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Applied and Environmental Microbiology, March 2004, p. 1865-1868, Vol. 70, No. 3
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.3.1865-1868.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717
Received 13 June 2003/ Accepted 12 December 2003
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We previously documented rapid microbial oxidation of As(III) in an acid-sulfate-chloride-type geothermal spring in Norris Geyser Basin, Yellowstone National Park (9). This shallow spring is fed by a nearly constant geothermal source water (63°C, pH 3.1) containing
35 µM As(III). The prokaryote microbial community in this spring forms visually and chemically distinguishable mats. A filamentous yellow microbial mat containing visible amounts of S0 (63 to 60°C) is present 0 to
3.5 m from the spring source and changes to a brown, Fe(III) oxyhydroxide filamentous microbial mat (51 to 55°C) at
3.5 to 5 m from the spring source (9). Chemical analysis of the aqueous and solid phases documented high rates of As(III) oxidation in the brown mat region, and the role of microorganisms in As(III) oxidation was confirmed in assays that showed no As(III) oxidation in the formaldehyde-killed samples (9). The PCR-generated 16S ribosomal DNA clone libraries representing the yellow and brown mat regions were dominated by Hydrogenobaculum- and Desulfurella-like sequences (7). However, since the phylogenetic data could not predict which population(s) was involved in the As(III) oxidation, the present study was conducted to initiate isolation and characterization of the As(III)-oxidizing microorganism(s) in this spring for use in modeling important and dominant biogeochemical features found in this spring type.
Sampling, enrichment, and isolation.
Brown microbial mat material was aseptically sampled and transferred to sterile 70-ml serum bottles and submerged with 35 ml of spring water sampled from above the mat. The bottles were sealed on site with sterile butyl rubber stoppers and transported to the laboratory. The phylogenetic information from community clone libraries (7) indicated that H2 metabolism was potentially important in the resident community and guided the initial headspace gas treatments, which included (i) filter-sterilized air, (ii) filter-sterilized air enriched with 10% CO2, (iii) filter-sterilized gaseous N2 [N2(g)] for anaerobic incubations, and (iv) filter-sterilized 85% H2(g) plus 10% CO2(g) plus 5% air. Killed controls (4% formaldehyde) were included, and all bottles were amended with 50 µM As(III) (as NaAsO2) and incubated at 55°C. After 7 days of incubation, As(III) oxidation was measured using hydride generation atomic absorption spectrophotometry (see reference 9) and found to occur only in those treatments containing H2(g). Denaturing gradient gel electrophoresis (DGGE) (described previously [7]) was used to assess enrichment progress and showed that the microorganisms in the H2(g) treatment appeared to be a subset of the original microbial community (Fig. 1, compare lanes 1 and 2).
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FIG. 1. Documentation of enrichment and isolation of Hydrogenobaculum sp. strain H55. PCR-DGGE analysis of 16S ribosomal DNA fragments derived from organisms present in the original mat sample (lane 1), after initial H2 gas headspace enrichment (lane 2), and in subsequent culture transfers with continued selection under H2 and microaerobic conditions and with screening for As(III) oxidation (lane 3, third transfer; lane 4, sixth transfer) and of the eventual pure culture Hydrogenobaculum sp. strain H55 (lane 5). DNA was extracted and PCR amplified by methods previously described (7).
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Isolate characterization.
The nearly full-length 16S rRNA gene of H55 was PCR cloned and sequenced (GenBank accession no. AY268103) by previously described protocols (7). BLAST analysis determined the closest match to be Hydrogenobaculum acidophilum (98% identical to accession no. D16296). The incubation temperature and medium pH were varied in order to establish the optimum temperature and pH for H55 as being 55 to 60°C and 3.0, respectively, which are in close agreement with the corresponding values for the environment from which H55 was isolated (55°C and pH 3.1). Under optimum conditions, the H55 doubling time was approximately 25 h. No growth was observed with various carbon compounds (including formate and acetate) in a defined medium or in complex media containing yeast extract or tryptone, suggesting that H55 may be an obligate autotroph.
Filtrates of mature H55 cultures did not oxidize As(III) (results not shown), indicating that the oxidation activity was intimately associated with the cell. Kinetic parameters were estimated for whole cells by substrate saturation assays initiated by suspending washed cells (1.0 x 106 per ml) in the synthetic growth medium amended with various As(III) concentrations. Linear plots of As(III) oxidation versus time determined As(III) oxidation rates, which were then plotted against substrate concentrations and analyzed via nonlinear regression to calculate values for Km and Vmax based on the Michaelis-Menten equation (Fig. 2).
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FIG. 2. H55 As(III) oxidation kinetics. Shown are As(III) oxidation rates () as a function of initial As(III) concentration. Rate data were fit to the Michaelis-Menten equation by using nonlinear regression (shown by the line) to estimate the kinetic parameters Km and Vmax. Rates are the mean changes in As(V) concentration measured in 1-ml assay volumes (1.0 x 106 cells · ml-1) from triplicate cultures, and error bars (where visible) represent 1 standard error of the mean.
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FIG. 3. Sensitivity of Hydrogenobaculum sp. strain H55 to arsenic. (A) Growth response of Hydrogenobaculum strain H55 as a function of increasing concentrations of As(V) () or As(III) ( ). (B) Effects of various phosphate concentrations on the growth of H55 in the presence of 0.75 mM As(III) (shaded bar) or 0.75 mM As(V) (filled bar) compared to growth occurring in the absence of As (open bar). Cultures were inoculated to an initial optical density (measured at A595) of 0.02. Results in both panels are from one of two independent experiments demonstrating similar responses. Each value is the mean of results for three replicate cultures for each As concentration. Error bars (where visible) depict 1 standard error of the mean.
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Other previous work at this thermal spring had also found that As(III) oxidation was not measurable where aqueous sulfide levels ranged from 60 to 80 µM (12), even though Hydrogenobaculum populations were present (7). Therefore, the effect of aqueous sulfide on As(III) oxidation by the H55 isolate was investigated by adding 60 µM H2S and 30 µM As(III) to H55 cultures to mimic measured concentrations in the spring (9). Normal As(III) oxidation patterns were observed in cultures not treated with H2S, but the presence of H2S inhibited As(III) oxidation (Fig. 4). Furthermore, the addition of sulfide as a spike midway through the experiment correlated with an immediate arrest of As(III) oxidation (Fig. 4). Noninoculated controls failed to show any As(III) oxidation or any reduction of As(V) due to H2S at the concentrations used (Fig. 4). We also note that the negative effect of sulfide on As(III) oxidation was not correlated with cell viability since the growth of H55 was not inhibited by 60 µM sulfide (results not shown).
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FIG. 4. Influence of aqueous sulfide on As(III) oxidation by Hydrogenobaculum sp. strain H55. Levels of As(III) oxidation in cultures (1.0 x 106 cells · ml-1, 5% air, 55°C, pH 3.0) where sulfide was omitted ( ) or added at the beginning of the experiment ( ) or as a spike (indicated by arrow) after 2 h of incubation () are shown. Additional controls included noninoculated medium containing 30 µM As(III) ( ) or 30 µM As(V) (as Na2HAsO4 · 7H2O) plus 60 µM S(-II) (as Na2S) ( ). Equilibrium equations were used to calculate and correct for the partitioning of aqueous H2S and H2S(g) in the serum bottle headspace. Culture samples were taken every 0.5 h for As speciation and analysis as described previously (9). Results are from one of two independent experiments demonstrating this response, where each data point is the mean of results of three replicate samples. Error bars (not visible) depict 1 standard error of the mean.
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1% O2) with CO2 as the primary carbon source and H2 as the primary energy source. These conditions were expected to favor the Hydrogenobaculum-like organisms whose presence in this spring were previously documented (7). Also, the temperature and pH optima of the isolate corresponded to values for in situ conditions (9) and serve as minimum points of relevancy that link this organism to the environment and biogeochemistry being studied. The maximum rate of As(III) oxidation by isolate H55 was estimated to be approximately 0.7 x 10-9 µmol · cell-1 · min-1 (Fig. 2), but at typical in situ As(III) concentrations, As(III) oxidation rates might approach 2.2 x 10-10 µmol · cell-1 · min-1. Based on previous estimates of total As(III) oxidation at this site (0.2 µmol of AsIII oxidized · min-1 · cm of sediment-3; calculated from data in reference 9), an H55 population density of approximately 9 x 108 cells · cm of sediment-3 would be necessary to account for all of the As(III) oxidization. However, the many other Hydrogenobaculum-like populations that inhabit this spring (7) may also contribute to As(III) oxidation. The physiologic basis for As(III) oxidation by H55 is unclear. It appears to be unable to utilize As(III) as an energy source for chemolithoautotrophic growth (results not shown), yet a detoxification basis also can be questioned because H55 is more sensitive to As(V). The addition of dissolved Fe(III) to H55 samples did not influence As(III) oxidation. This finding is consistent with previous in-field assays that found no As(III) oxidation with biocide-treated mat sediment samples (9) containing Fe(III) oxyhydroxides and aqueous Fe [mainly Fe(II)] and suggests that the Fe(III) in this mat environment (either solid phase or dissolved) likely contributes little to measured As(III) oxidation rates, at least relative to those catalyzed by H55 or other similarly behaving microorganisms. The profound negative effect of sulfide on As(III) oxidation by H55 implies that the absence of As(III) oxidation in regions of the spring containing appreciable levels of sulfide (9) may be due to sulfide inhibition of microbial As(III) oxidases. Future studies at this spring will attempt to further refine our understanding of microbe-arsenic interactions and to determine the relative importance of H2, H2S, and As(III) as primary energy inputs for the total microbial community.
This work was supported by funding from the National Aeronautics and Space Administration (NAG5-8807), the National Science Foundation (MCB-0132022), and the Montana Agricultural Experiment Station (911310 and 911398).
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