Ken Feldman and Sanjay Joshi have written peer reviewed articles in Advanced Aquaria on bacteria counts in reef aquarium.
http://www.advancedaquarist.com/2011/3/aafeature
Conclusions of this article are:
Overall, the major conclusions from these water column bacteria removal experiments are
GAC (Granular Activated Carbon) filtration does not remove bacteria from the water column.
Protein skimming (bubbles) removes approximately 30 - 40% of the bacteria in the water column of carbon-treated or organic rich water, but the remainder is not susceptible to bubble-based removal.
Steady state bacteria populations in skimmed reef tank water are not subject to further skimmer-based bacteria removal - there is a baseline value that the skimmer will not go below.
Conclusions from earlier research articles are:
Our earlier research on the topic of carbon nutrient levels in marine aquaria (Feldman, 2008; Feldman, 2009; Feldman, 2010) has provided experimental documentation for four conclusions that impact on TOC management in our reef tanks:
Reef aquaria utilizing active filtration (GAC, skimming) maintain equilibrium TOC levels within the range found on healthy tropical reefs.
Protein skimming (i.e., bubbles) is not very effective at removing TOC from aquarium water, depleting typical reef tank water of only ~ 20 - 35% of the post-feeding TOC present.
GAC filtration is quite effective at stripping reef tank water of its TOC load, removing 60 - 85% of the TOC present.
And, quite intriguingly, the natural biological filtration, which starts with bacteria and other microbes, is remarkable in its capacity to remediate reef tank water of TOC, easily removing 50% or more of the post-feeding TOC increase in tank water.
Conclusions (2) and (3) describe the consequences of mechanical filtration on TOC levels, but the 4th conclusion emphasizes the importance of the "hidden" part of the remediation equation, bacterial predation, for gaining an understanding of the dynamics of carbon commerce in our aquaria. In fact, this observation, coupled with the advent of Carbon Dosing strategies for nutrient export, led to a new series of questions regarding the perhaps pivotal role of bacteria, or at least skimmable water column bacteria, in successful reef aquarium husbandry.