Ecosystems Biology Approaches To Determine Key Fitness Traits of Soil Microorganisms

Wednesday, 17 December 2014: 9:45 AM
Eoin Brodie1,2, Kateryna Zhalnina1,2, Ulas Karaoz2, Heejung Cho1,2, Erin E Nuccio3, Shengjing Shi1, Mary Suzanne Lipton4, Jizhong Zhou5, Jennifer Pett-Ridge6, Trent Northen2 and Mary Firestone1, (1)University of California Berkeley, Berkeley, CA, United States, (2)Lawrence Berkeley National Laboratory, Berkeley, CA, United States, (3)Lawrence Livermore National Laboratory, Chemical Sciences Division, Livermore, CA, United States, (4)Pacific Northwest National Laboratory, Richland, WA, United States, (5)University of Oklahoma Norman Campus, Norman, OK, United States, (6)Lawrence Livermore National Laboratory, Livermore, CA, United States
The application of theoretical approaches such as trait-based modeling represent powerful tools to explain and perhaps predict complex patterns in microbial distribution and function across environmental gradients in space and time. These models are mostly deterministic and where available are built upon a detailed understanding of microbial physiology and response to environmental factors. However as most soil microorganisms have not been cultivated, for the majority our understanding is limited to insights from environmental ‘omic information. Information gleaned from ‘omic studies of complex systems should be regarded as providing hypotheses, and these hypotheses should be tested under controlled laboratory conditions if they are to be propagated into deterministic models.

In a semi-arid Mediterranean grassland system we are attempting to dissect microbial communities into functional guilds with defined physiological traits and are using a range of ‘omics approaches to characterize their metabolic potential and niche preference. Initially, two physiologically relevant time points (peak plant activity and prior to wet-up) were sampled and metagenomes sequenced deeply (600-900 Gbp). Following assembly, differential coverage and nucleotide frequency binning were carried out to yield draft genomes. In addition, using a range of cultivation media we have isolated a broad range of bacteria representing abundant bacterial genotypes and with genome sequences of almost 40 isolates are testing genomic predictions regarding growth rate, temperature and substrate utilization in vitro. This presentation will discuss the opportunities and challenges in parameterizing microbial functional guilds from environmental ‘omic information for use in trait-based models.