Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314:1464–1467

Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA–based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment. Amajor challenge of environmental sci-ence is the identification of microbialspecies capable of catalyzing important activities in situ (1). PCR-based techniques that use single genes as proxies for organisms or key microbial activities continue to provide valuable insights into microbial community diversit