Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities

Abstract

Two acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration. Acidithiobacillus, Ferrovum, Gallionella, Leptospirillum, Ferrimicrobium, Acidiphilium, and Acidocella were all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. IMPORTANCEThis study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites. N iche models use environmental and geochemical information to explain and predict the composition and diversity of microbial communities. In these models, different geochemical conditions act as key niche parameters controlling microbial community composition. For example, pH (1-4),...

Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run

“…This mechanism could explain the higher Fe(II) oxidation rates in alga-dominated than in alga-poor sites (11). The same mechanism could explain why the field iron oxidation rates at Scalp Level Run were 20 times greater than the rates in dark laboratory chemostats inoculated with sediment from Scalp Level Run (36). However, the phototrophs are also producing organic carbon, which could be used in dissimilatory iron reduction.…”

“…High-throughput sequencing was performed on samples SL 8.5, SL 25, and SL 82 using an Illumina MiSeq as described previously (36,43). Briefly, the V4 region of the 16S rRNA gene was amplified using primers 515f and 806r with attached sequencing barcodes and adaptors and pooled in equimolar quantities for sequencing.…”

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China

“…The microbial communities in subsurface environments rely on chemoheteroautotrophic/chemolithoautotrophic redox reactions of organic/inorganic compounds for sources of energy. As such, spatial heterogeneities and length of time in the system can affect the microbial community dynamics (Ramette and Tiedje ; Kara and Shade ; McAllister et al ; Hatosy et al ; Sheng et al ). Understanding the metabolism, distribution, and underlying drivers of these extremophiles has the potential to improve our understanding of environmental bioremediation, biotechnology development, and exploration of ancient communities presented or thrived on the early earth or other planets.…”

“…The geochemical conditions of the deep continental subsurface are characterized by low dissolved oxygen (DO) concentrations, high or low temperature and pressure, high radiation (from decay of radioactive elements), high or low pH and high salinity (Lovley and Chapelle 1995;Rothschild and Mancinelli 2001;Roadcap et al 2006;Dong and Yu 2007). These unique geochemical conditions typically control the underground microbial niche regimes in multiple extreme environments such as lake sediments, hot, cold and acidic springs, and groundwater with high salinity (Siering et al 2006;Chaudhary et al 2009;Brown et al 2011;Xiong et al 2012;Macalady et al 2013;Marina et al 2014;Sheng et al 2016a). Microorganisms can tolerate these extreme environments, often by employing novel metabolic and biogeochemical processes (Lovley and Chapelle 1995;Rothschild and Mancinelli 2001;Dong and Yu 2007).…”

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA

“…Decades of research on the microbiology of metal sulfides have improved our management of sulfidic mine wastes (5,6) and led to new strategies for mineral extraction (7,8). Although important new microorganisms are still being discovered in low pH environments (e.g., see references 9 and 10), many of the taxa common to extremely acidic mine drainage are now well known (11)(12)(13), as are some of the environmental factors that control their distribution (e.g., see references [14][15][16][17][18][19][20][21].…”