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Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition

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Abstract

Groundcover management systems (GMS) are important in managing fruit-tree orchards because of their effects on soil conditions, nutrient availability, tree growth and yields. We employed a polyphasic approach, incorporating measures of soil microbial abundance, activity and community composition, to study the long-term effects of different GMS on biotic and abiotic factors in an orchard soil. Four GMS treatments – Pre-emergence residual herbicides (Pre-H), post-emergence herbicide (Post-H), mowed-sod (Grass), and hardwood bark mulch (Mulch) – were established in 2-m-wide strips within tree rows in an apple orchard in 1992, and have been maintained and monitored annually until the present. We have measured soil water and nutrient availability, tree growth, and yields annually from 1993 to 2003. Soil nematode numbers and trophic groups were evaluated in July and Oct. 2001, and Sept. 2003. Numbers of culturable bacteria and fungi, soil respiratory activity, eubacterial and fungal community composition were determined in May and Sept. 2003. The Pre-H treatment soil had the fewest culturable bacteria, while the Grass treatment had the largest population of culturable fungi. Soil nematode population size and diversity were also affected by GMS treatments; the Pre-H treatment had the lowest ratio of (bacteriovores + fungivores) to plant parasitic nematodes. Soil respiration rates were higher in the Mulch than in other treatments during a 40-day incubation period. Hierarchical cluster dendrograms of denaturing gradient gel electrophoresis (DGGE) fingerprints for eubacterial community 16S rRNA genes indicated that Post-H and Grass treatments clustered together and separately from the Pre-H and Mulch treatments, which were also grouped together. The influence of GMSs on the fungal community, as assessed by PCR-DGGE of the internal transcribed spacer (ITS) region, was not as pronounced as that observed for bacteria. Soil fungal community composition under the Mulch differed from that under other treatments. The effects of GMS on soil microbial community abundance, activity, and composition were associated with observed differences in soil organic matter inputs and turnover, nutrient availability, and apple tree growth and yields under the different GMS treatments.

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Abbreviations

DGGE:

denaturing gradient gel electrophoresis

GMS:

groundcover management system

ITS:

internal transcribed spacer

PCR:

polymerase chain reaction

References

  • K Alef (1998) Soil respiration K Alef P Nanniperi (Eds) Methods in Applied Soil Microbiology and Biochemistry Academic Press New York 224–217

    Google Scholar 

  • R I Amann W Ludwig K H Schleifer (1995) ArticleTitlePhylogenetic identification and in situ detection of individual microbial-cells without cultivation Microbiol. Rev. 59 143–169 Occurrence Handle1:CAS:528:DyaK2MXkvVGmurk%3D Occurrence Handle7535888

    CAS  PubMed  Google Scholar 

  • H Ferris T Bongers R G M Goede Particlede (2001) ArticleTitleA framework for soil food web diagnostics: Extension of the nematode faunal analysis concept Appl. Soil Ecol. 18 13–29

    Google Scholar 

  • T A Forge E Hogue G Neilsen D Neilsen (2003) ArticleTitleEffects of organic mulches on soil microfauna in the root zone of apple: Implications for nutrient fluxes and functional diversity of the soil food web Appl. Soil Ecol. 22 39–54

    Google Scholar 

  • J L Garland A L Mills (1991) ArticleTitleClassification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization Appl. Environ. Microbiol. 57 2351–2359

    Google Scholar 

  • K M Goh D R Pearson M J Daly (2001) ArticleTitleEffects of apple orchard production systems on some important soil physical, chemical and biological quality parameters Biol. Agric. Hortic. 18 269–292

    Google Scholar 

  • T Greweling M Peech (1965) Chemical Soil Tests Cornell Agricultural Experimental Station Ithaca, NY

    Google Scholar 

  • H Heuer R M Kroppenstedt J Lottmann G Berg K Smalla (2002) ArticleTitleEffects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors Appl. Environ. Microbiol. 68 1325–1335 Occurrence Handle1:CAS:528:DC%2BD38XitFSjs7Y%3D Occurrence Handle11872484

    CAS  PubMed  Google Scholar 

  • E J Hogue G H Neilsen (1987) ArticleTitleOrchard floor vegetation management Hortic. Rev. 9 377–430 Occurrence Handle1:CAS:528:DyaL1cXls1Gls7s%3D

    CAS  Google Scholar 

  • D U Hooper D E Bignell V K Brown L Brussaard J M Dangerfield D H Wall D A Wardle D C Coleman K E Giller P Lavelle W H Vander Putten P C De Ruiter J Rusek W L Silver J M Tiedje V Wolters (2000) ArticleTitleInteractions between aboveground and belowground biodiversity in terrestrial ecosystems: Patterns, mechanisms, and feedbacks Bioscience 50 1049–1061

    Google Scholar 

  • B A Jaffee G S Abawi W F Mai (1982) ArticleTitleRole of soil microflora and Pratylenchus penetrans in an apple replant disease Phytopathology 72 247–251

    Google Scholar 

  • P F Kable W F Mai (1968) ArticleTitleInfluence of soil moisture on Pratylenchus penetrans Nematologica 14 101–122

    Google Scholar 

  • P Marschner E Kandeler B Marschner (2003) ArticleTitleStructure and function of the soil microbial community in a long-term fertilizer experiment Soil Biol. Biochem. 35 453–461 Occurrence Handle10.1016/S0038-0717(02)00297-3 Occurrence Handle1:CAS:528:DC%2BD3sXhvFGrt7w%3D

    Article  CAS  Google Scholar 

  • P Marschner G Neumann A Kania L Weiskopf R Lieberei (2002) ArticleTitleSpatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.) Plant Soil 246 167–174 Occurrence Handle1:CAS:528:DC%2BD38XnvFKhtbo%3D

    CAS  Google Scholar 

  • P Marschner C H Yang R Lieberei D E Crowley (2001) ArticleTitleSoil and plant specific effects on bacterial community composition in the rhizosphere Soil Biol. Biochem. 33 1437–1445 Occurrence Handle1:CAS:528:DC%2BD3MXmtFSlsrk%3D

    CAS  Google Scholar 

  • J M Melillo J D Aber J F Muratore (1982) ArticleTitleNitrogen and lignin control of hardwood leaf litter decomposition dynamics Ecology 63 621–626 Occurrence Handle1:CAS:528:DyaL38XkvFWjurk%3D

    CAS  Google Scholar 

  • W Merbach E Mirus G Knof R Remus S Ruppel R Russow A Gransee J Schulze (1999) ArticleTitleRelease of carbon and nitrogen compounds by plant roots and their possible ecological importance J. Plant Nutr. Soil Sci.-Z. Pflanzenernahr. Bodenkd. 162 373–383 Occurrence Handle1:CAS:528:DyaK1MXltlGltr8%3D

    CAS  Google Scholar 

  • I A Merwin (2004) ArticleTitleGroundcover management effects on orchard production, nutrition, soil, and water quality New York Fruit Quarterly 12 25–29

    Google Scholar 

  • Merwin I A 2003 Orchard-floor management systems. In: Apple-Botany, Production and Uses, Ed Ferree D C, Warrington I J. CABI Publishing

  • I A Merwin J A Ray T S Steenhuis J Boll (1996) ArticleTitleGroundcover management systems influence fungicide and nitrate-N concentrations in leachate and runoff from a New York apple orchard J. Am. Soc. Hortic. Sci. 121 249–257

    Google Scholar 

  • I A Merwin W C Stiles (1994) ArticleTitleOrchard groundcover management impacts on apple tree growth and yield, and nutrient availability and uptake J. Am. Soc. Hortic. Sci. 119 209–215

    Google Scholar 

  • I A Merwin W C Stiles H M Vanes (1994) ArticleTitleOrchard groundcover management impacts on soil physical-properties J. Am. Soc. Hortic. Sci. 119 216–222

    Google Scholar 

  • G Muyzer (1999) ArticleTitleDGGE/TGGE a method for identifying genes from natural ecosystems Curr. Opin. Microbiol. 2 317–322 Occurrence Handle1:CAS:528:DyaK1MXkt1Cms7w%3D Occurrence Handle10383868

    CAS  PubMed  Google Scholar 

  • G Muyzer E C Dewaal A G Uitterlinden (1993) ArticleTitleProfiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA Appl. Environ. Microbiol. 59 695–700 Occurrence Handle1:CAS:528:DyaK3sXit1Kktrk%3D Occurrence Handle7683183

    CAS  PubMed  Google Scholar 

  • G Muyzer K Smalla (1998) ArticleTitleApplication of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology Anton. Van Leeuw. Int. J. Gen. Mol. Microbiol. 73 127–141 Occurrence Handle1:CAS:528:DyaK1cXjsVaqtbs%3D

    CAS  Google Scholar 

  • G H Neilsen E J Hogue T Forge D Neilsen (2003) ArticleTitleMulches and biosolids affect vigor, yield and leaf nutrition of fertigated high density apple HortScience 38 41–45 Occurrence Handle1:CAS:528:DC%2BD3sXitleis7Y%3D

    CAS  Google Scholar 

  • E A Paul M F Clark (1996) Soil Microbiology and Biochemistry Academic Press San Diego

    Google Scholar 

  • G Psarras I A Merwin A N Lakso J A Ray (2000) ArticleTitleRoot growth phenology, root longevity, and rhizosphere respiration of field grown ‘Mutsu’ apple trees on ‘Malling 9’ rootstock J. Am. Soc. Hortic. Sci. 125 596–602

    Google Scholar 

  • A Rumberger S Yao I A Merwin E B Nelson J E Thies (2004) ArticleTitleRootstock 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 Occurrence Handle1:CAS:528:DC%2BD2cXpsF2ls7s%3D

    CAS  Google Scholar 

  • P Saetre E Bääth (2000) ArticleTitleSpatial variation and patterns of soil microbial community structure in a mixed spruce-birch stand Soil Biol. Biochem. 32 909–917 Occurrence Handle1:CAS:528:DC%2BD3cXltVCrur4%3D

    CAS  Google Scholar 

  • D L Taylor T D Bruns (1997) ArticleTitleIndependent, specialized invasions of ectomycorrhizal mutualism by two nonphotosynthetic orchids Proc. Nat. Acad. Sci. USA 94 4510–4515 Occurrence Handle1:CAS:528:DyaK2sXjtV2js70%3D Occurrence Handle9114020

    CAS  PubMed  Google Scholar 

  • C M Tu (1996) ArticleTitleEffect of selected herbicides on activities of microorganisms in soils J. Environ. Sci. Health Part B-Pestic. Contam. Agric. Wastes 31 1201–1214

    Google Scholar 

  • F Wintzingerode Particlevon U B Gobel E Stackebrandt (1997) ArticleTitleDetermination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis FEMS Microbiol. Rev. 21 213–229 Occurrence Handle9451814

    PubMed  Google Scholar 

  • B D Walsh A F MacKenzie D J Buszard (1996a) ArticleTitleSoil nitrate levels as influenced by apple orchard floor management systems Can. J. Soil Sci. 76 343–349 Occurrence Handle1:CAS:528:DyaK28XmtVSqu7g%3D

    CAS  Google Scholar 

  • B D Walsh S Salmins D J Buszard A F MacKenzie (1996b) ArticleTitleImpact of soil management systems on organic dwarf apple orchards and soil aggregate stability, bulk density, temperature and water content Can. J. Soil Sci. 76 203–209

    Google Scholar 

  • D A Wardle G W Yeates K I Bonner K S Nicholson R N Watson (2001) ArticleTitleImpacts of ground vegetation management strategies in a kiwifruit orchard on the composition and functioning of the soil biota Soil Biol. Biochem. 33 893–905 Occurrence Handle1:CAS:528:DC%2BD3MXksVOrtbs%3D

    CAS  Google Scholar 

  • M R Werner (1997) ArticleTitleSoil quality characteristics during conversion to organic orchard management Appl. Soil Ecol. 5 151–167

    Google Scholar 

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Authors and Affiliations

  1. Department of Horticulture, Cornell University, 21 Plant Science Building, Ithaca, NY, 14853, USA

    Shengrui Yao & Ian A. Merwin

  2. Department of Plant Pathology, Michigan State University, East Lansing, MI, 48824, USA

    George W. Bird

  3. Department of Plant Pathology, Cornell University, Geneva, NY, 14456, USA

    George S. Abawi

  4. Department of Crop and Soil Sciences, Cornell University, 719 Bradfield Hall, Ithaca, NY, 14853, USA

    Janice E. Thies

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  1. Shengrui Yao
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  2. Ian A. Merwin
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  3. George W. Bird
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  4. George S. Abawi
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  5. Janice E. Thies
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Correspondence to Janice E. Thies.

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Yao, S., Merwin, I.A., Bird, G.W. et al. Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition. Plant Soil 271, 377–389 (2005). https://doi.org/10.1007/s11104-004-3610-0

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