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Karasev ES, Hosid SL, Aksenova TS, Onishchuk OP, Kurchak ON, Dzyubenko NI, Andronov EE, Provorov NA. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized ( sym) Genes in the Polytypic Species Neorhizobium galegae. Int J Mol Sci 2023; 24:16696. [PMID: 38069024 PMCID: PMC10706768 DOI: 10.3390/ijms242316696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Nodule bacteria (rhizobia) represent a suitable model to address a range of fundamental genetic problems, including the impacts of natural selection on the evolution of symbiotic microorganisms. Rhizobia possess multipartite genomes in which symbiotically specialized (sym) genes differ from core genes in their natural histories. Diversification of sym genes is responsible for rhizobia microevolution, which depends on host-induced natural selection. By contrast, diversification of core genes is responsible for rhizobia speciation, which occurs under the impacts of still unknown selective factors. In this paper, we demonstrate that in goat's rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus, representing two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis), the evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, the evolution of core genes occurs under the impacts of driving selection (dN/dS > 1), while the evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, the evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism in both gene groups and the impacts of driving selection on core gene evolution are more pronounced in bv. orientalis than in bv. officianalis, reflecting the diversities of their respective host plant species. In bv. orientalis, a highly significant (P0 < 0.001) positive correlation is revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis, this correlation is of low significance (0.05 < P0 < 0.10). For sym genes, the correlation between p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data, along with the functional annotation of core genes implemented using Gene Ontology tools, suggest that the evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis, evolution presumably depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented, suggesting that gene nucleotide polymorphism may be extended by driving selection only in ecologically versatile organisms capable of supporting a broad spectrum of gene alleles in their gene pools.
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Affiliation(s)
- Evgeny S. Karasev
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Sergey L. Hosid
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Tatiana S. Aksenova
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Olga P. Onishchuk
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Oksana N. Kurchak
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Nikolay I. Dzyubenko
- All-Russia Research Institute of Plant Genetic Resources, 190031 St. Petersburg, Russia;
| | - Evgeny E. Andronov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
| | - Nikolay A. Provorov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
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2
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Quides KW, Lee Y, Hur T, Atamian HS. Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers. BIOLOGY 2023; 12:biology12020277. [PMID: 36829553 PMCID: PMC9953586 DOI: 10.3390/biology12020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.
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Affiliation(s)
- Kenjiro W. Quides
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Yoobeen Lee
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Teresa Hur
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Hagop S. Atamian
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Correspondence:
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3
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Microbial eco-evolutionary dynamics in the plant rhizosphere. Curr Opin Microbiol 2022; 68:102153. [DOI: 10.1016/j.mib.2022.102153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 01/08/2023]
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4
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Batstone RT, Burghardt LT, Heath KD. Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont. Proc Biol Sci 2022; 289:20220477. [PMID: 35858063 PMCID: PMC9277234 DOI: 10.1098/rspb.2022.0477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.
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Affiliation(s)
- Rebecca T. Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Liana T. Burghardt
- Department of Plant Science, The Pennsylvania State University, 103 Tyson Building, University Park, PA, 16802 USA
| | - Katy D. Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 286 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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5
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Epstein B, Burghardt LT, Heath KD, Grillo MA, Kostanecki A, Hämälä T, Young ND, Tiffin P. Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Mol Ecol 2022. [PMID: 35793264 DOI: 10.1111/mec.16602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.
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Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Liana T Burghardt
- Department of Plant Sciences, The University of Pennsylvania, University Park, Pennsylvania, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Adam Kostanecki
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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Dinges ZM, Phillips RK, Lively CM, Bashey F. Post‐association barrier to host switching maintained despite strong selection in a novel mutualism. Ecol Evol 2022; 12:e9011. [PMID: 35784049 PMCID: PMC9204852 DOI: 10.1002/ece3.9011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/25/2022] Open
Abstract
Following a host shift, repeated co‐passaging of a mutualistic pair is expected to increase fitness over time in one or both species. Without adaptation, a novel association may be evolutionarily short‐lived as it is likely to be outcompeted by native pairings. Here, we test whether experimental evolution can rescue a low‐fitness novel pairing between two sympatric species of Steinernema nematodes and their symbiotic Xenorhabdus bacteria. Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations. We selected the most productive infections, co‐passaging this novel mutualism nine times to determine whether selection could improve the fitness of either or both partners. We found that neither partner showed increased fitness over time. Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift. Thus, post‐association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists.
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Affiliation(s)
- Zoe M. Dinges
- Department of Biology Indiana University Bloomington Indiana USA
| | | | - Curtis M. Lively
- Department of Biology Indiana University Bloomington Indiana USA
| | - Farrah Bashey
- Department of Biology Indiana University Bloomington Indiana USA
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Klein M, Stewart JD, Porter SS, Weedon JT, Kiers ET. Evolution of manipulative microbial behaviors in the rhizosphere. Evol Appl 2022; 15:1521-1536. [DOI: 10.1111/eva.13333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Malin Klein
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Justin D. Stewart
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington USA
| | - James T. Weedon
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - E. Toby Kiers
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
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8
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Quides KW, Weisberg AJ, Trinh J, Salaheldine F, Cardenas P, Lee HH, Jariwala R, Chang JH, Sachs JL. Experimental evolution can enhance benefits of rhizobia to novel legume hosts. Proc Biol Sci 2021; 288:20210812. [PMID: 34034525 PMCID: PMC8150021 DOI: 10.1098/rspb.2021.0812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host–symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host–symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jerry Trinh
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Fathi Salaheldine
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Paola Cardenas
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Ruchi Jariwala
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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