Abstract
Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroRespTM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N2-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.
Highlights
Microbial communities in agricultural soils may contribute to plant growth and may be affected by farming practices (Emmerling et al, 2001; Pérez-Piqueres et al, 2006)
In the mineral fertilization–soil experiment, MF decreased the abundances of Proteobacteria and Bacteroidetes, while it increased the abundance of Actinobacteria, Firmicutes, and Thaumarchaeota (Table 3)
Olive saplings increased the relative abundance of five N-fixing genera of Proteobacteria (Bradyrhizobium, Rhizobium, Microvirga, Azoarcus, and Burkholderia), three genera of Actinobacteria (Arthrobacter, Frankia, and Micromonospora), and six symbiotroph fungal genera (Rhizophagus, Glomus, Gigaspora, Serendipita, Inocybe, and Hydnum), while it reduced four pathotrophic genera (Acremonium, Macrophomina, Fusarium, and Verticillium)
Summary
Microbial communities in agricultural soils may contribute to plant growth and may be affected by farming practices (Emmerling et al, 2001; Pérez-Piqueres et al, 2006). In crops cultivated in soils with a low content of organic matter, such as what is commonly the case with olive tree crops (Romanyà and Rovira, 2011), microbial communities are found to be mainly concentrated around plant roots (Glick, 2018). Organic fertilization can substantially increase soil organic matter in olive grove soils (García-Ruiz and Ochoa, 2012) and, affects soil microbial communities (Landa et al, 2014). Fertilization in organically managed olive tree groves is based on the use of organic amendments, mainly compost. Olive mill waste compost is commonly used in olive tree groves (Muktadirul Bari Chowdhury et al, 2013) due to its environmental and agronomic benefits (Sellami et al, 2007; Aviani et al, 2010; Akratos et al, 2017)
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