The idea of epicPCR (Emulsion, Paired Isolation and Concatenation PCR) is to link functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation.
The article describing the proof-of-concept for epicPCR was published in the ISME journal and the detailed protocol can be found from Protocol exchange.
http://www.nature.com/ismej/journal/v10/n2/full/ismej2015124a.html
https://www.nature.com/protocolexchange/protocols/4095/publications/3073