Isolation and exploitation of microorganisms from anthropized ecosystems characterised by heavy pollution: Application to bioremediation processes

Bioaugmentation might be an economic way to recover contaminated matrices by exploiting allochthonous and autochthonous microorganisms adapted to tolerate matrix toxicity and able to degrade the contaminating pollutants by producing enzymes with activities that are able to oxidize the toxic compounds. At the same time, those contaminated matrices can be a source of microorganisms whose features are suited for innovative bio-based processes not necessarily limited to bioremediation by bioaugmentation. An anthropogenic environment, contaminated by heavy hydrocarbons was source of two different microorganisms of high interest: an Ascomycete, and a chemolithoautotrophic Gammaproteobacterium. The isolated Ascomycete was found to be able to metabolise diesel oil as sole carbon source and to produce ligninolytic enzymes during hydrocarbon catabolism. The fungus was also found to be highly effective as candidate for bioaugmentation of highly contaminated hot spots of the original matrix. This species was able to co-metabolically degrade a high concentration of Total Petroleum Hydrocarbon contamination (54,000 ppm) by 43.0% within 60 days, and to also stimulate autochthonous microbial hydrocarbon putative degraders. The Gammaproteobacterium showed adaptations to haloalkaliphilic conditions and high metabolic flexibility in comparison with its closest taxonomical relatives. It was able to efficiently perform sulphide oxidation in haloalkaline conditions at 1 mmol-S/(mg-N*h) at 0.25 NL/min air flow rate. The isolate was classified as a new strain of Thioalkalivibrio sulfidiphilus sp. showing a higher capability of adaptation to pH and a higher optimal sodium concentration for growth, when compared to Thioalkalivibrio sulfidiphilus sp. HL-EbGr7, type strain of the species. The genome of the new isolate was sequenced and annotated. The comparison with the genome of Thioalkalivibrio sulfidiphilus sp. HL-EbGr7 showed a duplication of an operon encoding for a putative primary sodium extruding pump and the presence of a sodium/proton antiporter with optimal efficiency at halo-alkaline conditions, that might be involved in the capacity of the strain to adapt to very diverse growth conditions.