Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards

Abstract

Iron (Fe) deficiency in crop production is a worldwide problem which often results in chlorosis in grapevines, particularly in calcareous soils. Siderophores secreted by microorganisms and Strategy II plants can chelate Fe and other metals in soil solution, and siderophore-Fe complexes can then be utilized by plants and microbes. Plants may also shift rhizosphere conditions to favor siderophore-producing microbes, which can increase plant available Fe. Between-row cover crops (barley, rye, wheat, wheat/vetch) were planted as living mulch to address grapevine chlorosis by enhancing soil health in two vineyards in central Washington. The objectives of the current study were to (1) enrich for siderophore-producing organisms from within the indigenous rooting zone community of ‘Concord’ grapevines, and (2) perform comparative genomics on putative siderophore producing organisms to assess potentially important Fe acquisition-related functional domains and protein families. A high-throughput, chrome azurol S (CAS)-based enrichment assay was used to select siderophore-producing microbes from ‘Concord’ grapevine root zone soil. Next-generation whole genome sequencing allowed the assembly and annotation of ten full genomes. Phylogenetic analysis revealed two distinct clades among the genomes using the 40 nearest neighbors available in the public database, all of which were of the Pseudomonas genus. Significant differences in functional domain abundances were observed between the clades including iron acquisition and metabolism of amino acids, carbon, nitrogen, phosphate, and sulfur. Diverse mechanisms of Fe uptake and siderophore production/uptake were identified in the protein families of the genomes. The sequenced organisms are likely pseudomonads which are well-suited for iron scavenging, suggesting a potential role in Fe turnover in vineyard systems.

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Acknowledgments

The authors wish to thank Kalyani Muhunthan for assistance in laboratory procedures and the members of the Davenport Lab for assistance with sampling and plant tissue analyses.

Funding

Funding was provided by the Washington State Concord Grape Research Council, by the Washington State University BioAg program, and by the USDA/NIFA through Hatch project 1014527.

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Contributions

Ricky W. Lewis performed whole genome sequencing, processed and analyzed the sequencing data, and assisted with manuscript writing. Anjuman Islam gathered samples, performed the microplate siderophore production assay, extracted DNA, and assisted with manuscript writing. Lee Opdahl assisted with whole genome sequencing, interpretation of results, and manuscript writing. Tarah S. Sullivan and Joan R. Davenport conceived of the experimental design and assisted with sample gathering, interpretation of results, and manuscript writing.

Corresponding author

Correspondence to Tarah S. Sullivan.

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Lewis, R.W., Islam, A., Opdahl, L. et al. Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards. Microb Ecol 78, 699–713 (2019). https://doi.org/10.1007/s00248-019-01324-8

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Keywords

  • Rhizosphere function
  • Chrome azurol S (CAS) enrichment
  • Microbial cheating
  • Grapevine microbiome
  • Pseudomonas genomics
  • Grapevine nutrition