Functional biodiversity of Pseudomonas species in biofilm communities degrading polycyclic aromatic hydrocarbons

Abstract

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous pollutants that persist in the environment for a long time. These compounds are very stable, highly hydrophobic and very difficult for bacteria to degrade. However, bacteria can help each other within a community making the degradation process viable. Therefore, the aim of this work was to find a community able to degrade different PAHs crystals, characterize it and try to understand how the community works. Soil and sediment samples were collected at 3 different sites in Germany. Microcosms were constructed with soil or sediment samples, sterile water or medium and slides with a mixture of PAH crystals. Samples were taken over time; DNA and PAHs were extracted from the slides to characterize the community by SSCP and to measure the remaining PAH. Bacteria were isolated from the soil and from biofilms formed on the crystals for comparison with the taxonomic units found in the SSCP gel and to construct artificial communities. The communities from the microcosms were diverse and the one from a polluted creek could degrade higher amounts of PAHs than the others. It was able to degrade several PAHs, including very complex compounds like benzo(a)pyrene and benzo(b)fluoranthene. This community contained mainly Proteobacteria and Actinobacteria. Artificial communities constructed with isolates from this microcosm were able to colonized PAH crystals and degrade it, but isolates from the sediment failed to do so, proving that enrichments from microcosm is an efficient tool so select PAH degraders. The genus Pseudomonas was not detected in these communities by culture-independent methods, but was isolated in all the different approaches used, leading to the conclusion that these bacteria are not main degraders in soil, but had competitive advantages under laboratory conditions. Thus, intrinsic communities from sediment and soil play an important role in degrading pollutants in the environment.