I’m happy to be co-author on a study that was just published by Ann Arfken, a PhD student at the Virginia Institute for Marine Science (VIMS). The study evaluated the composition of the microbial community associated with eastern oyster Crassostrea virginica to determine if oysters play a role in denitrification. Denitrification is an ecologically significant anaerobic microbial metabolism. In the absence of oxygen certain microbes use other oxidized compounds as electron acceptors. Nitrate (NO3–) is a good alternate electron acceptor, and the process of reducing nitrate to nitrite (NO2), and ultimately to elemental nitrogen (N2), is called denitrification. Unfortunately nitrate is needed by photosynthetic organisms like plants and phytoplankton, so the removal of nitrate can be detrimental to ecosystem health. Oxygen is easily depleted in the guts of higher organisms by high rates of metabolic activity, creating a niche for denitrification and other anaerobic processes.
To evaluate denitrification in C. virginica, Arfken et al. coupled actual measurements of denitrification in sediments and oysters with an analysis of microbial community structure in oyster shells and digestive glands. We then used paprica with a customized database to predict the presence of denitrification genes, and validated the predictions with qPCR.
I was particularly happy to see that the qPCR results agreed well with the paprica predictions for the nosZ gene, which codes for the enzyme responsible for reducing nitrous oxide (N2O) to N2. I believe this is the first example of qPCR being used to validate metabolic inference – which currently lacks a good method for validation. Surprisingly however (at least to me), denitrification in C. virginica was largely associated with the oyster shell rather than the digestive gland. We don’t really know why this is. Arfken et al. suggests rapid colonization of the oyster shell by denitrifying bacteria that also produce antibiotic compounds to exclude predators, but further work is needed to demonstrate this!