New iDIRECT framework could help scientists better understand biological systems by disentangling direct from indirect relationships in association networks.
News Articles Archives
Bacterial community composition impacts the transformation of carbon in soils
Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, ENIGMA researchers characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. I
ENIGMA researchers identify hundreds of new enzymes
Filling Gaps in Bacterial Metabolism with Computation and High-throughput Genetics: An analysis of genetic data from many different kinds of bacteria identified hundreds of new enzymes.
Using microcalorimetry and thermodynamic modeling to examine effects of thermal stress
Hunt KA, von Netzer F, Gorman-Lewis D, Stahl DA. (2022) Microbial maintenance energy quantified and modeled with microcalorimetry. Biotechnol Bioeng. 2022 Jun 9; [DOI]:10.1002/bit.28155. {PMID}: 35680566 OSTI:1874049 All known biology is driven by the partitioning of energy released from nutrient consumption, either into building new cells or maintaining cellular integrity required for viability. The energy […]
Discovering microbial adaptations to subsurface niches
Gushgari-Doyle, S; L.M. Lui, T.N. Nielsen, X. Wu, R.G. Malana, F.L. Poole II, M.W.W. Adams, A.P. Arkin, R. Chakraborty (2022) Genotype to ecotype in niche environments: Adaptation of Arthrobacter to carbon availability and environmental conditions. ISME Comm. [DOI]:10.1038/s43705-022-00113-8 OSTI:1860268 Different niche micro-environments can affect the structure and function of microbial communities. Terrestrial subsurface environments exhibit […]
Whole genome sequence reveals molecular mechanisms underlying adaptation of Rhodanobacter strains to multiple stressors
The Genomic Features Underlying Adaptation of Rhodanobacter Strains to Stressful Conditions (denitrification processes, heavy metal resistance, and restriction-modification systems) present at ENIGMA Field Site ORR. Rhodanobacter species have been found dominant in the subsurface of Oak Ridge Reservation (ORR) site contaminated with acid, nitrate, metal radionuclides, and other heavy metals. Recently, multiple Rhodanobacter strains have […]
Sampling Down Well In Situ Microbial Colonization Conditions
LJ McKay*, HJ Smith*, E Barnhart, HD Schweitzer, RR Malmstrom, D Goudeau, MW Fields (2021) Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane Nature ISME Journal [DOI]:10.1038/s41396-021-01139-x PMID: 34689183 Development of activity-based metagenomics, enabled the identification of translationally active microorganisms and associated functional capacity Demonstration on terrestrial subsurface […]
Uncovering metal tolerance mechanisms using ENIGMA tools and Analysis
Thorgersen, M.P., .; J. Xue, E.L.W. Majumder, V.V. Trotter, X. Ge, F.L. Poole II, T.K. Owens, L.M. Lui, T.N. Nielsen, A.P. Arkin, A.M. Deutschbauer, G. Siuzdak, and M.W.W. Adams Deciphering microbial metal toxicity responses using RB-TnSeq and activity-based metabolomics. Applied and Environmental Microbiology 87 (21), e01037-21 (2021). [DOI]: 10.1128/AEM.01037-21] {PMID}:34432491 OSTI:1825256 Deciphering Microbial Metal […]