Microbial community functional change during vertebrate carrion decomposition

Examining the effect of post-depositional processes on the preservation and identification of stone tool residues from temperate environments: An experimental approach

Studying taphonomy is crucial for understanding how post-depositional processes impact archaeological remains. This knowledge is pivotal for accurately interpreting the archaeological record. Although taphonomy has a long tradition in archaeology, it is less developed in the analysis of stone tool residues compared to other subdisciplines. To address this gap, our study aims to further develop our understanding of the preservation potential of stone tool residues in temperate environments through actualist experiments. To achieve this, we develop a multidimensional experimental program that features the first biweekly monitoring of weathering processes on residues over a one-year cycle, aiming to understand the short-term effects of weathering immediately after tool discard. Additionally, the program involves the study of longer-term burial and weathering visual effects on different residue types within various previously unexplored depositional environments. This approach allows us to observe the visual effects of both weathering and burial processes and to improve our understanding of the different mechanisms involved in the diagenesis of stone tool residues. While known factors such as microbial activity and soil acidity play a primary role in residue decay, specific stone tool-related factors also prove important, underscoring the need to develop further a specific branch of taphonomy related to stone tool residues. Moreover, our results show that certain residue types may survive within these environments that are often considered as being hostile. A residue analysis of stone tools from temperate contexts may thus contribute unique data that can improve our understanding of past human behaviour. Future research with more diverse residue types and depositional conditions will permit further refinement of our understanding of how taphonomy affects residue preservation and enhance the reliability of residue identifications. As such, stone tool residue analysis will become firmly rooted within broader functional approaches to address how humans use stone tools and how this affects stone tool variability.

Mechanisms determining the multi-diversity of carrion visiting species along a gradient of carrion body mass

Resource availability and habitat heterogeneity are essential drivers of biodiversity, but their individual roles often remain unclear since both factors are often correlated. Here, we tested the more-individuals hypothesis (MIH) and the habitat-heterogeneity hypothesis (HHH) for bacteria, fungi, dipterans, coleopterans, birds, and mammals on 100 experimentally exposed carcasses ranging by three orders of magnitude in body mass. At the level of each carcass we found marginal or significant support for the MIH for bacteria, fungi, and beetles in spring and significant support for fungi, dipterans, and mammals in summer. The HHH was supported only for bacteria in spring, while it was supported for all groups except mammals in summer. Overall multidiversity always increased with body mass, with a steeper increase in summer. Abundance based rarefaction-extrapolation curves for three classes of body mass showed the highest species richness for medium-sized carcasses, particular for dipterans and microbes, supporting the HHH also among carcasses. These findings complement existing necromass studies of deadwood, showing there are more niches associated with larger resource amounts and an increasing habitat heterogeneity between carcasses most pronounced for medium-sized species. Higher resource amount led to increased diversity of carrion-consuming organisms in summer, particularly due to the increasing number of niches with increasing size. Our findings underline the importance of distributed large carrion as well as medium-sized carrion in ecosystems supporting overall biodiversity of carrion-consumers. Furthermore, the different responses in spring and summer may inform strategies of carrion enrichment management schemes throughout the year.

A review of multi-disciplinary decomposition research and key drivers of variation in decay

The decomposition of animal remains is a multifaceted process, involving ecological, biological, and chemical interactions. While the complexity is acknowledged through concepts like the necrobiome, it's unclear if this complexity is reflected in research. Appreciation of the complexity of decomposition is crucial for identifying sources of variation in estimations of time since death in medico-legal science, as well as building broader ecological knowledge of the decomposition process. To gain insights into the extent of multidisciplinary research in the field of decomposition science, we conducted an examination of peer-reviewed literature on four key drivers of variation: volatile organic compounds, microbes, drugs/toxins, and insects. Among 650 articles, we identified their scientific discipline, driver/s of variation investigated, and year of publication. We found that 19% explored relationships between two drivers, while only 4% investigated interactions between three. None considered all four drivers. Over the past three decades, there has been a steady increase in decomposition research publications, signifying its growing importance. Most research (79%) was linked to forensic science, highlighting opportunities for interdisciplinary collaboration in decomposition science. Overall, our review underscores the need to incorporate multidisciplinary approaches and theory into contemporary decomposition research.

Aquatic conditions & bacterial communities as drivers of the decomposition of submerged remains

Aquatic decomposition, as a forensic discipline, has been largely under-investigated as a consequence of the highly complex and influential variability of the water environment. The limitation to the adaptability of scenario specific results justifies the necessity for experimental research to increase our understanding of the aquatic environment and the development of post-mortem submersion interval (PMSI) methods of estimation. This preliminary research aims to address this contextual gap by assessing the variation in the bacterial composition of aquatic biofilms as explained by water parameter measurements over time, associated with clothed and bare decomposing remains. As part of three field investigations, a total of 9 still-born piglets (n = 3, per trial) were used as human analogues and were submerged bare or clothed in either natural cotton or synthetic nylon. Changes in the bacterial community composition of the water surrounding the submerged remains were assessed at 4 discrete time points post submersion (7, 14, 21 and 28 days) by 16 S rRNA gene Next Generation Sequencing analysis and compared to coinciding water parameter measurements (i.e. conductivity, total dissolved solids (TDS), salinity, pH, and dissolved oxygen (DO)). Bacterial diversity was found to change over time and relative to clothing type, where significant variation was observed between synthetic nylon samples and bare/cotton samples. Seasonality was a major driver of bacterial diversity, where substantial variation was found between samples collected in early winter to those collected in mid - late winter. Water parameter measures of pH, salinity and DO were identified to best explain the global bacterial community composition and their corresponding dynamic trajectory patterns overtime. Further investigation into bacterial community dynamics in accordance with varying environmental conditions could potentially lead to the determination of influential extrinsic factors that may drive bacterial activity in aquatic decomposition. Together with the identification of potential bacterial markers that complement the different stages of decomposition, this may provide a future approach to PMSI estimations.

From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees

For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.

Estimating postmortem interval based on oral microbial community succession in rat cadavers

The accurate estimation of the postmortem interval has been one of the crucial issues to be solved in forensic research, and it is influenced by various factors in the process of decay. With the development of high-throughput sequencing technology, forensic microbiology has become the major hot topic in forensic science, which provides new research options for postmortem interval estimation. The oral microbial community is one of the most diverse of microbiomes, ranking as the second most abundant microbiota following the gastrointestinal tract. It is remarkable that oral microorganisms have a significant function in the decay process of cadavers. Therefore, we collected outdoor soil to simulate the death environment and focused on the relationship between oral microbial community succession and PMI in rats above the soil. In addition, linear regression models and random forest regression models were developed for the relationship between the relative abundance of oral microbes and PMI. We also identified a number of microorganisms that may be important to estimate PMI, including: Ignatzschineria, Morganella, Proteus, Lysinibacillus, Pseudomonas, Globicatella, Corynebacterium, Streptococcus, Rothia, Aerococcus, Staphylococcus, and so on.

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.

Behavioral interactions are modulated by facilitation along a heterotrophic succession

Competition and facilitation drive ecological succession but are often hard to quantify. In this sense, behavioral data may be a key tool to analyze interaction networks, providing insights into temporal trends in facilitation and competition processes within animal heterotrophic succession. Here, we perform the first in-depth analysis of the factors driving temporal dynamics of carcass consumption by analyzing behavioral patterns (i.e., interactions) and community dynamics metrics (i.e., species richness, abundance, turnover, and diversity) in a Neotropical scavenger guild. For this purpose, we monitored goat carcasses using automatic cameras. From 573 reviewed videos, we registered 1784 intraspecific and 624 interspecific interactions, using intraspecific and interspecific aggressions (n = 2048) as a behavioral proxy of competition intensity. Our results show that resource availability shapes behavioral interactions between vultures, with a specific effect of the different species on behavioral and competition dynamics, showing the existence of a hierarchy between species. Furthermore, behavioral processes linked to carcass opening tended to be facilitative, related to moments of higher tolerance (i.e., lower aggressiveness), thus reducing competition intensity and also affecting community structure and dynamics. This novel framework demonstrates complex ephemeral successional processes characterized by a fluctuation in facilitation and competition intensity during the consumption of an unpredictable resource linked to key ecosystem processes.

Direct relationship between evapotranspiration rate (ETO) and vertebrate decomposition rate

When vertebrate scavenging is excluded, the Evapotranspiration Rate (ETo) of a given geographic region directly regulates the decomposition rate of unclothed vertebrate carrion, with any deviation attributed to insect activity. We conducted four decomposition experiments using pig carrion (Sus scrofa domesticus) over the span of two years (2018-2020) at a location in Davis, California. We used ETo, a variable that accounts for five climatic parameters (wind, temperature, humidity, solar radiation, and altitude) as the rate-determining variable of the decomposition process. We found ETo to have a strong (R2 = 0.98) predictive relationship with the decomposition rate. To account for maggot activity decomposing the carrion, we measured maggot weight in 2019 and 2020 using a novel method, and in 2020 we used FLIR imagery to measure maggot mass temperatures as a surrogate measurement of total maggot activity. Maggot activity was a significant predictor (p < 0.0001) of the decomposition rate, while maggot weight was not (p > 0.1). We hope to show the forensic entomology community the potential of using ETo. Future projects can incorporate ETo as a baseline to decomposition studies to determine if ETo remains the most accurate descriptor of decomposition and ultimately increase certainty in the Postmortem Interval (PMI).

Composition and functional diversity of bacterial communities during swine carcass decomposition

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.

Assessment of Fungal Succession in Decomposing Swine Carcasses (Sus scrofa L.) Using DNA Metabarcoding

The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes.

A synthesis of carcass decomposition studies conducted at a tropical (Aw) taphonomy facility: 2013-2022

Decomposition studies have been conducted in several regions of the world, but relatively few have investigated taphonomy in tropical environments. Even fewer have explored carcass decomposition during multiple tropical seasons, leaving the relationships between season and decomposition in tropical environments poorly understood. Ten decomposition studies using 30 carcasses were conducted in Honolulu, Hawaii, USA to start addressing this knowledge gap. These studies show that some postmortem processes were observed regardless of season. Carcass temperature and chemistry were spatiotemporally variable. Fly larval masses were consistently observed within 3 days (∼75 ADD) postmortem and carcasses lost 60%-90% of mass by 10 days (∼250 ADD) postmortem (Total Body Score ∼26). Season had a significant effect on decomposition, yet the warmest and most humid seasons did not always result in the most rapid and extensive decomposition. Seasonal variation appears to be less pronounced than at other tropical decomposition sites.

Insect Colonisation and the Decomposition Process in Aerated versus Watertight Burial Systems

In recent years, burial systems have covered increasingly higher costs due to the pollution caused by decomposition products. These products are understood as chemicals and microorganisms in the surrounding soil and groundwater and represent a topical issue. The purpose of this research was to ascertain the extent of decomposition when pig carcasses are buried in two different burial systems ("aerated" vs. "watertight") and catalogue the arthropods associated with burials at different time-points of removal from niches (after 6, 12, 24, 36, and 60 months). Thirteen taxa were collected in aerated niches, whereas five were collected in watertight niches. The initial access or exclusion of insect colonisers affected overall functional activity. Two Diptera species, Hydrotaea capensis and Megaselia scalaris, were the most abundant, supporting the hypothesis that insects can colonise carcasses in aerated burial systems. Furthermore, some species of bacteria have been documented as facilitators of the initial decomposition process of the carcass. Most bacterial colonies develop only in aerated niches. The trial showed that the first enzymatic-bacterial and insect actions helped promote the process of cadaveric decomposition and later skeletonisation, mainly when associated with aeration modes of the tomb/mound. The results obtained provide essential information on the process of human decomposition and taphonomy in cemeteries. Moreover, these data could benefit forensic science by adding information on insect colonisation and body modification in medico-legal investigations concerning the post-mortem interval in exhumed bodies and illegal burials.

Investigating the Timing and Extent of Juvenile and Fetal Bone Diagenesis in a Temperate Environment

It is well understood that intrinsic factors of bone contribute to bone diagenesis, including bone porosity, crystallinity, and the ratio of organic to mineral components. However, histological analyses have largely been limited to adult bones, although with some exceptions. Considering that many of these properties are different between juvenile and adult bone, the purpose of this study is to investigate if these differences may result in increased degradation observed histologically in fetal and juvenile bone. Thirty-two fetal (n = 16) and juvenile (n = 16) Sus scrofa domesticus femora subject to different depositions over a period of two years were sectioned for histological observation. Degradation was scored using an adapted tunneling index. Results showed degradation related to microbial activity in both fetal and juvenile remains across depositions as early as three months. Buried juvenile remains consistently showed the greatest degradation over time, while the blanket fetal remains showed more minimal degradation. This is likely related to the buried remains’ greater contact with surrounding soil and groundwater during deposition. Further, most of the degradation was seen in the subendosteal region, followed by the subperiosteal region, which may suggest the initial microbial attack is from endogenous sources.

Factors influencing carrion communities are only partially consistent with those of deadwood necromass

Research on decomposer communities has traditionally focused on plant litter or deadwood. Even though carrion forms highly nutrient-rich necromass that enhance ecosystem heterogeneity, the factors influencing saprophytic communities remain largely unknown. For deadwood, experiments have shown that different drivers determine beetles (i.e., decay stage, microclimate, and space), fungi (i.e., decay stage and tree species) and bacteria (decay stage only) assemblages. To test the hypothesis that similar factors also structure carrion communities, we sampled 29 carcasses exposed for 30 days that included Cervus elaphus (N = 6), Capreolus capreolus (N = 18), and Vulpes vulpes (N = 5) in a mountain forest throughout decomposition. Beetles were collected with pitfall traps, while microbial communities were characterized using amplicon sequencing. Assemblages were determined with a focus from rare to dominant species using Hill numbers. With increasing focus on dominant species, the relative importance of carcass identity on beetles and space on bacteria increased, while only succession and microclimate remained relevant for fungi. For beetle and bacteria with focus on dominant species, host identity was more important than microclimate, which is in marked contrast to deadwood. We conclude that factors influencing carrion saprophytic assemblages show some consistency, but also differences from those of deadwood assemblages, suggesting that short-lived carrion and long-lasting deadwood both provide a resource pulse with different adaptions in insects and microbes. As with deadwood, a high diversity of carcass species under multiple decay stages and different microclimates support a diverse decomposer community.

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.

The ephemeral resource patch concept

Ephemeral resource patches (ERPs) - short lived resources including dung, carrion, temporary pools, rotting vegetation, decaying wood, and fungi - are found throughout every ecosystem. Their short-lived dynamics greatly enhance ecosystem heterogeneity and have shaped the evolutionary trajectories of a wide range of organisms - from bacteria to insects and amphibians. Despite this, there has been no attempt to distinguish ERPs clearly from other resource types, to identify their shared spatiotemporal characteristics, or to articulate their broad ecological and evolutionary influences on biotic communities. Here, we define ERPs as any distinct consumable resources which (i) are homogeneous (genetically, chemically, or structurally) relative to the surrounding matrix, (ii) host a discrete multitrophic community consisting of species that cannot replicate solely in any of the surrounding matrix, and (iii) cannot maintain a balance between depletion and renewal, which in turn, prevents multiple generations of consumers/users or reaching a community equilibrium. We outline the wide range of ERPs that fit these criteria, propose 12 spatiotemporal characteristics along which ERPs can vary, and synthesise a large body of literature that relates ERP dynamics to ecological and evolutionary theory. We draw this knowledge together and present a new unifying conceptual framework that incorporates how ERPs have shaped the adaptive trajectories of organisms, the structure of ecosystems, and how they can be integrated into biodiversity management and conservation. Future research should focus on how inter- and intra-resource variation occurs in nature - with a particular focus on resource × environment × genotype interactions. This will likely reveal novel adaptive strategies, aid the development of new eco-evolutionary theory, and greatly improve our understanding of the form and function of organisms and ecosystems.

The devil is in the details: Variable impacts of season, BMI, sampling site temperature, and presence of insects on the post-mortem microbiome

Background

Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual's post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach.

Materials and methods

In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach.

Results

We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa.

Conclusion

The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.

Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition

Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles

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.

[Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem]

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.

Diverse Effects of Climate, Land Use, and Insects on Dung and Carrion Decomposition

Land-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.

MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study

Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72−168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.

Microbial traces and their role in forensic science

Forensic microbiology, also known as the microbiology of death, is an emerging branch of science that is still underused in criminal investigations. Some of the cases might be difficult to solve with commonly-used forensic methods, and then they become an operational field for microbiological and mycological analysis. The aim of our review is to present significant achievements of selected studies on the thanatomicrobiome (microorganisms found in the body, organs and fluids after death) and epinecrotic community (microorganisms found on decaying corpses) that can be used in forensic sciences. Research carried out as a part of the forensic microbiology deals with the thanatomicrobiome and the necrobiome - communities of microorganisms that live inside and outside of a putrefying corpse. Change of species composition observed in each community is a valuable feature that gives a lot of information related to the crime. It is mainly used in the estimation of post-mortem interval (PMI). In some criminal investigations, such noticeable changes in the microbiome and mycobiome can determine the cause or the actual place of death. The microbial traces found at the crime scene can also provide clear evidence of guilt. Nowadays, identification of microorganisms isolated from the body or environment is based on metagenome analysis and 16S rRNA gene amplicon-based sequencing for bacteria and ITS rRNA gene amplicon-based sequencing for fungi. Cultivation methods are still in use and seem to be more accurate; however, they require much more time to achieve a final result, which is an unwanted feature in any criminal investigation.

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.

Predicting the postmortem interval using human intestinal microbiome data and random forest algorithm

Gradual changes in microbial communities in a human body after death can be used to determine postmortem interval (PMI). In this study, gut microflora samples were collected from the vermiform appendix and the transverse colon of human cadavers with PMIs between 5 and 192 h. The results revealed that the appendix might be an excellent intestinal sampling site and the appendix flora had an inferred succession rule during human body decomposition. Firmicutes, Bacteroidetes, and their respective subclasses showed a predictable successionrule in relative abundance over time. A Random Forest regression model was developed to correlate human gut microbiota with PMI. We believe that our findings have increased the knowledge of the composition and abundance of the gut microbiota in human corpses, and suggest that the use of the human appendix microbial succession may be a potential method for forensic estimation of the time of death.

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition

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.

A walk on the dirt: soil microbial forensics from ecological theory to the crime lab

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.

Monitoring the dead as an ecosystem indicator

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.

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.

Carcasses at Fixed Locations Host a Higher Diversity of Necrophilous Beetles

Simple Summary

Whereas vertebrate scavengers have a higher diversity reported at randomly placed carcasses, the drivers of insect diversity on carrion, such as the exposure type (fixed versus random) or the carrion species, are still incompletely understood. We analyzed beetle diversity at differently exposed carcasses in the low-range mountain forest of the Bavarian Forest National Park in Germany. We tested if scavenging beetles, similarly to vertebrate scavengers, show a higher diversity at randomly placed carcasses compared to easily manageable fixed places. Ninety-two beetle species at 29 exposed wildlife carcasses (roe, red deer, and red foxes) were detected. Beetle diversity was higher at fixed locations possessing extended highly nutrient-rich cadaver decomposition islands as important refuges for threatened red-listed species, such as Necrobia violacea (Coleoptera: Cleridae). Particularly noticeable in our insect traps were the following two rare species, the “primitive” carrion beetle Necrophilus subterraneus (Coleoptera: Agyrtidae) and the false clown beetle Sphaerites glabratus (Coleoptera: Sphaeritidae). In Europe, only the species S. glabratus out of the genus Sphaerites is present. This emphasizes the importance of carrion for biodiversity conservation. We clearly show the relevance of leaving and additional providing wildlife carcasses in a dedicated place in protected forests for preserving very rare and threatened beetle species as essential members of the decomposing community.

Abstract

In contrast to other necromass, such as leaves, deadwood, or dung, the drivers of insect biodiversity on carcasses are still incompletely understood. For vertebrate scavengers, a richer community was shown for randomly placed carcasses, due to lower competition. Here we tested if scavenging beetles similarly show a higher diversity at randomly placed carcasses compared to easily manageable fixed places. We sampled 12,879 individuals and 92 species of scavenging beetles attracted to 17 randomly and 12 at fixed places exposed and decomposing carcasses of red deer, roe deer, and red foxes compared to control sites in a low range mountain forest. We used rarefaction-extrapolation curves along the Hill-series to weight diversity from rare to dominant species and indicator species analysis to identify differences between placement types, the decay stage, and carrion species. Beetle diversity decreased from fixed to random locations, becoming increasingly pronounced with weighting of dominant species. In addition, we found only two indicator species for exposure location type, both representative of fixed placement locations and both red listed species, namely Omosita depressa and Necrobia violacea. Furthermore, we identified three indicator species of Staphylinidae (Philonthus marginatus and Oxytelus laqueatus) and Scarabaeidae (Melinopterus prodromus) for larger carrion and one geotrupid species Anoplotrupes stercorosus for advanced decomposition stages. Our study shows that necrophilous insect diversity patterns on carcasses over decomposition follow different mechanisms than those of vertebrate scavengers with permanently established carrion islands as important habitats for a diverse and threatened insect fauna.

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n = 198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57 days) and 333.8 ADD (~37 days), respectively.

Microbial communities developing within bulk sediments under fish carcasses on a tidal flat

Animal carcasses are often brought into tidal flats where they are at the boundary between terrestrial and marine ecosystems. Since these carcasses act as microhabitats with large amounts of energy and nutrients, they likely develop unique bacterial assemblages in the ambient sediment, which in turn may stimulate colonization of other organisms such as protozoans. However, little is known about the microbial assemblages colonized in sediment around animal carcasses in the tidal zone. Herein we examined the bacterial and ciliophoran assemblages developed in association with fish carcasses by incubating the carcasses in the Higashiyachi tidal flat (Sendai, Japan). We collected sediment samples at 2, 9, and 42 days of incubation and analyzed the bacterial and ciliophoran assemblages by 16S and 18S rRNA gene amplicon sequencing. We observed significant differences in the composition and relative abundance of bacterial and ciliophoran operational taxonomic units (OTUs) between the sediments with and without the carcasses. Our analyses suggest that these unique assemblages were created through the direct effects of the carcass and indirect effects through interactions between bacteria and ciliophorans. These results also suggest that animal carcasses developed a temporally unique microbial food web in the sediments close to the carcasses, although it disappeared for several weeks.

Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus

Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.

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.

Volatile organic compounds in variably aged carrion impacted by the presence of the primary colonizer, Cochliomyia macellaria (Diptera: Calliphoridae)

The attraction and colonization of vertebrate remains by carrion-associated arthropods are processes largely governed by olfaction. As remains decompose, they emit a bouquet of volatile organic compounds (VOCs), which in part originate from endogenous and exogenous microbes surrounding the carcass or from the carcass itself. The composition and concentration of VOCs are influenced by the presence and abundance of microbial species and arthropods. Blowfly species, such as Cochliomyia macellaria, play a critical role in nutrient recycling and the decomposition process of carrion. Gas chromatography-mass spectroscopy analysis was used to identify and classify volatile emissions from insect-colonized (with C. macellaria) and uncolonized rat carcasses, as well as a standard Gainesville diet, over a 10-day period. There were significant differences in composition and abundance of compounds present in each treatment, with significant effects of time, and different compound composition between treatments. Notable indicator compounds included, but were not limited to, indole, dimethyl disulfide, and dimethyl trisulfide. A high compound richness, and a low compound diversity, was detected over the 10-day period. The indicator compounds detected across all treatments were found to be of microbial origin, highlighting the importance of microbes in decomposition processes and arthropod attraction to carrion. This study also discusses the significant impact of necrophagous arthropods to the VOC profile of carrion. The results of this study provide insight into the changes in decomposition VOCs over time, with an explanation of compounds in high concentration known to be attractive to carrion-colonizing arthropods.

Microbial succession from a subsequent secondary death event following mass mortality

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.

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.

Omics era in forensic medicine: towards a new age

Background/aim

Forensic medicine and sciences is a multidisciplinary branch of science, which frequently benefit from novel technologies. State of the art omics technologies have begun to be performed in forensic medicine and sciences, particularly in postmortem interval, intoxication, drugs of abuse, diagnosis of diseases and cause of death. This review aims to discuss the role and use of great omics (metabolomics, proteomics, genomics and transcriptomics) in forensic sciences, in detail.

Materials and methods

A detailed review of related literature was performed, and studies were subdivided as per the type of omics.

Results and conclusion

Omics seems as a revolutionary step in forensic science and sure carries it towards a new age. The number of forensic studies utilizing omics steadily increases in last years. Omics strategies should be used together in order to gather more accurate and certain data. Additional studies need to be performed to incorporate omics into routine forensic methodology.

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts

Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.

Influence of Substrate Age and Interspecific Colonization on Oviposition Behavior of a Generalist Feeder, Black Soldier Fly (Diptera: Stratiomyidae), on Carrion

Variation in resource utilization plays a significant role in determining the success or failure of a species. Generalist species across numerous taxa have exhibited success in feeding strategies for a variety of reasons. This study investigated the colonization and oviposition habits of a generalist carrion-feeder, Hermetia illucens L. (Diptera: Stratiomyidae), to varying conditions of carrion decay and colonization. Oviposition treatments consisted of combinations of variably aged decaying rats, both uncolonized and colonized with a heterospecific carrion-feeder. The black soldier fly exhibited a greater preference for oviposition on aged carrion, regardless of carcass colonization status. However, when presented with the option to colonize a plant-based diet, there was a significantly greater (40.4%) oviposition response to this diet. Results of this study highlight the ability of the black soldier fly to colonize fresh or aged carrion with or without a primary colonizer present, further supporting the recognition of this species as a generalist. These data demonstrate potential inaccuracies in the utility of H. illucens as time of colonization indicator species for legal investigations, and, in some regard, can be considered an exploitative niche-specialist (i.e., relying on plant-carrion interface for immature development) when found in association with carrion.

Succession of bacterial communities on carrion is independent of vertebrate scavengers

The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.

Fear the reaper: ungulate carcasses may generate an ephemeral landscape of fear for rodents

Animal carcasses provide an ephemeral pulse of nutrients for scavengers that use them. Carcass sites can increase species interactions and/or ephemeral, localized landscapes of fear for prey within the vicinity. Few studies have applied the landscape of fear to carcasses. Here, we use a mass die-off of reindeer caused by lightning in Norway to test whether rodents avoided larger scavengers (e.g. corvids and fox). We used the presence and abundance of faeces as a proxy for carcass use over the course of 2 years and found that rodents showed the strongest avoidance towards changes in raven abundance (β = -0.469, s.e. = 0.231, p-value = 0.0429), but not fox, presumably due to greater predation risk imposed by large droves of raven. Moreover, the emergence of rodent occurrence within the carcass area corresponded well with the disappearance of raven during the second year of the study. We suggest that carcasses have the potential to shape the landscape of fear for prey, but that the overall effects of carcasses on individual fitness and populations of species ultimately depend on the carcass regime, e.g. carcass size, count, and areal extent, frequency and the scavenger guild. We discuss conservation implications and how carcass provisioning and landscapes of fear could be potentially used to manage populations and ecosystems, but that there is a gap in understanding that must first be bridged.

Molecular characterization of gut microbial shift in SD rats after death for 30 days

To observe the temporal shifts of the intestinal microbial community structure and diversity in rats for 30 days after death. Rectal swabs were collected from rats before death (BD) and on day 1, 5, 10, 15, 20, 25, and 30 after death (AD). Bacteria genomic DNA was extracted and V3 + V4 regions of 16S rRNA gene were amplified by PCR. The amplicons were sequenced at Illumina MiSeq sequencing platform. The bacterial diversity and richness showed similar results from day 1 to 5 and day 10 to 25 all presenting downtrend, while from day 5 to 10 showed slightly increased. The relative abundance of Firmicutes and Proteobacteria displayed inverse variation in day 1, 5, 10 and that was the former decreased, the latter increased. Bacteroidetes, Spirochaete and TM7 in day 15, 20, 25, 30 was significantly decline comparing with BD. Enterococcus and Proteus displayed reduced trend over day 1, 5, 10 and day 10, 15, 20, 25, respectively, while Sporosarcina showed obvious elevation during day 15, 20, 25. Accordingly, there was a certain correlation between intestinal flora succession and the time of death. The results suggested that intestinal flora may be potential indicator to aid estimation of post-mortem interval (PMI).

Cold Case Experiment Demonstrates the Potential Utility of Aquatic Microbial Community Assembly in Estimating a Postmortem Submersion Interval

Microbial community assembly (MCA) of both human and nonhuman animal carcasses provides indicators useful for estimating the postmortem interval (PMI) in terrestrial settings. However, there are fewer studies estimating postmortem submersion intervals (PMSIs) in aquatic habitats. No aquatic studies to date assessed MCA in the context of a death investigation, with all previous studies focusing on important basic ecological questions. Within the context of a cold case investigation, we performed an experiment using replicate adult swine carcasses to describe postmortem MCA variability within a nonflowing aquatic habitat. Using high-throughput sequencing of carcass postmortem microbiomes, we described MCA variability and identified key taxa associated with decomposition in an aquatic habitat similar to the cold case body recovery site. We also modeled key taxa for estimating PMSIs, modeling within ±3 days (mean square error) postmortem using random forest regression. Our findings show significant changes in microbial communities as decomposition progressed, and several taxa were identified as important indicator taxa which may be useful for future estimates of PMSI. While descriptive, this study provides initial findings quantifying MCA variability within a nonflowing aquatic habitat. Within the context of the cold case investigation, we discuss how postmortem microbial samples collected at the time of body recovery could have been an important piece of evidence for understanding the PMSI of recovered remains. Additional experimental studies are needed to explicitly test and identify mechanisms associated with postmortem MCA variability in other habitats and under different temperature (e.g., seasons) conditions.