Forest Rohwer's work on the microbiology of coral reefs was the basis for an undergraduate seminar course I did. We had articles that were from other labs, but his work framed the course and had some of the best papers. In discussing the overdominance of algae on dying coral reefs, students assume the algae is eating the coral or killing the coral by blocking light. Instead, it turns out the algae is suffocating the coral by making a bunch of sugar that feeds bacterial growth and that bacteria uses up all the local O2. It's a phenominal story and the students loved the discussion of these articles in class:
Kline, D. et al (2006). Role of elevated organic carbon levels and microbial activity in coral mortality. Mar Ecol Prog Ser. 314:119-125.
Smith, J.E. et al. (2006). Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. Ecol Lett. Jul;9(7):835-45
Hi there, since I deal with marine viruses look at this review papers
Wommack, K.E., Colwell, R.R., 2000. Virioplankton: Viruses in aquatic ecosystems. Microbiology and Molecular Reviews, 64, 2180-2185.
Suttle, C.A., 2005. Viruses in the sea. Nature, 437, 356–361.
Suttle, C.A., 2007. Marine viruses – major players in the global ecosystem. Nature Reviews Microbiology, 5, 801–812.
Jacquet, S., Miki, T., Noble, R.T., Peduzzi, P., Wilhelm, S., 2010. Viruses in aquatic ecosystems: important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology. Advanced Oceanography Limnology, 1, 71–101.
Hi, here three nice articles on microbial associations:
Hollants, J., F. Leliaert, O. de Clerck and A. Willems. 2013. What we can learn from sushi: A review on seaweed-bacterial associations. FEMS Microbiol Ecol. 83: 1-16.
Wahl, M., F. Goecke, A. Labes, S. Dobretsov and F. Weinberger. 2012. The second skin: Ecological role of epibiotic biofilms on marine organisms. Front. Microbio. 3: 292.
McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110(9):3229-36 PMC3587249
I'm partial to the 2005 Giovannoni Science paper describing the smallest genome of a free-living bacterium. "Genome streamlining in a cosmopolitan oceanic bacterium."