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

Abstract

The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil microbiome samples were collected in tropical eastern Mexico (Veracruz, 19°28' N & 96° 52' W), with annual average temperature and rainfall of 24.8° C, and 882.6 mm, respectively. Upon DNA soil-microbiome extraction, the V3-V4 16S rRNA region was amplified, and sequenced (Illumina). Results were analyzed with QIIME based on the EzBioCloud reference. Diverse phyla (n=16), classes (n=40), orders (n=90), families (n=135) and genera (n=333) were identified. The diversity index values were similar in both treatments, with Shannon's being 9.7 and Simpson's 0.99. While the phylum Proteobacteria was more abundant in CAM-soils and classified as copiotrophic, the phylum Acidobacteria was more abundant in OAM-soils and classified as oligotrophic. This classification may be related to the application of microorganisms and their effect on the soils state of organic matter and carbon fractions. Our research outcomes indicate that the application of bio-fertilizers promoted an increased presence of Acidobacteria, a phylum positively correlated with organic matter while significantly involved in carbon sequestration. Undisputable, metagenomics emerges as an interesting up-to-date genomic technology for unveiling the hidden content of the soil microbiome black box.