Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina

• Published in: Applied and environmental microbiology Vol. 85; no. 19
• Main Authors: Steen, Andrew D, Kevorkian, Richard T, Bird, Jordan T, Dombrowski, Nina, Baker, Brett J, Hagen, Shane M, Mulligan, Katherine H, Schmidt, Jenna M, Webber, Austen T, Royalty, Taylor M, Alperin, Marc J
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01-10-2019
• Subjects: Communities; Deoxyribonucleic acid; DNA; DNA repair; Environmental Microbiology; Enzymes; Estuaries; Extracellular enzymes; Gingipain; Heterotrophic microorganisms; Kinetics; Methionine; Microorganisms; Organic carbon; Organic matter; Ornithine; Peptidase; Peptidases; Phenylalanine; Rivers; Sediments; Single-stranded DNA; Substrates; extracellular enzymes; anaerobes; deep subsurface; heterotrophs; sediments; peptidases
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.00102-19

Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low 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 (
) decreased with increasing sediment depth, although
expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (
) 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.
Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO
, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.