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Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity

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Abstract

Apple replant disease (ARD) is a soil-disease syndrome of complex etiology that affects apple tree roots in replanted orchards, resulting in stunted tree growth and reduced yields. To investigate whether different groundcover management systems (GMSs) influence subsequent ARD severity, we grew apple seedlings in an outdoor nursery in pots containing orchard soil from field plots where four GMSs had been maintained for 14 years in an orchard near Ithaca, NY, USA. The GMS treatments were: (1) pre-emergence herbicide (Pre-H), bare soil strips maintained by applying tank-mixed glyphosate, norflurazon and diuron herbicides annually; (2) post-emergence herbicide (Post-H), sparse weed cover maintained by applying glyphosate in May and July each year; (3) mowed sod grass (Mowed Sod); and (4) bark mulch (Mulch). Soils were also sampled from the grass drive lane maintained between the trees in the orchard (Grass Lane). Sampled soils (Orchard soil) were either pasteurized or left untreated, placed into 4-L pots, and planted with one apple seedling per pot. After 3 months of growth, soil (Bioassay soil) and apple tree roots (Bioassay roots) were sampled from each pot and microbial populations colonizing samples were characterized. Seedling growth was reduced in soils sampled from all four GMS treatments compared to the Grass Lane soils. Among the GMS treatments, seedling biomass was greater in Pre-H than in the Post-H soil. Soil microbial communities and nutrient availability differed among all four GMS treatments and the Grass Lane. Root-lesion (Pratylenchus sp.) nematode populations were higher in the Mowed Sod than in the other GMS treatments. Soil bacterial and fungal community composition was assessed in Orchard and Bioassay soils and Bioassay roots with a DNA fingerprinting method (T-RFLP). Redundancy analysis indicated that soils sampled from the different GMS treatments differentially influenced seedling biomass. A clone library of 267 soil bacteria was developed from sampled Orchard soils and Bioassay roots. These communities were dominated by Acidobacteria (25% of sequences), Actinobacteria (19%), δ-Proteobacteria (12%), β-Proteobacteria (10%), and these ratios differed among the GMS soils. Members of the family Comamonadaceae were detected only in tree-row soil, not in the Grass Lanes. The dominant sequences among 145 cloned fungi associated with apple seedling roots were Fusarium oxysporum (16% of sequences), an uncultured soil fungus submitted under DQ420986 (12%), and Rhodotorula mucilaginosa (9%). In a redundancy analysis, factors including fungal and oomycete community compositions, soil respiration rates, population sizes of culturable bacteria and fungi, soil organic matter content, and nutrient availability, were not significant predictors of apple seedling biomass in these soils. Different GMS treatments used by apple growers may influence subsequent ARD severity in replanted trees, but edaphic factors commonly associated with soil fertility may not reliably predict tree-root health and successful establishment of replanted orchards.

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Abbreviations

AMMI:

Additive Main effects with Multiplicative Interaction

ARD:

Apple Replant Disease

DGGE:

Denaturing Gradient Gel Electrophoresis

GMS:

Groundcover Management Systems

ITS:

Internal Transcribed Spacer

OTU:

Operational Taxonomic Unit

PCA:

Principal Component Analysis

RDA:

Redundancy Analysis

T-RFLP:

Terminal Restriction Fragment Length Polymorphism

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Acknowledgements

Our research was funded by a United States Department for Agriculture-Integrated Research Extension and Education Program, Alternatives for Methyl Bromide grant. We thank Dr. George Abawi from the New York State Agricultural Experiment Station in Geneva for conducting the nematode counts.

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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

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  1. Angelika St. Laurent
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  2. Ian A. Merwin
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  3. Janice E. Thies
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Correspondence to Ian A. Merwin.

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Responsible Editor: Petra Marschner.

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St. Laurent, A., Merwin, I.A. & Thies, J.E. Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity. Plant Soil 304, 209–225 (2008). https://doi.org/10.1007/s11104-008-9541-4

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