16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L

• Published in: Brazilian journal of biology 2023, Vol.83, p.1-9
• Main Authors: Andrade, P. H. M., Machado, P. C., Paula, A. F., Paganin, A. C. L., Rezende, G. S., Matheucci Jr, E., Carvalho, L. M., Freire, C. C. M., Cunha, A. F., Lacava, P. T.
• Format: Article
• Language: English
• Subjects: 16S rRNA; Acidobacteria; Actinobacteria; Agricultural management; Agricultural practices; Agricultural production; Agrochemicals; Bacteria; Bacteroidetes; BIOLOGY; Climatic conditions; Coffea arabica; Coffee; DNA barcoding; Environmental changes; Environmental impact; Farming; Fertilization; Firmicutes; Laboratories; Microbial activity; Microbiomes; Microbiota; Microorganisms; Next-generation sequencing; Nocardioides; Organic farming; Plant growth; Proteobacteria; Rhizobiales; rhizospheric soil; Soil analysis; Soil erosion; Soil management; Sphingomonadaceae; Taxonomy; Verrucomicrobia
• ISSN: 1519-6984; 1678-4375; 1678-4375
• DOI: 10.1590/1519-6984.274070

Abstract Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop. Resumo Coffea sp. é cultivada em muitos países tropicais. O Brasil sempre adotou práticas agrícolas intensivas, mas a cafeicultura orgânica é um sistema alternativo baseado na não utilização de agrotóxicos e no manejo racional dos solos. A análise Metabarcode 16S utilizando o sequenciamento de última geração foi desenvolvida para identificar e comparar a diversidade da comunidade bacteriana rizosférica de Coffea arabica L. em duas áreas de cultivo em São Paulo, Brasil. Dourado usa agricultura convencional, enquanto Ribeirão Corrente usa agricultura orgânica. Encontramos ampla composição taxonômica, com sequências de 24 filos, 55 classes, 61 ordens, 146 famílias e 337 gêneros. Os três filos mais abundantes foram Proteobacteria (38,27%), Actinobacteria (15,56%) e Acidobacteria (16,10%). Na agricultura orgânica, os 3 primeiros foram a família Sphingomonadaceae, ordem Rhizobiale