Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1073/pnas.2117814119
Licence creative commons licence
Title (Primary) Stabilizing microbial communities by looped mass transfer
Author Li, S.; Abdulkadir, N.; Schattenberg, F.; Nunes da Rocha, U.; Grimm, V.; Müller, S.; Liu, Z.
Source Titel Proceedings of the National Academy of Sciences of the United States of America
Year 2022
Department OESA; UMB
Volume 119
Issue 17
Page From e2117814119
Language englisch
Topic T7 Bioeconomy
T5 Future Landscapes
Keywords highlight; microbial ecology; metacommunity assembly; stability; microbial community cytometry; single-cellanalytics
Abstract Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx  were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.
Persistent UFZ Identifier
Li, S., Abdulkadir, N., Schattenberg, F., Nunes da Rocha, U., Grimm, V., Müller, S., Liu, Z. (2022):
Stabilizing microbial communities by looped mass transfer
Proc. Natl. Acad. Sci. U.S.A. 119 (17), e2117814119 10.1073/pnas.2117814119