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Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils

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Abstract

Background and aims

The avocado-producing area of southern Spain includes conventional orchards and organic orchards that use different organic amendments. To gain insight into the effects of these amendments, physicochemical properties and microbial communities of the soil were analysed in a representative set of commercial and experimental orchards.

Methods

The population size of several groups of culturable microorganisms was determined by plating on different selective media. Bacterial community structure was studied by denaturing gradient gel electrophoresis (DGGE)

Results

Commercial composts showed the largest effects, especially the animal compost, enhancing the population sizes of some microbial groups and affecting bacterial community structure in superficial and deep soil layers. Moreover, animal and vegetal compost, manure and blood meal addition are related to high bacterial diversity in the superficial soil layer.

Conclusions

All of the organic amendments used in this study affect soil properties in one or more of the characteristics that were analysed. Culturable microbial population data revealed the most evident effects of some of the organic treatments. However, molecular analysis of soil bacterial communities by DGGE allowed the detection of the influence of all of the analysed amendments on bacterial community composition. This effect was stronger in the superficial layer of the avocado soil.

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Acknowledgements

We want to thank David Sarmiento from SAT “TROPS” for assistance in sampling design and sample collection. We would also like to thank the owners of the orchards in which the study was conducted, the members of our laboratory for their inestimable help with the microbial analysis and Juan A. Torés for his assistance during various parts of the project. We are especially grateful to Jose M. Farré for his helpful ideas and discussion, which were absolutely essential for this project, and for allowing us to include his experimental orchards in the study. This work was supported by Plan Estratégico BIOÁNDALUS, CICE-Junta de Andalucía (BIOÁNDALUS 08/1/l1.1), and by Plan Nacional I+D+I from Ministerio de Ciencia e Innovación (MCI) (AGL08-05453-C02-01), co-financed by FEDER funds (EU). N. Bonilla was supported by a PhD fellowship from the FPU program of MCI.

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Authors and Affiliations

  1. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC). Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071, Málaga, Spain

    Nuria Bonilla, Francisco M. Cazorla & Antonio de Vicente

  2. Departamento de Genética y Microbiología, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Spain

    Maira Martínez-Alonso & Núria Gaju

  3. IHSM-UMA-CSIC, Departamento de Fruticultura, EE “La Mayora”, 29750, Algarrobo costa, Spain

    José M. Hermoso & Jorge J. González-Fernández

  4. Departamento de Protección de cultivos, Instituto de Agricultura Sostenible (IAS-CSIC) Finca Alameda del Obispo, 4084-14080, Córdoba, Spain

    Blanca B. Landa

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  1. Nuria Bonilla
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  2. Francisco M. Cazorla
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Corresponding author

Correspondence to Francisco M. Cazorla.

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Responsible Editor: Harsh P. Bais.

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Table S1

Physicochemical properties of the soils. Mean values of four replicate samples analysis and standard deviations in brackets. (DOC 48 kb)

Fig. S1

Effect of organic treatments on culturable microbial populations of the soil in the three analysed sampling campaigns. Statistical analyses were performed separately for superficial soil (black bars) and deep soil (white bars). Only significant differences between treated and control soil of the same orchard were considered (TP was compared with SAR). Significant differences (P < 0.05) are marked with *. AL, “La Alegría” with almond shells; ALC, “La Alegría” control; MY, “La Mayora” with almond shells; MYC, “La Mayora” control; BRA, “Barranco” with animal compost; BRV, “Barranco” with vegetal compost; BRC, “Barranco” control; TP, “Tío Palomo” commercial orchard with manure and blood meal; SAR, “Sarmiento” conventional commercial orchard (EPS 1204 kb)

Fig. S2

Location of the avocado orchards included in this study. 1, “Sarmiento”; 2, “Tío Palomo”; 3, “La Alegría”; 4, “Barranco”; 5, “La Mayora” (EPS 7971 kb)

Fig. S3

Effect of the amendment with almond shells on bacterial community composition of the superficial soil. Native image of the DGGE gel. AL, “La Alegría” with almond shells; ALC, “La Alegría” control; MY, “La Mayora” with almond shells; MYC, “La Mayora” control (EPS 1923 kb)

Fig. S4

Effect of the amendment with almond shells on bacterial community composition of the deep soil. Native image of the DGGE gel. AL, “La Alegría” with almond shells; ALC, “La Alegría” control; MY, “La Mayora” with almond shells; MYC, “La Mayora” control (EPS 1739 kb)

Fig. S5

Effect of the amendment with animal and vegetal compost on bacterial community composition of the superficial soil. Native image of the DGGE gel. BRA, “Barranco” with animal compost; BRV, “Barranco” with vegetal compost; BRC, “Barranco” control (EPS 1696 kb)

Fig. S6

Effect of the amendment with animal and vegetal compost on bacterial community composition of the deep soil. Native image of the DGGE gel. BRA, “Barranco” with animal compost; BRV, “Barranco” with vegetal compost; BRC, “Barranco” control (EPS 2066 kb)

Fig. S7

Bacterial DGGE profiles from superficial soil of organic and conventional avocado orchards. TP, “Tío Palomo” commercial orchard with manure and blood meal; SAR, “Sarmiento” conventional commercial orchard (EPS 1730 kb)

Fig. S8

Bacterial DGGE profiles from deep soil of organic and conventional avocado orchards. TP, “Tío Palomo” commercial orchard with manure and blood meal; SAR, “Sarmiento” conventional commercial orchard (EPS 1020 kb)

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Bonilla, N., Cazorla, F.M., Martínez-Alonso, M. et al. Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils. Plant Soil 357, 215–226 (2012). https://doi.org/10.1007/s11104-012-1155-1

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