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Sci Rep
2016 Dec 12;6:38850. doi: 10.1038/srep38850.
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Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes.
Robinson G
,
Caldwell GS
,
Wade MJ
,
Free A
,
Jones CLW
,
Stead SM
.
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Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.
Figure 1. (a) The mean (±standard error) growth rate and (b) the mean (±standard error) biomass density of Holothuria scabra (n = 4) reared in tanks with either a stratified oxic-anoxic and fully oxic sand sediment.
Figure 2. The relative abundance of the bacterial reads classified at phylum level (including Proteobacteria sub-classes) from the different sediment redox regimes and depths.Each bar represents the mean of treatment replicates (n = 3).
Figure 3. The phylogenetic distribution of microbial lineages associated with the two different sediment redox regimes (oxic-anoxic and oxic).Lineages with linear discriminant analysis (LDA) values of 5.0 or higher as determined by effect size measurements (LEfSe) are displayed. The six rings of the cladogram stand for domain (innermost), phylum, class, order, family and genus. Enlarged circles in dark green and red are differentially abundant taxa identified as taxonomic biomarkers in the two different redox regime treatments (red = oxic-anoxic sediment, green = oxic sediment). Light green circles are biomarkers with LDA scores of less than 5.0. Labels are shown at the phylum level only.
Figure 4. Bacterial phyla with significantly different relative abundances between the oxic-anoxic and oxic redox regimes (Kruskal-Wallis test).Data are presented as log normalised relative abundances.
Figure 5. A principal components analysis biplot of the correlation between the bacterial community composition and the environmental parameters plotted as vectors.
Figure 6. The mean proportion (%) and the difference in the mean proportion of gene counts at level two of the BRITE functional hierarchy between oxic-anoxic and oxic treatments with 95% confidence intervals.Significant differences in gene abundances were determined using two-sided Welch’s t-tests (alpha = 0.05) with a Bonferroni multiple test correction to control for false discovery rate.
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