Hydrobiologia 401: 1–8, 1999. J.P. Zehr & M.A. Voytek (eds), Molecular Ecology of Aquatic Communities. © 1999 Kluwer Academic Publishers. Printed in the Netherlands. 1 Molecular ecology of aquatic communities: reflections and future directions J. P. Zehr 1 & M. A. Voytek 2 1 Department of Biology, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY 12180-3590, U.S.A. Current address for J.P. Zehr: Ocean Sciences Department, Earth and Marine Sciences Building, University of California, Santa Cruz, CA 95064, U.S.A. 2 U.S. Geological Survey, MS430, 12201 Sunrise Valley Drive, Reston, VA 20192, U.S.A. Key words: aquatic ecology, molecular techniques, molecular ecology Abstract During the 1980s, many new molecular biology techniques were developed, providing new capabilities for studying the genetics and activities of organisms. Biologists and ecologists saw the promise that these techniques held for studying different aspects of organisms, both in culture and in the natural environment. In less than a decade, these techniques were adopted by a large number of researchers studying many types of organisms in diverse environments. Much of the molecular-level information acquired has been used to address questions of evolution, biogeography, population structure and biodiversity. At this juncture, molecular ecologists are poised to contribute to the study of the fundamental characteristics underlying aquatic community structure. The goal of this overview is to assess where we have been, where we are now and what the future holds for revealing the basis of community structure and function with molecular-level information. Introduction Studies of freshwater and marine communities have played an integral role in the history and development of the science of ecology (Lindeman, 1942; Hutchin- son, 1957; Paine, 1980). Ecology has matured during the past quarter century, with theoretical and quant- itative developments in the description and modeling of populations, communities and ecosystems (Jones & Lawton, 1995). In parallel, the development of mo- lecular biological techniques has spawned new ways of looking at organisms in the environment, assessing biological processes and activities (Zehr, 1998; Zehr & Hiorns, 1998), and studying population genetics and species distributions (Medlin et al., 1995; Vanoppen et al., 1995; Palumbi, 1996; Geller, 1998; Graves, 1998; Parker et al., 1998). The trajectories of ecological theory and molecular biology technique development have converged during this decade, and the application of molecular tech- niques has begun to provide information relevant to ecological questions. Ecological studies have focused on different levels and scales ranging from individual organisms to species, populations and ecosystems, and these different perspectives are now being integrated (Grimm, 1995). Given the complexity of ecosystems and ecological interactions, it could be questioned whether the extension of these studies to the scale of molecules has anything to offer the study of com- munity and ecosystem ecology. Nonetheless, aquatic biology and ecology have already benefited from mo- lecular approaches (for reviews, see Falkowski & LaRoche, 1991; Joint, 1995; Burton, 1996; Cook- sey, 1998; Parker et al., 1998). The objective of this discussion is to develop a framework for integrating molecular biology into community ecology and com- munity structure studies, thus making a link from spatial scales of molecules to ecosystems that may foster new avenues of ecological research. Molecular biology contributions to aquatic ecology Some of the fundamental concepts that have driven studies in aquatic ecology at the community and eco- system levels are: