The biochemical alteration of soil beneath a decomposing carcass

Transient hypoxia drives soil microbial community dynamics and biogeochemistry during human decomposition

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products.

The taphonomic effects of long-term burial in the South African Highveld

Taphonomy studies the environmental effects on remains from the time of deposition to the time of recovery and has been integrated into the field of forensic anthropology. The changes to skeletal remains are dependent on the method of disposal and the surrounding environment. This study focused on buried remains where the type and chemical composition of the soil and the microorganisms present need to be considered. The aim was to investigate the type, frequency, and correlations of the taphonomic alterations of buried domestic pigs. Six taphonomic alterations were observed which included depositional staining, adipocere formation, bone weathering, acidic soil corrosion, and plant, and animal activity. Depositional staining, weathering and plant activity were the most common alterations followed by adipocere which was present on 92.3% of the remains. The bones were mostly stained dark brown and brown; however, the trunk region was the only region to present with black staining. The right sides were darker than the left due to the body positioning as most pigs were placed on their right sides and thus were in direct contact with the cadaver decomposition island. Additionally, the right sides presented with more adipocere as well as increased plant activity suggesting that the soil retained water. Darker stains were correlated with a more complete skeleton as adipocere provides some protection. The study confirms that there are various complicated relationships between different taphonomic alterations. A good understanding of them is needed in forensic anthropology to assist in reconstructing the events that occur after death.

Bridging the gap between decomposition theory and forensic research on postmortem interval

Knowledge of the decomposition of vertebrate animals has advanced considerably in recent years and revealed complex interactions among biological and environmental factors that affect rates of decay. Yet this complexity remains to be fully incorporated into research or models of the postmortem interval (PMI). We suggest there is both opportunity and a need to use recent advances in decomposition theory to guide forensic research and its applications to understanding the PMI. Here we synthesise knowledge of the biological and environmental factors driving variation in decomposition and the acknowledged limitations among current models of the PMI. To guide improvement in this area, we introduce a conceptual framework that highlights the multiple interdependencies affecting decay rates throughout the decomposition process. Our framework reinforces the need for a multidisciplinary approach to PMI research, and calls for an adaptive research cycle that aims to reduce uncertainty in PMI estimates via experimentation, modelling, and validation.

Rewilding by large ungulates contributes to organic carbon storage in soils

The concept of rewilding, which focuses on managing ecosystem functions through self-regulation by restoring trophic interactions through introduced animal species with little human intervention, has gained increasing attention as a proactive and efficient approach to restoring ecosystems quickly and on a large scale. However, the science of rewilding has been criticized for being largely theory-based rather than evidence-based, with available data being geographically biased towards the Netherlands and Scandinavian countries, and a lack of objective data on rewilding effects on soil processes and C sequestration. In response to a call for data-driven experimental rewilding projects focused on national contexts, we collected unique data on the effects of large herbivore rewilding on soil properties from eight sites in the Czech Republic. These include sites with a wide range of edaphic characteristics that were grazed by Exmoor ponies, European bison, and back-bred Bos primigenius cattle (singly or in combination) for 2-6 years on areas ranging from ≈30 to ≈250 ha. Despite the relatively short duration of rewilding actions and considerable variability in the response rate of soil properties to grazing, our results indicate improved nutrient availability (evidenced by higher nitrification rate or higher soluble nitrogen concentration) and accelerated ecosystem metabolism (higher soil microbial biomass and dissolved carbon content). On longer-grazed pastures, rewilding contributed to soil carbon sequestration associated with increased water holding capacity and improved soil structure. However, other soil properties (reduced dissolved P concentration or total P content) showed signs of low P availability in the soils of the rewilding sites. Therefore, carcass retention should be considered where possible. Our data, although limited in number and geographic coverage, allow us to conclude that large ungulate rewilding has the potential to enhance soil carbon sequestration and related ecosystem services in rewilding areas. At the same time, we urge similar monitoring as an essential part of other rewilding projects, which will ultimately allow much more robust conclusions about the effects of this management on soils.

Soil elemental changes during human decomposition

Mammalian decomposition provides pulses of organic matter to the local ecosystem creating ephemeral hotspots of nutrient cycling. While changes to soil biogeochemistry in these hotspots have been described for C and N, patterns associated with deposition and cycling of other elements have not received the same attention. The goal of our study was to evaluate temporal changes to a broad suite of dissolved elements in soils impacted by human decomposition on the soil surface including: 1) abundant mineral elements in the human body (K, Na, S, P, Ca, and Mg), 2) trace elements in the human body (Fe, Mn, Se, Zn, Cu, Co, and B), and 3) Al which is transient in the human body but common in soils. We performed a four-month human decomposition trial at the University of Tennessee Anthropology Research Facility and quantified elemental concentrations dissolved in the soil solution, targeting the mobile and bioavailable fraction. We identified three groups of elements based on their temporal patterns. Group 1 elements appeared to be cadaver-derived (Na, K, P, S) and their persistence in soil varied based upon soluble organic forms (P), the dynamics of the soil exchange complex (Na, K), and gradual releases attributable to microbial degradation (S). Group 2 elements (Ca, Mg, Mn, Se, B) included three elements that have greater concentrations in soil than would be expected based on cadaver inputs alone, suggesting that these elements partially originate from the soil exchange (Ca, Mg), or are solubilized as a result of soil acidification (Mn). Group 3 elements (Fe, Cu, Zn, Co, Al) increased late in the decomposition process, suggesting a gradual solubilization from soil minerals under acidic pH conditions. This work presents a detailed longitudinal characterization of changes in dissolved soil elements during human decomposition furthering our understanding of elemental deposition and cycling in these environments.

Viability of African Swine Fever Virus with the Shallow Burial with Carbon Carcass Disposal Method

African swine fever (ASF) is a highly contagious swine disease with high mortality. In many countries, culling pigs infected and exposed to the ASF virus is mandatory to control the disease, which poses a real challenge in the disposal of large numbers of carcasses during ASF outbreaks. Shallow burial with carbon (SBC) Thanks ew mortality disposal method developed from deep burial and composting. The present study investigates the effectiveness of SBC in disposing of ASF virus-infected pigs. The real-time PCR results showed that DNA of the ASF virus was still detected in bone marrow samples on day 56, while the virus isolation test revealed that the infectious ASF virus was destroyed in both spleen and bone marrow samples on day 5. Interestingly, decomposition was found to occur rapidly in these shallow burial pits. On day 144, only large bones were found in the burial pit. In general, the results of this study indicated that SBC is a potential method for the disposal of ASF-infected carcasses; however, further studies are needed to provide more scientific evidence for the efficacy of SBC in different environment conditions.

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.

Virus viability in spiked swine bone marrow tissue during above-ground burial method and under in vitro conditions

The emergence of high consequence animal diseases usually requires managing significant mortality. A desirable aspect of any carcass management method is the ability to contain and inactivate the target pathogen. The above-ground burial (AGB) technique was recently developed and proposed as an alternative carcass management method. Here, we investigate the tenacity of swinepox virus (SwPV), as a surrogate model for African swine fever virus (ASFV) in swine carcasses during the AGB process. For this, SwPV was inoculated intrafemorally in 90 adult swine carcasses, which were subsequently disposed under AGB conditions. Bone marrow samples were recovered periodically throughout 12 months and virus viability was assessed by virus isolation (VI), whereas the presence of SwPV DNA was evaluated by quantitative polymerase chain reaction (qPCR). Additionally, an in vitro study assessed the inactivation rate of SwPV, Senecavirus A (SVA), and bovine viral diarrhoea virus (BVDV). Viral suspensions were mixed with bone marrow material and maintained at 21-23°C for 30 days. Virus viability was assessed by VI and viral titration. In the field study, SwPV remained viable only in 11 (55%) bone marrow samples collected on day 7; only viral DNA (and not infectivity) was detected afterwards. SwPV inactivation was estimated to have occurred by day 11. The in vitro testing revealed a variable tenacity of the studied viruses. The viability period was estimated in 28, 80, and 118 days, respectively, for BVDV, SwPV, and SVA. Overall, these findings indicate that the AGB technique was effective in quickly inactivating SwPV. Additionally, the SwPV inactivation rate is comparable to ASFV under field studies and poses a potential model for preliminary ASFV inactivation studies with reduced biosecurity requirements. Moreover, this study contributes to understanding the inactivation kinetics of viruses under specific conditions, which is critical when designing and applying countermeasures in case of biosecurity breaches in sites managing animal mortality.

The impact of the decomposition process of shallow graves on soil mite abundance

Burial of a cadaver results in a slower decomposition rate, due to more stable below-ground temperatures and restricted access to necrophagous insects. In such circumstances, analysis of the soil mesofauna, with emphasis on mites (Acari) may be more valuable in time-of-death estimations. The production of volatile organic compounds of cadaveric decay results in changes, especially in the soil pH, which in turn would affect the abundance and diversity of the associated mites. In general, the effects of decomposition and the consequently altered pH levels on the abundance of mites in shallow graves, as well as the effects of fluctuating above-ground environmental parameters (temperature, relative humidity, and precipitation) remain unknown. Here, we found that the decay of three pig cadavers buried in shallow graves (<30 cm below) caused a significant increase in the soil pH throughout decomposition, from neutral to alkaline. Cadaver decay attracted an abundance of mites: with 300 mites collected from the three pig cadavers compared to 129 from the control soil samples at the same depth. Mites rapidly became more abundant in cadaver-associated soils than in control soils after the fresh stage. Increasing soil pH had a positive impact on the abundance of mites in graves and there was a significant interaction between cadaver body temperature and soil pH. Above-ground fluctuations in temperature, relative humidity, and precipitation were found to have no significant direct effect on mite abundance in grave or control soils.

Assessing optical remote sensing for grave detection

The application of an effective and ready-to-use tool for discovering clandestine graves is crucial for solving a number of cases where disappearance of people is involved. This is the case in Mexico, where the government drug war has resulted in a large number of missing people that has been estimated to be over 40,000 since the year 2006. In this article, we report results from an experimental study on simulated animal graves detection using several techniques from optical remote sensing. Results showed that several spectral indices from hyperspectral and/or multispectral sensors may be used to detect N-enriched vegetation. Thermal imagery was also effective to detect underground voids through differential thermography, although this was only effective for detecting large graves with bare terrain. Lastly, while dense pointclouds reconstructed from oblique aerial photography was able to detect vegetation regrowth over the pits, the terrain subsidence was not sufficiently large to be detected with this technique, even in the case of mechanical removal of vegetation.

Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH₄⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH₄⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

Icilio Guareschi and his amazing "1897 reaction"

Organic chemistry honors Icilio Guareschi (1847-1918) with three eponymic reactions, the best known ones being the Guareschi synthesis of pyridones and the Guareschi-Lustgarten reaction. A third Guareschi reaction, the so-called "Guareschi 1897 reaction", is one of the most unusual reactions in organic chemistry, involving the radical-mediated paradoxical aerobic generation of hydrocarbons in near-neutral water solution. A discussion of the mechanism of this amazing reaction, the only metal-free process that generates hydrocarbons, and the implications of the approach in biology and geosciences mirrors the multifaceted scientific personality of the discoverer. Thus, Guareschi's eclectic range of activities spans a surprising variety of topics, overcoming the boundaries of the traditional partition of chemistry into organic, inorganic, and analytical branches and systematically crosses the divide between pure and applied science as well as between the history of chemistry and the personal contributions to its development.

A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics

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.

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.

Insect reproductive behaviors are important mediators of carrion nutrient release into soil

Current declines in terrestrial insect biomass and abundance have raised global concern for the fate of insects and the ecosystem services they provide. However, the ecological and economic contributions of many insects have yet to be quantified. Carrion-specializing invertebrates are important mediators of carrion decomposition; however, the role of their reproductive activities in facilitating this nutrient pulse into ecosystems is poorly understood. Here, we investigate whether insects that sequester carrion belowground for reproduction alter soil biotic and abiotic properties in North American temperate forests. We conducted a field experiment that measured soil conditions in control, surface carrion alone, and beetle-utilized carrion treatments. Our data demonstrate that Nicrophorus beetle reproduction and development results in changes in soil characteristics which are consistent with those observed in surface carrion decomposition alone. Carrion addition treatments increase soil labile C, DON and DOC, while soil pH and microbial C:N ratios decrease. This study demonstrates that the decomposition of carrion drives soil changes but suggests that the behaviors of insect scavengers play an important role in the release of carrion nutrients directly into the soil by sequestering carrion resources in the ecosystem where they were deposited.

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

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.

Soil chemistry dynamics of Sus scrofa carcasses with and without delayed Diptera colonization

Under normal circumstances, insects such as blow flies will oviposit and larvae will colonize a carcass as soon as possible. However, insect colonization on a carcass may be delayed due to the effects of wrapping, shallow burial, addition of lime derivatives to mitigate scavenging and odor, or extreme weather. The impacts of delayed insect colonization on carcass decomposition and its subsequent effect on soil chemistry profiles have not been examined to date. The objectives of this study were to determine soil chemistry dynamics associated with porcine carcasses experiencing delayed insect colonization for 7-day or 14-day. Soil chemistry profiles such as ammonium-N (NH₄ -N), orthophosphate-P (PO₄ -P), and dissolved organic carbon (DOC) were significantly different among treatments: insect inclusion (immediate access of blow fly colonization on porcine carcasses), 7-day insect exclusion and 14-day insect exclusion (blow fly access was delayed up to 7-day and 14-day). Furthermore, significant differences of soil chemical profiles were detected between days of decomposition and soil regions. Soil moisture, NH₄ -N, PO₄ -P, and DOC were significantly higher when insects were excluded from the porcine carcass suggesting loss of tissue from larval feeding reduced the mass of nutrients entering the soil. This study provides useful information for forensic science in cases where insect colonization is delayed for a period of time postmortem and soil chemistry in the cadaver decomposition island is considered for estimating postmortem interval.

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.

Forensic taphonomy: Characterization of the gravesoil chemistry using a multivariate approach combining chemical and volatile analyses

Soil thanatochemistry, defined as the study of the chemical changes occurring during the decomposition of buried corpses, is a young and inadequately documented field of research. In this study, we aim to determine the effects of decomposition on soil physico-chemical properties by combining pedological, chemical, and volatile analyses of soils surrounding buried animals. We examined chemical and volatile changes over time occurring throughout the soil column in two common soil-texture types (sandy loam and loam). We buried dead rats and let them decompose for two months. During their excavations, we characterized the physico-chemical conditions of three soil layers above the rats and one layer below, including (1) pH, dry matter, and electrical conductivity, (2) organic carbon and total nitrogen, (3) bioavailable nutrients (K, Na, Mg, Ca, and P), and (4) volatile organic compounds. Multivariate analyses (permMANOVA) revealed that a decaying rat is associated with changes in soil chemical characteristics in both soil types. However, the observed changes were not homogenous throughout the soil columns. Conditions in soil layers nearest the cadavers changed most during decomposition. We generated a predictive model by combining chemical and volatile analyses (10 % error rate), allowing us to identify key gravesoil indicators that could be used to reveal the former existence of a buried corpse in loam and sandy loam (indicators in order of importance): organic carbon, calcium, pH, conductivity, dimethyl-disulfide, and nitrogen.

Stability of African Swine Fever Virus in Carcasses of Domestic Pigs and Wild Boar Experimentally Infected with the ASFV "Estonia 2014" Isolate

Europe is currently experiencing a long-lasting African swine fever (ASF) epidemic, both in domestic pigs and wild boar. There is great concern that carcasses of infected wild boar may act as long-term virus reservoirs in the environment. We evaluated the tenacity of ASF virus (ASFV) in tissues and body fluids from experimentally infected domestic pigs and wild boar, which were stored on different matrices and at different temperatures. Samples were analysed at regular intervals for viral genome and infectious virus. ASFV was most stable in spleen or muscles stored at -20 °C and in blood stored at 4 °C. In bones stored at -20 °C, infectious virus was detected for up to three months, and at 4 °C for up to one month, while at room temperature (RT), no infectious virus could be recovered after one week. Skin stored at -20 °C, 4 °C and RT remained infectious for up to three, six and three months, respectively. In urine and faeces, no infectious virus was recovered after one week, irrespective of the matrix. In conclusion, tissues and organs from decomposing carcasses that persist in the environment for a long time can be a source of infection for several months, especially at low temperatures.

Scavenging by threatened turtles regulates freshwater ecosystem health during fish kills

Humans are increasing the frequency of fish kills by degrading freshwater ecosystems. Simultaneously, scavengers like freshwater turtles are declining globally, including in the Australian Murray-Darling Basin. Reduced scavenging may cause water quality problems impacting both ecosystems and humans. We used field and mesocosm experiments to test whether scavenging by turtles regulates water quality during simulated fish kills. In the field, we found that turtles were important scavengers of fish carrion. In mesocosms, turtles rapidly consumed carrion, and water quality in mesocosms with turtles returned to pre-fish kill levels faster than in turtle-free controls. Our experiments have important ecological implications, as they suggest that turtles are critical scavengers that regulate water quality in freshwater ecosystems. Recovery of turtle populations may be necessary to avoid the worsening of ecosystem health, particularly after fish kills, which would have devastating consequences for many freshwater species.

Estimating the Postmortem Interval of Wild Boar Carcasses

Knowledge on the postmortem interval (PMI) of wild boar (Sus scrofa) carcasses is crucial in the event of an outbreak of African swine fever in a wild boar population. Therefore, a thorough understanding of the decomposition process of this species in different microhabitats is necessary. We describe the decomposition process of carcasses exposed in cages. Trial 1 compared a wild boar and a domestic pig (Sus scrofa domesticus) under similar conditions; Trial 2 was performed with three wild boar piglets in the sunlight, shade, or in a wallow, and Trial 3 with two adult wild boar in the sun or shade. The wild boar decomposed more slowly than the domestic pig, which shows that standards derived from forensic studies on domestic pigs are not directly applicable to wild boar. The carcasses exposed to the sun decomposed faster than those in the shade did, and the decomposition of the carcass in the wallow took longest. To assess the state of decomposition, we adapted an existing total body scoring system originally developed for humans. Based on our studies, we propose a checklist tailored to wild boar carcasses found in the field that includes the most important information for a reliable PMI estimation.

Are soil testate amoebae and diatoms useful for forensics?

Two of the main goals of forensic science are (1) to estimate the time since death, or post mortem interval (PMI) and (2) to find the site where a dead body was buried. Soil testate amoebae and diatoms may be useful indicators for these goals. However, the structure and patchiness of the habitat appears to be a main driver for the amoeba and diatom soil communities (e.g., individual density). In case the soil substrate is very dry and nutrient-poor (as in our study), the influence of a dead body on the soil microfaunal community may be superimposed by natural environmental heterogeneity, especially soil moisture content. Further studies are necessary to clarify if protist abundance data are helpful for forensic investigations.

Thanatomicrobiome composition profiling as a tool for forensic investigation

Thanatomicrobiome, or the postmortem microbiome, has been recognized as a useful microbial marker of the time and location of host death. In this mini-review, we compare the experimental methods commonly applied to thanatomicrobiome studies to the state-of-the-art methodologies in the microbiome field. Then, we review present findings in thanatomicrobiome studies, focusing on the diversity of the thanatomicrobiome composition and prediction models that have been proposed. Finally, we discuss potential improvements and future directions of the field.

Inorganic elemental analysis of decomposition fluids of an in situ animal burial

In homicide investigations, it is critically important that post-mortem (PMI) and post-burial interval (PBI) of buried victims are determined accurately. However, clandestine graves can be difficult to locate; and the detection rates for a variety of search methods can be very low. This paper presents elemental analysis results of 18 months of decomposition fluids from an in situ buried animal cadaver used as a human clandestine burial proxy. Study results showed potassium, sulphate and sodium are key detectable elements which mirror observed conductivity temporal changes from this and other studies. Seasonal rainfall has a strong influence on both fluid generation and subsequent concentration which needs to be accounted for. Study implications suggest inorganic elements could provide both detection and potential dating of discovered clandestine burials.

Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval

Criminal investigations of suspected murder cases require estimating the post-mortem interval (PMI, or time after death) which is challenging for long PMIs. Here we present the case of human remains found in a Swiss forest. We have used a multidisciplinary approach involving the analysis of bones and soil samples collected beneath the remains of the head, upper and lower body and "control" samples taken a few meters away. We analysed soil chemical characteristics, mites and nematodes (by microscopy) and micro-eukaryotes (by Illumina high throughput sequencing). The PMI estimate on hair 14C-data via bomb peak radiocarbon dating gave a time range of 1 to 3 years before the discovery of the remains. Cluster analyses for soil chemical constituents, nematodes, mites and micro-eukaryotes revealed two clusters 1) head and upper body and 2) lower body and controls. From mite evidence, we conclude that the body was probably brought to the site after death. However, chemical analyses, nematode community analyses and the analyses of micro-eukaryotes indicate that decomposition took place at least partly on site. This study illustrates the usefulness of combining several lines of evidence for the study of homicide cases to better calibrate PMI inference tools.

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.

Pyrosequencing-based assessment of microbial community shifts in leachate from animal carcass burial lysimeter

This study examined the use of microbial community structure as a bio-indicator of decomposition levels. High-throughput pyrosequencing technology was used to assess the shift in microbial community of leachate from animal carcass lysimeter. The leachate samples were collected monthly for one year and a total of 164,639 pyrosequencing reads were obtained and used in the taxonomic classification and operational taxonomy units (OTUs) distribution analysis based on sequence similarity. Our results show considerable changes in the phylum-level bacterial composition, suggesting that the microbial community is a sensitive parameter affected by the burial environment. The phylum classification results showed that Proteobacteria (Pseudomonas) were the most influential taxa in earlier decomposition stage whereas Firmicutes (Clostridium, Sporanaerobacter, and Peptostreptococcus) were dominant in later stage under anaerobic conditions. The result of this study can provide useful information on a time series of leachate profiles of microbial community structures and suggest patterns of microbial diversity in livestock burial sites. In addition, this result can be applicable to predict the decomposition stages under clay loam based soil conditions of animal livestock.

Soil Microbial Forensics

Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.

The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death

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.

Design and evaluation of a bioreactor with application to forensic burial environments

Existing forensic taphonomic methods lack specificity in estimating the postmortem interval (PMI) in the period following active decomposition. New methods, such as the use of citrate concentration in bone, are currently being considered; however, determining the applicability of these methods in differing environmental contexts is challenging. This research aims to design a forensic bioreactor that can account for environmental factors known to impact decomposition, specifically temperature, moisture, physical damage from animals, burial depth, soil pH, and organic matter content. These forensically relevant environmental variables were characterized in a soil science context. The resulting metrics were soil temperature regime, soil moisture regime, slope, texture, soil horizon, cation exchange capacity, soil pH, and organic matter content. Bioreactor chambers were constructed using sterilized thin-walled polystyrene boxes housed in calibrated temperature units. Gravesoil was represented using mineral soil (Ultisols), and organic soil proxy for Histosols, horticulture mix. Gravesoil depth was determined using mineral soil horizons A and Bt2 to simulate surface scatter and shallow grave burial respectively. A total of fourteen different environmental conditions were created and controlled successfully over a 90-day experiment. These results demonstrate successful implementation and control of forensic bioreactor simulating precise environments in a single research location, rather than site-specific testing occurring in different geographic regions. Bone sections were grossly assessed for weathering characteristics, which revealed notable differences related to exposure to different temperature regimes and soil types. Over the short 90-day duration of this experiment, changes in weathering characteristics were more evident across the different temperature regimes rather than the soil types. Using this methodology, bioreactor systems can be created to replicate many different clandestine burial contexts, which will allow for the more rapid understanding of environmental effects on skeletal remains.

Estimating Time Since Death from Postmortem Human Gut Microbial Communities

Postmortem succession of human-associated microbial communities ("human microbiome") has been suggested as a possible method for estimating postmortem interval (PMI) for forensic analyses. Here we evaluate human gut bacterial populations to determine quantifiable, time-dependent changes postmortem. Gut microflora were repeatedly sampled from the proximal large intestine of 12 deceased human individuals as they decayed under environmental conditions. Three intestinal bacterial genera were quantified by quantitative PCR (qPCR) using group-specific primers targeting 16S rRNA genes. Bacteroides and Lactobacillus relative abundances declined exponentially with increasing PMI at rates of Nt=0.977e(-0.0144t) (r2=0.537, p<0.001) and Nt=0.019e(-0.0087t) (r2=0.396, p<0.001), respectively, where Nt is relative abundance at time (t) in cumulative degree hours. Bifidobacterium relative abundances did not change significantly: Nt=0.003e(-0.002t) (r2=0.033, p=0.284). Therefore, Bacteroides and Lactobacillus abundances could be used as quantitative indicators of PMI.

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.

Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval

Bacteria are taphonomic agents of human decomposition, potentially useful for estimating postmortem interval (PMI) in late-stage decomposition. Bone samples from 12 individuals and three soil samples were analyzed to assess the effects of decomposition and advancing time on bacterial communities. Results indicated that partially skeletonized remains maintained a presence of bacteria associated with the human gut, whereas bacterial composition of dry skeletal remains maintained a community profile similar to soil communities. Variation in the UniFrac distances was significantly greater between groups than within groups (p < 0.001) for the unweighted metric and not the weighted metric. The members of the bacterial communities were more similar within than between decomposition stages. The oligotrophic environment of bone relative to soft tissue and the physical protection of organic substrates may preclude bacterial blooms during the first years of skeletonization. Therefore, community membership (unweighted) may be better for estimating PMI from skeletonized remains than community structure (weighted).

Nitrous oxide, methane and carbon dioxide dynamics from experimental pig graves

Twelve pig carcasses were buried in single, shallow and deep (30 and 90 cm, respectively) graves at an experimental site near Ottawa, Ontario, Canada, with three shallow and three deep wrapped in black plastic garbage bags. An additional six carcasses were left at the surface to decompose, three of which were bagged. Six reference pits without remains were also dug. The objective of this three-year study was to examine the biogeochemistry and utility of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) in grave detection and whether grave depth or cadaver condition (bagged versus bare) affected soil pore air concentrations and emission of the three gases. Graves showed significantly higher (α=0.05) concentrations and surface fluxes of N2O and CO2 than reference pits, but there was no difference in CH4 between graves and reference pits. While CH4 decreased with depth in the soil profiles, N2O and CO2 showed a large increase compared to reference pits. Shallow graves showed significantly higher emissions and pore air concentrations of N2O and CO2 than deep graves, as did bare versus bagged carcasses.