Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

Abstract

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.

Fig 1. Experimental design.

Schematic representation and description of the bioreactor setup and sampling schedule.

Fig 2. Microbial activity within the reacted groundwater.

(a) Dehydrogenase activity and (b) total protein (± standard deviation) of planktonic communities (i.e. reacted groundwater) in bioreactors from filtered (open square) and unfiltered (closed square) groups. (c) Variation in hydrogenase activity versus total protein.

Fig 3. Most abundant bacterial OTUs.

The top 20 most abundant OTUs, combined into the same taxon if classified similarly, for planktonic communities in filtered (Panel A) and unfiltered treatments (Panel B) over time, and within plankton and biofilm communities at the end of the experiment (day 23; Panel C).

Fig 4. The genus Zoogloea relative abundance over time.

Planktonic Zoogloea spp. mean relative abundance (± standard error bars) over time within filtered and unfiltered bioreactors. Zoogloea abundance differed over time and between filtered and unfiltered bioreactors. Notably, Zoogloea had a time x filtered/unfiltered interaction—its abundance increased over time in filtered bioreactors and remained similar over time in unfiltered bioreactors.

Fig 5. Bacterial community dynamics over time.

Non-metric Multidimensional scaling (NMDS) ordinations for bacterial planktonic communities over time for filtered (circles) and unfiltered (triangles) samples (Panel A) and for biofilm (gray symbols) and planktonic communities (black symbols) at the end of the experiment (day 23; Panel B).