Argonne National Laboratory. University of Chicago
Department of Ecology & Evolution
IL, United States
Microbial communities: temporal and biogeographic structure
Coming primarily from a marine background I have been very interested in how bacteria exist in such a fluid matrix. Specifically, what determines how microbes exist when the medium in which they live is moving around so much? My research site in the Western English Channel has demonstrated that even though the sampling location is flushed with new water every two weeks, the same communities of microbes appear year after year.
This highlights that microbes exist in robust and well-defined communities in this ecosystem. My ongoing research is to determine how true this is for all ecosystems around the planet.
There are a nonillion bacteria in the world (1 x 1030 cells) give or a take a few quadrillion. This almost incomprehensible number is greater than the number of stars in the known universe. To date no one has ever fully characterized the biodiversity of a microbial sample. Even the simplest communities seem to have a never-ending ‘tail’ of rare microorganisms, some of which seem to respond to episodic events producing ‘blooms’, while others seem to just exist in this rare state. We have now applied more the 20 million sequences to one sample from a marine ecosystem and still failed to catalogue all the diversity therein. Until we are able to fully characterize one of these communities, every effort to describe the global extent of microbial diversity will be extrapolative. Understanding biodiversity in any ecosystem, gives you an appropriate metric by which to describe it. Until we can do that we are describing the relative abundance of a subset of a given community. Understanding this concept, and exploring the limits of diversity are fundamental to my research goals.
Microbial Metabolic Dynamics
Microbes are vital to the success of life on this planet. They perform the vast majority of all metabolic processes, and also control health in every living organism on this planet. My lab uses metagenomics (literally meaning ‘beyond the genome’) to characterize the metabolic potential of a microbial community. We also use metatranscriptomics to explore the genes that are transcribed in every cell in a community. We then turn the sequence data into metabolic information by ascribing function to each potential gene or transcript and then defining their metabolic activity. Through comparison between one sample and another we can effectively describe how the metabolic activity of a community changes over time or space. This is essential to exploring functional and trophic interactions in a community, i.e. who eats who, who feeds of what, and who needs what?
Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, Gilbert JA, Chu H. 2014. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbial Ecology. 10.1111/1574-6941.12289
Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D. 2014. Saliva from Obese individuals suppresses the released of aroma compounds from wine. PLoS ONE 9(1): e85611. doi:10.1371/journal.pone.0085611.
Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicus D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. 2014. Metagenomics reveals sediment microbial community response to the Deepwater Horizon oil spill. ISME Journal. 23rd Jan 2014. doi:10.1038/ismej.2013.254
Peer X, Gilbert JA, An GC. 2014. Examining the Microbial Ecological Dynamics of Clostridium difficile Infections and the Efficacy of Fecal Microbiome Transplant (FMT) using an Agent-based Model. Journal of Surgical Research 186 (2), 689.
Gilbert JA, van der Lelie D, Zarraonaindia I. 2014. Microbial terroir for wine grapes. PNAS. 111 (1), 5-6.