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The microbial diversity and abundance in surface snow at different altitudes (5300 and 5504 m above sea level), a moraine lake and a glacial stream in the Yala Glacier on the southern slope of the Himalayas were investigated through a 16S rRNA gene clone library and flow cytometry approaches. Cell abundance in different habitats changed from 1.1 × 10 to 25 × 10 cells mL, with the highest abundance in the moraine lake and the lowest abundance in the snow at 5504 m. Microbial communities in the snow were significantly different from those in the moraine lake and stream, although they were similar within snow and within the aquatic habitats. The two snow libraries were both dominated by Cyanobacteria, which accounted for about half of the total, followed by the Alphaproteobacteria and Firmicutes. The moraine lake and stream libraries were dominated by the Bacteroidetes and Betaproteobacteria, followed by the Actinobacteria. The results indicated that snow and water were highly diverse systems even in the same glacier. Microbial communities in the snow on the Yala Glacier were distinctly different from those in the East Rongbuk Glacier on the northern slope of Himalayas. However, microbes in the moraine lakes at two glaciers had similar community features. The snow habitat was easily affected by various environmental factors, while the aquatic habitats were comparatively stable in different glaciers. [ABSTRACT FROM AUTHOR]