Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Connecting Microbial Genotype to Phenotype in Bacterial Strains from a Dynamic Subsurface Ecosystem Using ENIGMA ‘Environmental Atlas’

Authors:

R. Chakraborty1* (rchakraborty@lbl.gov), A. M. Deutschbauer1,2, J-M. Chandonia1, A. Yadav1, M. de Raad1, A. Codik1, M. Chen1, A. E. Kazakov1, S. Priya1, T. J. Lie4, V. Bhanot1, M. N. Price1, M. P. Thorgersen3, L. M. Lui1, V. V. Trotter1, J. R. Hahn1, B. W. Biggs1, J. L. Goff3, T. N. Nielsen1, V. Mutalik1, H. K. Carlson1, A. Mukhopadhyay1, P. J. Walian1, M. W. W. Adams3, D. A. Stahl4, T. R. Northen1, A. P. Arkin1,2, P. D. Adams1,2

Institutions:

1Lawrence Berkeley National Laboratory; 2University of California–Berkeley; 3University of Georgia–Athens; 4University of Washington–Seattle

Goals

The goal of ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) is to develop theoretical, technological, and scientific approaches to gain a predictive and mechanistic understanding of the biotic and abiotic factors that constrain microbial communities’ assembly and activity in dynamic environments. To link genetic, ecological, and environmental factors to the structure and function of microbial communities, ENIGMA uses a systems biology approach to integrate and develop laboratory, field, and computational methods.

Abstract

The project has made significant progress towards developing an “ENIGMA Environmental Atlas” and mapping genotype to phenotype for a significant number of diverse subsurface microbes from a field site, the Oak Ridge Field Research Center (ORFRC). This Atlas includes a growing collection of close to 3000 isolates across diverse phyla. Enrichment and isolation efforts reveal that microbial necromass is a major nutrient source for the community, and one recent success includes isolation of novel nitrous oxide reducers from the field site. High-resolution electron microscopy images have revealed unique morphotypes and features of ENIGMA isolates based on growth and nutrient conditions. Researchers are also isolating novel phages and phage tail–like bacteriocins (tailocins) from the field site. The systematic study of bacteria-phage and tailocin interactions will provide novel insights into microbial community dynamics and functional genomics. Genome sequencing of over 1,100 bacterial isolates to date has revealed both macro and microdiversity, such as in Sediminibacterium sp., with regards to denitrification genes. To facilitate analyses of these genomes, the team has developed scalable, web-based portals for rapid comparative genomics (https://fast.genomics.lbl.gov/cgi/search.cgi), including those that can readily incorporate newly sequenced genomes (https://iseq.lbl.gov/genomes). Applying diverse high-throughput phenotypic and genome-wide mutant libraries, researchers have investigated the physiology of strains under in situ conditions, and results indicate differential phenotypes in outer membrane genes under transient and chronic metal exposure in Pantoea sp. In addition, the team has discovered a novel origin of replication in this strain that allows transformation and expression of non-native genes. Such capability may allow a similar exploration of the metabolism and gene functions in other strains. Here, the team highlights several instances where the ENIGMA Atlas is used to better understand the complexities that govern microbial function in the environment and presents progress on the development of such a unique community-usable platform.

Funding Information

This material by ENIGMA, a Science Focus Area at Lawrence Berkeley National Laboratory, is based upon work supported by the U.S. DOE, Office of Science, BER program under contract number DE-AC02-05CH11231.