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Home Faculty Chester B. Zarnoch, Ph.D.

Chester B. Zarnoch, Ph.D.


My laboratory at Baruch College performs research in benthic ecology with emphasis on shellfish and nutrient cycling.
Our efforts aim to address questions related to ecosystem restoration and aquaculture. Currently, my students and I are working on projects that address:

1) the ecological implications of benthic habitat restoration (i.e. oyster reefs, salt marsh) in New York estuaries
2) the physiological ecology of bivalves

These projects are a result of collaborations with faculty from other academic institutions, government scientists, non-profit groups, and aquaculture industry partners.

We have also worked closely with colleagues at the Brooklyn College’s Aquatic Research and Environmental Assessment Center in urban aquaculture research and development.

Chester B. Zarnoch, Ph.D.

Associate Professor
Biology and Environmental Studies

Department of Natural Science
Baruch College
City University of New York (CUNY)

17 Lexington Avenue, Box A-0506
New York, NY 10010
Phone: (646) 660-6239

Graduate School Faculty Member
The Graduate Center
Biology Department – Ecology, Evolutionary Biology, and Behavior

City University of New York (CUNY)

365 Fifth Avenue
New York, NY 10016


Mechanisms of nutrient retention in restored salt marshes: Will marsh restoration in eutrophic ecosystems provide ecosystem services of nitrogen removal and carbon sequestration?

Salt marshes play a critical role in the structure and function of coastal ecosystems, including the reduction of anthropogenic inorganic nitrogen (N) loading.  Salt marshes have experienced significant declines over the last century, due in part to eutrophication.  Large scale salt marsh restoration efforts are common worldwide, and are often motivated towards regaining lost ecosystem services such as N removal, carbon (C) sequestration, and mitigation of storm surge. Many restorations are underway in the eutrophic Hudson River estuary, but it is not clear if restored marshes have the capacity for N removal and C retention in eutrophic environments. In the proposed research, we will measure how eutrophic conditions alter biogeochemical cycles in urban salt marshes.  We will measure N removal and C retention across a chronosequence of restored salt marshes in Jamaica Bay to determine the age and environmental conditions under which salt marsh restoration may become an effective strategy for ecosystem services in eutrophic environments. Our results will illustrate how controls on different pathways of N cycling within urban salt marshes may lead to the sustained N availability or promote N removal from the ecosystem. 

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Pollution of estuaries from human activities such as agriculture and urbanization has disrupted the global cycling of elements including carbon and nitrogen (N) and reduced stocks of coastal fisheries worldwide. Enhanced water quality in New York City has stimulated interest in reviving the previously abundant eastern oyster to the Hudson-Raritan estuary. Oysters filter the overlying water for food particles, and then deposit their waste to the sediments below. The delivery of N-rich waste to sediments may stimulate the microbial transformation of biologically active N into inert N gas. This process is the only pathway through which N is permanently removed from aquatic ecosystems; however, the environmental conditions under which oysters could enhance the activity of N-cycling microbes have not been previously examined.

In this study my colleague, Timothy Hoellein from Loyola University Chicago (formerly of Baruch College), and I are examining how two important factors, oyster density and water column N concentration, control the influence of oysters on sediment N cycling. We are quantifying rates of oyster filtration, excretion, and sediment N transformations seasonally for two years at four sites in Jamaica Bay, New York.  Recently, we have expanded this work to include measurements at recently created oyster reefs in the Hudson-Raritan estuary.  These experiments will document the potential for the re-introduction of eastern oysters to enhance N removal in urbanized ecosystems.

A physiological comparison of wild and selectively bred hard clams, Mercenaria mercenaria

Aquaculture is the fastest growing sector of global food production and the hard clam aquaculture industry is a major contributor to such growth. Hard clam selective breeding programs have used a variant ( Mercenaria mercenaria var. notata ) of the native hard clam for large-scale production. It is distinguished from native clams by brown bands on the shell surface and through selection shows improved growth performance. Although notata clams are widely used by clam hatcheries, the physiological basis for improved growth has yet to be thoroughly investigated.

My undergraduate students and I have been exploring the bioenergetics of growth to identify the relationship of phenotypic variability of growth and genetic causes in wild and selected clams. Laboratory studies conducted to test physiological hypotheses may explain the greater growth in selected clams. In addition, measurements made on rates of ingestion in wild and selected clams in Peconic Bay (NY) will help to understand how feeding rates may change under natural food and temperature conditions. The end result should include a greater understanding of the physiological advantages and disadvantages associated with selection for fast growth and data that guides strain selection for aquaculture and restoration.

Novel methodologies to overwinter cultured hard clams in the Northeast U.S.

This project is experimentally examining new overwintering technologies for cultured hard clam juveniles in ME, NY, and NJ. The new methodology is based on 12 years of successful overwintering of cultured juvenile soft shell clams in Maine. An initial overwintering trial with hard clams during the winter of 2006-2007 at the Downeast Institute (DEI), Beals, Maine resulted in > 99% survival over 177-days.  Similar results have been found during the winters of 2007-2008 and 2008-2009, thereby substantiating these preliminary results and warranting large-regional tests of this methodology.   However, these tests were performed with clams produced from wild ME broodstock.  Previous work has shown that selected clams are more vulnerable to overwinter mortality than wild clams.

In this study PIs from Rutgers University, University of Maine at Machias, and Baruch College will perform two experimental field trials from Nov 2010 to April 2011, and Nov 2011 to April 2012 in the three states to examine spatial and temporal variation in the new overwintering technique. Commercial quantities of local hard clam seed (2 sizes: 6-8 mm; 8-10 mm) will be overwintered in each state for a 6-month period. To determine if success is related to strain type (aquacultured vs. native), we will conduct a reciprocal study by taking seed originating/reared in each state, and overwintering seed in the other states. In each state, we will compare survival of overwintered seed using the new technique to survival of seed overwintered in protected field plots, as is the current, standard, practice. Biochemical assays will be conducted on clams from all size classes and origins at each field site overwintered using the new methodology to measure energy use through the overwintering period and to determine if the ME genetic stock is better adapted to temperature stress by using less energy stores. Simultaneously measuring biochemical composition and environmental parameters should also provide an understanding of how the various clam strains respond physiologically to local conditions and culture methods.


  1. Hoellein, T. J., Zarnoch, C., Bruesewitz, D. A., & DeMartini, J. In Press, Contributions of freshwater mussels (Unionidae) to nutrient cycling in an urban river: Filtration, recycling, storage, and removal. Biogeochemistry

  2. Zarnoch, C., Hoellein, T., Furman, B., & Peterson, B. In Press. Eelgrass meadows, Zostera marina, facilitate the ecosystem service of nitrogen removal during simulated nutrient pulses in Shinnecock Bay, New York, USA. Marine Pollution Bulletin.

  3. Handel, S. N., Marra, J., Kaunzinger, C. (lead authors), Bricelj, V.M., Zarnoch, C., Burger, J., Camhi, M., Rosenbaum, H. C., Colon, C. P., Jensen, O. P., & Schlesinger, M. D. (contributing authors). 2016 Change and Resilience of Jamaica Bay’s Ecological Systems. In E.W. Sanderson, W.D. Solecki, J.R. Waldman, A.S. Parris (Ed.), Prospects for Resilience:  Insights from New York City’s Jamaica Bay (pp. 304). Island Press.

  4. Lindemann, S., C.B. Zarnoch, D. Castignetti, and T.J. Hoellein. 2016. 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.

  5. Landau, B., D. Jones, C.B. Zarnoch, and M.L. Botton. 2015 Development of aquaculture methods to enhance horseshoe crab populations: An example from Delaware Bay. In: R.H. Carmichael, M.L. Botton, P.K.S. Shin, and S.G. Cheung (Eds).   Changing Global Perspectives on Biology, Conservation and Management of Horseshoe Crabs. Springer Publishers.  

  6. Zarnoch, C.B., J.N. Kraeuter, B.F. Beal, V.M. Bricelj, G. Flimilin, and D. Bushek, D. 2015. Geographic origin and culture method influence the overwinter mortality of juvenile hard clams, Mercenaria mercenaria (L.) Aquaculture 440: 48-59.

  7. Hoellein T.J.,C.B. Zarnoch, and R. E. Grizzle. 2015. Eastern oyster (Crassostrea virginica) filtration, biodeposition, and sediment nitrogen cycling at two oyster reefs with contrasting water quality in Great Bay Estuary (New Hampshire, USA).  Biogeochemistry122: 113-129.

  8. Hoellein T.J. and C.B. Zarnoch. 2014. Effect of eastern oysters (Crassostrea virginica) on sediment carbon and nitrogen dynamics in an urban estuary. Ecological Applications24: 271-286. Featured in the Photo Gallery of the Bulletin of Ecological Society of America. 95: 82-84

  9. Zarnoch, C.B. and M.P. Schreibman. 2012. Growth and reproduction of eastern oysters, Crassostrea virginica, in a New York City estuary; Implications for restoration. Urban Habitats, Vol 7:1.Available at:

  10. Zarnoch, C.B.and M. Sclafani. 2010. Overwinter mortality and spring growth in selected and non-selected juvenile Mercenaria mercenariaAquatic Biology11: 53-63.

  11. Zarnoch, C.B., M.P. Schreibman, R.T  Colesante, and M.B. Timmons. 2010. Growth characteristics of walleye, Sander vitreus, using recirculating aquaculture system (RAS) technology. Journal of Applied Aquaculture  22:285-296.

  12. Tzafrir-Prag, T., I. Lupatsch, M.P. Schreibman, and C.B. Zarnoch. 2010. Estimation of nutrient requirements for Atlantic horseshoe crabs (Limulus polyphemus; Linnaeus) grown in captivity. Journal of the World Aquaculture Society, 41(6): 874-883.

  13. Schreibman, M.P. and C.B. Zarnoch. 2009. Urban Aquaculture: using New York as a model. Pp 1148-1162.  In: Burrell, G. and Allan, G. (Eds.) New Technologies in Aquaculture. Woodhead Publishing Limited. Cambridge, UK.

  14. Schreibman, M.P. and C.B. Zarnoch. 2009. Aquaculture methods and early growth of juvenile horseshoe crabs (Limulus polyphemus). Pp 501-511.  In: Botton, M., Tanacredi, J. and Smith, D. (Eds.) Biology and Conservation of Horseshoe Crabs.  Springer Ltd., New York

  15. Zarnoch, C.B. and Schreibman, M.P., 2008.  Influence of temperature and food availability on the biochemical composition and mortality of juvenile Mercenaria mercenaria (L.) during the over-winter period. Aquaculture274: 81-91.8.

  16. Zarnoch, C.B., A. Surier, R. Karney, M.P. Schreibman and S. Gamss. 2008. Influence of triploidy on the biochemical composition and fiber size of bay scallop (Argopecten irradians; Lamarck) adductor muscle. In: Russo R (Ed) Aquaculture I. Dynamic Biochemistry, Process Biotechnology and Molecular Biology2 (Special Issue 1), 68-71.

  17. Schreibman, M.P. and C.B. Zarnoch. 2005.  Urban Aquaculture in Brooklyn, NY, USA. Pp 207-221, In: Costa-Pierce, B.A., Edwards, P., Baker, D., and Desbonnet, A. (Eds.). Urban Aquaculture. CABI Publishing; Cambridge, MA.



ENV 1020 Principles of Ecology

The fundamentals of theoretical and applied ecology are presented with an emphasis on various ecosystems. The importance of understanding ecology in relation to environmental quality is stressed. Laboratory exercises include study of materials recycling and energy flow; effects of environmental stress and water population, population growth, and carrying capacity; and developmental changes in ecosystems.

ENV 3001 Introduction to Environmental Science

An exploration of the science behind the laws that control natural systems and their influence on the environment.  Emphasis is placed on the interaction of humans with the environment.  The course demonstrates that environmental science is an inter-disciplinary science founded in ecology.  Students gain skills to critically assess current environmental issues.

BIO/ENV 3020 Biology of Invertebrates

An introduction to the biology of selected groups of terrestrial, freshwater, and marine invertebrate animals. Students explore evolutionary themes and functional approaches to invertebrate animal biology through a broad survey of the invertebrate phyla. Within the coverage of each group, unique aspects of morphology, physiology, and behavior are discussed in light of the selective forces that have favored their evolution. Other topics will include examples from the recent literature that illustrate aspects of ecology, behavior, or economic utility of the group under consideration.