According to Matt Kane, program director in NSF's Division of Molecular and Cellular Biosciences, the findings shed light on how bacteria and other microbes function collectively.
"This work simultaneously reconstructed the genome sequences for a five-membered microbial community from nature," Kane said. "It goes beyond previous achievements, such as those that sequenced the entire genome of single, isolated species or efforts that gathered genomic content from a microbial community but stopped short of constructing the individual genomes within it."
The researchers first screened several biofilms with a technique called FISH-fluorescence in situ hybridization-before settling on the particular pink sample a soup of several strains typical of acid mine drainages. They then applied to their selected community a genomics approach usually put to an individual species-"random shotgun sequencing."
This meant extracting DNA directly from the sample and a "small insert library." Once the sequences of short pieces of DNA were obtained, computer processing linked them to generate large genomic fragments that could be assigned to specific organisms within the community.
The researchers reconstructed nearly complete genomes of two organisms-strains of the bacterium Leptospirillum and of the archaeon Ferroplasma-and partial genomes of three other microbes. According to the researchers' Nature article, such recovery "from an environmental sample is an advance in the study of natural microbial communities."
According to Banfield, "The transition to this genome-level study of real populations opens the way for new understanding of speciation and evolution."
Further analysis of each organism's gene complement yielded clues about which microbes are most likely responsible for which services in this acid-adapted, self-sustaining community.