DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene 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 for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Nitrogen to phosphorus ratio shapes the bacterial communities involved in cellulose decomposition and copper contamination alters their stoichiometric demands

“…As already observed in previous studies (e.g. Leflaive et al 2008;Lemmel et al 2019), our results evidenced positive correlations between the intensity of microbial functions and the diversity: cellulose mass losses were significantly and positively related to bacteria OTU numbers, Chao1 richness and Shannon diversity indices. This suggests that only a few bacterial taxa are capable of surviving in environment with highly imbalanced N and P, and these species are probably less efficient in decomposing cellulose under high N:P ratios.…”

Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network

“…This result also supported to some extent the conclusion in Section 3.1 that some bacteria use intermediate metabolites to grow. The degradation trend of PHE was consistent with the results of community diversity and richness, indicating that the PHE degradation level was positively correlated with bacterial abundance, and that the cooperation between strains led to more efficient PAH degradation [32].…”

Anaerobe isolation from denitrifying benzene-degrading enrichment culture and their capacity to mineralize benzene

“…They are known nitrogen-fixing symbionts mostly found naturally in legumes (Mousavi et al, 2014) and have been identified in anaerobic microbial communities degrading acetate under sulfate-reducing conditions (Bin Hudari et al, 2020), and benzene under nitrate-reducing conditions (Eziuzor et al, 2022), which is the original inoculum for the isolation attempt. ANPR was also found to be the dominant phenanthrene degrader aerobically in gradient anthropized soils (Lemmel et al, 2019). They are likely found in the examples stated above as nitrogen-fixing opportunists due to the presence of nitrate reducers, thereby, contributing to the dissimilatory inorganic nitrogen metabolism…”