Phyllosphere bacterial assembly in citrus crop under conventional and ecological management

Abstract

Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.

Keywords: Agricultural management; Agroecology; Foliar copper; New generation sequencing; Phyllosphere; XRF.

Figure 1. Bacterial distribution in the phyllosphere at the phyllum level.

The graphic shows the results for 16S rRNA sequencing using Illumina MiSeq plataform, demonstrating bacterial taxonomy and relative abundance for triplicate samples from conventional and ecological areas, respectively.

Figure 2. Comparison of alpha diversity for bacterial community.

Rarefaction curve representing the alpha diversity of the bacterial community sctructure of the citrus phyllosphere under ecological and conventional management.

Figure 3. Beta diversity for bacterial community using multivariate statistics.

Coordinate analysis (PCoA) demonstrating bacterial community assemblage in conventional agriculture (red) and ecological (blue), based on the weighted Unifrac method. Data is based on 16 rRNA gene sequences. The eigenvalues displayed on the diagram axes refer to the percentage variation of the respective axis.

Figure 4. Microchemical maps obtained by micro-XRF for Cu in the surface of Citrus sp. leaves.

Microchemical maps obtained by micro-XRF for Cu in the surface of Citrus sp. leaves conventional (A and B) and ecological management (C and D) on copper-based products application day (on the left) and 15 days-after (on the right). The Rh K-alpha Compton peak was used for correcting the maps.