Final Report Modeling and Decision Support Tools Based on the Effects of Sediment Geochemistry and Microbial Populations on Contaminant Reactions in Sediments SERDP Project ER-1495 September 2011 Jeanne M. VanBriesen Carnegie Mellon University Todd Bridges U.S. Army Engineer Research and Development Center (ERDC) Table of Contents Abstract ......................................................................................................................................... iii Executive Summary ..................................................................................................................... iv List of Acronyms ......................................................................................................................... vii List of Figures ............................................................................................................................... ix List of Tables ................................................................................................................................ xi Acknowledgments ....................................................................................................................... xii 1 Objectives .................................................................................................................................. 1 2 Background ............................................................................................................................... 2 2.1 Fundamentals of PCBs ........................................................................................................ 3 2.2 Microbial Transformation of PCBs .................................................................................... 5 2.2.1 PCB Dechlorinating Microorganisms ....................................................................... 6 2.2.2 Factors Affecting PCB Dechlorination ..................................................................... 7 2.3 PCB Dechlorination Pathways and Processes .................................................................... 7 3 Materials and Methods .......................................................................................................... 11 3.1 Site Selection and Initial Characterization ........................................................................ 12 3.1.1 The Grasse River ..................................................................................................... 13 3.1.2 The Hudson River ................................................................................................... 13 3.2 Core Characterization ....................................................................................................... 13 3.3 Grab Sample Geochemical Analysis ................................................................................ 14 3.4 Congener-Specific PCB Analysis of Sediments ............................................................... 14 3.4.1 Extraction of PCBs from the Grab and Core 18M Sediment Samples ................... 14 3.4.2 Congener Specific PCB Analysis with the GC-µECD Method .............................. 14 3.5 Molecular Microbiological Analyses ................................................................................ 15 3.5.1 Genomic DNA Extraction....................................................................................... 16 3.5.2 Microbial Community Profiles by PCR-DGGE Analyses ...................................... 16 3.5.3 Clone Library for Bacteria in Core Segments ......................................................... 18 3.5.4 Quantitative Polymerase Chain Reaction (Q-PCR) ................................................ 18 3.6 Computational and Statistical Analyses Methods ............................................................. 19 3.6.1 Molar Dechlorination Product Ratio (MDPR) ........................................................ 19 3.6.2 Identification of Missing Pathways in Eight Processes .......................................... 20 3.6.3 Bayes Monte Carlo (BMC) Method for Process Occurrence ................................. 20 3.6.4 Decision Support Modeling Methods ..................................................................... 22 3.7 Microcosm Study Methods ............................................................................................... 22 3.7.1 Selection of PCB Congeners ................................................................................... 22 3.7.2 Sediment Characterization for Microcosm Preparation .......................................... 23 3.7.3 Preparation of PCB Spiked Sediments ................................................................... 24 3.7.3.1 Prepare the PCB Mixture ................................................................................... 24 3.7.3.2 Prepare the Spiked Sediment .............................................................................. 29 3.7.3.3 Prepare the Microbial Media .............................................................................. 29 3.7.3.4 Assemble the Microcosms ................................................................................. 29 3.7.4 Microcosm Sampling and Analysis ........................................................................ 30 i 3.7.4.1 Iron and Sulfide Analysis ................................................................................... 31 3.7.4.2 PCB Analysis ..................................................................................................... 31 3.7.5 DNA Extraction and Microbial Community Analysis ............................................ 31 4 Results and Discussion ........................................................................................................... 32 4.1 Task A-1. Grab Sample Sediment Characterization ......................................................... 32 4.1.1 Geochemical Characterization ................................................................................ 32 4.1.2 Microbial Analysis of Hudson and Grasse Sediment ............................................. 40 4.2 Task A-2. Characterization of Sediment Cores ................................................................ 51 4.2.1 Cesium Results........................................................................................................ 51 4.2.2 TOC, Geochemical Characteristics and Total PCBs .............................................. 56 4.2.3 Evidence of Reductive Dechlorination in Sediment Cores ..................................... 58 4.2.4 Changes in Congener Distributions in Cores from 1997 to 2006 ........................... 67 4.2.5 Microbiological Analysis of Grasse River Core 18M. ........................................... 71 4.2.5.1 PCR Detection of 6 Microbial Groups from the 8 Segments of Core 18M ....... 73 4.2.5.2 Group-Specific Microbial Community Profiles by DGGE Analyses ................ 74 4.2.5.3 Bacterial Clone Libraries from Two segments of Core 18M and the Grasse River Surficial Sample .................................................................................................... 79 4.2.5.4 Quantitative PCR for Group Specific Enumeration ........................................... 81 4.3 Task B. PCB Model Development.................................................................................... 86 4.3.1 Classification Trees for the Identification of Missing Pathways in Dechlorination Processes ........................................................................................................................... 86 4.3.1.1 Bayes Monte Carlo (BMC) for Process Occurrence .......................................... 96 4.4 Task C. Microcosm Study............................................................................................... 104 4.4.1 PCB Dechlorination in Microcosms Spiked with Two PCB Mixtures ................ 104 4.4.1.1 Shifts of Tracker Pair Ratios in Microcosms Spiked with PCB Mixture 1. ..... 106 4.4.1.2 Pathways Occurred in Microcosms Spiked with PCB Mixture 1 (No Sulfate or Iron Amendment) .......................................................................................................... 107 4.4.1.2.1 Target Chlorines in Microcosms with Sulfate Amendments .................... 108 4.4.1.2.2 Altered Dechlorination Preference in the Grasse Microcosms with Iron Amendments ............................................................................................................... 108 4.4.1.2.3 Evidence of Ferric Iron Reduction in Microcosms Spiked with PCBs ..... 108 4.4.1.2.4 Evidence of Methanogenesis ..................................................................... 110 4.4.1.2.5 Quantification of Putative Dechlorinating Microorganisms ..................... 113 4.5 Task D. Decision Support Model.................................................................................... 115 5 Conclusions and Implications for Future Research .......................................................... 120 Literature Cited ........................................................................................................................ 123 Appendix A. Raw Data Appendix B. List of Scientific and Technical Publications Appendix C. Modeling and Decion Support Tools White Paper ii Abstract The proper management of polychlorinated biphenyl (PCB)-contaminated sediment has proven to be a wide-spread, complex, and costly issue. PCBs are a primary contaminant driving risk at many Department of Defense facilities. There is a need for sound science and