Bacteria may play important roles in the biogeochemical cycling of coral reef fish feces and in the interactions between fishes and corals. This interaction potential was observed in a study of milkfish (Chanos chanos) aquaculture farms in the Philippines. Effluents from suspended fish pens created steep gradients of particulate organic carbon and other water characteristics that extended into nearby coral reefs. Highly similar bacterial phylotypes co-occurred in milkfish feces and in corals indicating the potential for transport of fecal particles and interaction with coral. In a separate study at Palmyra Atoll, bacteria abundances ranged 1̃0⁹ to 10¹¹ g⁻¹ dry wt among feces of parrotfish (Chlorurus sordidus), snapper (Lutjanus bohar), and surgeonfish (Acanthurus nigricans). Bacteria in parrotfish feces grew at a rate of 2̃ x 10⁸ cells g⁻¹ dry wt feces h⁻¹ . To improve our ability to observe growing marine bacteria, I tested a method for using the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU), which becomes incorporated during DNA synthesis and can be detected using c̀lick' chemistry combined with epifluorescence microscopy. The percentage of EdU-labeled bacteria ranged from 6̃% to 18% during a time course incubation of natural seawater assemblages. Additionally, cell specific signal intensities could be quantified, demonstrating the method's potential for determining individual cell growth rate. Other studies addressed phylotype composition of feces-associated assemblages. Analyses of feces-derived 16S rRNA gene clones revealed that Vibrionaceae dominated parrotfish and snapper feces. Many of these genes clustered phylogenetically to cultured Vibrio spp. and Photobacterium spp. Other Vibrionaceae- like sequences comprised a distinct phylogenetic group that may represent 'feces-specific' taxa. PCR primers specific to this f̀ish feces vibrio-like' group (FFV-L) were used to screen 'aged' parrotfish feces. FFV-L could be detected in feces collected over several days, indicating that feces may permit persistence of FFV-L in reefs. In addition to FFV-L, other bacteria phylotypes consistently occurred in aged feces, as determined via denaturing gradient gel electrophoresis (DGGE) analyses. To test the responses of coral-associated bacteria during short-term interactions with feces, both in situ and aquaria experiments were performed whereby corals were challenged with acute feces doses. The results reinforce the potential for bacteria transfer between feces and corals. Meanwhile, acute challenges with parrotfish feces did not impair the overall health of three coral species

Denitrifying microbes sequentially reduce nitrate (NO₃ ^-) to nitrite (NO₂ ^-), NO, N₂O, and N₂ through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NO_x ^-) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NO_x ^-. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.