Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition
Introduction
Cadaver decomposition is a complex process that begins with post-mortem changes such as algor mortis, rigor mortis and livor mortis followed by soft tissue decomposition through the processes of autolysis, putrefaction, decay and skeletonization [1], [2], [3], [4], [5], [6]. The soft tissue decomposition stages are characterized by protein, carbohydrate and lipid catabolisms in the body [1], [2], [5]. The rate of cadaver decomposition can be influenced by both biotic and abiotic factors, which can vary between above- and underground situations [2], [3]. Studies which compared above- [7], [8], [9] and underground [10], [11], [12] scenarios have shown that cadaver decomposition rate is slower in the latter.
The application of fatty acid-based techniques, such as phospholipid fatty acid and fatty acid methyl ester analyses, and molecular techniques, such as polymerase chain reaction (PCR), denaturing/temperature gradient gel electrophoresis (T/DGGE) and terminal restriction length polymorphism (T-RFLP) with next generation sequencing for microbial community profiling, are beginning to elucidate the complex relationships between cadaver decomposition, nutrient cycling and soil microbial community dynamics in a forensic context [6], [13], [14], [15], [16], [17], [18]. For example, some sub-surface studies by Bergmann et al. [19] and Olakanye et al. [20] recorded spatial and temporal changes in soil bacterial diversity relative to burial depth and decomposition time, respectively. Also, aboveground studies by Lauber et al. [21] that investigated the roles of microorganisms in cadaver ecogenomics recorded changes in 16S rRNA bacterial, 16S rRNA archaeal, and 18S rRNA fungal communities in sterile and non-sterile soils with differences between skin-associated and grave soil during the active and advanced decay stages. Thus, several researchers have illustrated and suggested that changes in epinecrotic and burial soil microbial diversity can be a potential “post-mortem microbial clock” tool for PMI estimation [15], [16].
Although the possible use of forensic ecogenomics as a novel suite of techniques for crime scene investigation is gaining momentum [15], [16], [17], [19], [22], [23], more detailed studies are required to elucidate fully the interactions between soil ecology and cadaver decomposition (cadaver decomposition-mediated soil ecology changes). Consequently, the values of different microbial ecology tools in this novel context, including profiling platforms that are accessible to most researchers and practitioners, must be considered while taking full cognizance of their limitations. To explore this, two different carbon sources (S. scrofa domesticus and Agrostis/Festuca spp) were buried and studied over a one-year period (July 2013 to July 2014). The specific research questions were:
- (i)
What are the effects of abiotic factors such as temperature/pH on decompositional soil biodiversity?;
- (ii)
Will Sus scrofa domesticus and plant matter decompositions illicit the same trends or shifts in biodiversity compared to the soil only controls?;
- (iii)
Which biochemical and molecular markers (microbial community indices) can be employed reliably during S. scrofa domesticus decomposition? Thus, DGGE profiling was complemented by ecological community indices measurements of Shannon–Wiener and Simpson diversity, taxa richness and evenness.
Section snippets
Soil collection and characterization
Twenty kilograms of sandy clay loam soil was dug from a well secured site at Bishop Burton College of Agriculture, Lincolnshire, UK (Lat. 53.27°N, Long. 0.52°W) [24] and stored in a sterilized 25 l airtight bucket. To ensure homogeneity, the soil was milled thoroughly (Retsch SM 100, Retsch, Haan, Germany) and sieved (ASTM—standard soil sieve No 10; 2 mm mesh). The sandy clay loam soil was constituted (w/w) by 21% clay, 21% silt and 58% sand (Forestry Commission, Surrey, UK) and physicochemical
Temperature
Between days 0 and 60, the average microcosm temperature was 25.1 °C ± 0.31 while the atmosphere was 19.2 °C ± 0.19. The seasonal weather change then resulted in a temperature decrease that was marked from days 120 to 180 with an average of 8 °C ± 0.26. For days 300 to 365 temperature increases were apparent with an average of 14.5 °C ± 0.14. The two-way ANOVA showed a statistically significant difference (p < 0.001) between the atmospheric and microcosm temperatures but no difference (p > 0.05) between the S.
Discussion
Studies of cadaver decomposition and its interactions with, and effects on, soil ecology have highlighted the potential of forensic ecogenomics as a powerful tool to estimate PMI and identify clandestine graves through changes in microbial communities [14], [15], [16], [20], [21], [22], [23]. Although this tool has potential advantages compared with conventional methods for estimating PMI, most studies have, however, only considered a single carbon source (the cadaver) while dual sources can
Conclusion
Abiotic factors such as temperature and pH are key variables in taphonomic studies. This research identified interesting trends, as revealed by an accessible ecogenomics technique and multiple and robust statistical analyses, that could be useful in identifying a cadaver grave by targeting specific microbial community diversity changes. In this study microcosms were used but an extensive whole carcass program is in progress and should result in more comprehensive data by targeting specific
Acknowledgments
The authors thank Lorraine White for granting site access for soil collection.
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