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Development of a taxon-discriminating molecular marker to trace and quantify a mycorrhizal inoculum in roots and soils of agroecosystems

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Abstract

Crop inoculation with Glomus cubense isolate (INCAM-4, DAOM-241198) promotes yield in banana, cassava, forages, and others. Yield improvements range from 20 to 80% depending on crops, nutrient supply, and edaphoclimatic conditions. However, it is difficult to connect yield effects with G. cubense abundance in roots due to the lack of an adequate methodology to trace this taxon in the field. It is necessary to establish an accurate evaluation framework of its contribution to root colonization separated from native arbuscular mycorrhizal fungi (AMF). A taxon-discriminating primer set was designed based on the ITS nrDNA marker and two molecular approaches were optimized and validated (endpoint PCR and quantitative real-time PCR) to trace and quantify the G. cubense isolate in root and soil samples under greenhouse and environmental conditions. The detection limit and specificity assays were performed by both approaches. Different 18 AMF taxa were used for endpoint PCR specificity assay, showing that primers specifically amplified the INCAM-4 isolate yielding a 370 bp-PCR product. In the greenhouse, Urochloa brizantha plants inoculated with three isolates (Rhizophagus irregularis, R. clarus, and G. cubense) and environmental root and soil samples were successfully traced and quantified by qPCR. The AMF root colonization reached 41–70% and the spore number 4–128 per g of soil. This study demonstrates for the first time the feasibility to trace and quantify the G. cubense isolate using a taxon-discriminating ITS marker in roots and soils. The validated approaches reveal their potential to be used for the quality control of other mycorrhizal inoculants and their relative quantification in agroecosystems.

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Acknowledgements

YR thanks technical support of Itamar Garcia from Mycorrhiza lab at Embrapa-Agrobiology, Seropédica, RJ, and Boris Beaker from Phytopathology lab at Faculty of Bioscience Engineering, Department of Applied Sciences, Ghent University. Authors also want to thank María Mariana Pérez Jorge, who reviewed the English version of the manuscript.

Funding

This research was sponsored by CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil)-MES/CUBA, Edital nº 046/2013, project 213/13, and by the Vliruos TEAM project with Ghent University, Belgium (Arbuscular mycorrhizal fungi as an efficient tool to improve the agricultural production of small-scale local farmers in Cuba).

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Authors and Affiliations

  1. Arbuscular Mycorrhizal Group, Department Biofertilizers and Plant Nutrition, Instituto Nacional de Ciencias Agrícolas (INCA) Gaveta Postal No 1 San José de Las Lajas, 32700, Mayabeque, Cuba

    Yakelin Rodríguez-Yon & Ramón Antonio Rivera

  2. Department of Botany, Center for Life Science and Health, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, RJ, 22290-255, Brazil

    Camila Maistro-Patreze

  3. Mycorrhiza Laboratory, Embrapa Agrobiologia, BR 464, km 07, Bairro Ecologia, Seropédica, RJ, 23891-000, Brazil

    Orivaldo Jose Saggin-Junior

  4. Plant Pathology Group, Centro Nacional de Sanidad Agropecuaria (CENSA), Mayabeque, Cuba

    Madelaine Quiñones

  5. Department of Applied Sciences, Faculty of Bioscience Engineering, Ghent University, V. Vaerwyckweg 1, 9000, Ghent, Belgium

    Geert Haesaert

  6. Agroécologie, AgroSup Dijon, CNRS, Université Bourgogne, INRAE, Université Bourgogne Franche-Comté, 21000, Dijon, France

    Diederik van Tuinen

Authors
  1. Yakelin Rodríguez-Yon
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  2. Camila Maistro-Patreze
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  3. Orivaldo Jose Saggin-Junior
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  4. Ramón Antonio Rivera
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  5. Madelaine Quiñones
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  6. Geert Haesaert
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  7. Diederik van Tuinen
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Corresponding author

Correspondence to Yakelin Rodríguez-Yon.

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Rodríguez-Yon, Y., Maistro-Patreze, C., Saggin-Junior, O.J. et al. Development of a taxon-discriminating molecular marker to trace and quantify a mycorrhizal inoculum in roots and soils of agroecosystems. Folia Microbiol 66, 371–384 (2021). https://doi.org/10.1007/s12223-020-00844-y

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