Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

Abstract

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

“…The bioreactors also remained at a higher pH than the source water throughout the experiment (Figure 1). This trend was observed in previous experiments using these reactors 25, 29 , and may reflect dissolution of calcium carbonate from clay minerals in the sediment-derived biofilm coupons (Figure S5). Despite this difference, the convergence of the bioreactor communities over the first 18 days suggests that pH was not the dominant parameter shaping these communities, and that the geochemical environment shaped and stabilized the establishing microbial community in the reactors.…”

“…In terms of organic acids, the FW305 groundwater has previously been shown to be oligotrophic 25, 29 with transient lactate and acetate peaks which decreased back to initial concentrations over time 29 . In the current work, FW305 groundwater and control bioreactors exhibited <1 µM fluctuations in formate and acetate.…”

“…The local geological and microbial features of the ORR background study site has been well described previously 13–15 . We established small, in-field bioreactors located within a mobile laboratory in the background area to obtain and study in-situ groundwater and the associated microbial communities directly from an established well 25, 29 . Groundwater was pumped from well FW305 into a sterile, 1L source reservoir container at a rate of 100 mL min −1 , resulting in a residence time of 8 minutes to minimize any “bottle effect” (Figure S1A).…”

“…Groundwater was pumped from well FW305 into a sterile, 1L source reservoir container at a rate of 100 mL min −1 , resulting in a residence time of 8 minutes to minimize any “bottle effect” (Figure S1A). The source reservoir and bioreactors were continuously flushed with 13% O 2 /87% N 2 gas (Airgas, Radnor PA) to supply the bioreactors with in-situ dissolved oxygen levels of 2.2-6.3 ppm O 2 as previously described 25, 29 .…”

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

“…These surrogates include laboratory microcosms (Lee and Lee 2017 ), in field biofilm reactors (King et al . 2017 ; Christensen et al . 2018 ), or sediment fines from backwashed pumps (Cardenas et al .…”