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In this study, bioassessment data collected between 1998 and 2005 were synthesized and analyzed for streams and rivers throughout the San Diego Hydrologic Region to provide a spatial and temporal context for the results of several monitoring projects conducted between 1998 and 2005 and to ascertain the applicability of the Southern California benthic macroinvertebrate index of biological integrity (SoCal B-IBI) to the region's streams. The water quality of the sites studied in the region, as reflected by temporal and spatial analyses of SoCal B-IBI scores, was found to be quite poor. When streams were analyzed individually most showed stable scores over the time frame of the study with some showing better scores in the fall. Spatially, scores were found to be better farther away from the coast in the upstream reaches of the watersheds. This study further explored the applicability of the SoCal B-IBI to a focused geographic region by demonstrating the necessity of each component metric to the assignment of biological condition. Although all component metric scores were deemed to be necessary, the percent intolerant individuals score had a more significant effect in driving impairment. The analysis of the component metrics of the SoCal B-IBI provides useful insights to the changes in scores among and between the sampled sites in the region's watersheds. Based on this study, natural resource management agencies responsible for managing water quality should incorporate regular measures of biological integrity into their water quality programs to ascertain regional and temporal trends. DOI: 10.1061/(ASCE)EE.1943-7870.0000193 CE Database subject headings: Biological processes; Watershed management; Assessment; Water quality; California. Author keywords: Bioassessment; Biological integrity; Watershed assessment; Biocriteria.

Microbial community composition and diversity change along chemical gradients, leading to the expectation that microbial community information might provide new gradient characterizations. Here we examine stream bacteria composition and diversity along a strong chemical gradient in Central Appalachian streams. Coal mining in the region generates alkaline mine drainage (AlkMD), causing dramatic increases in conductivity, alkalinity, sulfate and metals sufficient to degrade stream macrobiota communities throughout the ecoregion. In this study, we examined the relationship between water and biofilm chemistry and biofilm bacteria taxonomic composition in streams where active and reclaimed surface coal mines occupied 0-96% of watershed surface area. We incubated wood veneers in each stream site for 4 months to develop biofilms on similar substrates. We sampled water chemistry at the time of deployment and collection, and after 1 month. Following incubation, we collected biofilms for microbial and chemical characterization. Microbial composition was determined by pyrosequencing 16S rRNA amplicons. Biofilm subsamples were analyzed by inductively coupled plasma mass spectrometry to determine metal concentrations. Our results show that microbial community composition differed significantly between AlkMD-exposed and AlkMD-unexposed sites, and that compositional dissimilarity increased with AlkMD loading. Diversity was not correlated with pH or extent of upstream mining, but instead correlated with biofilm concentrations of Cd, Mn, Zn and Ni. Within mined sites, the extent of upstream mining was negatively correlated with taxonomic richness. Despite major compositional shifts, functional capacity predicted with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) correlated with mining in only 3 of 43 level-2 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology groups. [ABSTRACT FROM AUTHOR]