A new study investigated complex interactions among four cross-feeding microorganisms in a synthetic community (SynCom) that converts cellulose to methane and carbon dioxide, paving the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems.
Environmental Simulations
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.
Decomposition decreases molecular diversity and ecosystem similarity of soil organic matter
ENIGMA researchers collaborated with the Lehmann Lab at Cornell University to find that microbial decomposition drives significant variability in the molecular richness and diversity of soil organic matter between soil horizons and ecosystems.
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 […]
Automating Culturing Technology Aids In Scaling Bacterial Growth Experiments
An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates Hunt, KA; J Forbes, F Taub, N Elliott, J Hardwicke, R Petersen, N Stopnisek, DAC Beck, DA Stahl; Journal of Microbiological Methods, [DOI]:10.1016/j.mimet.2021.106294 For decades, the cloudiness (turbidity) of a culture has been used to monitor the […]
Scientists Uncover Mechanistic Evidence on How Cooperation Evolves in Mutualistic Microbial Communities
February 21, 2021-Researchers map early adaptive events in evolution of mutualistic interactions with a broad range of applications for biotechnology, medicine and environment.
Turkarslan, Serdar; N. Stopnisek, A.W Thompson, C.E Arens, J.J Valenzuela, J. Wilson, K.A Hunt, J. Hardwicke, S. Lim, Y.M Seah, Y. Fu, L. Wu, J-Z Zhou, K.L Hillesland, D.A Stahl, N.S Baliga (2021) Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions. ISME Journal [doi]: 1038/s41396-021-00919-9 OSTI ID: 1773759.The Science…Organisms from different species often interact in ways that benefit both organisms – a common ecological interaction called mutualism. Researchers have found evidence for how cooperativity in one example of mutualism, syntrophy, is established across evolutionary timescales. They have uncovered striking evidence that mutations accumulated during the evolution of syntrophy generate synergistic epistasis or positive genetic interactions among rare individuals of a microbial community. These genetic interactions increase cooperativity within these rare microbial assemblages enabling their persistence at very low frequency within a larger productive population.
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
JANUARY 2021 Using systems analysis to elucidate the roles that hydrogen sulfide and cysteine play in inhibiting the growth of a nitrate-reducing Otwell AE, Carr AV, Majumder ELW, Ruiz MK, Wilpiszeski RL, Hoang LT, Webb B, Turkarslan S, Gibbons SM, Elias DA, Stahl DA, Siuzdak G, Baliga NS. 2021. Sulfur metabolites play key system-level roles […]
Challenging Carbon Nitrogen Ratios in a Dual-Pathway Actinobacterium
March 3, 2021-Vuono D.C., Read R.W., Hemp J., Sullivan B.W., Arnone, J.A., Neveux I., Blank R.R., Loney E., Miceli D., Winkler M-K.H., Chakraborty R., Stahl D.A., Grzymski J.J. 2019. Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium. Frontiers in Microbiology Vol 10, 3 [doi]:3389/fmicb.2019.00003{PMID}:30723459 PMCID:PMC6349771 OSTI:156058. In this study, we tested the effects of C:NO3− ratio and substrate concentration on pathway selection between ammonification and denitrification in the dual-pathway organism Intrasporangium calvum C5. We challenge the paradigm that C:NO3− ratio controls pathway selection based on a simple principle: ratios do not account for substrate concentrations, which can impose resource limitation for C or NO3−