An RNA-based analysis of changes in biodiversity indices in response to Sus scrofa domesticus decomposition

Abstract

Despite emergent research initiatives, significant knowledge gaps remain of soil microbiology-associated cadaver decomposition. Nevertheless, preliminary studies have shown that the vast diversity and complex interactions of soil microbial communities have great potential for forensic applications such as clandestine grave location and postmortem interval estimation. This study investigated changes in soil bacterial communities during pig (Sus scrofa domesticus) leg decomposition. 16S rRNA, instead of the usually applied 16S rDNA marker, was used to compare the metabolically active bacteria. Total bacterial RNA was extracted from soil samples of three different layers on day 3, 28 and 77 after the shallow burial of a pig leg. The V3 region of the 16S rRNA was amplified, analysed by RT-PCR DGGE, and compared with control soil bacterial community profiles. Statistically significant differences in soil bacterial biodiversity were observed. For the control, bacterial diversity (H′) and species richness (S) of the three layers averaged 2.48±0.14 (H′) and 18.8±2.5 (S), respectively, while for the test soil increases (p=0.027) were recorded between day 3 (H′=2.71±0.02; S=21.3±2.0) and 28 (H′=3.46±0.32; S=60.3±16.9), particularly in the middle (10–20cm) and bottom (20–30cm) soil layers. Between day 28 and 77 the diversity and richness then decreased on average for all three layers (H′=3.43±0.20; S=60.0±17.3) but remained higher than on day 3. Thus, responses in soil bacterial profiles and activity to carcass decomposition, detected and characterised by RNA-based DGGE, could be used together with RNA sequencing data, changes in physico-chemical variables (carbon, nitrogen, phosphorus, temperature, redox potential, water activity and pH) and conventional macroecology markers (e.g. insects and vegetation), to develop a suite of analytical protocols for different forensic scenarios.