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The transport and processing of nutrients and organic matter in streams are important functions that influence the condition of watersheds and downstream ecosystems. In this study, we investigated the effects of streambed sediment removal on biogeochemical cycling in Fawn River, a gravel-bottomed river in Indiana, U.S.A. We measured stream metabolism as well as nitrogen (N) and phosphorus (P) retention in both restored and unrestored reaches of Fawn River to examine how sediment removal affected multiple biogeochemical functions at the reach scale. We also assessed the properties of restored and unrestored streambed sediments to elucidate potential mechanisms driving observed reach-scale differences. We found that sediment removal led to lower rates of primary productivity and ecosystem respiration in the restored reach, likely due to macrophyte removal and potentially due to changes to sediment organic matter quality. We found minimal differences in N and P retention, suggesting that these processes are controlled at larger spatial or temporal scales than were examined in this study. Denitrification enzyme activity was lower in sediments from the restored reach compared to the unrestored reach, suggesting that restoration may have decreased N removal. Our results indicate that most near-term changes in biogeochemical function following restoration could be attributed to macrophyte removal, although effects from sediment removal may emerge over longer timescales.

Theoretical constructs, such as the river continuum concept, predict that the composition of benthic fauna in rivers will be different from that of headwater streams. There exists a need to modify, for use on larger rivers, the bioassessment techniques commonly used on small streams. Using aquatic macroinvertebrates and the "reference condition" approach, we developed and tested a multimetric index for use on the rivers of Idaho. Reference sites were selected to represent the best current conditions (i.e., least impacted) among Idaho rivers. The index performed well in distinguishing reference sites from sites displaying some form of anthropogenic impairment. Individual metrics used in the index included: number of EPT taxa, total number of taxa, percent dominant taxon, percent Elmidae, and percent predators. The index we developed for Idaho rivers was essentially a modification of a framework designed for small streams, suggesting that techniques, including data analysis, currently used for streams can be adapted for use on larger rivers. Adapting these methods for use in rivers is primarily a matter of (1) selecting metrics relevant to the rivers of interest; (2) expanding the field sampling to encompass the greater habitat area and, potentially, heterogeneity of rivers; and (3) selecting an appropriate form of data analysis. The approach we describe here should be applicable to geographic regions other than Idaho.