Campus Directory

My research interest is marine microbial biogeochemistry, addressing questions related to:

• characterizing underlying controls on phytoplankton and bacterial processes in aquatic systems.
• quantifying microbial food web dynamics
• understanding microbial responses to coastal nutrient pollution.

I primarily work in urbanized estuaries (Delaware Bay and San Francisco Bay Estuary) where coastal pollution, including large-scale nutrient fertilization, has had major impacts on the microbial community. In addition to estuarine work, I have also conducted research in the Gulf of the Farallones National Marine Sanctuary, the Equatorial Pacific Ocean, the Chukchi Sea (Arctic Ocean) and in Antarctica.  

 

 

2024

Dugdale, R.C.;A.E.Parker, F.P. Wilkerson, 2024. Patterns in Anthropogenic Nitrogen and Water Quality Leading to Phytoplankton Blooms in Urban Estuaries. J. Mar. Sci. Eng. 2024, 12, 2029. https:// doi.org/10.3390/jmse12112029 

2022

Glibert, P. M, F. P. Wilkerson, R. C. Dugdale, A. E. Parker. 2022. Ecosystem Recovery in Progress? Initial Nutrient and Phytoplankton Response to Nitrogen Reduction from Sewage Treatment Upgrade in the San Francisco Bay Delta. Nitrogen. doi:10.3390/nitrogen3040037.

2021

Parker, A.E., P. W. Lehman. 2021. Powering Life in the Water, Phytoplankton in the San Francisco Estuary. Frontiers for Young Minds. https://doi: 10.3389/frym.2021.611976

2020

Sohm, J.A., Niederberger, T.D., Parker, A.E., Tirindelli, J., Gunderson, T., Cary, S.C., Capone, D.G., Carpenter, E.J., 2020. Microbial Mats of the McMurdo Dry Valleys, Antarctica: Oases of Biological Activity in a Very Cold Desert. Front. Microbiol. 11, 537960–537960. https://doi.org/10.3389/fmicb.2020.537960

Coyne, K.J., Parker, A.E., Lee, C.K., Sohm, J.A., Kalmbach, A., Gunderson, T., Leόn-Zayas, R., Capone, D.G., Carpenter, E.J., Cary, S.C., 2020. The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiaa010

Stumpner, E.B., Bergamaschi, B.A., Kraus, T.E.C., Parker, A.E., Wilkerson, F.P., Downing, B.D., Dugdale, R.C., Murrell, M.C., Carpenter, K.D., Orlando, J.L., Kendall, C., 2020. Spatial variability of phytoplankton in a shallow tidal freshwater system reveals complex controls on abundance and community structure. Sci. Total Environ. 700, 134392. https://doi.org/10.1016/J.SCITOTENV.2019.134392

2019

Kimmerer, W.J., Wilkerson, F.P., Downing, B.D., Dugdale, R.C., Gross, E.S., Kayfetz, K., Khanna, S., Parker; Alexander. E, Thompson, J., 2019. Effects of Drought and the Emergency Drought Barrier on the Ecosystem of the California Delta. San Fr. Estuary Watershed Sci. 17.

Niederberger, T.D., Bottos, E.M., Sohm, J.A., Gunderson, T., Parker, A., Coyne, K.J., Capone, D.G., Carpenter, E.J., Cary, S.C., 2019. Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils. Front. Microbiol. 10, 621. https://doi.org/10.3389/fmicb.2019.00621

2017

Kraus, T.E.C., Carpenter, K.D., Bergamaschi, B.A., Parker, A.E., Stumpner, E.B., Downing, B.D., Travis, N.M., Wilkerson, F.P., Kendall, C., Mussen, T.D., 2017. A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium. Limnol. Oceanogr. 62, 1234–1253. https://doi.org/10.1002/lno.10497

Otten, T.G., Paerl, H.W., Dreher, T.W., Kimmerer, W.J., Parker, A.E., 2017. The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary. Environ. Microbiol. 19, 3619–3637. https://doi.org/10.1111/1462-2920.13860

2016

Dahm, C.N., Parker, A.E., Adelson, A.E., Christman, M.A., Bergamaschi, B.A., 2016. Nutrient Dynamics of the Delta: Effects on Primary Producers. San Fr. Estuary Watershed Sci. 14. https://doi.org/10.15447/sfews.2016v14iss4art4

Dugdale, R.C., Wilkerson, F.P., Parker, A.E., 2016. The effect of clam grazing on phytoplankton spring blooms in the low-salinity zone of the San Francisco Estuary: A modelling approach. Ecol. Modell. 340, 1–16. https://doi.org/10.1016/J.ECOLMODEL.2016.08.018

Glibert, P.M., Wilkerson, F.P., Dugdale, R.C., Raven, J.A., Dupont, C.L., Leavitt, P.R., Parker, A.E., Burkholder, J.M., Kana, T.M., 2016. Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen‐enriched conditions. Limnol. Oceanogr. 61, 165–197. https://doi.org/10.1002/LNO.10203@10.1002/(ISSN)1939-5590.STABLE-ISOTOPES

2015

Lee, J., Parker, A.E., Wilkerson, F.P., Dugdale, R.C., 2015. Uptake and inhibition kinetics of nitrogen in Microcystis aeruginosa: Results from cultures and field assemblages collected in the San Francisco Bay Delta, CA. Harmful Algae 47, 126–140. https://doi.org/10.1016/J.HAL.2015.06.002

Buck, C.M., Wilkerson, F.P., Parker, A.E., Dugdale, R.C., 2014. The Influence of Coastal Nutrients on Phytoplankton Productivity in a Shallow Low Inflow Estuary, Drakes Estero, California (USA). Estuaries and Coasts 37, 847–863. https://doi.org/10.1007/s12237-013-9737-6

Wilkerson, F.P., Dugdale, R.C., Parker, A.E., Blaser, S.B., Pimenta, A., 2015. Nutrient uptake and primary productivity in an urban estuary: using rate measurements to evaluate phytoplankton response to different hydrological and nutrient conditions. Aquat. Ecol. 49, 211–233. https://doi.org/10.1007/s10452-015-9516-

2014

Cohen, R.A., Wilkerson, F.P., Parker, A.E., Carpenter, E.J., 2014. Ecosystem-Scale Rates of Primary Production Within Wetland Habitats of the Northern San Francisco Estuary. Wetlands 34, 759–774. https://doi.org/10.1007/s13157-014-0540-3

Glibert, P.M., Wilkerson, F.P., Dugdale, R.C., Parker, A.E., Alexander, J., Blaser, S., Murasko, S., 2014. Phytoplankton communities from San Francisco Bay Delta respond differently to oxidized and reduced nitrogen substrates—even under conditions that would otherwise suggest nitrogen sufficiency. Front. Mar. Sci. 1, 17. https://doi.org/10.3389/fmars.2014.00017

Glibert, P.M., Dugdale, R.C., Wilkerson, F., Parker, A.E., Alexander, J., Antell, E., Blaser, S., Johnson, A., Lee, J., Lee, T., Murasko, S., Strong, S., 2014. Major – but rare – spring blooms in 2014 in San Francisco Bay Delta, California, a result of the long-term drought, increased residence time, and altered nutrient loads and forms. J. Exp. Mar. Bio. Ecol. 460, 8–18. https://doi.org/10.1016/J.JEMBE.2014.06.001

2013

Dugdale, R.C., Wilkerson, F.P., Parker, A.E., 2013. A biogeochemical model of phytoplankton productivity in an urban estuary: The importance of ammonium and freshwater flow. Ecol. Modell. 263, 291–307. https://doi.org/10.1016/J.ECOLMODEL.2013.05.015

2012

Brooks, M.L., Fleishman, E., Brown, L.R., Lehman, P.W., Werner, I., Scholz, N., Mitchelmore, C., Lovvorn, J.R., Johnson, M.L., Schlenk, D., van Drunick, S., Drever, J.I., Stoms, D.M., Parker, A.E., Dugdale, R., 2012. Life Histories, Salinity Zones, and Sublethal Contributions of Contaminants to Pelagic Fish Declines Illustrated with a Case Study of San Francisco Estuary, California, USA. Estuaries and Coasts 35, 603–621. https://doi.org/10.1007/s12237-011-9459-6

Dugdale, R., Wilkerson, F., Parker, A.E., Marchi, A., Taberski, K., 2012. River flow and ammonium discharge determine spring phytoplankton blooms in an urbanized estuary. Estuar. Coast. Shelf Sci. 115, 187–199. https://doi.org/10.1016/J.ECSS.2012.08.025

Kimmerer, W.J., Parker, A.E., Lidström, U.E., Carpenter, E.J., 2012. Short-Term and Interannual Variability in Primary Production in the Low-Salinity Zone of the San Francisco Estuary. Estuaries and Coasts 35, 913–929. https://doi.org/10.1007/s12237-012-9482-2

Kress, E., Parker, A.E., Wilkerson, F.P., Dugdale, R.C., 2012. Assessing phytoplankton communities in the Sacramento and San Joaquin Rivers using microscopic and indirect analytical approaches. Interag. Ecol. Progr. Newsl. 25, 43–55.

Lefebvre, S.C., Benner, I., Stillman, J.H., Parker, A.E., Drake, M.K., Rossignol, P.E., Okimura, K.M., Komada, T., Carpenter, E.J., 2012. Nitrogen source and pCO2 synergistically affect carbon allocation, growth and morphology of the coccolithophore Emiliania huxleyi: potential implications of ocean acidification for the carbon cycle. Glob. Chang. Biol. 18, 493–503. https://doi.org/10.1111/j.1365-2486.2011.02575.x

Parker, A.E., Dugdale, R.C., Wilkerson, F.P., 2012. Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary. Mar. Pollut. Bull. 64, 574–586. https://doi.org/10.1016/J.MARPOLBUL.2011.12.016

Parker, A.E., Hogue, V.E., Wilkerson, F.P., Dugdale, R.C., 2012. The effect of inorganic nitrogen speciation on primary production in the San Francisco Estuary. Estuar. Coast. Shelf Sci. 104–105, 91–101. https://doi.org/10.1016/J.ECSS.2012.04.001

Parker, A.E., Kimmerer, W.J., Lidström, U.U., 2012. Reevaluating the Generality of an Empirical Model for Light-Limited Primary Production in the San Francisco Estuary. Estuaries and Coasts 35, 930–942. https://doi.org/10.1007/s12237-012-9507-x

2011

Brzezinski, M.A., Baines, S.B., Balch, W.M., Beucher, C.P., Chai, F., Dugdale, R.C., Krause, J.W., Landry, M.R., Marchi, A., Measures, C.I., Nelson, D.M., Parker, A.E., Poulton, A.J., Selph, K.E., Strutton, P.G., Taylor, A.G., Twining, B.S., 2011. Co-limitation of diatoms by iron and silicic acid in the equatorial Pacific. Deep Sea Res. Part II Top. Stud. Oceanogr. 58, 493–511. https://doi.org/10.1016/J.DSR2.2010.08.005

Dugdale, R., Chai, F., Feely, R., Measures, C., Parker, A., Wilkerson, F., 2011. The regulation of equatorial Pacific new production and pCO2 by silicate-limited diatoms. Deep Sea Res. Part II Top. Stud. Oceanogr. 58, 477–492. https://doi.org/10.1016/J.DSR2.2010.08.008

Parker, A.E., Wilkerson, F.P., Dugdale, R.C., Marchi, A.M., Hogue, V.E., Landry, M.R., Taylor, A.G., 2011. Spatial patterns of nitrogen uptake and phytoplankton in the equatorial upwelling zone (110°W–140°W) during 2004 and 2005. Deep Sea Res. Part II Top. Stud. Oceanogr. 58, 417–433. https://doi.org/10.1016/J.DSR2.2010.08.013

Strutton, P.G., Palacz, A.P., Dugdale, R.C., Chai, F., Marchi, A., Parker, A.E., Hogue, V., Wilkerson, F.P., 2011. The impact of equatorial Pacific tropical instability waves on hydrography and nutrients: 2004-2005. Deep Sea Res. Part II Top. Stud. Oceanogr. 58, 284–295. https://doi.org/10.1016/J.DSR2.2010.08.015

2009

Kirchman, D.L., Hill, V., Cottrell, M.T., Gradinger, R., Malmstrom, R.R., Parker, A., 2009. Standing stocks, production, and respiration of phytoplankton and heterotrophic bacteria in the western Arctic Ocean. Deep. Res. Part II Top. Stud. Oceanogr. 56, 1237–1248.

Sharp, J.H., Yoshiyama, K., Parker, A.E., Schwartz, M.C., Curless, S.E., Beauregard, A.Y., Ossolinski, J.E., Davis, A.R., 2009. A Biogeochemical View of Estuarine Eutrophication: Seasonal and Spatial Trends and Correlations in the Delaware Estuary. Estuaries and Coasts 32, 1023–1043. https://doi.org/10.1007/s12237-009-9210-8

2006

Cottrell, M.T., Malmstrom, R.R., Hill, V., Parker, A.E., Kirchman, D.L., 2006. The metabolic balance between autotrophy and heterotrophy in the western Arctic Ocean. Deep Sea Res. Part I Oceanogr. Res. Pap. 53, 1831–1844. https://doi.org/10.1016/J.DSR.2006.08.010

Parker; A.E, Fuller; J., Dugdale, R.C., 2006. Estimating dissolved inorganic carbon concentrations from salinity in San Francisco Bay for use in 14C-primary production studie. Interag. Ecol. Progr. Newsl. 19, 17–22.

2005

Parker, A.E., 2005. Differential supply of autochthonous organic carbon and nitrogen to the microbial loop in the Delaware Estuary. Estuaries 28, 856–867. https://doi.org/10.1007/BF02696015

2004

Sharp, J.H., Beauregard, A.Y., Burdige, D., Cauwet, G., Curless, S.E., Lauck, R., Nagel, K., Ogawa, H., Parker, A.E., Primm, O., Pujo-Pay, M., Savidge, W.B., Seitzinger, S., Spyres, G., Styles, R., 2004. A direct instrument comparison for measurement of total dissolved nitrogen in seawater. Mar. Chem. 84, 181–193. https://doi.org/10.1016/J.MARCHEM.2003.07.003

OCN 100 Marine Biology

OCN110 Marine Ecology

OCN 305 Introduction to Occean Science Research

OCN 310 / 310 Oceanographic Instruments and Analysis

OCN 330 Marine Microbial Ecology

Requesting a Letter of Recommendation

Ideally, we have worked together in more than one class (or independent project).  The better that I know you, the more specific I can be in my letter of recommendation about your strengths – and provide you with a strong letter of support. 

Please make an appointment with me at least three weeks before the deadline.  During our meeting we will discuss the specifics about the job / graduate program / internship that you are interested in applying for; plan to explain why you think I will be able to write a strong letter for you. 

Ahead of our meeting, prepare written information about you and the position that you are applying for. Again, the more information that you can provide about the position, the better the letter that I can prepare for you.  Here is what I will need in written materials.

• A description of the job or graduate school(s) to which you are applying.
• Clearly indicate deadline dates.
• All application forms and materials with the relevant portions filled in by you.
• Provide a resume or CV (ideally the same document that you will send as part of your application) Your resume should highlight experiences and skills.
• A written description of your career interests and aspirations—why are you applying to this position? This is often referred to as a “statement of purpose” in graduate school applications.