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Contamination at the Doe Savannah River Site

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Contamination at the Doe Savannah River Site MICROBIAL DIVERSITY ASSOCIATATED WITH METAL- AND RADIONUCLIDE- CONTAMINATION AT THE DOE SAVANNAH RIVER SITE (SRS), SOUTH CAROLINA, USA by QI YE (Under the Direction of Chuanlun Zhang) ABSTRACT The goal of this dissertation is to utilize an integrated approach of molecular microbiology (cloning, sequencing, and real-time PCR) and microbial lipid biomarker to understand microbial diversity, and the factors and mechanisms shaping microbial community structure in the heavily contaminated soils at the Savannah River Site of the US Department of Energy in South Carolina, USA. The first task of this dissertaton was to determine the effect of heavy metals (As, Co, Cr, Cu, Pb, and Ni) on the microbial diversity in the effluent channel of the waste water from a coal-generated power plant. The predominance of antibiotic resistant species near the source water indicated that heavy metal concentrations are likely to serve as selective pressure for antibiotic and metal tolerant bacteria and genes. Members of heterotrophic clostridia in D-area may directly participate in metal reduction or provide electron donors for the metal-reducing microorganisms. Another task was undertaken to examine the microbial community structures in heavy metal (eg. nickel) and radionuclides (eg., uranium) contaminated soils in the M-area. Members of sulfate-reducing and iron-reducing bacteria, especially Geobacter species may play an important role in immobilizing the metals and radionuclides in the uranium-contaminated sites. The third task was to determine the diversity and abundance of ammonium-oxidizing archaea in metal- and organic- contaminated soils at the Savannah River Site. To the best of my knowledge, this dissertation marks the first demonstration of microbial community changes in the heavily contaminated soils at the Savannah River Site, and demonstrated that the microbial community structure and abundance changed along with heavy metal and radionuclide gradients. This implies that it is feasible to bio-stimulate the indigenous microbial populations for bioremediation of contaminants at the Savannah River Site. INDEX WORDS: Savannah River Site, Bioremediation, 16 rRNA, Functional genes, Iron-reducing Bacteria, Sulfate-reducing Bacteria, GDGT, Ammonium-Oxidizing Crenarchaeota, Heavy metal, Radionuclide MICROBIAL DIVERSITY ASSOCIATATED WITH METAL- AND RADIONUCLIDE- CONTAMINATION AT THE DOE SAVANNAH RIVER SITE (SRS), SOUTH CAROLINA, USA by QI YE B.S. East China Normal University, China, 1992 M.S. University of Missouri-Columbia, 2002 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirement for the Degree DOCTOR OF PHYLOSOPHY ATHENS, GEORGIA 2007 © 2007 Qi Ye All Rights Reserved MICROBIAL DIVERSITY ASSOCIATATED WITH METAL- AND RADIONUCLIDE- CONTAMINATION AT THE DOE SAVANNAH RIVER SITE (SRS), SOUTH CAROLINA, USA by QI YE Major Professor: Chuanlun Zhang Committee: Robert E. Hodson Ming-Yi Sun William B. Whitman Juergen Wiegel Electronic Copy Approved: Maureen Grasso Dean of the Graduate School The University of Georgia December 2007 ACKNOWLEDGEMENTS I would like to gratefully and sincerely thank my major professor, Dr. Chuanlun Zhang, for his guidance, understanding and patience during my graduate studies at The University of Georgia. Throughout my doctoral work, he encouraged me to develop independent thinking and research skills and greatly assisted me with scientific writing. I am also very grateful for having an exceptional doctoral committee and wish to thank Drs. Robert Hodson, Ming-Yi Sun, William Whitman and Juergen Wiegel for their valuable discussion, continual support and encouragement. I would like to thank for members of my lab, past and present, Zhiyong Huang, Yiliang Li, Wenjun Li, Yundan Pi, Weidong Zhao, for their cooperation and various help during my dissertation study. I acknowledge the support of the faculty and staff in the marine sciences department and Savannah River Ecology Laboratory. Special thanks go to my parents and husband, for their unwavering support during the past years. iv TABLE OF CONTENTS page ACKNOWLEDGEMENTS ……………………………………………………………...iv LIST OF TABLES……………………………………………………………………….vii LIST OF FIGURES …………………...…………………………………………………ix CHAPTER 1. INTRODUCTION AND CHAPTER REVIEW…………………………….1 2. MICROBIAL BIOREMDIATION OF METAL- AND RADIONUCLIDE- CONTAMINATED SOILS AND GROUNDWATER……………………...10 3. MICROBIAL DIVERSITY AND GEOCHEMICAL DYNAMICS ASSOCIATED WITH METAL- CONTAMINATION AT THE DOE SAVANNAH RIVER SITE (SRS), SOUTH CAROLINA, USA…………...33 4. MICROBIAL COMMUNITY CHANGES ALONG THREE HEAVY METAL AND RODIONUCLIEDS GRADIENTS AT M-AREA OF SAVANNAH RIVER SITES, SOUTH CAROLINA, USA………………...88 5. THE DIVERSITY AND ABUNDANCE OF AMMONIUM-OXIDATION ARCHAEA IN HEAVILY CONTAMINATED SOILS AT DOE SAVANNAH RIVER SITE (SRS), SOUTH CAROLINA, USA………….120 6. SUMMARY………………………………………………………………...178 v APPENDIX 1. GLOBAL OCCURRENCE AND BIOGEOGRAPHIC PATTERNING OF PUTATIVE ARCHAEAL AMOA GENES IN TERRESTRIAL HOT SPRINGS……………………………………………………………………….182 2. ARCHAEAL LIPIDS AND 16S RRNA GENES CHARACTERIZING GAS HYDRATE-IMPACTED SEDIMENTS IN THE GULF OF MEXICO……….214 vi LIST OF TABLES Page Table 3.1. Heavy metal data for two samples analyzed from the Source Location and Creek Downstream, D-area. …………………………….……………...………..60 Table 3.2. Classification and number of 16S rRNA gene sequences in the Source location (DHC). …………………………………………………………………………..61 Table 3.3. Relative abundance of operation taxonomic units (OTU) among bacterial taxon within the IRM and IRS clone libraries. ………………………..………...62 Table 4.1. Heavy metal data for three samples analyzed from the LTH-ST system. .....104 Table 4.2.1. Comparison of Diversity of Three Soils in the M-area. ……………..…...105 Table 4.2.2. Pair-wise comparison demonstrating the genetic overlap of 16S rRNA genes Between the two sites. ……………...……………………………………….….106 Table 4.3. Summary of phylogenetic distribution of 16S rRNA clones from samples Lower Tim Branch (LTH), Steed Pond (ST) and Beaver Pond (BP). …………107 Table 4.4. Summary of the 16S rRNA gene sequences affiliation in phylogentic tree based on the most closely related GenBank member sequences. …………...…………108 Table 4.5. Diversity and composition of abundant Acidobacteria phylum in heavy metal contaminated samples, SRS. ………………………….………………………..109 Table 4.6. Percent sequence similarity and three SRS library distribution of selected OTUs within Acidobacteria. ………………………...…………………………110 Table 5.1. Sample description. ………………………………………………………...156 Table 5.2. Summary of primers used in this study. …………………………………....157 vii Table 5.3. 16S rRNA archaeal sequences similarity analysis of representative clones from soils sediment of Savannah River Site, USA. ………………………………….158 Table 5.4. Archaeal amoA sequences similarity analysis of representative clones from Soils and sediment of Savannah River Site, USA. ………………………….....160 Table 5.5. Observed richness and diversity estimators based on different methods derived from both archaeal 16S rRNA gene and Archaeal amoA gene clone libraries from six soil and sediment samples from Savannah River Site, USA. ……………....161 Table 5.6. Q-PCR for Crenarchaeota, archaeal amoA gene(AOA) and bacterial amoA gene (AOB) from six samples collected from three areas, SRS. ………….…...162 Table 5.7. Relative abundance of glycerol dialkyl glycerol tetraethers (GDGTs) in Soils and sediment collected from Savannah River Sites, USA. ………………163 viii LIST OF FIGURES Page Figure 3.1. A picture showing the location which collected both mat (red) and sediment (black) samples from the downstream creek at SRS D-area. …..………………..63 Figure 3.2. Rarefaction analysis of soil bacterial 16S rRNA gene libraries from three clone libraries (DHC, IRM, IRS). …………………………………………….....65 Figure 3.3. Phylogenetic relationship to the Acidobacteria and Acitinobacteria of partial 16S rRNA gene sequences from the dowonstream location. ................................67 Figure 3.4. Phylogenetic relationship to the Chloroflexi of partial 16S rRNA gene sequences from the dowonstream location. ………………….………………….69 Figure 3.5. Phylogenetic relationship to the Cynobacteria of partial 16S rRNA gene sequences from the dowonstream location. ……………………………………..71 Figure 3.6. Phylogenetic relationship to the Clostridia of partial 16S rRNA gene sequences from the dowonstream location. ……………………………………..73 Figure 3.7. Phylogenetic relationship to the Bacilius and other groups in Firmicutes of partial 16S rRNA gene sequences from the dowonstream location. …………...75 Figure 3.8. Phylogenetic relationship to the Alphaproteobacteria of partial 16SrRNA gene sequences from the dowonstream location. …………………………………….77 Figure 3.9. Phylogenetic relationship to the Betaproteobacteria of partial 16S rRNA gene sequences from dowonstream location. …………………..……79 ix Figure 3.10. Phylogenetic relationship to the Deltaproteobacteria of partial 16S rRNA gene sequences from the dowonstream location. ……..…………………………81 Figure 3.11. Phylogenetic relationship to the Planctomycete ,Verrucomicrobia, Eukaryota, and Bacterioidete partial 16S rRNA gene sequences from the dowonstream location. ………………………………………………………………………….83 Figure 3.12.A. Fatty Acid profiles of two samples (surface mat and sediment below) at the downstream location at the SRS D-area. ……………………………………85 Figure 3.12.B. Variations of δ13C ratios of 14:0, 16:0, 18:1 ω7c, 18:0, 22:0, 24:0 fatty acids, and TOC in same sample described in Figure 3.12.A. …………………...85 Figure 4.1. Rarefaction analysis of soil bacterial
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