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Effect of Eastern Oysters (Crassostrea virginica) and Seasonality on Nitrite Reductase Gene Abundance (nirS, nirK, nrfA) in an Urban Estuary

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Abstract

The influence of oysters on nitrogen (N) cycling has received increased research attention. Previous work focused on fluxes of N solutes and gases, but the effects on microbes responsible for N transformations are unknown. In May 2010, we deployed eastern oysters (Crassostrea virginica) in mesh cages above sand-filled boxes at four sites across a nutrient gradient in Jamaica Bay, New York City. In fall and winter, we used quantitative PCR to measure abundance of 16S rRNA and nitrite reductase genes for denitrification (nirS and nirK) and dissimilatory nitrate reduction to ammonium (nrfA) in sediment. We measured water column nutrients and chlorophyll a, sediment C:N and organic matter (OM), exchangeable ammonium (NH4 +), ammonification, nitrification, and denitrification potential (DNP). Oysters did not affect gene abundance in fall, when we predicted that their influence would be strongest, or in winter. However, gene abundance was significantly different among sites and seasons. Factors which explained 16S rRNA, nirS, and nirK gene abundance included sediment OM, water column N, and chlorophyll a, similar to previous research. Abundance of nrfA was lower than that of nir genes and positively related to sediment C:N, suggesting OM lability may drive the balance between nir and nrfA. Finally, nirS and nirK abundance was unrelated to DNP, which is consistent with variable results from the literature. More studies that combine molecular techniques with N transformation rates in the context of oyster reefs are needed. Results will advance models which predict the ecosystem effects of reef conservation and restoration under variable environmental conditions.

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Acknowledgments

Funding was provided by the National Science Foundation Awards DEB-0918952 and MRI-0959876, PSC-CUNY Research Awards, Eugene Lang Junior Faculty Fellowship, and Loyola University Chicago Provost Fellowship and Biology Summer Research Fellowship. We thank graduate students Allison Mass Fitzgerald, Michael Hassett, Corrina Singleman, and Kayla Turek and undergraduate assistants Elizabeth Humphrey, Narendra Paramanand, Swathi Mummini, Doris Law, Angeline David, Simon Morgan, Steven Polaskey, Gena Isreal, Owen McKenna, Adam Pink, Yana Zak, Nouran Aly, Vitaly Zaharov, Hanen Yan, Kevin Kucher, Jemi Jacob, and Sanne Lynham for field and laboratory assistance. We thank Dr. Stefan Kanzok for qPCR support. Institutional support was provided by Baruch College, Loyola University Chicago, Gateway National Recreation Area, Jamaica Bay Wildlife Refuge Visitor Center, NYS Department of Environmental Conservation, and the Jamaica Bay Institute.

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  1. Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL, 60660, USA

    Samantha Lindemann, Domenic Castignetti & Timothy J. Hoellein

  2. Department of Natural Sciences, Baruch College and Graduate Center, City University of New York, Box A-0506, 17 Lexington Ave, New York, NY, 10010, USA

    Chester B. Zarnoch

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  1. Samantha Lindemann
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ESM 1

Mean (±SE) relative abundance of functional gene copy numbers per abundance of 16S rRNA gene copies from Floyd Bennett Field (FB), Wildlife Refuge (WR), Mott’s Basin (MB), and Spring Creek (SC) for nirS in A) fall and B) winter, nirK in C) fall and D) winter, nrfA in E) fall and F) winter (GIF 50 kb)

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Lindemann, S., Zarnoch, C.B., Castignetti, D. et al. Effect of Eastern Oysters (Crassostrea virginica) and Seasonality on Nitrite Reductase Gene Abundance (nirS, nirK, nrfA) in an Urban Estuary. Estuaries and Coasts 39, 218–232 (2016). https://doi.org/10.1007/s12237-015-9989-4

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