Our first open access paper has just been accepted at PLoS One! And it’s a good one. Dylan & I looked at the effects of different lab protocols on the main variables measured by microbial ecologists (richness, community similarity). We also compared Illumina & 454 Pyrosequencing of the same samples and publish our fungal ITS primers for Illumina. If you’re thinking about doing microbial ecology with NGS data it’s worth taking a look.
Smith DP and Peay KG. (in press). Sequence depth, not PCR replication, improves ecological inference from Next Generation DNA Sequencing PLoS One.