June 8 2021. An effective cultivation and isolation strategy using natural complex carbon source recovers diverse and novel bacteria from the terrestrial subsurface. The Science…. Despite rapid technological advances in modern molecular tools for identification of key microbial taxa and critical metabolic processes in a given environment, a complete interpretation of omics-based data is still constrained by the unavailability of reference genomes and physiologically characterized isolates. Challenges in microbial cultivation/isolation in the laboratory have impeded the ability of microbiologists to fully investigate the roles and function of microbes in terrestrial subsurface ecosystems. To date scientists have only been able to cultivate less than 2% of microbes on Earth in the laboratory.
Discovery Support Yields Phage Tailocin Insights
April 7, 2021-To ensure that the ENIGMA research program remains vibrant 10% of funding is set aside annually for a Discovery program. ENIGMA researchers may propose new, short-term, research projects that either explore a new research theme or develop a new technical capability. These proposals are reviewed internally and funds allocated on the basis of merit and potential impact. One proposal by Mutalik and Carim as Early Career Scientists combined efforts across multiple ENIGMA labs: Arkin, Deutschbauer, Chakraborty, Walian has recently been published.
Carim, ; AL. Azadeh, AE. Kazakov, MN. Price, P. Walian, LM. Lui, TN. Nielsen, R Chakraborty, AM. Deutschbauer, VK. Mutalik, AP. Arkin (2021) Systematic discovery of Pseudomonad genetic factors involved in sensitivity to tailocins. ISME Journal [doi]:10.1038/s41396-021-00921-1OSTI ID: 1773739
These insights are highlighted by the LBL Newscenter https://newscenter.lbl.gov/2021/04/07/bacterial-homing-missiles/
The success of this work is being followed up with more discovery efforts in biochemistry and imaging.
Microbial Nitrate Removal in a Highly Contaminated Environment is Limited by the Essential Metal Molybdenum
Apr 7, 2021-Molybdenum limitation in the Oak Ridge Reservation contaminated environment, caused by iron and aluminium precipitation, affects nitrate reduction by microorganisms. The Science…The Oak Ridge Reservation (ORR) in Tennessee is a uniquely acidic, high-nitrate- and high-metal-contaminated environment. Although nitrate can be removed by microbes living in this environment, a limited concentration of soluble Molybdenum (Mo) in the ORR reduces biological denitrification. Two studies now reported the reason why Mo is limited and revealed the mechanisms used by some nitrate-reducing microbes to overcome Mo limitation and survive in these extreme conditions.
An Integrated Conceptual Microbial Ecology Framework
March 24, 2021-AHolistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. The Science Microbial communities serve critical roles in all ecosystems and have a profound impact on human health, environmental health, and industrial capabilities. As such, it is desirable to have robust, actionable directions for the intervention of microbial community function. However, the multiscale, stochastic, Spatio-temporal and diverse nature of microbial processes makes it difficult to achieve predictive understanding of microbial systems, despite the large body of microbial ecology research. To aid efforts that are building predictive understanding from genes to ecosystems, we have developed a conceptual modeling framework (FICSME) that models the composition,
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 […]
New Tools Allow for Faster Mapping of Large Numbers of Phage Resistant Genes
Oct 13, 2020-
Mutalik, V.K.; B.A. Adler, H.S. Rishi, D. Piya, C. Zhong, B. Koskella, E.M. Kutter, R. Calendar, P.S. Novichkov, M.N. Price, A.M. Deutschbauer, A.P. Arkin (2020) High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biology [doi]:10.1371/journal.pbio.3000877 OSTI:1714384
Phage work supported by ENIGMA Discovery to develop new tools for use towards mission critical questions is highlighted in https://newscenter.lbl.gov/2020/12/10/phages-natures-hidden-arsenal/
How Much Microbial Community Composition Is Driven by Selection How Much by Chance
Nov 23, 2020-Life on our planet consists of many communities of plants, animals, and microbes. These communities are shaped by complex ecological processes. Those processes include natural selection, migration, and random shifts in births and deaths. Quantifying the relative importance of these processes is a major challenge in ecology research. The challenge is especially great for the ecology of microbes. This study develops an approach named iCAMP. This approach is based on the concept that different processes can govern different groups of species in a diverse community. iCAMP showed excellent performance on simulated microbial communities. When applied to real-world grassland microbial communities, iCAMP revealed that environmental changes altered the relative importance of the ecological processes.