Brent Hughes, PhD


PhD University of California, Santa Cruz

Assistant Professor, Sonoma State University  Department of Biology

Click to view Brent’s CV

Current Research in the Hughes Lab at Sonoma State University

“Research in the Hughes Lab at Sonoma State seeks to determine the processes that affect the stability of coastal ecosystems. Our research centers around coastal habitats – seagrass, salt marsh, and kelp (aka foundation species) – which provide valuable ecosystem services, yet are threatened by human activities. Current research in the Hughes Lab focuses on four themes: 1) the consequences of predator recovery on the functioning and stability of ecosystems, 2) the relative influence of climatic drivers and anthropogenic threats of coastal ecosystems, 3) the role of foundation species in structuring nearshore diversity and functioning and in turn the drivers maintaining foundation species stability, and 4) informing management and restoration on the processes that drive ecosystem resilience. Our research relies on collaborations with both the research and conservation communities, such as the Elkhorn Slough National Estuarine Research Reserve, U.S. Geological Survey, and U.S. Fish and Wildlife Service. These partnerships are critical for managing coastal resources, and facilitate dialogue between academia, management, industry, and the general public.”

Dissertation Focus:

For my doctoral research at UCSC I am investigating the effects of anthropogenic nutrient inputs on coastal ecosystems; including diversity, trophic food webs, and ecosystem function. Currently, this work focuses on estuaries on the central and northern California coast with an emphasis on Elkhorn Slough, an estuary with some of the highest reported nutrient inputs in the world, as well as moderate to hypereutrophication. This anthropogenic disturbance allows me to test hypotheses related to functioning and resilience in seagrass and fish communities. I am combining analyses of long-term ecological and physical data sets with laboratory and field experiments to tease out the important biological and physical drivers of estuarine ecosystems. BrentHughes2The results from these studies are informing coastal resource managers (National Estuarine Research Reserve, Central Coast Regional Water Quality Control Board) on the consequences of nutrient loading in coastal environments.

For my masters thesis at Moss Landing Marine Labs, I studied the effects of the large intertidal kelp Egregia menziesii on benthic community dynamics and diversity. This study demonstrated that Egregia and morphologically similar brown algal species can have both negative and positive effects on community diversity depending on variation in density and local environmental conditions. Egregia has the opposite effect on community diversity than what has been previously reported for foundation species because it negatively affects biodiversity in stressful environments, but has a positive effect in less stressful environments.



Hughes, B.B., R. Eby, E. Van Dyke, M.T. Tinker, C. Marks, K.S. Johnson, K. Wasson. 2013. Recovery of a top predator mediates negative eutrophic effects on seagrass. Proceedings of the National Academy of Sciences USA 110:1513-1518. See PDF

Hughes, B., M. Levey, J. Brown, M. Fountain, A. Carlisle, S. Litvin, W. Heady, M. Gleason, C. Greene. 2014. Nursery functions of U.S. west coast estuaries: the state of knowledge for juveniles of focal invertebrate and fish species. A technical report for The Nature Conservancy and The Pacific Marine and Estuarine Fish Habitat Partnership. In Press. 180 pp.

Hughes, B., M. Fountain, A. Carlisle, M. Levey, M. Gleason. 2012. The impacts of nutrient loading and environmental conditions on the fish assemblage and available nursery habitat in Elkhorn Slough. The Nature ConservancySee PDF

Overstrom-Coleman, M.O., B.B. Hughes, S.D. Connell, M.H. Graham. 2013. Habitat associations in tropical kelp systems: comparisons to temperate paradigms. In reviewMarine Ecology Progress Series.

Heim, W.H., M. Stephenson, B.B. Hughes, A. Newman, M. Marvin-DiPasquale, J.M. Holloway, K.H. Coale. 2013. Spatial distribution of solid phase total mercury in Yolo Bypass, CA. USA: implications for land use management of mercury contaminated floodplains. In reviewScience of the Total Environment. 

Hughes, B.B., J. Haskins , K. Wasson, and E. Watson. 2011. Identifying factors that influence expression of eutrophication in a central California estuary. Marine Ecology Progress Series 439:31-43. See PDF

Hughes, B.B. 2010. Variable effects of a kelp foundation species on rocky intertidal diversity and species interactions in central California. Journal of Experimental Marine Biology and Ecology 393:90-99.

Hughes, B., Haskins, J., Wasson, K. 2010. Assessment of the effects of nutrient loading in estuarine wetlands of the Elkhorn Slough watershed: a regional eutrophication report card. Elkhorn Slough Technical Report Series 2010:1.

Hughes, B. 2009. Synthesis for management of eutrophication issues in Elkhorn Slough. Elkhorn Slough Technical Report Series 2009:1.

Stepehnson, M., J. Negrey, and B. Hughes. 2009. Spatial and temporal trends of methyl mercury in California bays and harbors: A bioaccumulation approach to assess fish and water quality. California State Water Resources Control Board Technical Report.

Stephenson, M., W. Heim, B.B. Hughes, A. Bonnema and K. Coale. 2008. Methylmercury loading studies in Delta wetlands. CALFED Mercury Project, Task 5.3a.

Hernandez, G.C., B. Hughes and M. Graham. 2006. Reproductive longevity of drifting kelp Macrocystis pyrifera (Phaeophyceae) in Monterey Bay, USA. Journal of Phycology 42:1199-1207. See PDF


Hughes, B.B., M. Fountain, A. Carlisle, M. Gleason, M. Levey. 2014. Climate impacts to fish diversity and nursery function of a highly threatened estuary. In review. Proceedings of the National Academy of Sciences.

Hughes, B.B., K. Hammerstrom, N. Grant, *U. Hoshijima. 2014. A trophic cascade dictates a phase shift from macroalgae to seagrass in a macroalgal dominated estuary. In prep. Target journal: Ecology Letters. *Indicates Undergraduate Student Researcher

Mahoney, B., S. Honig, *J. Glanz, B.B. Hughes. 2014. Use of seagrass beds as indicators of environmental stress in the rocky intertidal. In prep. Target journal: Marine Ecology Progress Series. *Indicates Undergraduate Student Researcher