Investigating microbial cycling of recalcitrant organic matter in marine sediments using natural isotope respirometry in a novel, carbon-free bioreactor

Marine sediments harbor complex microbial communities that play a key role in the cycling of carbon and nutrients. Reactions initiated by microbial enzymes at the molecular scale drive the rate and extent of organic matter degradation to CO₂ and CH₄. Organic matter is comprised of multiple carbon pools with different intrinsic turnover times. It is hypothesized that microbes will degrade younger pools with more labile compounds, while older pools with refractory compounds will remain unutilized. However, many studies have shown that microbes are capable of respiring older, refractory pools of organic matter in a number of environments. In order to better understand microbial carbon cycling and the fate of recalcitrant organic matter, we constructed a novel bioreactor system to measure carbon isotopes during microbial degradation of complex organic matter. This system enables us to measure the natural isotopic signature (δ¹³C and Δ¹⁴C ) of microbially-respired CO₂, thereby allowing us to determine the age of the organic matter that is being respired. We investigated microbial carbon utilization in sediments from Falmouth, MA and observed a pattern of successive microbial respiration such that several peaks appear over the course of a 7-day incubation. Δ¹⁴C signatures of CO₂ fractions collected during incubation ranged from -185 to +70‰ with the majority of CO₂ appearing to be modern. This indicates that the microbial community is primarily are respiring labile organic matter from fast cycling pools. Interestingly, the observation of multiple peaks with similar Δ¹⁴C signatures suggests that organic matter is degraded in a step-wise manner by a succession of microbial taxa. Illumina sequencing of 16S rRNA genes will identify these successions of bacteria (and archaea), while enzymatic analyses may help determine the metabolic pathways that correspond to each peak. Our study will provide a molecular-level framework for organic matter degradation and provide insight into patterns of microbial carbon utilization, linking these observations to genomic and metabolomics information.