Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmaxexpressed on a per cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.
Approximately 150 Pg of organic carbon resides in subsurface sediments (Ciais et al. 2013). Understanding the preservation, transformation, and remineralization of this carbon is a prerequisite to understanding the global carbon cycle. Extracellular enzymes are required by subsurface heterotrophic microbes to access complex molecules from this reservoir (Arnosti 2011) and thus, influence carbon turnover. Identifying which microbes produce which extracellular enzymes and under what conditions has remained a challenge. Here, it is proposed to apply bottom-up metaproteomics, metatranscriptomics, and shotgun-metagenomics on subsurface microbe communities from the White Oak River estuary to help close this knowledge gap.