I thought I'd use the opportunity of a recent publication to introduce my lab group to you - from right (clockwise, sitting): Katherine Williams (she focuses on antibiotic resistance and susceptibility profiles of coral-associated bacteria, and resistance in the Genus Vibrio), Ben Neely (he's our non-coral guy - every lab needs one - he recently defended his doctoral research and should be turning in his dissertation soon), Maria Vizcaino (she is holding Kaya, Nikole's daughter - Maria is the lab's chemist, and is well on her way to characterizing the structure of several antimicrobials from a coral-associated bacterium), Nikole Kimes (she is a doctoral student in the lab, and it is her work that I mention below), and Dr. Wes Johnson (the lab's postdoc, fisherman, golfer and baker - Wes is working on bacterial diversity associated with coral, and is at present focused on the analysis of the Vibrio coralliilyticus genome). The image doesn't include a master's student with the group (his name is Joe Pollock - and he is in a conjoint program with the College of Charleston and James Cook University, where he works with Drs. Bette Willis and David Bourne) and I'll use this as an excuse to talk about him more on another post). This image was taking about two years ago now - and since it was taken, Kaya has turned two years old! Guess I need another photo, don't you think?
~~~~~
Our functional genomics work was a collaboration with Drs. Joe Zhou and Joy Van Nostrand - Joe is the Director of the Institute for Environmental Genomics at the University of Oklahoma, and it's his group that has developed the microbial functional gene array, GeoChip [you can read an earlier publication from his group on the GeoChip microarray here, He et al. 2007 The ISME Journal 1:67-77 ). This was a nice collaboration for the lab, especially since Joy received her PhD with my group in 2006 - it was fun working with her again.
~~~~~
~image credit: Dr. Ernesto Weil, University of Puerto Rico-Mayaguez~
Well, so it went like this: Nikole went down to Puerto Rico, and with the help of Dr. Ernesto Weil (whom the whole world knows) collected samples from a number of different corals. Based on the prevalence of disease in Montastraea faveolata, and the presence of visually healthy and diseased colonies, Nikole used samples from this coral to assess their biogeochemical cycling potential using GeoChip 2.0. She flew down to Dr. Zhou's lab, and worked closely with Joy - initially there was some troubleshooting needed in order to get good quality DNA for the array - and finally they were surprised (and quite thrilled) by the large number of 'hits' they observed on the array. Nikole them spent quite a bit of time analyzing the large dataset that resulted.
There are still many questions - and we plan in the future to broaden the coral samples that we examine using this approach. Our data also reflects functional 'potential' so of course an RNA-based approach is something we're discussing - as well as laboratory studies looking at expression of specific functional genes/biogeochemical pathways.
~~~~~
For an abstract of the work, and the citation, see below:
A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states.
Kimes, N.E., J.D. Van Nostrand, J.Z. Zhou, E. Weil and P.J. Morris. 2009. The functional potential of microbial communities associated with Montastraea faveolata from the southern coast of Puerto Rico. Environmental Microbiology. DOI: 10.1111/j.1462-2920.2009.02113.x.
