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. 2016 Mar 14:6:23012.
doi: 10.1038/srep23012.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

Jaejoon Jung  1 , Laurent Philippot  2 , Woojun Park  1
Affiliations

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

Jaejoon Jung et al. Sci Rep. .

Abstract

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

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Figures

Figure 1
Figure 1. Schematic description of experimental design and quantitation of microbial communities in microcosms based on 16S rRNA gene copy number.
(a) Soil was serially diluted and inoculated to sterilized soil slurry microcosms subjected to metagenomic analysis and experiments. (b) Copy number of the 16S rRNA gene in the 10−2-inoculated samples and (c) 10−5-inoculated samples. C, control; D, diesel-spiked soil; DR, diesel-spiked soil and red clay; DP, diesel-spiked soil and processed red clay.
Figure 2
Figure 2. Analysis of microbial communities using rRNA gene sequences and MG-RAST.
Taxa with abundance <5% are presented as “Others.” (a) Phyla (b) Genera C, control; D, diesel-spiked soil; DR, diesel-spiked soil and red clay; DP, diesel-spiked soil and processed red clay.
Figure 3
Figure 3. Genes related to alkane oxidation in microcosms of differing biodiversity.
Gene abundance and taxonomic affiliation at the phylum level were determined using the KEGG Orthology and M5NR databases, respectively, from MG-RAST. Taxa with abundance <5% are presented as “Others.” C, control; D, diesel-spiked soil; DR, diesel-spiked soil and red clay; DP, diesel-spiked soil and processed red clay. (a) phylum (b) genus.
Figure 4
Figure 4. Diesel biodegradation in microcosms after 6 weeks.
Residual percentages were calculated based on the major diesel components (alkane chain length C9–C20). D, diesel-spiked soil; DR, diesel-spiked soil and red clay; DP, diesel-spiked soil and processed red clay.
Figure 5
Figure 5. Abundance of genes related to denitrification in microcosms of differing biodiversity and microbial community structure.
Taxa with abundance <5% are presented as “Others.” (a) phylum (b) genus C, control; D, diesel-spiked soil; DR, diesel-spiked soil and red clay; DP, diesel-spiked soil and processed red clay.
Figure 6
Figure 6. Nitrate reduction by microbial communities in microcosms of differing biodiversity and varying structure.
(a) C2 and C5 (b) D2 and D5 (c) DR2 and DR5 (d) DP2 and DP5. NI indicates no inoculation (sterile soil) to show that reduction of nitrate was performed by biological processes.
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References

    1. Sutherland W. J. et al. Identification of 100 fundamental ecological questions. J Ecol 101, 58–67 (2013).
    1. Balvanera P. et al. Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett 9, 1146–1156 (2006). - PubMed
    1. Philippot L. et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J 7, 1609–1619 (2013). - PMC - PubMed
    1. Wu J. et al. Testing biodiversity-ecosystem functioning relationship in the world’s largest grassland: overview of the IMGRE project. Landscape Ecol 10.1007/s10980-015-0155-y (2015). - DOI
    1. Hodgson D. J., Rainey P. B. & Buckling A. Mechanisms linking diversity, productivity and invasibility in experimental bacterial communities. Proc Biol Sci 269, 2277–2283 (2002). - PMC - PubMed

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