Jed Fuhrman, Ph.D.

CBIOMES Project: Microbial growth, interactions and biogeographies from ‘omics data

This project contributes multiple ways towards pursuit of overall CBIOMES goals of improving our conceptual and computational models of biological systems in the global ocean. Our participation primarily includes the provision of microbial biogeographic data (i.e. what organisms are found where and when) and other microbial data, plus biological oceanographic knowledge facilitating the development and evaluation of regional and global models. The data and knowledge specifically are on the identities, distributions, functions, rates (including growth) and interactions of a broad array of microorganisms, including bacteria, archaea, viruses and protists. We also work with modelers to provide various levels of “reality checks” in the microbial processes and interactions within the models. Specific aspects of the project are as follows: (1) Comprehensive observed global biogeographies, including seasonality and interannual dynamics where available, that can be used to set up model initial conditions and to compare model outcomes to observed biogeographies and seasonalities. Community composition is assessed through the use of PCR with “universal” rRNA primers (bacteria, archaea, protists and phytoplankton) from large scale ocean transects covering all ocean basins and multiple years Thousands of samples are being analyzed in our lab this way. Viruses are assessed from informatic analyses of metagenomes available for most of these transects. (2) Evaluation of different indicator genes and transcripts for predicting taxon-resolved traits like growth rates and nutritional status, and then applying these to existing metagenomes and metatranscriptomes in a biogeographic context. (3) Dividing microbial communities into workable bins for models by working with modelers to optimize the various tradeoffs between simplicity and accuracy. (4) Aligning model outputs with field data on global microbial distributions and interactions to iteratively improve models. Interactions and microbial associations will be assessed from statistical analyses of the global field data.

Bio:
Jed Fuhrman (S.B. MIT, 1977; Ph.D., Scripps Institution of Oceanography 1981) holds an endowed chair in the Department of Biological Sciences at the University of Southern California. Previously, he was on the faculty at SUNY Stony Brook (1981-88). His research aims to improve our understanding of the structure and function of marine microbial systems, including viruses, bacteria, archaea and protists, through field measurements, laboratory studies and modeling. His development (with Farooq Azam) of an approach to measure in situ growth of marine bacteria via DNA synthesis showed these bacteria consume about half the marine primary production, ushering widespread recognition of the global importance of the “microbial loop.” His lab was the first to measure the impact of viral infection on marine bacteria and cyanobacteria, showing through observations, experiments and modeling that it has many implications for ecosystem function. His lab also discovered abundant marine archaea that are primary marine agents of nitrification. Initiating one of the longest marine microbial time series in 2000 (off Los Angeles, still running), his lab showed annually repeating and predictable patterns in prokaryotic community composition and long-term stability of average composition, despite short-term fluctuations, implying feedback controls (competition, cooperation, grazing and viral infection) that he aims to model. His collaboration with computational biologists to develop and apply microbial association networks has begun to map the niche spaces and interactions among microbes and environmental factors. This was facilitated by his lab’s development of a high-resolution “universal” rRNA sequencing pipeline (for prokaryotes and eukaryotes together), also furthered by computational approaches he and his collaborators developed to better extract information about viral infection processes from metagenomic and metatranscriptomic data. Fuhrman is a Fellow of the American Association for the Advancement of Science, the American Academy of Microbiology, the Association for the Sciences of Limnology and Oceanography (from which he was awarded the G. Evelyn Hutchinson Medal in 2006) and the American Academy of Arts and Sciences.