TY - JOUR
T1 - Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
AU - Burghardt, Liana T.
AU - Epstein, Brendan
AU - Guhlin, Joseph
AU - Nelson, Matt S.
AU - Taylor, Margaret R.
AU - Young, Nevin D.
AU - Sadowsky, Michael J.
AU - Tiffin, Peter
N1 - Funding Information:
ACKNOWLEDGMENTS. We thank the editor and four anonymous reviewers for comments that greatly improved the manuscript. Funding was provided by NSF Grant IOS-1237993 and USDA-HATCH Award MIN-71-030.
Publisher Copyright:
© 2018 National Academy of Sciences. All Rights Reserved.
PY - 2018/3/6
Y1 - 2018/3/6
N2 - Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the “evolve and resequence” approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
AB - Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the “evolve and resequence” approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
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U2 - 10.1073/pnas.1714246115
DO - 10.1073/pnas.1714246115
M3 - Article
C2 - 29453274
AN - SCOPUS:85042936235
SN - 0027-8424
VL - 115
SP - 2425
EP - 2430
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 10
ER -