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Lecture Series One Earth: Impacts and countermeasures to global change and effects on the biosphere

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Speaker: Dr. Aurélie Cébron, Research Scientist, CNRS, LIEC UMR 7360 Faculté des Sciences et Technologie, Université de Lorraine, France
Event date: Wednesday, 01 February 2023 12:00 pm - 01:00 pm
Place: Biotech II (BT2), RIKEN room
6, avenue du Swing
4367 Belvaux

Stable isotope probing, a tool to assess the PAH-degradation and identity of degrading bacteria in industrial wasteland soils and plant rhizosphere 

Microbial degradation in plant rhizosphere (rhizodegradation) is a promising soil remediation strategy for polycyclic aromatic hydrocarbons (PAHs) frequently polluting post-industrial environments. However, the effect of plants on PAH dissipation rates and overall microbial community diversity and activity, is still unclear. Working on aged-contaminated soils, from industrial wastelands, we used phenanthrene as a model of PAH and studied the short-term dynamics of pollutants, microbial communities and PAH-degrading bacteria. To specifically target metabolically active PAH-degraders and monitor the fate of PAH, microcosms were spiked with 13 C-labelled phenanthrene in three independent stable isotope probing (SIP) experiments that will be presented.

Firstly, we compared 13 C-phenanthrene degradation and 13 C-labelled bacteria in ten different soils with various initial PAH contamination (Lemmel et al. 2019). Surprisingly, the PHE degradation rate was not directly correlated to the initial level of PAHs in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified and supported the hypothesis that cooperation between strains led to a more efficient PAH degradation. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE-degraders.

Secondly, in batch microcosms, we studied the impact of root exudate addition. We highlighted for the first time that the presence of root exudates did not influence the rate of phenanthrene-degradation but modified the functional community diversity. Interestingly, two distinct populations were active, Pseudoxanthomonas and Microbacterium strains were the main PAH-degraders without exudates, while Pseudomonas and Arthrobacter strains were the main PAH-degraders with exudates (Cébron et al. 2011).

Finally, to better evaluate the impact of plant root exudates, small two-compartment microcosms were designed to compared bare and ryegrass-planted soils. Actively growing roots were allowed to colonize soil spiked with 13 C-phenanthrene for 10 days. Phenanthrene concentrations were significantly lower after 10 days in bare soil than in planted soil. Carbon compounds from root exudates might be preferentially consumed instead of phenanthrene. The abundance of bacteria increased over the time course for both rhizospheric and bare soil, but plants favored the transcription of PAH-degrading genes from Actinobacteria (Thomas & Cébron, 2016). After 10 days, 16S rRNA gene sequencing revealed that 13 C-phenanthrene was metabolized by consortia dominated by Sphingomonas or Sphingobium depending on the presence of plant. The metagenome characterization, based on shotgun sequencing of the 13 C-DNA fractions, allowed us to reconstruct the whole phenanthrene-degradation pathway of the consortia. Complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps (Thomas et al., 2019).


- Cébron A, Louvel B, Faure P, France-Lanord C, Chen Y, Murrell C, Leyval C (2011) Root exudates modify bacterial diversity of phenanthrene-degraders in PAH-polluted soil but not phenanthrene degradation rates. Environmental Microbiology. 13:722-736.

- Thomas F, Cébron A (2016) Short-Term rhizosphere effect on available carbon sources, phenanthrene degradation, and active microbiome in an aged-contaminated industrial soil. Frontiers in Microbiology. 7 :92.

- Lemmel F, Maunoury-Danger F, Leyval C, Cébron A (2019). DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils. FEMS Microbiology Ecology, 95(12), fiz181.

- Thomas F, Corre E, Cébron A (2019) Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. The ISME Journal, 13(7), 1814-1830.

The One Earth lecture series is financially supported by the National Research Fund (FNR, RESCOM/2022/SR/16983801) and the Luxembourg Society for Microbiology (LSfM).