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

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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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References

  1. Davenport JR, Stevens RG (2006) High soil moisture and low soil temperature are associated with chlorosis occurrence in Concord grape. Hortscience 41:418–422

    Article  CAS  Google Scholar 

  2. Pradubsuk S, Davenport JR (2010) Seasonal uptake and partitioning of macronutrients in mature ‘Concord’ grape. J Am Soc Hortic Sci 135:474–483

    Article  Google Scholar 

  3. Abadia J, Vazquez S, Rellan-Alvarez R, El-Jendoubi H, Abadia A, Alvarez-Fernandez A, Lopez-Millan AF (2011) Towards a knowledge-based correction of iron chlorosis. Plant Physiol Biochem 49:471–482. https://doi.org/10.1016/j.plaphy.2011.01.026

    Article  CAS  PubMed  Google Scholar 

  4. Garcia-Mina JM, Bacaicoa E, Fuentes M, Casanova E (2013) Fine regulation of leaf iron use efficiency and iron root uptake under limited iron bioavailability. Plant Sci 198:39–45. https://doi.org/10.1016/j.plantsci.2012.10.001

    Article  CAS  PubMed  Google Scholar 

  5. Singh K, Singh Y, Upadhyay AK, Mori S (2011) Phytosiderophore-based molecular approach for enhanced iron acquisition to increase crop production under high pH calcareous soils. Indian J Agric Sci 81:679–689

    CAS  Google Scholar 

  6. Colombo C, Palumbo G, He JZ, Pinton R, Cesco S (2014) Review on iron availability in soil: interaction of Fe minerals, plants, and microbes. J Soils Sediments 14:538–548. https://doi.org/10.1007/s11368-013-0814-z

    Article  CAS  Google Scholar 

  7. Kim SA, Guerinot ML (2007) Mining iron: iron uptake and transport in plants. FEBS Lett 581:2273–2280. https://doi.org/10.1016/j.febslet.2007.04.043

    Article  CAS  PubMed  Google Scholar 

  8. Lopez-Millan AF, Grusak MA, Abadia A, Abadia J (2013) Iron deficiency in plants: an insight from proteomic approaches. Front Plant Sci 4. https://doi.org/10.3389/fpls.2013.00254

  9. Rajaie M, Tavakoly AR (2018) Iron and/or acid foliar spray versus soil application of Fe-EDDHA for prevention of iron deficiency in Valencia orange grown on a calcareous soil. J Plant Nutr 41:150–158. https://doi.org/10.1080/01904167.2017.1382523

    Article  CAS  Google Scholar 

  10. Bavaresco L, Goncalves M, Civardi S, Gatti M, Ferrari F (2010) Effects of traditional and new methods on overcoming lime-induced chlorosis of grapevine. Am J Enol Vitic 61:186–190

    CAS  Google Scholar 

  11. Gamble AV, Howe JA, Delaney D, van Santen E, Yates R (2014) Iron chelates alleviate iron chlorosis in soybean on high pH soils. Agron J 106:1251–1257. https://doi.org/10.2134/agronj13.0474

    Article  CAS  Google Scholar 

  12. Smith BR, Cheng LL (2006) Fe-EDDHA alleviates chlorosis in ‘Concord’ grapevines grown at high pH. Hortscience 41:1498–1501

    Article  CAS  Google Scholar 

  13. Oburger E, Gruber B, Schindlegger Y, Schenkeveld WDC, Hann S, Kraemer SM, Wenzel WW, Puschenreiter M (2014) Root exudation of phytosiderophores from soil-grown wheat. New Phytol 203:1161–1174. https://doi.org/10.1111/nph.12868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Puschenreiter M, Gruber B, Wenzel WW, Schindlegger Y, Hann S, Spangl B, Schenkeveld WDC, Kraemer SM, Oburger E (2017) Phytosiderophore-induced mobilization and uptake of Cd, Cu, Fe, Ni, Pb and Zn by wheat plants grown on metal-enriched soils. Environ Exp Bot 138:67–76. https://doi.org/10.1016/j.envexpbot.2017.03.011

    Article  CAS  Google Scholar 

  15. Saha M, Sarkar S, Sarkar B, Sharma BK, Bhattacharjee S, Tribedi P (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut Res 23:3984–3999. https://doi.org/10.1007/s11356-015-4294-0

    Article  CAS  Google Scholar 

  16. Jin CW, Li GX, Yu XH, Zheng SJ (2010) Plant Fe status affects the composition of siderophore-secreting microbes in the rhizosphere. Ann Bot 105:835–841. https://doi.org/10.1093/aob/mcq071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Masalha J, Kosegarten H, Elmaci O, Mengel K (2000) The central role of microbial activity for iron acquisition in maize and sunflower. Biol Fertil Soils 30:433–439

    Article  CAS  Google Scholar 

  18. Desai A, Archana G (2011) Role of siderophores in crop improvement

  19. Ahmed E, Holmstrom SJM (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208. https://doi.org/10.1111/1751-7915.12117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ahmed E, Holmstrom SJM (2015) Siderophore production by microorganisms isolated from a podzol soil profile. Geomicrobiol J 32:397–411. https://doi.org/10.1080/01490451.2014.925011

    Article  CAS  Google Scholar 

  21. Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF (2018) Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558:440–444. https://doi.org/10.1038/s41586-018-0207-y

    Article  CAS  PubMed  Google Scholar 

  22. Barber MF, Eldel NC (2015) Buried treasure: evolutionary perspectives on microbial iron piracy. Trends Genet 31:627–636. https://doi.org/10.1016/j.tig.2015.09.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Popat R, Harrison F, da Silva AC, Easton SAS, McNally L, Williams P, Diggle SP (2017) Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production. Proc R Soc B Biol Sci 284:20170200. https://doi.org/10.1098/rspb.2017.0200

    Article  CAS  Google Scholar 

  24. Castro RO, Bucio JL (2013) Small molecules involved in transkingdom communication between plants and rhizobacteria. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere. Wiley, Hoboken, pp 295–307

    Chapter  Google Scholar 

  25. Butaite E, Baumgartner M, Wyder S, Kummerli R (2017) Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nat Commun 8:414. https://doi.org/10.1038/s41467-017-00509-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. O’Brien S, Lujan AM, Paterson S, Cant MA, Buckling A (2017) Adaptation to public goods cheats in Pseudomonas aeruginosa. Proc R Soc B Biol Sci 284:20171089. https://doi.org/10.1098/rspb.2017.1089

    Article  CAS  Google Scholar 

  27. Lewis RW, LeTourneau MK, Davenport JR, Sullivan TS (2018) ‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes. Plant Physiol Biochem 129:429–436. https://doi.org/10.1016/j.plaphy.2018.06.011

    Article  CAS  PubMed  Google Scholar 

  28. Davenport JR, Stevens RG, Whitley KM (2008) Spatial and temporal distribution of soil moisture in drip-irrigated vineyards. Hortscience 43:229–235

    Article  Google Scholar 

  29. Singer SD, Davenport JR, Hoheisel G-A, Moyer M (2018) Vineyard nutrient management in Washington State.

  30. Bremner J (1996) Nitrogen-total Methods of Soil Analysis Part 3—Chemical Methods: 1085–1121

  31. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56. https://doi.org/10.1016/0003-2697(87)90612-9

    Article  CAS  PubMed  Google Scholar 

  32. Allen B, Drake M, Harris N, Sullivan T (2017) Using KBase to assemble and annotate prokaryotic genomes. Curr Protoc Microbiol 46:1E.13.1–1E.13.18. https://doi.org/10.1002/cpmc.1037.

    Article  Google Scholar 

  33. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. https://doi.org/10.1089/cmb.2013.0084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Wu Y-W, Simmons BA, Singer SW (2015) MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605–607

    Article  CAS  PubMed  Google Scholar 

  36. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome research: gr. 186072.186114.

  37. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M (2013) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Price MN, Dehal PS, Arkin AP (2010) FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. https://doi.org/10.1371/journal.pone.0009490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Perez-Miranda S, Cabirol N, George-Tellez R, Zamudio-Rivera L, Fernandez F (2007) O-CAS, a fast and universal method for siderophore detection. J Microbiol Methods 70:127–131

    Article  CAS  PubMed  Google Scholar 

  41. Sullivan TS, Ramkissoon S, Garrison VH, Ramsubhag A, Thies JE (2012) Siderophore production of African dust microorganisms over Trinidad and Tobago. Aerobiologia 28:391–401. https://doi.org/10.1007/s10453-011-9243-x

    Article  Google Scholar 

  42. Aznar A, Dellagi A (2015) New insights into the role of siderophores as triggers of plant immunity: what can we learn from animals? J Exp Bot 66:3001–3010. https://doi.org/10.1093/jxb/erv155

    Article  CAS  PubMed  Google Scholar 

  43. Lamont IL, Martin LW (2003) Identification and characterization of novel pyoverdine synthesis genes in Pseudomonas aeruginosa. Microbiology 149:833–842

    Article  CAS  PubMed  Google Scholar 

  44. Moon CD, Zhang XH, Matthijs S, Schafer M, Budzikiewicz H, Rainey PB (2008) Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. BMC Microbiol 8:7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Meyer JM, Abdallah MA (1978) The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physico-chemical properties. J Gen Microbiol 107:319–328

    Article  CAS  Google Scholar 

  46. Hohnadel D, Meyer JM (1988) Specificity of pyoverdine-mediated iron uptake among fluorescent Pseudomonas strains. J Bacteriol 170:4865–4873

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Mirleau P, Delmorme S, Philippot L, Meyer JM, Mazurier S, Lemanceau P (2000) Fitness in soil and rhizosphere of Pseudomonas fluorescens C7R12 compared with a C7R12 mutant affected in pyoverdine synthesis and uptake. FEMS Microbiol Ecol 34:35–44

    Article  CAS  PubMed  Google Scholar 

  48. Cunrath O, Geoffroy VA, Schalk IJ (2016) Metallome of Pseudomonas aeruginosa: a role for siderophores. Environ Microbiol 18:3258–3267. https://doi.org/10.1111/1462-2920.12971

    Article  CAS  PubMed  Google Scholar 

  49. Baldi F, Gallo M, Battistel D, Barbaro E, Gambaro A, Daniele S (2016) A broad mercury resistant strain of Pseudomonas putida secretes pyoverdine under limited iron conditions and high mercury concentrations. Biometals 29:1097–1106. https://doi.org/10.1007/s10534-016-9980-y

    Article  CAS  PubMed  Google Scholar 

  50. O'Brien S, Hesse E, Lujan A, Hodgson DJ, Gardner A, Buckling A (2018) No effect of intraspecific relatedness on public goods cooperation in a complex community. Evolution 72:1165–1173. https://doi.org/10.1111/evo.13479

    Article  PubMed  PubMed Central  Google Scholar 

  51. Buyer JS, DeLorenzo V, Neilands JB (1991) Production of the siderophore aerobactin by a halophilic pseudomonad. Appl Environ Microbiol 57:2246–2250

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Sandy M, Butler A (2009) Microbial iron acquisition: marine and terrestrial siderophores. Chem Rev 109:4580–4595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Valvano MA, Silver RP, Crosa JH (1986) Occurrence of chromosome- or plasmid-mediated aerobactin iron transport systems and hemolysin production among clonal groups of human invasive strains of Escherichia coli K1. Infect Immun 52:192–199

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Fischbach MA, Lin H, Liu DR, Walsh CT (2006) How pathogenic bacteria evade mammalian sabotage in the battle for iron. Nat Chem Biol 2:132–138

    Article  CAS  PubMed  Google Scholar 

  55. Chen LM, Dick WA, Streeter JG (2000) Production of aerobactin by microorganisms from a compost enrichment culture and soybean utilization. J Plant Nutr 23:2047–2060. https://doi.org/10.1080/01904160009382164

    Article  CAS  Google Scholar 

  56. Thode SK, Rojek E, Kozlowski M, Ahmad R, Haugen P (2018) Distribution of siderophore gene systems on a Vibrionaceae phylogeny: database searches, phylogenetic analyses and evolutionary perspectives. PLoS One 13:e0191860. https://doi.org/10.1371/journal.pone.0191860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Dertz EA, Raymond KN (2003) Siderophores and transferrins. In: Que L, Tolman WB (eds) Comprehensive coordination chemistry II. Elsevier, Ltd., Philadelphia

    Google Scholar 

  58. Miethke M, Marahiel MA (2007) Siderophore-based iron acquisition and pathogen control. Microbiol Mol Biol Rev 71:413–451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Dean CR, Neshat S, Poole K (1996) PfeR, an enterobactin-responsive activator of ferric enterobactin receptor gene expression in Pseudomonas aeruginosa. J Bacteriol 178:5361–5369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Michel L, Bachelard A, Reimmann C (2007) Ferripyochelin uptake genes are involved in pyochelin-mediated signaling in Pseudomonas aeruginosa. Microbiology 153:1508–1518

    Article  CAS  PubMed  Google Scholar 

  61. Cline GR, Powell PE, Szaniszlo PJ, Reid CPP (1982) Comparison of the abilities of hydroxamic, synthetic, and other natural organic acids to chelate iron and other ions in nutrient solution. Soil Sci Soc Am J 46:1158–1164

    Article  CAS  Google Scholar 

  62. Llamas MA, Sparrius M, Kloet R, Jimenez CR, Vandenbroucke-Grauls C, Bitter W (2006) The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J Bacteriol 188:1882–1891. https://doi.org/10.1128/jb.188.5.1882-1891.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Lee K, Lee KM, Go J, Ryu JC, Ryu JH, Yoon SS (2016) The ferrichrome receptor A as a new target for Pseudomonas aeruginosa virulence attenuation. FEMS Microbiol Lett 363. https://doi.org/10.1093/femsle/fnw104

  64. Hannauer M, Barda Y, Mislin GLA, Shanzer A, Schalk IJ (2010) The ferrichrome uptake pathway in Pseudomonas aeruginosa involves an Iron release mechanism with acylation of the siderophore and recycling of the modified desferrichrome. J Bacteriol 192:1212–1220. https://doi.org/10.1128/jb.01539-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Rudolf M, Stevanovic M, Kranzler C, Pernil R, Keren N, Schleiff E (2016) Multiplicity and specificity of siderophore uptake in the cyanobacterium Anabaena sp PCC 7120. Plant Mol Biol 92:57–69. https://doi.org/10.1007/s11103-016-0495-2

    Article  CAS  PubMed  Google Scholar 

  66. Grosse C, Scherer J, Koch D, Otto M, Taudte N, Grass G (2006) A new ferrous iron-uptake transporter, EfeU (YcdN), from Escherichia coli. Mol Microbiol 62:120–131. https://doi.org/10.1111/j.1365-2958.2006.05326.x

    Article  CAS  PubMed  Google Scholar 

  67. Cao J, Woodhall MR, Alvarez J, Cartron ML, Andrews SC (2007) EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E-coli O157 : H7. Mol Microbiol 65:857–875. https://doi.org/10.1111/j.1365-2958.2007.05802.x

    Article  CAS  PubMed  Google Scholar 

  68. Rajasekaran MB, Mitchell SA, Gibson TM, Hussain R, Siligardi G, Andrews SC, Watson KA (2010) Isolation and characterisation of EfeM, a periplasmic component of the putative EfeUOBM iron transporter of Pseudomonas syringae pv. Syringae. Biochem Biophys Res Commun 398:366–371. https://doi.org/10.1016/j.bbrc.2010.06.072

    Article  CAS  PubMed  Google Scholar 

  69. Temtrirath K, Okumura K, Maruyama Y, Mikami B, Murata K, Hashimoto W (2017) Binding mode of metal ions to the bacterial iron import protein EfeO. Biochem Biophys Res Commun 493:1095–1101. https://doi.org/10.1016/j.bbrc.2017.09.057

    Article  CAS  PubMed  Google Scholar 

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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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Authors and Affiliations

  1. Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman, WA, USA

    Ricky W. Lewis, Anjuman Islam, Lee Opdahl & Tarah S. Sullivan

  2. Irrigated Agriculture Research and Extension Center, Washington State University, 24106 N. Bunn Road, Prosser, WA, USA

    Joan R. Davenport

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  1. Ricky W. Lewis
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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.

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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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