title: Epilithlic associates
design: To determine the impact of territorial damselfish on microbial communities, we examined the bacterial composition of the EAM inside and outside damselfish territories. In the field, ten 50 mL EAM samples were collected from control plots outside of Stegastes’ territories, inside S. apicalis’ territories and inside S. nigricans’ territories. For the collections from S. apicalis’ and S. nigricans’ territories, samples were taken across two damselfish colonies, and each sample came from a different damselfish territory. Samples were immediately snap-frozen in liquid nitrogen, stored at -80C [39] and transported to James Cook University (JCU) for processing and DNA extractions.  Samples were homogenized under liquid nitrogen, DNA was isolated using a PowerPlant DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA) following the manufacturer’s instructions and DNA quality was checked using a nanodrop. 27f and 519r univeral reverse primers and the V1-V3 region of the 16S gene were used for amplification with a single-step 30 cycle PCR using a HotStarTaq Plus Master Mix Kit (Qiagen, Valencia, CA, USA). MR DNA, a next generation sequencing and bioinformatics provider (Shallowater, TX, USA), performed the PCR (under the following conditions: 94C for 3 minutes, 28 cycles of 94C for 30 seconds, 53C for 40 seconds and 72C for 1 minute; 72C for 5 minutes). All amplicon products were mixed in equal concentrations and purified using Agencourt ampure beads (Agencourt Bioscience Corporation, MA, USA) and sequenced with Roche 454 FLX titanium instruments and reagents according to manufacturer’s guidelines.