Evaluating the laboratory flume microbiome as a window into natural hyporheic zone biogeochemistry

Riverbeds are hotspots for microbially-mediated biogeochemical reactions. Understanding these reactions requires frequent, spatially-distributed measurements since they exhibit pronounced spatial variability and are dynamic across timescales. It is challenging to resolve riverbed biogeochemical cycling in situ, as uncontrolled natural settings make data generation and interpretation difficult. Alternatively, laboratory experiments are conducted to investigate natural processes but rely on a common assumption that ex situ microbial processes are representative of natural systems. Flume experiments capture spatiotemporal variability and thus are provide an ideal capability for laboratory investigations of riverbed biogeochemistry; however, there has been no quantitative evaluation of flume microbiomes in comparison to natural settings. In order for a laboratory flume to be a meaningful tool for investigating microbially-mediated processes, it must host a microbiome similar to natural systems. To evaluate this fundamental assumption, we compare the sediment-associated microbiome of a large laboratory flume, analyzed through 16S rRNA gene sequencing, to microbiomes from riverbed sediments as well as a variety of other natural ecosystems. Overall the flume microbiome bears strong similarities to natural microbiomes from riverbed sediments and diverges from microbiomes found in other ecosystems. Flume experiments are therefore likely to be representative of natural microbially-mediated processes, suggesting that they can be powerful tools for investigating riverbed biogeochemistry.