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Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil

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Abstract

Apple replant disease (ARD) is a soil-borne disease complex that affects young apple trees in replanted orchards, resulting in stunted growth and reduced yields. Newly developed rootstock genotypes with tolerance to ARD may help to control this disease. We determined the effects of rootstock genotype rotations during orchard renovation, by investigating root-zone soil microbial consortia and the relative severity of ARD on seven rootstock genotypes (M.9, M.26, G.30, G.41, G.65, G.935, and CG.6210) planted in soil where trees on four of those same rootstocks (M.9, M.26, G.30 and CG.6210) had grown for the previous 15 years. Rootstock genotyping indicated that genetic distances among rootstocks were loosely correlated with their differential responses to ARD. Root-zone fungal and bacterial community composition, assessed by DNA fingerprinting (T-RFLP), differed between M.26 and CG.6210. Soil bacterial communities were influenced most by which rootstock had grown in the soil previously, while fungal communities were influenced more by the current replanted rootstock. In a clone library of bacteria from M.26 and CG.6210 root-zone soil, β-Proteobacteria was the most abundant phylum (25% of sequences). Sequences representing the Burkholderia cepacia complex were obtained only from CG.6210 soil. Rootstock genotypes that were grown in the orchard soil previously affected subsequent ARD severity, but replanting with the same or closely related rootstocks did not necessarily exacerbate this disease problem. Our results suggest that genotype-specific interactions with soil microbial consortia are linked with apple rootstock tolerance or susceptibility to ARD.

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Abbreviations

AMMI:

Additive main effects with multiplicative interaction

ANOVA:

Analysis of variance

ARD:

Apple replant disease

OTU:

Operational taxonomic units

T-RFLP:

Terminal restriction fragment length polymorphism

References

  • Benizri E, Piutti S, Verger S, Pagès L, Vercambre G, Poessel JL, Michelot P (2005) Replant diseases: bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting. Soil Biol Biochem 37:1738–1746

    Article  CAS  Google Scholar 

  • Bevivino A, Dalmastri S, Tabacchioni S, Chiarini L (1998) Efficacy of Burkholderia cepacia: effects of seed treatment on disease suppression and growth promotion of maize. FEMS Microbiol Ecol 27:225–237

    Article  CAS  Google Scholar 

  • Bruns T, White TJ, Taylor JW (1991) Fungal molecular systematics. In: Johnston RF (ed) Annual review of ecology and systematics. Annual Reviews Inc., Palo Alto, pp 525–564

    Google Scholar 

  • Časka V, Vančura V, Hudská G, Přikryl Z (1982) Rhizosphere micro-organisms in relation to apple replant problem. Plant Soil 69:187–197

    Article  Google Scholar 

  • Chan C, Yang X, Fu Y, Feng Z, Sha L, Casper P, Zou X (2006) 16S RNA gene analyses of bacterial community structures in the soils of evergreen broadleaved forests in southwest China. FEMS Microbiol Ecol 58:247–259

    Article  CAS  PubMed  Google Scholar 

  • Culman SW, Gauch HG, Blackwood CB, Thies JE (2008) Analysis of T-RFLP data using AOV and ordination methods: a comparative study. J Microbiol Meth 75:55–63

    Article  CAS  Google Scholar 

  • Cummins JN, Aldwinckle HS (1974) Breeding apple rootstocks. HortScience 9:367–372

    Google Scholar 

  • De Clercq D, van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer J (2006) Rhodanobacter spathiphylli sp nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix. Int J Syst Evol Micr 56:1755–1759

    Article  Google Scholar 

  • Fazio G, Robinson TL, Aldwinckle HS, Mazzola M, Leinfelder M, Parra R (2005) Traits of the next wave of Geneva apple rootstocks. Compact Fruit Tree 38(3):7–11

    Google Scholar 

  • Gauch HG Jr (2007) MATMODEL Version 3.0: Open source software for AMMI and related analyses. Cornell University, Ithaca, NY, 14853. Accessible at: http://www.css.cornell.edu/staff/gauch/matmodel.html

  • Gauch HG Jr, Furnas RE (1991) Statistical analysis of yield trials with MATMODEL. Agron J 83:916–920

    Article  Google Scholar 

  • Hebbar KP, Martel MH, Heulin T (1998) Suppression of pre- and postemergence damping-off in corn by Burkholderia cepacia. Eur J Plant Pathol 104:29–36

    Article  Google Scholar 

  • Hokanson SC, Szewc McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus X domestica Borkh. core subset collection. Theoretical and Applied Genetics 97:671–683

    Article  CAS  Google Scholar 

  • Isutsa DK, Merwin IA (2000) Malus germplasm varies in resistance or tolerance to apple replant disease in a mixture of New York orchard soils. HortScience 35:262–268

    Google Scholar 

  • Leinfelder M, Merwin IA (2006) Rootstock selection, pre-plant soil treatments, and tree planting positions as factors in managing apple replant disease. HortScience 41:394–401

    Google Scholar 

  • Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van De Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed 10:217–241

    Article  CAS  Google Scholar 

  • Mai WF, Abawi GS (1981) Controlling replant diseases of pome and stone fruits in Northeastern United-States by preplant fumigation. Plant Dis 65:859–864

    Article  Google Scholar 

  • Mai WF, Merwin IA, Abawi GS (1994) Diagnosis, etiology, and management of replant problems in New York cherry and apple orchards. Acta Hort 363:33–41

    Google Scholar 

  • Manici LM, Ciavatta C, Kelderer M, Ershmaumer G (2003) Replant problems in South Tyrol: role of fungal pathogens and microbial population in conventional and organic apple orchards. Plant Soil 256:315–324

    Article  CAS  Google Scholar 

  • Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Enivron Microbiol 64:795–799

    CAS  Google Scholar 

  • Matsushita A (1990) F-2702 a new antifungal antibiotic produced by Gluconobacter oxidans F2702 I. Taxonomy and production. Jikeikai Med J 37:325–334

    Google Scholar 

  • Mazzola M (1998) Elucidation of the microbial complex having a causal role in the development of apple replant disease in Washington. Phytopathology 88:930–938

    Article  CAS  PubMed  Google Scholar 

  • Mazzola M (1999) Transformation of soil microbial community structure and Rhizoctonia-suppressive potential in response to apple roots. Phytopathology 89:920–927

    Article  CAS  PubMed  Google Scholar 

  • Mergaert J, Cnockaert MC, Swings J (2002) Fulvimonas soil gen. nov., sp. nov., a gamma-proteobacterium isolates from soil after enrichment on acetylated starch plastic. Int J Syst Evol Micr 52:1285–1289

    Article  CAS  Google Scholar 

  • Moeseneder M-M, Arrieta J-M, Muyzer G, Winter C, Herndl G-J (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518–3525

    CAS  PubMed  Google Scholar 

  • Nalin R, Simonet P, Vogel TM, Normand P (1999) Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bact 49:19–23

    Article  Google Scholar 

  • Norelli JL, Holleran HT, Johnson WC, Robinson TL, Aldwinckle HS (2003) Resistance of Geneva and other apple rootstocks to Erwinia amylovora. Plant Dis 87:26–32

    Article  Google Scholar 

  • Rom RC, Carlson RF (1987) Rootstocks for fruit crops. Wiley, NY, p 494

    Google Scholar 

  • Rumberger A, Yao S, Merwin IA, Nelson EB, Thies JE (2004) Rootstock genotype and orchard replant position rather than soil fumigation or compost amendment determine tree growth and rhizosphere bacterial community composition in an apple replant soil. Plant Soil 264:247–260

    Article  CAS  Google Scholar 

  • Rumberger A, Merwin IA, Thies JE (2007) Microbial community development in the rhizosphere of apple trees at a replant site. Soil Biol Biochem 39:1645–1654

    Article  CAS  Google Scholar 

  • St. Laurent A, Merwin IA, Thies JE (2008) Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity. Plant Soil 304:209–225

    Article  CAS  Google Scholar 

  • Wallace RB, Johnson MJ, Suggs SV, Ken-ichi M, Bhatt R, Keiichi I (1981) A set of synthetic oligodeoxyribonucleotide primers for DNA sequencing in the plasmid vector pBR322. Gene 16:21–26

    Article  CAS  PubMed  Google Scholar 

  • Yao S, Merwin IA, Abawi GS, Thies JE (2006) Soil fumigation and compost amendment alter soil microbial community composition but do not improve tree growth or yield in an apple replant site. Soil Biol Biochem 38:587–599

    Article  CAS  Google Scholar 

  • Yoon JH, Kang SJ, Oh TK (2006) Dokdonella koreensis gen. nov, sp. nov., isolated from soil. Int J Syst Evol Micr 56:145–150

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Crop and Soil Science, Cornell University, Ithaca, NY, 14853, USA

    Angelika St. Laurent & Janice E. Thies

  2. Department of Horticulture, Cornell University, Ithaca, NY, 14853, USA

    Ian A. Merwin & Michael G. Brown

  3. Plant Genetic Resources, USDA-ARS, Geneva, NY, 14456, USA

    Gennaro Fazio

Authors
  1. Angelika St. Laurent
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  2. Ian A. Merwin
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  3. Gennaro Fazio
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  4. Janice E. Thies
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  5. Michael G. Brown
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Correspondence to Ian A. Merwin.

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Responsible Editor: Hans Lambers.

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St. Laurent, A., Merwin, I.A., Fazio, G. et al. Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil. Plant Soil 337, 259–272 (2010). https://doi.org/10.1007/s11104-010-0522-z

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