Effects of agriculture management on fungal phyllosphere diversity in vineyards and its relationship with native forests
- Published
- Accepted
- Subject Areas
- Agricultural Science, Biodiversity, Conservation Biology
- Keywords
- amplicon sequencing, Chile, ecosystem services, organic management, yeast, Mediterranean biome
- Copyright
- © 2018 Castañeda et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Effects of agriculture management on fungal phyllosphere diversity in vineyards and its relationship with native forests. PeerJ Preprints 6:e26928v1 https://doi.org/10.7287/peerj.preprints.26928v1
Abstract
Agriculture is one of the main drivers of land conversion and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carmenere grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on phyllosphere in vineyards. After conducting deep amplicon sequencing, no significant differences in fungal diversity indices and community structure were detected between organic and conventional vineyards, suggesting that the phyllosphere microorganisms of grapevines are highly resilient to agricultural treatments. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different between habitats. Nevertheless, the native forest had more unidentified genera and OTUs unique to this habitat than did the vineyards. Cladosporium, Aureobasidium, and Endoconidioma were more abundant in vineyards, whereas Davidiella, Didymella, and Erysiphie were more abundant in forests. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Rarefaction plots for ITS2 and D2 fungal amplicons
Rarefaction plots indicating the number of OTUs for (A) ITS2 and (B) D2. Panel C shows the relationship between phylogenetic diversity and the number of D2 reads. Samples were collected from forest leaves (dark green), grape leaves (green), and grape berries (purple).
Comparison of relative abundances of operational taxonomic units (OTUs) between conventional and organic vineyards
Fold-changes were estimated. This table indicates the OTU identity, the normalized mean between groups, the log2 fold change and its standard error, the Wald statistics and their P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the taxonomic assignment from phylum to genus. Blue rows indicate OTUs that were significantly more abundant in conventional vineyards whereas red rows indicate OTUs that were significantly more abundant in organic vineyards.
Comparison of relative abundances of genera between conventional and organic vineyards using an ANOVA
This table indicates the taxonomic assignment for each OTU, the F statistic and its P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the mean relative abundance of each genus in the vineyards and forest. Red rows indicate genera that were significantly more abundant in organic vineyards. No genus was significantly more abundant in conventional vineyards.
Comparison of relative abundances of operational taxonomic units (OTUs) between grape berries and grape leaves
Fold-changes were determined. This table indicates the OTU identity, the normalized mean between groups, the log2 fold change and its standard error, the Wald statistics and their P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the taxonomic assignment from phylum to genus. Green rows indicate OTUs that were significantly more abundant in grape leaves whereas purple rows indicate OTUs that were significantly more abundant in grape berries.
Comparison of relative abundances of genera between grape berries and grape leaves using an ANOVA
This table indicates the taxonomic assignment of each OTU, the F statistic and its P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the mean relative abundance of each genus in vineyards and forest. Green rows indicate genera that were significantly more abundant in grape leaves whereas purple rows indicate genera that were significantly more abundant in grape berries.
Comparison of relative abundances of operational taxonomic units (OTUs) between grape and native forest leaves
Fold-changes were determined. This table indicates the OTU identity, the normalized mean between groups, the log2 fold change and its standard error, the Wald statistics and their P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the taxonomic assignment from phylum to genus. Green rows indicate OTUs that were significantly more abundant in the native forests, whereas dark green rows indicate OTUs that were significantly more abundant in vineyards.
Comparison of relative abundances of genera between grape and native forest leaves using an ANOVA
This table indicates the taxonomic assignment of each OTU, the F statistic and its P-values, the P-value corrected for multiple comparisons (False Discovery Rare; FDR), and the mean relative abundance of each genus in the vineyards and forest. Green rows indicate genera that were significantly more abundant in native forests whereas dark green rows indicate genera that were significantly more abundant in the vineyards.