Microbial ecology; Cooperation; Spatial ecology; Microbial communities; Range expansion; Denitrification; Evolutionary ecology; Antibiotic resistance
Ruan Chujin, Ramoneda Josep, Chen Guowei, Johnson David R., Wang Gang (2021), Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations, in ISME Communications
, 1(1), 54-54.
Goldschmidt Felix, Caduff Lea, Johnson David R. (2021), Causes and consequences of pattern diversification in a spatially self-organizing microbial community, in The ISME Journal
, 15(8), 2415-2426.
Ciccarese Davide, Anita Zuidema, Valeria Merlo, Johnson David R (2020), Interaction-dependent effects of surface structure on microbial spatial self-organization, in Philosophical Transactions of the Royal Society B
, 375, 20190246.
Johnson David R, Stephan Noack (2020), Editorial overview: Causes and biotechnological application of microbial metabolic specialization, in Current Opinion in Biotechnology
, 62, iii-iv.
Borer Benedict, Ciccarese Davide, Johnson David, Or Dani (2020), Spatial organization in microbial range expansion emerging from trophic dependencies and successful lineages, in Communications Biology
, 3, 685.
Lilja Elin E., Johnson David R. (2019), Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage, in BMC Evolutionary Biology
, 19(1), 129.
Tecon Robin, Mitri Sara, Ciccarese Davide, Or Dani, van der Meer Jan Roelof, Johnson David R. (2019), Bridging the Holistic-Reductionist Divide in Microbial Ecology, in mSystems
, 4, e00265-18.
Ciccarese Davide, Johnson David R (2019), Functional microbial landscapes, in Moo-Young Murray (ed.), Elsevier: Permagon, Amsterdam, 42-51.
CiccareseDavide, MicaliGabriele, BorerBenedict, RuanChujin, OrDani, JohnsonDavid R., Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment, in The ISME Journal
A vast amount of the natural microbial world lives attached to surfaces, such as the microbial communities residing in the human gut, in soil ecosystems, or on particulate matter in the open ocean. An inherent behavior of surface-attached microbial communities is that they must, at some point in their existence, undergo range expansion. A range expansion occurs when microbial communities expand into previously unoccupied space. Range expansions likely occur as a series of successive expansions, where one microbial strain expands first (the primary expansion) and one or more other microbial strains expand afterwards (secondary expansions). While successive range expansions are pervasive in nature, the consequences of successive range expansions remain poorly understood. How might successive range expansions affect the evolutionary processes acting on microbial communities? How might they affect the ecological functioning and stability of microbial communities? In this proposal, I postulate two potentially general consequences of successive range expansions. The first is that successive range expansions should promote the transfer of genes between different microbial strains, such as the transfer of antibiotic resistance genes in the human gut. The main hypothesis is that successive range expansions increase the number of cell-cell contacts between different strains, thus increasing the probability of gene transfer between those strains. To address this hypothesis, I propose specific experiments to address the following questions:•Do successive range expansions promote the transfer of genes between different microbial strains?•After acquiring beneficial genes, can recipient cells proliferate and establish within a successive range expansion? •How does the magnitude of benefits bestowed by newly acquired genes affect the proliferation and establishment of recipient cells?The second consequence is that temporal fluctuations between cooperation and conflict between different microbial strains during range expansions may cause ecosystems to collapse. The main hypothesis is that cooperation and conflict promote the emergence of different spatial cell arrangements, and these spatial cell arrangements are in conflict with each other (i.e. the arrangements that emerge during cooperation are detrimental during competition and vice versa). Fluctuations between cooperation and conflict may therefore destabilize ecosystems and promote their eventual collapse. To address this hypothesis, I propose specific experiments to address the following questions: •Do temporal fluctuations between cooperation and conflict promote the eventual collapse of ecosystems during range expansions?•Do feedbacks emerge that mitigate the destabilizing effects of such temporal fluctuations, thus slowing or preventing ecosystem collapse?•If ecosystems escape collapse, what are the mechanisms that enable escape?Together, answering these questions will significantly advance our basic understanding about the evolutionary and ecological consequences of microbial range expansions. Given that every surface-attached microbial community must undergo range expansions, the insights gained will be of potential importance for nearly any surface-attached microbial community, including those important for the environment, biotechnology, and human health and disease.