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Further, and critically, our understanding of in situ microbial activity and interactions is still quite incomplete. It has become clear that studying the tropical reef environment requires some modifications of methods from traditional temperate marine microbial ecology to accurately quantify essential parameters (e.g. Torreton and Dufour, 1996a for FDDC conversion to specific growth rate, ?; Wild et?al., 2006; Garren and Azam, 2010 for enumeration of bacterial cells), and these breakthroughs are helping to constrain and quantify critical pieces of the puzzle such as bacterial abundance, growth rates, and production rates (Table?1). And thus, while the questions we highlight (Fig.?3) address some of the current gaps in our understanding of reef microbial ecology, many are questions that have been asked previously. The reason to revisit them [http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase] is that new technologies (including NanoSIMS, super resolution microscopy, high-speed imaging techniques, confocal Raman microspectroscopy, next-generation sequencing, and microfluidics) are becoming accessible to marine microbial ecologists that can help answer the questions in a quantitative and mechanistic way (Table?2). We further stress the need to develop in situ microscopy. In this new era of microbial ecology, some researchers are considering phage therapy as a potential response to global increases [http://www.selleckchem.com/PI3K.html /www.selleckchem.com/PI3K.html] in coral disease (Efrony et?al., 2007; 2009) and the ability to employ the rapidly advancing concepts and techniques from biomedicine is ever more accessible (Bourne et?al., 2009). Studies of coral reef ecology and microbial diseases of corals would also benefit by learning from the highly dynamic field of human health considerations of microbial [http://www.selleckchem.com/products/ch5424802.html Selleckchem Alectinib] pathogenesis and the ecology of microbial diseases. Indeed, future discoveries in coral�Cmicrobe interactions may ��return the favours�� through potential applicability to human�Cmicrobe interactions. The time is ripe for microbial ecologists to discover and create an integrated and mechanistic understanding of coral reef functioning; however, they will need the help of natural resource managers working in coral reef ecosystems. In the context of long-term survival and conservation of coral reef ecosystems, the need for this work is immediate. There are powerful and logistically simple ways now possible in which resource managers and microbial ecologists might collaborate to greatly advance our understanding of coral reef microbial ecology and microbial pathogenesis. Most coral reef managers and researchers lack access to specialized technologies in field settings around the world. However, it could be straightforward to collect samples during regular monitoring routines and send them to specialize laboratories for analyses and archiving.