The author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report: Document Title: Biomarkers of Human Decomposition Ecology and the Relationship to Postmortem Interval Author(s): Franklin E. Damann, Ph.D. Document No.: 241440 Date Received: March 2013 Award Number: 2008-DN-BX-K165 This report has not been published by the U.S. Department of Justice. To provide better customer service, NCJRS has made this Federally- funded grant report available electronically. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. This document is a research report submitted to the U.S. Department of Justice. This report has not been published by the Department. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. Final Technical Report National Institute of Justice Award Number: 2008-DN-BX-K165 Biomarkers of Human Decomposition Ecology and the Relationship to Postmortem Interval Franklin E. Damann, PhD National Museum of Health and Medicine Silver Spring, MD 20910 30 September 2012 This document is a research report submitted to the U.S. Department of Justice. This report has not been published by the Department. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. Abstract Microbial putrefaction of a corpse leaves signatures in the landscape and bone. Within this relationship exists the potential for refining models of postmortem interval (PMI) estimation based on increased understanding of the physicochemical characteristics and bacterial metagenomic profiles of the human decomposition environment. Therefore, microbial biomarkers and characterization of gravesoil ecology have a great potential to benefit the work of forensic anthropologists in interpreting postmortem history. Unfortunately, this potential is only recently becoming realized and suffers from a lack of basic research. Using bone and soil samples acquired from The University of Tennessee Anthropology Research Facility (ARF), this study provides baseline physicochemical and bacterial community data for developing methods to estimate better estimate PMI. This project evaluated the physicochemical and microbial characteristics of ARF soils, non- ARF soils, and skeletal tissue exposed to various levels of human decomposition and advancing PMIs. Soil was evaluated for eight different physicochemical parameters and a biological similarity matrix of identified bacterial taxa from sequencing the 16S rRNA gene was generated from soil and bone. Results of the physicochemical analyses from ARF landscape soils demonstrated no differences among the decomposition sample groups inside the facility, while all sample groups inside were significantly different (p ≤ 0.05) from the non-ARF samples. Bacterial community data augmented the physicochemical data, by identifying significant differences inside the ARF between decomposition sites with constant decomposition and those with little to no decomposition, suggesting microbial sensitivity to slight ecological change. Sites with a lot of decomposition contained elevated levels of chemoorganotrophic and sulfate-reducing bacteria, and a reduction in Acidobacteria, indicating a change in the community of underlying bacteria in response to carcass enrichment and ammonification of the soil. Temporally-related trends in bacterial metagenomic profiles were observed among the PMI samples of gravesoil and bone. Regardless of origin (gravesoil or bone), the same bacterial phyla (Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes) were observed; only the relative abundance changed over time. Proteobacteria were most abundant in all samples and the most fluctuation among samples Page 2 of 90 This document is a research report submitted to the U.S. Department of Justice. This report has not been published by the Department. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. occurred with Firmicutes, Bacteroidetes, and Actinobacteria. Firmicutes appeared more frequently in the earlier samples than did Bacteroidetes and Actinobacteria. Bacteroidetes dominated the middle phase to the 20 month PMI sample, at which time Actinobacteria dominated the three phyla at the 48 month terminus of this project. Thirty years of decomposition research at the ARF has forced a shift in the underlying bacterial community in response to the enrichment of the soil with increased nitrogen and carbon-containing compounds. The results of this basic research provide baseline data for further exploration regarding the biogeochemical relationships among microbial organisms, soil characteristics, cadaver decomposition, and advancing PMI. Page 3 of 90 This document is a research report submitted to the U.S. Department of Justice. This report has not been published by the Department. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. Table of Contents Abstract ........................................................................................................................................... 2 Table of Contents .......................................................................................................................... 4 List of Figures ................................................................................................................................ 5 List of Tables ................................................................................................................................. 6 Executive Summary ........................................................................................................................ 7 Chapter 1 Introduction .................................................................................................................. 12 1.1 Statement of the Problem .................................................................................................... 12 1.2 Statement of Research Rationale ........................................................................................ 12 1.3 Literature Review................................................................................................................ 13 Chapter 2 General Field and Laboratory Methods ....................................................................... 17 2.1 Sample Collection ............................................................................................................... 17 2.2 Physicochemical Parameters ............................................................................................... 18 2.3 Molecular Methods ............................................................................................................. 20 Chapter 3 Physicochemical Environment of the ARF Soil Landscape ........................................ 27 3.1 Introduction ......................................................................................................................... 27 3.2 Sample Selection ................................................................................................................. 27 3.3 Analytical Methods ............................................................................................................. 28 3.4 Results and Discussion ....................................................................................................... 28 3.5 Conclusions ......................................................................................................................... 29 Chapter 4 Bacterial Communities of the ARF Soil Landscape .................................................... 34 4.1 Introduction ......................................................................................................................... 34 4.2 Sample Selection ................................................................................................................. 34 4.3 Analytical Methods ............................................................................................................. 34 4.4 Results and Discussion ....................................................................................................... 35 4.5 Conclusions ......................................................................................................................... 37 Chapter 5 An Investigation into the Relationship of Postmortem Interval and the Physicochemical Parameters of Gravesoils .................................................................................. 48 5.1 Introduction ......................................................................................................................... 48 5.2 Sample Selection ................................................................................................................. 48 5.3 Analytical Methods ............................................................................................................. 48 5.4 Results and Discussion ....................................................................................................... 49 5.4 Conclusions