Delbeek and SPrung's "Reef Aquarium" Vol III. The first two volumes are good but vol III does an excellent job of looking at and expalining the different filtering methods. Research over the last few years has found Dissolved Organic Carbon, DOC, has a huge influence on corals and algae and some forms help corals and some forms promote corals disease. Forest Rohwer's "Coral Reefs in the Microbial Seas" is an excellent introduction to theis subject. WHile it's technically a thesis paper,
Jasper de Goeij's work on sponges adds an additional diamension to the role of DOC on reefs and is book length (and it's a free download

) Below are some links to videos you may find informative:
"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title (Paper back is ~$20, Kindle is ~$10), both deal with the conflicting roles of the different types of DOC in reef ecosystems. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems
Changing Seas - Mysterious Microbes
Nitrogen cycling in hte coral holobiont
BActeria and Sponges
Maintenance of Coral Reef Health (refferences at the end)
Optical Feedback Loop in Colorful Coral Bleaching
Richard Ross What's up with phosphate"