Department of Pathogenic Fungi, Division of Fungal Resources and Development

<p>Average relative abundance of bacterial phyla composition in root apex samples from teeth with post-treatment apical periodontitis.</p

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment

<div><p>The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. <i>Coriolopsis floccosa</i>. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and <i>C. floccosa</i>-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.</p></div

Functional microbial diversity characteristics (mean±standard deviation) obtained from unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CORDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p><i>S_f</i> –Functional richness.</p><p><i>H_f</i>–Functional Shannon index.</p><p><i>J_f</i>–Functional evenness.</p><p>For each variable, data followed by different letter are significantly different according to Tukey's HSD test (P≤0.05).</p

PCoA based on unweighted UniFrac distances of bacterial community found in unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CORDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p>Percent variability explained by each principal coordinate is shown in parentheses after each axis legend.</p

PCoA based on Euclidean distances of community level physiological profile (CLPP) dataset for unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CORDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p>Percent variability explained by each principal coordinate is shown in parentheses after each axis legend.</p

Phylogenetic fungal diversity characteristics obtained from unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CORDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p>Values in parenthesis are 95% confidence intervals as calculated using MOTHUR.</p><p><i>S_p</i> – Phylogenetic richness.</p><p><i>H_p</i>– Phylogenetic Shannon index.</p><p><i>J_p</i>– Phylogenetic evenness.</p><p>Diversity t test was performed for each amended sample with its control (* significant differences, p≤0.05).</p

Relative abundance of the different bacterial phyla (A) and orders of <i>Alphaproteobacteria</i> (B) found in unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p>Relative abundance of the different bacterial phyla (A) and orders of <i>Alphaproteobacteria</i> (B) found in unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CDOR) at 0 (T0), 30 (T1) and 60 (T2) days.</p

PCoA based on unweighted UniFrac distances of fungal community found in unamended soil (C) and soil amended with untransformed DOR (DOR) or <i>C. floccosa</i>–transformed DOR (CORDOR) at 0 (T0), 30 (T1) and 60 (T2) days.

<p>Percent variability explained by each principal coordinate is shown in parentheses after each axis legend.</p

Composition of fungal community in the soil studied based on 28S rRNA gene pyrosequencing at phylum (A) and class (B) level.

<p>Composition of fungal community in the soil studied based on 28S rRNA gene pyrosequencing at phylum (A) and class (B) level.</p

Average relative abundance of the top most abundant bacterial genera (left bars), and proportion of occurrence among the root apex samples from teeth with post-treatment apical periodontitis (right bars).

<p>Average relative abundance of the top most abundant bacterial genera (left bars), and proportion of occurrence among the root apex samples from teeth with post-treatment apical periodontitis (right bars).</p