Antonie van Leeuwenhoek 81: 487–507, 2002. © 2002 Kluwer Academic Publishers. Printed in the Netherlands. 487 Characterizing man-made and natural modifications of microbial diversity and activity in coastal ecosystems Hans W. Paerl 1,∗ , Julianne Dyble 1 , Luke Twomey 1 , James L. Pinckney 2 , Joshua Nelson 3 & Lee Kerkhof 3 1 Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, USA; 2 Department of Oceanography, Texas A & M University, College Station, TX 77843-3146, USA; 3 Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901-8521, USA ( ∗ Author for correspondence; E-mail: hpaerl@email.unc.edu) Key words: Bacteria, climate change, eutrophication, microbial consortia, nutrient cycling, phytoplankton, pollution, water quality Abstract The impacts of growing coastal pollution and habitat alteration accompanying human encroachment are of great concern at the microbial level, where much of the ocean’s primary production and biogeochemical cycling takes place. Coastal ecosystems are also under the influence of natural perturbations such as major storms and flooding. Distinguishing the impacts of natural and human stressors is essential for understanding environmentally-induced change in microbial diversity and function. The objective of this paper is to discuss the applications and merits of recently developed molecular, ecophysiological and analytical indicators and their utility in examining anthropo- genic and climatic impacts on the structure and function of coastal microbial communities. The nitrogen-limited Neuse River Estuary and Pamlico Sound, North Carolina are used as examples of ecosystems experiencing both anthropogenic (i.e., accelerating eutrophication) and climatic stress (increasing frequencies of tropical storms and hurricanes). Additional examples are derived from a coastal monitoring site (LEO) on the Atlantic coast of New Jersey and Galveston Bay, on the Gulf of Mexico. In order to assess structure, function, and trophic state of these and other coastal ecosystems, molecular (DNA and RNA-based) characterizations of the microbial taxa involved in carbon, nitrogen and other nutrient transformations can be combined with diagnostic pigment-based indicators of primary producer groups. Application of these methods can reveal process-level microbial community responses to environmental variability over a range of scales. Experimental approaches combined with strategic monitoring utilizing these methods will facilitate: (a) understanding organismal and community responses to environmental change, and (b) synthesizing these responses in the context of ecosystem models that integrate physical, chemical and biotic variability with environmental controls. Introduction We have entered a new millennium with the notable distinction that more than 70% of the world’s hu- man population resides within 100 km of the coast (Vitousek et al. 1997). Understanding man-induced ecological change and the subsequent impacts on biodiversity, coastal water quality, habitat and fisheries resources are major research and management chal- lenges worldwide. Deterioration of coastal ecosystems appears to be accelerating, but there is a paucity of knowledge on how complex aquatic communities are being altered in structure and function. To further complicate matters, anthropogenic stresses are often accompanied by large-scale climatic perturbations, possibly signaling a period of climatic change (Gray et al. 1996; Landsea et al. 1998; Golden- berg et al. 2001). During Fall 1999, Hurricanes Den- nis, Floyd and Irene inundated the eastern seaboard of the USA. Coastal North Carolina received up to 1 m of rainfall, causing a 200–500 year flood in the watershed of the Pamlico Sound, the US’s 2nd largest estuarine system. Sediment and nutrient-laden flood- waters displaced over 80% of the Sound’s volume, depressed salinity by 70%, and accounted for half the annual nitrogen (N) load to this N-sensitive system