Salinity and bacterial diversity: to what extent does the concentration of salt affect the bacterial community in a saline soil?

Abstract

In this study, the evaluation of soil characteristics was coupled with a pyrosequencing analysis of the V2-V3 16S rRNA gene region in order to investigate the bacterial community structure and diversity in the A horizon of a natural saline soil located in Sicily (Italy). The main aim of the research was to assess the organisation and diversity of microbial taxa using a spatial scale that revealed physical and chemical heterogeneity of the habitat under investigation. The results provided information on the type of distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH. The analysis of bacterial 16S rRNA showed differences in bacterial composition and diversity due to a variable salt concentration in the soil. The bacterial community showed a statistically significant spatial variability. Some bacterial phyla appeared spread in the whole area, whatever the salinity gradient. It emerged therefore that a patchy saline soil can not contain just a single microbial community selected to withstand extreme osmotic phenomena, but many communities that can be variously correlated to one or more environmental parameters. Sequences have been deposited to the SRA database and can be accessed on ID Project PRJNA241061.

Figure 1. Number of sequences assigned by RDP multiclassifier for each site at each taxonomic level.

Figure 2. Rarefaction curves of the sites.

These curves were obtained considering only the taxonomic assignments that reached the genus level in the RDP multiclassifier analysis.

Figure 3. Richness values compared to Chao1 indexes.

As shown in this plot almost all sites have a relevant number of putative “unseen genera” according to the Rarefaction analysis (Fig. 3).

Figure 4. Heatmap of Phyla assignments.

The heatmap reports the normalized values of the taxonomic assignments at phylum level. Each value has been normalized following this criterion: Where X_ij is the occurrence of the phyla ‘j’ in the site ‘i’ and N is the number of site in the dataset (in this case 9). Using this transformation each phyla assignment can be compared in all sites independently from its order of magnitude.

Figure 5. Canonical Correlation Analysis (CCA) based on community data matrix.

The salinity levels and the pH levels of each site have been fitted onto the CCA ordination analysis in order to inspect the relevance of these two factors in relation to the bacterial communities distribution.

Figure 6. Correlations between relative abundances of different taxonomic groups and soil salinity.

Circles represent the soil sites. Spearman rank correlation coefficient (r) with the related P values are shown for each taxonomic group.

Figure 7. Principal component analysis of bacterial communities as affected by soil properties, based on the abundance of bacterial phyla.

Every vector points to the direction of increase for a given variable so that soil sites with similar bacterial communities, are localized in similar positions in the diagram.

Figure 8. Piecharts based on the abundance (%) of bacterial phyla.

Every pie shows the percent of the abundance (%) of the bacteria phyla.