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The grazing and subsequent defecation Selleckchem PI3K inhibitor patterns of mobile reef organisms (such as fish and invertebrates) provide another such mechanism (Johannes et?al., 1972; Smriga et?al., 2010). In thinking about the various connections among the microbial habitats discussed thus far, it is important to consider the time component and the role sediments might play as an archive of anthropogenic influence. For instance, Cu and Zn contamination in reef sediments can reach high levels from a single ship grounding (Negri et?al., 2002; Jones, 2007) such that small amounts of the sediment are toxic to coral larvae and inhibit settlement (Negri et?al., 2002; Smith et?al., 2003). The selection pressure of these metals can shift sediment bacterial community composition, and increase the incidence of antibiotic resistance (Nogales et?al., 2011). This metal signature may persist in the sediments and/or the associated bacterial communities for many years to come with unexplored consequences for overall ecosystem function. This is an example of why we need to understand the propagation of sublethal perturbations through the ecosystem to be able to predict the responses and resilience of coral reefs to future change. Given the strong coupling in coral reef ecosystems, it is not possible to clearly separate benthic and pelagic processes, and thus we need Tryptophan synthase to understand the holobiont within the continuum of benthic and pelagic environments. In a similar context, each Alectinib price of these environments encompasses many different microscale niches that can change the dynamics of benthic-pelagic interactions depending on the physical processes and various types of external forcing at play. In the pelagic environment, for example, we know that organic matter aggregates such as marine snow and phytoplankton are point sources of high concentrations of organic matter that vary on the millimetre scale, and are profoundly important for the functioning of ocean basin scale pelagic marine ecosystems (Azam, 1998; Seymour et?al., 2000; Kiorboe and Jackson, 2001; Long and Azam, 2001). Similarly, we can consider how microscale architecture and its heterogeneous distribution may regulate some mechanisms of microbial interactions. Spatial heterogeneity within coral microbial communities has been documented on the scale of centimetres (Rohwer et?al., 2001), but has rarely been investigated on a smaller scale. For example, one potential mechanism to consider is local organic matter enrichment within the coral mucus layer by expelled zooxanthellae (Paul et?al., 1986; Jones and Yellowlees, 1997; Baghdasarian and Muscatine, 2000; Wild et?al., 2005; Garren and Azam, 2010), which could act as a hotspot for microbial growth, as in the case of rapid and profuse colonization by Vibrio cholerae of the marine dinoflagellate Lingulodinium polyedrum (Mueller et?al., 2007).