A step towards understanding Polycyclic Aromatic Hydrocarbons degradation by microbial communities

Transcription

1 7th Annual Conference on the Advances in Land Contamination Assessment and Remediation A step towards understanding Polycyclic Aromatic Hydrocarbons degradation by microbial communities Kevin Bayle Ph.D. Infrastructure and environnement group

2 Context and objectives approach 2

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4 Pollutant resistant to degradation in the environment Chemical processes Photolytic processes Biological processes Organic pollutant Organic pollutant Organic pollutant Organic pollutant 4

5 Polycyclic Aromatic Hydrocarbons The potential for biodegradation of PAH contaminants by microbes has been demonstrated for a single compound or a mixture of a small number of chemicals (<5). 5

6 New analytical tools need to be deployed! 6

7 Former manufactured gas plant 7

8 and objective 8

9 Chemistry Biology Fingerprinting of contaminants within samples collected Composition of the microbial communities. 9

10 Chemistry Quantifying the real concentration of PAHs bioaccessible to indigenous soil microorganisms. Fingerprinting of contaminants within samples collected Identifying transformation products that might cause higher environmental risk than parent compounds 10

11 Allows the separation and detection of thousands of compounds 11

12 Identifying members of the microbial community Understanding the dynamic of the microbial ecosystems Biology analysis Composition of the microbial communities 12

13 Several months 13

14 Concentration µg/l Context Several months Naphtalene concentration Month Correlation between degradation of compounds and composition of microbial communities? Identification of new degraders? 14

15 approach

16 Amplicon DNA extraction Data analysis Which organisms are present? 16s rrna sequencing Amplification by PCR 16

17 tics sickle: Quality Trimming BayesHammer: Noise Removal (Kmer) pandaseq: Overlap Forward and Reverse Reads usearch/vsearch: De novo/reference Based Chimera Detection usearch/vsearch: Dereplicate Duplicate Sequence, Annotate with Cluster Sizes, Sort by Decreasing Cluster Sizes 1 23 ChimeraSlayer 4 usearch/vsearch: OTU Clustering CREST/RDP LCA Classifier: Generate Taxonomic Levels Breakdown Qiime/muscle/mafft/FastTree: Generate phylogenetic tree

18 Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Category_1 Category_1 Category_2 Category_2 Category_2 OTU_ OTU_ OTU_ OTU_

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21 16 PAHs US EPA list (United States Environmental Protection Agency)

22 Correlation of pathways 16S rrna (predicted) vs WGS (actual) Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2015). Tax4Fun: predicting functional profiles from metagenomic 16S rrna data. Bioinformatics, 31(17),

23 Tax4Fun 23

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25 But which pathways to choose? 358 pathways from below 25

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28 A first step towards creating a model able to comprehend the bioremediation of PAHs by microbial communities Additional samples required Anyone can help? Understand the synergy in microbial cooperation Identification of new PAHs degraders Possible future bio augmentation? 28

29 Dr. Caroline Gauchotte-Lindsay Dr. Umer Z. Ijaz Dr. Thomas J. Aspray 29

30 Thank you for your attention! 30