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Project Area and Sampling Sites 



The project area is located within the Middle Rockies Ecoregion (USEPA 2000) in 

 Madison County, Montana. At higher elevations, vegetation is mainly mixed conifer forest, 

 with alpine tundra on the highest peaks. At lower elevations, vegetation is mainly mixed 

 grassland and sagebrush steppe (USDA 1976, Woods et al. 1999). The main land uses are 

 livestock grazing and irrigated agriculture. 



Periphyton samples were collected at 20 sites on 14 streams (Table 1). The study 

 streams are in the Ruby River hydrologic unit (USGS HUC 1 0020003). The Ruby River, along 

 with the Big Hole and the Beaverhead Rivers, are the three main tributaries of the Jefferson 

 River. Streams in the project area are classified B-l in the Montana Surface Water Quality 

 Standards. 



Methods 



Periphyton samples were collected following standard operating procedures of the 

 MDEQ Planning, Prevention, and Assistance Division. Using appropriate tools, microalgae 

 were scraped, brushed, or sucked from natural substrates in proportion to the importance of those 

 substrates at each study site. Macroalgae were picked by hand in proportion to their abundance 

 at the site. All collections of microalgae and macroalgae were pooled into a common container 

 and preserved with Lugol's (IKT) solution. 



The samples were examined to estimate the relative abundance and rank by biovolume of 

 diatoms and genera of soft (non-diatom) algae according to the method described in Bahls 

 (1993). Soft algae were identified using Smith (1950), Prescott (1962, 1978), John et al. (2002), 

 and Wehr and Sheath (2003). These books also served as references on the ecology of the soft 

 algae, along with Palmer (1969, 1977). 



After the identification of soft algae, the raw periphyton samples were cleaned of organic 

 matter using sulfuric acid, potassium dichromate, and hydrogen peroxide. Then permanent 

 diatom slides were prepared using Naphrax, a high refractive index mounting medium, following 



