ENIGMA researchers demonstrated the development and application of a markerless deletion mutagenesis system in nitrate-reducing bacterium Rhodanobacter denitrificans. This method marks a crucial step in advancing Rhodanobacter as a model denitrifying bacterium for the study of denitrification in groundwater ecosystems and diverse molecular mechanisms of low-pH resistance.
Environmental Atlas
Two model phages characterized by new CRISPR based technology extensible to diverse phages
ENIGMA researchers demonstrated for the first time that they can, on a genome-wide scale, identify phage genes that are essential (or not) to infecting bacteria, and then replace non-essential DNA with distinctive barcode tags. Their method could unlock potent biotechnology applications.
Novel Protocol Leverages Automatic Liquid Transfer to Prepare Hundreds of Microbial Cell Cultures for Proteomic Analysis
ENIGMA researchers detailed a step-by-step protocol that consists of cell lysis in alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. This protocol, combined with previously established automated protein quantification and protein normalization protocols, provides a rapid, cost-effective method to prepare LC-MS proteomic samples from bacteria and non-filamentous fungi cell cultures.
Microbial Communities Vary Widely Underground, Even When Close
Study finds that geochemistry and hydrogeology can influence community type and function, even when those communities are only 10 cm apart.
Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins
Using new barcoded screening technology, ENIGMA researchers uncovered genome-wide targets of diverse including single-stranded RNA-phages (ssRNA-phages)-derived protein antibiotics to efficiently identify the host mechanisms targeted in bacteriolysis. The novel approach could have significant applications for characterizing the hundreds of putative Sgl identified in genomic databases and recent studies.
Examining adaptations of a dominant bacterial species at a contaminated subsurface site
Leveraging comparative genomics, community analysis, and geochemical data to understand adaptations that facilitate survival of a dominant community member in the contaminated Oak Ridge Reservation subsurface.
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.
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 […]