If you read TFA, you'll see that 1) they did sequence DNA, 2) they found many, many species which are not the usual ones associated with contamination due to methodology, and 3) they found organisms that can theoretically survive in the extreme and varied environments believed to be present in the lake (thermophiles near suspected geothermal areas, halophiles in brackish/salty water, etc). As a microbiologist, I find it fascinating that the authors not only provide a list of species, but go so far as to paint a complete picture of how each could possibly exist in a completely functioning ecosystem. For example, they found organisms responsible for carbon and nitrogen fixation, and hypothesize that these same species will also be found throughout the lake water in their various niches.