Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa

<div><p>The role of rhizosphere microbial communities in the degradation of hydrocarbons remains poorly understood and is a field of active study. We used high throughput sequencing to explore the rhizosphere microbial diversity in the alfalfa and barley planted oil contaminated soil samples. The analysis of 16s rRNA sequences showed <i>Proteobacteria</i> to be the most enriched (45.9%) followed by <i>Bacteriodetes</i> (21.4%) and <i>Actinobacteria</i> (10.4%) phyla. The results also indicated differences in the microbial diversity among the oil contaminated planted soil samples. The oil contaminated planted soil samples showed a higher richness in the microbial flora when compared to that of untreated samples, as indicated by the Chao1 indices. However, the trend was different for the diversity measure, where oil contaminated barley planted soil samples showed slightly lower diversity indices. While the clustering of soil samples grouped the oil contaminated samples within and across the plant types, the clean sandy soil samples formed a separate group. The oil contaminated rhizosphere soil showed an enrichment of known oil-degrading genera, such as <i>Alcanivorax</i> and <i>Aequorivita</i>, later being specifically enriched in the contaminated soil samples planted with barley. Overall, we found a few well known oil-degrading bacterial groups to be enriched in the oil contaminated planted soil samples compared to the untreated samples. Further, phyla such as <i>Thermi</i> and <i>Gemmatimonadetes</i> showed an enrichment in the oil contaminated soil samples, indicating their potential role in hydrocarbon degradation. The findings of the current study will be useful in understanding the rhizosphere microflora responsible for oil degradation and thus can help in designing appropriate phytoremediation strategies for oil contaminated lands.</p></div

Number of reads per sample after filtering singleton OTUs.

<p>Number of reads per sample after filtering singleton OTUs.</p

Species richness indicated by Chao1 rarefaction measure.

<p>CS: Clean sandy soil; BC: Control oil contaminated bulk soil without barley plants; BO: Barley planted oil contaminated rhizosphere soil; AC: Control oil contaminated bulk soil without alfalfa plants; AO: Alfalfa planted oil contaminated rhizosphere soil.</p

PCoA plot of samples using unweighted UniFrac analysis.

<p>CS: Clean sandy soil; BC: Control oil contaminated bulk soil without barley plants; BO: Barley planted oil contaminated rhizosphere soil; AC: Control oil contaminated bulk soil without alfalfa plants; AO: Alfalfa planted oil contaminated rhizosphere soil.</p

Summary of read count after various filtering steps.

<p>Summary of read count after various filtering steps.</p

Phylum level distribution of microbial population across samples.

<p>Phyla represented by at least 0.5% of the total assigned sequences (11 of total 36 phyla) are shown here. CS: Clean sandy soil; BC: Control oil contaminated bulk soil without barley plants; BO: Barley planted oil contaminated rhizosphere soil; AC: Control oil contaminated bulk soil without alfalfa plants; AO: Alfalfa planted oil contaminated rhizosphere soil.</p

Species diversity estimated by Shannon index.

<p>CS: Clean sandy soil; BC: Control oil contaminated bulk soil without barley plants; BO: Barley planted oil contaminated rhizosphere soil; AC: Control oil contaminated bulk soil without alfalfa plants; AO: Alfalfa planted oil contaminated rhizosphere soil.</p

UPGMA clustering of samples based on phylogenetic distribution.

<p>CS: Clean sandy soil; BC: Control oil contaminated bulk soil without barley plants; BO: Barley planted oil contaminated rhizosphere soil; AC: Control oil contaminated bulk soil without alfalfa plants; AO: Alfalfa planted oil contaminated rhizosphere soil.</p

Summary of raw and quality filtered reads per sample.

<p>Summary of raw and quality filtered reads per sample.</p

Shannon and Chao1 indexes for each sample.

<p>Shannon and Chao1 indexes for each sample.</p