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Chapter 7 : Microorganisms and Processes Linked to Uranium Reduction and Immobilization
Category: Applied and Industrial Microbiology; Environmental Microbiology
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This chapter focuses on the microorganisms and electron transfer processes that are likely to impact the reductive immobilization of U(VI) in the contaminated terrestrial subsurface. It offers a perspective on how microbial eukaryotes may play a role in U(VI) biotransformation, and ends with a discussion of the nonreductive immobilization of U(VI) through microbially facilitated precipitation with phosphate. The mobility of uranium in porous media is mainly controlled by complexation and redox reactions. Extensive microbial community characterization has revealed a diverse assemblage of microbes encompassing all phyla within the domain Bacteria in the subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC). Recent work shows that the subsurface Geobacter clade exhibits a remarkable genotypic and phenotypic plasticity and the 16S rRNA marker is not diagnostic for this plasticity. Field studies indicate that microbially mediated, reductive immobilization is a promising strategy for the remediation of U(VI) contamination in subsurface environments. To direct the function of subsurface microbial communities, and to achieve the aims of bioremediation and natural attenuation, genome-enabled studies are needed to directly link the phylogenetic structure with the metabolic activity of U(VI)-transforming microbial groups in situ. Expanded sequencing efforts will no doubt provide a clearer view of subsurface microbial community structure, but pure-culture studies are required for development of techniques to evaluate in situ function through quantification of gene expression patterns.
Schematic summarizing the predominant biogeochemical reactions and processes impacting U(VI) mobility in the contaminated subsurface. U(IV) in the solid phase is represented by uraninite (UO2), but other mineral forms may be present. 10.1128/9781555817190.ch7.f1
Phylogenetic tree of U(VI)-reducing microorganisms. Bootstrapped neighbor-joining trees were generated using partial and full-length 16S rRNA gene sequences obtained from the National Center for Biotechnology Information and from the DOE’s Joint Genome Institute. Sequences were aligned using the software package Greengenes ( DeSantis et al., 2006 ) and analyzed within the phylogenetic software package MEGA ( Kumar et al., 2008 ). Bootstrap values greater than 50% are indicated at each node, and polytomies indicate branching points that were not consistently supported by bootstrap analyses. Organisms for which genome sequences are available are highlighted in grey, with all the 16S rRNA genes present in the genome compressed into a single cluster. The number of 16S rRNA genes present in the genome is indicated in brackets adjacent to the accession number. Relevant references are indicated for each organism. Species shown to conserve energy using U(VI) as a sole electron acceptor are indicated with a black box. The scale bar represents 0.05 substitutions per nucleotide position. Missing from the tree are the short gene sequences from the genome of Cellulomonas flavigena ATCC 482 (NZ_ABTJ00000000), as well as several organisms for which no sequences were available, including Pseudomonas denitrificans ATCC 13867, Pseudomonas sp. CRB5, and Veillonella alcalescens (formerly Micrococcus lactilyticus). 10.1128/9781555817190.ch7.f2
Taxonomic profiling of small-subunit rRNA gene sequences recovered from cultivation-independent analyses of uranium-contaminated environments a