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

Abstract

Vertebrate decomposition processes have important ecological implications and, in the case of human decomposition, forensic applications. Animals, especially domestic pigs (Sus scrofa), are frequently used as human analogs in forensic decomposition studies. However, recent research shows that humans and pigs do not necessarily decompose in the same manner, with differences in decomposition rates, patterns, and scavenging. The objective of our study was to extend these observations and determine if human and pig decomposition in terrestrial settings have different local impacts on soil biogeochemistry and microbial activity. In two seasonal trials (summer and winter), we simultaneously placed replicate human donors and pig carcasses on the soil surface and allowed them to decompose. In both human and pig decomposition-impacted soils, we observed elevated microbial respiration, protease activity, and ammonium, indicative of enhanced microbial ammonification and limited nitrification in soil during soft tissue decomposition. Soil respiration was comparable between summer and winter, indicating similar microbial activity; however, the magnitude of the pulse of decomposition products was greater in the summer. Using untargeted metabolomics and lipidomics approaches, we identified 38 metabolites and 54 lipids that were elevated in both human and pig decomposition-impacted soils. The most frequently detected metabolites were anthranilate, creatine, 5-hydroxyindoleacetic acid, taurine, xanthine, N-acetylglutamine, acetyllysine, and sedoheptulose 1/7-phosphate; the most frequently detected lipids were phosphatidylethanolamine and monogalactosyldiacylglycerol. Decomposition soils were also significantly enriched in metabolites belonging to amino acid metabolic pathways and the TCA cycle. Comparing humans and pigs, we noted several differences in soil biogeochemical responses. Soils under humans decreased in pH as decomposition progressed, while under pigs, soil pH increased. Additionally, under pigs we observed significantly higher ammonium and protease activities compared to humans. We identified several metabolites that were elevated in human decomposition soil compared to pig decomposition soil, including 2-oxo-4-methylthiobutanoate, sn-glycerol 3-phosphate, and tryptophan, suggesting different decomposition chemistries and timing between the two species. Together, our work shows that human and pig decomposition differ in terms of their impacts on soil biogeochemistry and microbial decomposer activities, adding to our understanding of decomposition ecology and informing the use of non-human models in forensic research.

At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics

“…Specifically, because of lack of thermoregulation, ambient temperatures ( Goff, 2009 ) greatly affect the shift in nutrient availability and can thereby affect microbial community dynamics. Thus, while most studies have been performed in the United States ( Metcalf et al, 2013 ; Pechal et al, 2018 ; DeBruyn et al, 2021 ) with a few in Australia, Japan, and the United Kingdom ( García et al, 2020 ), post-mortem microbiome research in a wider range of climates should be encouraged.…”

“…Moreover, many microbial cells contain robust cell walls that leave them better protected against degradation compared to human cells ( Sijen, 2015 ). Nevertheless, the focus of microbial forensics to date has been predominantly on gut and soil samples ( Metcalf et al, 2013 , Metcalf et al, 2016 ; Pechal et al, 2014 ; Javan et al, 2016b ; Burcham et al, 2019 ; DeBruyn et al, 2021 ), whereas research on forensic implementation of the (post-mortem) microbiome of the female reproductive tract, skin, and oral cavity is lagging behind. Therefore, in this review, we provide a critical assessment of current research on the vaginal, skin, and oral/salivary microbiome in relation to their potential application in forensics, especially sexual assault and femicide cases.…”

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

“…In terrestrial settings, nutrient-rich fluids from decomposing animal carcasses are flushed into the surrounding soil during decomposition, altering soil chemistry and increasing soil microbial activity. Changes in soil chemistry include increased electrical conductivity, ammonium concentrations, and dissolved organic carbon and nitrogen content ( 1 – 3 ). Soil microbes also respond to decomposition products, resulting in altered community composition and activity.…”

“…Moisture also affects decomposition by mediating microbial activity ( 13 ). However, even when extrinsic factors are controlled for, such as when multiple carcasses start decomposition at the same time and experience the same local environmental conditions, differential decomposition patterns have been observed among individuals ( 1 , 2 , 14 ), suggesting that intrinsic factors may also impact decomposition patterns. Genetics, age, sex, diet, body mass index (BMI), and diseases (including therapeutic interventions) can lead to differences in body physiology or chemistry and microbiome between individuals ( 15 – 20 ) that may ultimately impact decomposer activity during decomposition.…”

“…Changes in soil chemistry and microbial succession in response to human decomposition have been suggested as potential markers to estimate the postmortem interval (PMI) as evidence in death investigations ( 21 – 23 ); therefore, understanding sources of variation in human decomposition is critical for forensic applications. Both extrinsic and intrinsic factors are sources of variability that can impact PMI; however, a majority of decomposition studies have focused only on extrinsic factors ( 1 , 10 , 24 – 27 ). A few terrestrial decomposition studies have shown that the inclusion of BMI in soil chemistry-based PMI models improves model prediction ( 2 , 28 ).…”