Changes in soil microbial communities during subsurface decompositions

Abstract

A cadaver is an energy source with an important role in nutrient recycling. Its decomposition is a complex process attributable to microbial, vertebrate and invertebrate scavenger metabolic activities, which impact the surrounding environmental microbiota with potentially novel forensic applicability if key knowledge gaps are addressed. To investigate subsurface microbiome shifts as a novel tool to establish postmortem microbial clock and augment postmortem interval (PMI) estimations, four studies were made with pigs /piglets as human taphonomic proxies. Study I used a pig leg (Sus scrofa domesticus) buried in sandy loamy soil in a sealed polyethylene container for 98 days while Study II compared S. scrofa domesticus and plant litter (Agrostis/Festuca spp) decomposition over 365 days in triplicate microcosms. Study III (300 days) examined two decomposition substrates (whole piglets and Agrostis/Festuca spp), individually and together. Finally, an in situ Study (IV) consisted triplicate burials of piglets and Oak (Quercus robur) leaf litter were monitored for 270 days.
For the studies, a combination of environmental variables and molecular analyses were employed. Specifically, analyses/interpretation of the PCR-DGGE fingerprints by richness, Shannon-Wiener and Simpson ecological indices and Illumina Miseq next-generation sequencing were used to determine decomposition-mediated dynamics on soil microbial community diversity, structure and composition. Overall, both pH and temperature changes aligned with microbial community profile shifts and were important variables for PMI estimation. The DGGE-based profiling of the 16S rRNA bacterial gene appeared the most suitable for S. scrofa domesticus PMI estimation, while ecological indices of the fungal 18S rRNA gene were better indicators of plant litter decomposition. Some unique taxa, such as Sphingobacteriaceae and Xanthomonadaceae, provided preliminary indicators to differentiate between pig and plant vegetation decomposition as illustrated in Study II. Likewise, taxa such as Sphingobacteriaceae and Alcaligenaceae were identified during the summer season as potential indicators for piglet and piglet + plant litter in Study III whereas
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Planctomycetaceae and Sphingobacteriaceae were likely indicators to differentiate between the two carbon substrates. Finally, the in situ epinecrotic community profiles in Study IV identified Anaerolineaceae and Methylophilaceae as microbial clock indicators for oak leaf litter and piglet, respectively, for decomposition locations in similar soil types. This research programme is one of the first to compare two decomposition substrates in the subsurface to illustrate potential applicability in PMI estimation.

Date of Award	27 Apr 2018
Original language	English
Awarding Institution	Teesside University
Supervisor	Timothy Thompson (Supervisor) & Theresia Ralebitso-Senior (Supervisor)