New Method for Counting Bacteria Associated with Coral Mucus

The extremely viscous and highly autofluorescent nature of coral mucus has been a major challenge in developing enumeration techniques and has limited our ability to study the ecological interactions among coral mucus layer (CML)-associated microbial communities. Only a few studies have used direct counts to quantify bacteria in the CML, and the methods and subsequent results vary widely. The techniques have included scanning electron microscopy (SEM) (34), phase-contrast microscopy (27), and epifluorescent microscopy using a variety of stains (acridine orange staining [8], SYBR gold [20], and 4′,6-diamidino-2-phenylindole [DAPI] [3]). Bacterial abundances reported from these studies spanned more than 5 orders of magnitude (from 1.6 × 102 cells [cm2]−1 using acridine orange [8] to 6.2 × 107 cells [cm2]−1 using SYBR gold [20]), and some of the studies are difficult to compare to each other because different units were used, such as cells ml−1 of mucus and cells (cm2)−1 of coral. Some variation in abundance is likely due to differences in mucus sampling methods and differences among coral species. However, the enormous quantity of autofluorescence emitted in green and red wavelengths found in most coral species creates a substantial challenge for reliably counting fluorescently stained cells in that portion of the spectrum, because many of the particles are bacterium sized. Many of these same particles could be visible with phase-contrast microscopy as well. Thus far, researchers quantifying CML-associated bacteria using epifluorescence microscopy have prepared their samples by following well-established protocols that were developed for seawater. We suggest that the viscous and autofluorescent nature of coral mucus may require some modifications from standard seawater protocols for epifluorescence microscopy to be most effective. SEM is an alternative to fluorescence-dependent techniques. It has the advantage of acquiring images with sufficient detail to distinguish among particles and cells, but this method is time-consuming, visualizes only the surface of the sample, and is not widely available or affordable enough for it to be a standard field protocol. An additional limitation is that most studies that have employed SEM for CML observation have found bacteria to be too dispersed to count in a reasonable number of micrographs (8, 19). Here we present a new method that disperses bacterial cells by enzymatically digesting the mucus with trypsin (an adaptation of routine cellular biology cell line culture procedures) and subsequently staining the cells with DAPI for rapid quantification using epifluorescence microscopy. DAPI fluoresces in the blue end of the spectrum, and its emission does not overlap with the autofluorescence of the mucus samples. This method is rapid, uses reagents and equipment readily available in microbial ecology laboratories, and can provide necessary information for studies of the ecology of microbial cells associated with mucus. It may also be helpful for studies of other aquatic gel-associated microbial communities. This visualization capability revealed that bacteria living with the reef-building coral Porites lobata were significantly smaller than their water-associated counterparts and that this difference is reduced in reefs heavily influenced by anthropogenic impacts. There is only one other report that we are aware of that observed small bacterial cell size in mucus from corals (of the genus Fungia), but that study did not quantify cell size (34). Given that mucus is a carbon-rich environment (6, 11, 12, 18, 24, 25, 31), this discovery is counterintuitive. It highlights questions regarding the ecological interactions that must occur in situ to select for small cell size in such a rich environment (3, 4, 7, 8, 11, 25, 34).