Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

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.

Facility‐specific ‘house’ microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking

“…The soil acts as a reservoir of these eukaryotic organisms, which can further migrate into the plant via xilema (Zhang et al ., 2012). Fungi members within the Orders Pleosporales and Hypocreales have been reported as endophytes of coffee plant in different producing regions, including Brazil, Colombia, Ethiopia, Hawaii Mexico, and Puerto Rico (Sette et al ., 2006; Vega et al ., 2010; Duong et al ., 2020).…”

“…2). These microbial groups have been reported to co‐exist as epiphytes, endophytes, or parasites on plant tree leaves in the tropics (Zhang et al ., 2012; Duong et al ., 2020).…”

Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario

“…At this step, microorganisms are very prevalent, highly variable and difficult to predict [ 60 , 61 ]. While other authors have discussed the microbial diversity associated to other components of the coffee plant, such as the rhizosphere, the episphere and endosphere [ 62 , 63 , 64 , 65 , 66 , 67 , 68 ], we have focused our review on the postharvest microbiota which, as described above, has been shown to be highly relevant to coffee quality and mycotoxin production.…”

“…For a detailed list of the relative abundances of the microorganisms identified by 7 of the 10 studies mentioned herein, we refer the reader to Duong et al [ 66 ] who has already provided a descriptive survey of the microorganisms identified through these studies (along with previous studies). Instead, we prefer to highlight some of the main hypotheses stemming from these works and discuss the future perspectives for better understanding of the influence of environmental factors on different stages of microbial life cycles.…”

Composting and Methane Emissions of Coffee By-Products

“…This could be attributed to the moisture suppressing the airflow since the material at that week is more compact. The pores in the feedstock are filled with water, favoring the formation of anaerobic conditions and methane emissions [31]. The emissions in the fifth week were the highest among the treatment compared to the control TC.…”