Spatial heterogeneity in genetic diversity and composition of bacterial symbionts in a single host species population

Abstract

Aims

Revealing genetic diversity in a root nodulation symbiosis under field conditions is critical to understand the formation of ecological communities of organisms associated with hosts and the nitrogen cycle in natural ecosystems. However, our knowledge of the genetic diversity of bacterial mutualists on a local scale is still poor because of the assumption that the genetic diversity of mutualistic bacteria is constrained by their hosts.

Methods

We thoroughly investigated the genetic diversity of Frankia in a local forest stand. We collected root nodules from 213 Alnus hirsuta seedlings covering the spatial range of the continuous population, which means that Alnus individuals occurred in a relatively homogeneous distribution in a continuous forest. Then, a phylogenetic and diversity analysis was performed for the nifD-K IGS region, including global Frankia sequences from Alnus hosts.

Results

The genetic diversity of Frankia detected even on a local scale measured as high as that shown by previous studies conducted on local and regional scales. Moreover, a genetic structure analysis revealed a spatially mosaic-like distribution of genetic variation in Frankia despite the small spatial scale.

Conclusions

The genetic diversity and composition of bacterial mutualists are heterogeneous on a local scale. Our findings demonstrate that genetically different bacterial symbionts simultaneously interact with a single host population and interaction partnerships spatially vary. The standing variation could produce dynamic ecological and evolutionary outcomes in a heterogeneous forest ecosystem.

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Data availability

The sequence data are deposited at DDBJ with accession numbers of LC482655–LC482672 and LC528956–LC529138.

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Acknowledgments

We thank Rei Sakai, Michio Ishihara, Takashi Hara, Yoshiaki Takahashi, Masayuki Watarai, Wataru Mamiya, Yuri Yabuhara, and members of Uryu Experimental Forest, Hokkaido University, for their field assistance.

Funding

This research was supported by Grant-in-Aid for JSPS Research Fellow to SK (16 J03194), Young Scientists A (16H0617908), and Scientific Research B (19H0297409) to SU.

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SK and SU designed and conducted the investigation, performed the molecular analysis, analyzed the data, and wrote the manuscript.

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Correspondence to Shinnosuke Kagiya.

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Kagiya, S., Utsumi, S. Spatial heterogeneity in genetic diversity and composition of bacterial symbionts in a single host species population. Plant Soil (2020). https://doi.org/10.1007/s11104-020-04583-4

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Keywords

  • Alnus hirsuta
  • Frankia
  • Genetic diversity
  • Local scale
  • nifD-K IGS region
  • Nitrogen-fixing bacteria
  • Root nodule symbiosis