Origin of biogeographically distinct ecotypes during laboratory evolution

Jacob J. Valenzuela, Selva Rupa Christinal Immanuel, James Wilson, Serdar Turkarslan, Maryann Ruiz, Sean M. Gibbons, Kristopher A. Hunt, Nejc Stopnisek, Manfred Auer, Marcin Zemla, David A. Stahl and Nitin S. Baliga ()
Additional contact information
Jacob J. Valenzuela: Institute for Systems Biology
Selva Rupa Christinal Immanuel: Institute for Systems Biology
James Wilson: Institute for Systems Biology
Serdar Turkarslan: Institute for Systems Biology
Maryann Ruiz: Institute for Systems Biology
Sean M. Gibbons: Institute for Systems Biology
Kristopher A. Hunt: University of Washington
Nejc Stopnisek: University of Washington
Manfred Auer: Southeast University
Marcin Zemla: Lawrence Berkeley National Laboratory
David A. Stahl: University of Washington
Nitin S. Baliga: Institute for Systems Biology

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300–1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H2 by low affinity hydrogenases of Mm in the same phase. The unutilized H2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.

Date: 2024
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DOI: 10.1038/s41467-024-51759-y

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