Skip to main content
SpringerLink
Log in

Site and Clone Effects on the Potato Root-Associated Core Microbiome and its Relationship to Tuber Yield and Nutrients

  • Published:
American Journal of Potato Research Aims and scope Submit manuscript

Abstract

The aim of this study was to describe the variability in the root-associated bacterial community due to location and clone, and to determine whether an underlying core bacterial community exists that might benefit the quality of the potato crop. Root-associated bacterial communities from one growing season were examined with 454 sequencing. Variance analysis using perMANOVA attributed 45.4 % and 24.1 % of the community variability to site and clone effects, respectively. A total of 123 bacterial operational taxonomic units were correlated with tuber yield and/or tuber nutrient content, a majority belong to the order Rhizobiales. Rhizobiales bacteria are recognized contributors to crop nitrogen needs for many legumes; however, no known symbiotic relationship between potato roots and nitrogen fixing bacteria exists. Within the Rhizobiales order, the genus Devosia is a major contributor to both the presence/absence core “bacteriome” and the sparse partial least squares core “bacteriome,” thus further exploration into this unknown relationship is warranted.

Resumen

El propósito de este estudio fue describir la variabilidad en la comunidad bacteriana asociada con la raíz debida a ubicación y clon, y determinar si existe una capa interna de comunidad bacteriana que pudiera beneficiar la calidad del cultivo de papa. Se examinaron las comunidades bacterianas asociadas a la raíz de un ciclo de cultivo con 454 secuenciaciones. El análisis de varianza usando perMANOVA atribuyó 45.4 % y 24.1 % de la variabilidad de la comunidad a los efectos de sitio y clon, respectivamente. Se correlacionó a un total de 123 unidades taxonómicas bacterianas operativas con el rendimiento de tubérculo y/o su contenido de nutrientes, la mayoría de las unidades pertenecen al orden Rhizobiales. Se reconoce a estas bacterias su contribución a los requerimientos de nitrógeno del cultivo para muchas leguminosas; no obstante, no se sabe que exista una relación simbiótica entre las raíces de la papa y bacterias fijadoras de nitrógeno. Dentro del orden Rhizobiales, el género Devosia en un contribuyente mayor tanto para la presencia como para la ausencia de la capa de “bacterioma” y los cuadros de capas parcialmente mas dispersos de “bacterioma”, de manera que esta garantizada la exploración adicional al interior de esta relación desconocida.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Adesemoye, A.O., H.A. Torbert, and J.W. Kloepper. 2009. Plant growth-promoting thizobacteria allow reduced application rates of chemical fertilizers. Microbial Ecology 58: 921–929.

    Article  CAS  PubMed  Google Scholar 

  • Badri, D.V., N. Quintana, E.G. El Kassis, H.K. Kim, Y.H. Choi, A. Sugiyama, R. Verpoorte, E. Martinoia, D.K. Manter, and J.M. Vivanco. 2009. An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiology 151: 2006–2017.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bakker, M.G., J.M. Bradeen, and L.L. Kinkel. 2013. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbiology Ecology 83: 596–606.

    Article  CAS  PubMed  Google Scholar 

  • Belimov, A.A., V.I. Safronova, T.A. Sergeyeva, T.N. Egorova, V.A. Matveyeva, V.E. Tsyganov, A.Y. Borisov, et al. 2001. Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. Canadian Journal of Microbiology 47: 642–652.

    Article  CAS  PubMed  Google Scholar 

  • Boone, D.R., R.W. Castenholz, G.M. Garrity, D.J. Brenner, N.R. Krieg, and J.T. Staley. 2005. Bergey’s Manual of Systematic Bacteriology. New York: Springer.

    Google Scholar 

  • Bossio, D.A., K.M. Scow, N. Gunapala, and K.J. Graham. 1998. Determinants of soil microbial communities: Effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microbial Ecology 36: 1–12.

    Article  CAS  PubMed  Google Scholar 

  • Broz, A.K., D.K. Manter, and J.M. Vivanco. 2007. Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa. The ISME Journal 1: 763–765.

    Article  CAS  PubMed  Google Scholar 

  • Cao, L., Z. Qiu, J. You, H. Tan, and S. Zhou. 2005. Isolation and characterization of endophytic streptomycete antagonists of fusarium wilt pathogen from surface-sterilized banana roots. FEMS Microbiology Letters 247: 147–152.

    Article  CAS  PubMed  Google Scholar 

  • Chiarini, L., A. Bevivino, C. Dalmastri, C. Nacamulli, and S. Tabacchioni. 1998. Influence of plant development, cultivar and soil type on microbial colonization of maize roots. Applied Soil Ecology 8: 11–18.

    Article  Google Scholar 

  • Chun, H., and S. Keles. 2010. Sparse partial least squares regression for simultaneous dimension reduction and variable selection. Journal of the Royal Statistical Society. Series B. Statistical Methodology 72: 3–25.

    PubMed Central  PubMed  Google Scholar 

  • Conn, K.L., G. Lazarovits, and J. Nowak. 1997. A gnotobiotic bioassay for studying interactions between potatoes and plant growth-promoting rhizobacteria. Canadian Journal of Microbiology 43: 801–808.

    Article  CAS  Google Scholar 

  • Fierer, N., J.L. Morse, S.T. Berthrong, E.S. Bernhardt, and R.B. Jackson. 2007. Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88: 2162–2173.

    Article  PubMed  Google Scholar 

  • Fred, E.B., I.L. Baldwin, and E. McCoy. 1932. Root Nodule Bacteria and Leguminous Plants. UW-Madison Libraries Parallel: Press.

    Google Scholar 

  • Gera Hol, W.H., W. de Boer, A.J. Termorshuizen, K.M. Meyer, J.H.M. Schneider, N.M. van Dam, J.A. van Veen, and W.H. van der Putten. 2010. Reduction of rare soil microbes modifies plant-herbivore interactions. Ecology Letters 13: 292–301.

    Article  Google Scholar 

  • Hamady, M., J.J. Walker, J.K. Harris, N.J. Gold, and R. Knight. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 5: 235–237.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • İnceoğlu, Ö., J.F. Salles, L. van Overbeek, and J.D. van Elsas. 2010. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Applied and Environmental Microbiology 76: 3675–3684.

    Article  PubMed Central  PubMed  Google Scholar 

  • İnceoğlu, Ö., W. Abu Al-Soud, J.F. Salles, A.V. Semenov, and J.D. van Elsas. 2011. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS ONE 6: e23321.

    Article  PubMed Central  PubMed  Google Scholar 

  • Jost, L. 2006. Entropy and diversity. Oikos 113: 363–375.

    Article  Google Scholar 

  • Kaneko, T., Y. Nakamura, S. Sato, K. Minamisawa, T. Uchiumi, S. Sasamoto, A. Watanabe, et al. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Research 9: 189–197.

    Article  PubMed  Google Scholar 

  • Kloepper, J.W., J. Leong, M. Teintze, and M.N. Schroth. 1980. Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 286: 885–886.

    Article  CAS  Google Scholar 

  • Knief, C., N. Delmotte, S. Chaffron, M. Stark, G. Innerebner, R. Wassmann, C. von Mering, and J.A. Vorholt. 2011. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. The ISME Journal 6: 1378–1390.

    Article  PubMed Central  PubMed  Google Scholar 

  • Kosslak, R.M., R. Bookland, J. Barkei, H.E. Paaren, and E.R. Appelbaum. 1987. Induction of Bradyrhizobium japonicum common nod genes by isoflavones isolated from Glycine max. Proceedings of the National Academy of Sciences 84: 7428–7432.

    Article  CAS  Google Scholar 

  • Lane, D.J., B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin, and N.R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proceedings of the National Academy of Sciences 82: 6955–6959.

    Article  CAS  Google Scholar 

  • Lundberg, D.S., S.L. Lebeis, S. Herrera Paredes, S. Yourstone, J. Gehring, S. Malfatti, J. Tremblay, et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86–90.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Manter, D.K., J.A. Delgado, D.G. Holm, and R.A. Stong. 2010. Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microbial Ecology 60: 157–166.

    Article  PubMed  Google Scholar 

  • Marchesi, J.R., T. Sato, A.J. Weightman, T.A. Martin, J.C. Fry, S.J. Hiom, and W.G. Wade. 1998. Design and evaluation of useful bacterium-specific pcr primers that amplify genes coding for bacterial 16S rRNA. Applied and Environmental Microbiology 64: 795–799.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Novy, R., and J. Stark. 2012. Western Regional & Tri-State Potato Variety Trial Reports. http://www.ars.usda.gov/Main/docs.htm?docid=21888. Accessed 30 May 2013.

  • Odum, E.P. 1950. Bird Populations of the Highlands (North Carolina) Plateau in Relation to Plant Succession and Avian Invasion. Ecology 31: 587.

    Article  Google Scholar 

  • Oksanen, J., F.G. Blanchet, R. Kindt, P. Legendre, P.R. Minchin, R.B. O’Hara, G.L. Simpson, P. Solymos, M.H.H. Stevens, and H. Wagner. 2013. vegan: Community Ecology Package R package version 2.0-7. http://CRAN.R-prject.org/package=vegan.

  • Pagan, J.D., J.J. Child, W.R. Scowcroft, and A.H. Gibson. 1975. Nitrogen fixation by Rhizobium cultured on a defined medium. Nature 256: 406–407.

    Article  CAS  Google Scholar 

  • Peiffer, J.A., A. Spor, O. Koren, Z. Jin, S.G. Tringe, J.L. Dangl, E.S. Buckler, and R.E. Ley. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences 110: 6548–6553.

    Article  CAS  Google Scholar 

  • Quince, C., A. Lanzén, T.P. Curtis, R.J. Davenport, N. Hall, I.M. Head, L.F. Read, and W.T. Sloan. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6: 639–641.

    Article  CAS  PubMed  Google Scholar 

  • Reitz, M., K. Rudolph, I. Schröder, S. Hoffmann-Hergarten, J. Hallmann, and R.A. Sikora. 2000. Lipopolysaccharides of Rhizobium etli strain G12 act in potato roots as an inducing agent of systemic resistance to infection by the cyst nematode Globodera pallida. Applied and Environmental Microbiology 66: 3515–3518.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rivas, R., E. Velázquez, A. Willems, N. Vizcaíno, N.S. Subba-Rao, P.F. Mateos, M. Gillis, F.B. Dazzo, and E. Martínez-Molina. 2002. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce. Applied and Environmental Microbiology 68: 5217–5222.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ryu, S.H., B.S. Chung, N.T. Le, H.H. Jang, P.-Y. Yun, W. Park, and C.O. Jeon. 2008. Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea. International Journal of Systematic and Evolutionary Microbiology 58: 633–636.

    Article  CAS  PubMed  Google Scholar 

  • Schloss, P.D., S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537–7541.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shade, A., and J. Handelsman. 2012. Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology 14: 4–12.

    Article  CAS  PubMed  Google Scholar 

  • Stackebrandt, E. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiology Toda 33: 152.

    Google Scholar 

  • Sturz, A.V., and B.R. Christie. 1998. The potential benefits from cultivar specific red clover -potato crop rotations. Annals of Applied Biology 133: 365–373.

    Article  Google Scholar 

  • Turnbaugh, P.J., R.E. Ley, M. Hamady, C.M. Fraser-Liggett, R. Knight, and J.I. Gordon. 2007. The Human Microbiome Project. Nature 449: 804–810.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Vanparys, B.K., L. Lebbe Heylen, and P. De Vos. 2005. Devosia limi sp. nov., isolated from a nitrifying inoculum. International Journal of Systematic and Evolutionary Microbiology 55: 1997–2000.

    Article  CAS  PubMed  Google Scholar 

  • Weinert, N., Y. Piceno, G.-C. Ding, R. Meincke, H. Heuer, G. Berg, M. Schloter, G. Andersen, and K. Smalla. 2011. PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiology Ecology 75: 497–506.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. United States Department of Agriculture, Agricultural Research Service, Soil-Plant-Nutrient Research, Fort Collins, Fort Collins, CO, 80526, USA

    Brittany A. Barnett & Daniel K. Manter

  2. San Luis Valley Research Center, Colorado State University, Center, CO, 81125, USA

    David G. Holm

  3. Texas A&M University Agricultural Research and Extension Center, Lubbock, TX, 79401, USA

    Jeffery W. Koym

  4. ANR Intermountain Research & Extension Center, University of California, Tulelake, CA, 96134, USA

    Robert G. Wilson

Authors
  1. Brittany A. Barnett
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David G. Holm
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jeffery W. Koym
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Robert G. Wilson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Daniel K. Manter
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel K. Manter.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(XLSX 369 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Barnett, B.A., Holm, D.G., Koym, J.W. et al. Site and Clone Effects on the Potato Root-Associated Core Microbiome and its Relationship to Tuber Yield and Nutrients. Am. J. Potato Res. 92, 1–9 (2015). https://doi.org/10.1007/s12230-014-9405-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12230-014-9405-9

Keywords

Search

Navigation