock carcass burial site were detected in the monitoring wells close to the leachate. This was likely because the release of carcass decomposition products, such as organic acids, to adjacent areas improved the suitability of the local environments for SRB, which were not abundant in the leachate. This study highlights the need to better understand microbial community dynamics along groundwater flow paths to evaluate bacterial transport in subsurface environments and provides new insights into the effective management of groundwater quality at both farm and regional scales.

Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp

Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (Galleria mellonella) larvae cadavers killed by Heterorhabditis nematodes and their Photorhabdus symbionts. We found that, although Photorhabdus strains did initially displace an Enterococcus-dominated community present in uninfected G. mellonella insect larvae, the cadaver community was not static. Twelve days postinfection, Photorhabdus shared the cadaver with Stenotrophomonas species. Consistent with this result, Stenotrophomonas strains isolated from infected cadavers were resistant to Photorhabdus-mediated toxicity in solid coculture assays. We isolated and characterized a Photorhabdus-produced antibiotic from G. mellonella cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased G. mellonella-associated Enterococcus growth, but not Stenotrophomonas growth, in vitro Finally, we showed that the Stenotrophomonas strains described here negatively affected Photorhabdus growth in vitro Our results add an important dimension to a broader understanding of Heterorhabditis-Photorhabdus biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a Heterorhabditis-Photorhabdus-parasitized insect cadaver.

IMPORTANCE

Understanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic in vitro microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers.

Microbial Signatures of Cadaver Gravesoil During Decomposition

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.

Microbial community assembly and metabolic function during mammalian corpse decomposition

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