Linking microbial populations and geochemical processes in soils, mine tailings, and geothermal environments

Abstract

The primary goal of this work was to identify and characterize the microbial populations responsible for transformations of As and 2,4-D in soils and waters. Chemical, spectroscopic, and microscopic techniques were used to characterize the aqueous and solid phase geochemistry of soils, mine tailings, and a geothermal spring. The role of specific microbial populations in these systems was examined using cultivation-independent molecular methods [total DNA extraction, 16S rDNA amplification, denaturing gradient gel electrophoresis (DGGE), and sequence analysis] coupled with either characterization of microorganisms isolated from the same systems, or inference of physiological characteristics from (i) closely related (16S rDNA sequence) cultured microorganisms and (ii) the geochemical environments in which they were detected. The microbial reduction of As(V) to As(III) and the subsequent effects on As mobilization in contaminated mine tailings was examined under transport conditions. Enhanced elution of As from mine tailings apparently resulted from the enrichment of aerobic As(V)-reducing Caulobacter leidyi, Sphingomonas yanoikuyae, and Rhizobium loti -like populations after liming. Arsenite was rapidly oxidized to As(V) via microbial activity in unsaturated Madison River Valley soil columns. Eight aerobic heterotrophic bacteria with varying As redox phenotypes were isolated from these columns. Three isolates, identified as Agrobacterium tumefaciens, Pseudomonas fluorescens, and Variovorax paradoxus -like organisms, were As(III) oxidizers and all were apparently important members of the soil microbial community responsible for net As(III) oxidation. Successional changes in microbial communities colonizing an As-rich acid-sulfate-chloride geothermal spring stream channel in Norris Geyser Basin of Yellowstone National Park were examined. Enhanced As(III) oxidation correlated in time and space with the appearance of three Hydrogenobaculum -like populations. The formation of an As(V)-rich hydrous-ferric-oxide mat correlated with the detection of Thiomonas, Acidimicrobium, and Metallosphaera —like populations whose nearest cultivated relatives (based on 16S rDNA sequence) were Fe-oxidizers. Fingerprints of microbial communities (DGGE) established under increasing concentrations of 2,4-D (0 - 500 mg kg'1) in batch soil microcosms showed that at least 100 mg kg'1 2,4-D was required to obtain apparent shifts in community structure. The microbial community selected at high 2,4-D concentrations was predominantly composed of Burkholderia -like populations, which harbored homologs of tfdA genes.