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*Corresponding author: Erika Nava-Reyna, CENID-RASPA-INIFAP. Km. 6.5 Margen derecha Canal Sacramento. C.P. 35140. Gómez Palacio, Durango, México. E-mail: nava.erika@inifap.gob.mx Received: 05 January 2020; Accepted: 11 April 2020 Cabrera-Rodríguez, et al. 264 Emir. J. Food Agric ● Vol 32 ● Issue 4 ● 2020 on humification of organic matter and conservation of microbial structures (Cotler et al., 2016; Ortega et al., 2016). Therefore, it is important to consider this type of organic practice in crops of economic interest, since in these crops conventional practices are usually employed, and they can affect the microbial structure of soil and, consequently, its fertility. One of the most economically and culturally important crops worldwide is coffee, with a harvesting area of 10.6 million ha and a production of 10.3 million tons. In Mexico, coffee (Coffea arabica L.) is also an important crop, harvested in more than 630,000 ha, a production of 158,323 tons while 250 million USD economic value. Nonetheless, from the total planted coffee area in Mexico, only 3.24% is classified as organic production; Chiapas, Veracruz and Puebla are the main producer’s states of both conventional and organic coffee, the latter standing out because of its high demand by North American and European markets. Coffee cultivation constitutes 0.66% of the national agricultural gross domestic product, with an annual per capita consumption of 0.6 kg (Flores, 2015; SAGARPA, 2017 and 2018). Because of such economic importance, diverse agricultural management practices have been proposed to maximize coffee production through the implementation of organicbased production systems to promote the recovery of the soil’s optimal status (SAGARPA, 2017). For these reasons, is important to identify and analyze the presence of microorganism communities in soils under organic production systems where organic practices are being implemented to conserve and enhance biotic resources available in coffee plantations (Hernández et al., 2018). Besides, it is fundamental to know the main processes that affect the soil fertility, such as the presence and dynamics of soil microorganisms (Barea et al., 2005; Carbonetto et al., 2014). Certainly, a better understanding of the dominant bacterial taxa in the soil will improve our understanding regarding the main MOS functional capabilities (Delgado et al., 2018). Nowadays, metagenomics is a tool for the study of bacterial communities used to determine, explore, and analyze microbial communities from diverse environments, through the sequencing of their genetic material (Cadena et al., 2016; Ospino et al., 2018). Previous studies have been carried out on coffee plantations to determine how the chemical and biological properties of soil are modified in response to organic or conventional management systems. Some of the most evaluated properties include pH, electrical conductivity, nitrogen, phosphorus, microbial biomass carbon, enzymatic activity, microbial respiration, and bacterial colony forming units (Chemura, 2014; Lammel et al., 2015; Velmourougane, 2016). Similarly, some studies have focused on the isolation and identification of bacteria in plant and rhizosphere organs, using various methodologies. These studies have confirmed the presence of endophytic bacteria in seeds, leaves, stems and roots, some of which have been isolated to evaluate the inhibition of diseasepromoting bacteria (Vega et al., 2005; Shiomi et al., 2006). Other studies have been addressed on identifying the bacteria in coffee cherries through the polymerase chain reaction of the 16S rRNA gene (Silva et al., 2000; Vilela et al., 2010; Oliveira et al., 2013). In addition, the role of various rhizobacteria as nitrogen fixers (Jimenez-Salgado et al., 1997), their potential to synthesize acetic acid and to degrade ethanol precursors (Muleta et al., 2009), as well as their importance as phosphate solubilizers (Muleta et al., 2013) have also been studied. Nonetheless, little is currently known about the response of soil bacterial communities to the type of management in coffee plantations, using the metagenomics approach in order to get a more accurate picture of the soil-microbiome structure and composition. Based on previous findings, we hypothesized that organic management, through the application of bio-fertilizers, could enhance the presence of bacteria involved in carbon sequestration (i.e. acidobacteria), and then, plant growth. Therefore, we determined the soil microbiome in coffee plantations managed under organic or conventional production systems, through massive 16S rRNA sequencing. Secondary objectives included: 1) to determine the bacterial structure and composition in soils, and 2) to establish the main changes in bacterial structure in soils under organic and conventional management. MATERIALS AND METHODS Location and environmental conditions of the study

emirates journal of food and agriculture

A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems