Although coral skeletons represent the most natural of all tested substrates, when regarding the ease of handling and removal of the biofilm, glass slides have the clear advantage in that their smooth, flat surfaces enable simple and rapid removal of most of the biofilm biomass. Considering that bacterial community structures on coral skeletons and glass slides were not significantly different, we propose the use of glass slides for future bioindicator studies. Both spatial and seasonal influences (i.e. changes in water quality including light, salinity, turbidity, chlorophyll α) on bacterial community structures may have been responsible for some of the variability among certain substrates,

rather Ku-0059436 clinical trial than the actual substrate type. We suggest that all of the substrate types used in this study

have RO4929097 relatively little influence on the bacterial community composition when examined after the relatively long deployment period (c. 48 days). Types of bacteria initially colonizing and settling on specific substrates may be different depending on the surface properties of the substrate, however, biofilms undergo distinct temporal shifts, where the effect of substrate type diminishes, and tend to form more similar community structures over time (Huggett et al., 2009; Chung et al., 2010). In the present study, distinct bacterial communities were identified at the two different locations suggesting that discrete bacterial communities develop in response to the different environmental parameters found at the different locations rather than different substrates. As our study sites were positioned at either ends of a clearly formed water quality gradient that is known from a continuous long-term monitoring program (Uthicke & Altenrath, 2010; Uthicke et al., 2010; Kriwy & Uthicke, 2011) and from recently measured

data (Table 1), we propose that this response was caused by differences in water quality at the two locations. The rationale to collect samples from two islands (representing extremes of a previously studied water quality gradient) and at two sampling times (representing the annual extremes in water temperature) was merely to test for substrate differences under a variety of environmental conditions, and thus extends the validity of this study. Given that differences between the bacterial Aspartate community compositions at different sites could be easily detected, reproducible patterns among replicates were produced, and tentatively 89.2% of the taxonomic affiliations of the T-RFs after comparison to sequence data produced from clone libraries were identified. This study therefore suggests that T-RFLP is a suitable and rapid, high-throughput fingerprinting method for detecting spatio-temporal and water quality-induced bacterial community shifts. Further support is given by the fact that dominant bacterial taxa identified using this method (e.