Coffee microbiota and its potential use in sustainable crop management. A review

Duong Benoit, Marraccini Pierre, Maeght Jean-Luc, Vaast Philippe, Lebrun Michel, Duponnois Robin. 2020. Coffee microbiota and its potential use in sustainable crop management. A review. Frontiers in Sustainable Food Systems, 4:607935, 31 p.

Journal article ; Article de recherche ; Article de revue à comité de lecture Revue en libre accès total
Published version - Anglais
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Abstract : Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Mots-clés Agrovoc : Coffea, Flore microbienne, Rhizobactérie, Micro-organisme du sol, Champignon du sol, Conduite de la culture, Agriculture durable, Agent de lutte biologique, Protection biologique des plantes

Mots-clés libres : Coffee, Biocontrol agents, Plant growth promoting agents, Core microbiota, Sustainable management

Classification Agris : P34 - Soil biology
P35 - Soil fertility
F08 - Cropping patterns and systems
F62 - Plant physiology - Growth and development
F04 - Fertilizing

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Auteurs et affiliations

  • Duong Benoit, Université de Montpellier (FRA)
  • Marraccini Pierre, CIRAD-BIOS-UMR IPME (VNM) ORCID: 0000-0001-7637-6811
  • Maeght Jean-Luc, IRD (FRA)
  • Vaast Philippe, CIRAD-PERSYST-UMR Eco&Sols (FRA)
  • Lebrun Michel, Université de Montpellier (FRA)
  • Duponnois Robin, IRD (FRA) - auteur correspondant

Source : Cirad-Agritrop (

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