Effects of agricultural management on the olive tree root microbiome

The aim of this study was to figure out the influence of manure amendment on the radicular (rhizosphere and root endosphere) microbial communities from olive trees. For this purpose, two adjacent olive orchards with different soil managements were surveyed: i) traditional management (TM) and ii) with manure amendment (MA). TM orchard was subjected to common agriculture procedures (including herbicides, mechanical plough and pesticides treatments), while MA cultivar did not receive any herbicides treatment, but a manure amendment was applied to the soil. For each orchard, 12 replicates (trees) were considered for analysis, all of them belonging to Picual variety. From each replicate and microhabitat, both bacterial and fungal communities were studied with the use of amplicon sequencing (pairedend 2x300-bp [PE 300] with the Illumina MiSeq platform). Raw reads were processed following our own tutorial, recently published in GitHub (https://nuriamw.github.io/micro4all/) and also available as an R package (micro4all). This tutorial includes analysis for ASV inferring with DADA2, ¿ and ß-diversity (index calculation, graphical representation and statistical analysis), differential abundance analysis with ANCOM-BC and taxonomical profiling (plots and tables). Moreover, microbial ecological networks were also studied with MENAP online tool. Our results showed that a higher fungal diversity was found in MA rhizosphere. However, no statistically significant differences were found for bacterial community at rhizosphere level, neither for fungal or bacterial endosphere community. Interestingly, community structure (ß-diversity) seemed to differ for both microhabitats (rhizosphere and root endosphere) and kingdoms (bacteria and fungi). Furthermore, network analysis showed that in both compartments TM microbial communities had closer interactions (i.e., a shorter geodesic distance) as well as a greater percentage of positive links. Regarding taxonomical profiles, it should be hig