MICROBIAL ECOLOGY Microb Ecol (2003) 46:200-215 DOI: 10.1007/s00248-002-0003-x © 2003 Springer-Verlag New York Inc. Structure and Seasonal Dynamics of Hyporheic Zone Microbial Communities in Free-Stone Rivers of the Western United States K.P. Feris, P.W. Ramsey, C. Frazar, M.C. Rillig, J.E. Gannon, W.E. Holben Microbial EcologyProgram, Division of Biological Sciences, The University of Montana, Missoula MT 59812-1002 USA Received: 22 October 2002; Accepted: 15 January 2003; Online publication: 13 June 2003 IABSTRACT The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6-96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pro- nounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone. Introduction Correspondence to: W.E. Holben; E-mail: bholben@selway.umt.edu The hyporheic zone is the region of saturated sediments beneath the channel of a stream [43] and is an important component of lotic ecosystems [16, 56, 58]. This transition