Bacterial populations and functions driving the decontamination of PAC polluted soils = Poblacions i funcions bacterianes implicades en la descontaminació de sòls contaminats amb CAPs

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment due to accidental spills during use, transport and storage of petroleum and coal derivatives. Their high chemical stability and hydrophobicity confers them recalcitrance. Because of their great persistence in the environment, toxicity and carcinogenicity, these compounds are on the list of priority pollutants. The most sustainable way to remove these compounds from soil without damaging its ecological structure and function is bioremediation. This technology uses the metabolic capabilities of microorganisms to decontaminate (degrade) polluted sites. Microorganisms act on the environment interconnected by metabolic networks, in which the byproducts generated by certain populations are utilized for others as a carbon source. Until recently, the PAH biodegradation studies were conducted by exposing individual compounds to pure strains. However, to improve the technology of bioremediation is necessary to unravel how these metabolic networks function in situ.

The main objective of this Thesis was to contribute to the elucidation of microbial processes occurring in situ during PAH biodegradation in soils. Thus, two main approaches were used.

First, the high molecular weight (HMW) PAH-degrading community of a creosote polluted soil was selected and characterized by new enrichment method using a biphasic system consisting of mineral medium and sand coated with a creosote NAPL previously biodegraded. Once the community became stable, its degrading potential was determined. In 12 weeks, consortium UBHP was able to significantly remove the compounds from 2 to 6 rings (90% fluoranthene, pyrene 90%, 66% benz(a)anthracene and chrysene 59%) and their alkylated derivatives. Key populations of this consortium were identified, based on their responses to specific substrates, phylogenetic, functional and metabolomic profiles, and recovery in pure culture. The phylotypes who played a key role in the degradation of HMW PAHs corresponded to Sphingobium, Sphingomonas, Achromobacter, Pseudomonas and Mycobacterium.

Furthermore, the microbial processes driving the PAH removal in situ during the laboratory bioestimulation of a real creosote polluted soil were investigated. The degradation kinetics of PAHs, oxy-PAHs and N-PACs, together with the formation and/or accumulation of possible acidic products were correlated with key phylotypes and community shifts. A real-time insight into the community dynamics was obtained from the combined analysis of changes in global (genes) and active (transcripts) microbial communities, both at the phylogenetic (16S rRNA) and functional (genes RHD) level. The addition of nutrients resulted in a significant and substantial biodegradation of PAHs with 2, 3, 4 and 5 aromatic rings (93%) and the N-PACs (85%) at 150 days of incubation. During the highest degradation rates there was a transient peak of accumulation of both oxy-PAH and acid metabolites, which were later removed by the microbial populations present in the soil. The nutrient addition also resulted in a higher expression levels in both functional and structural genes, and the genera involved in the disappearance of such compounds were identified as Pseudomonas, Pseudoxanthomons, Achromobacter, Sphingobium, Olivibacter and Mycobacterium.

Los hidrocarburos aromáticos policíclicos (HAPs) predominan en numerosos emplazamientos contaminados en Europa. Debido a su alta persistencia en el medio y elevada toxicidad y carcinogenicidad, están en las listas de contaminantes prioritarios. La única manera de eliminar estos compuestos del suelo sin dañar la estructura y las funciones ecológicas es la bioremediación, que utiliza las capacidades metabólicas de los microorganismos para la degradación o detoxificación de los contaminantes. Los microorganismos actúan en el suelo mediante redes metabólicas en las que los subproductos de degradación de unas poblaciones sirven de fuente de carbono para otras. Hasta hace pocos años los estudios de biodegradación de HAPs se basaban en cultivos puros y sustratos individuales. Para optimizar las técnicas de bioremediación es necesario saber cómo funcionan esas redes metabólicas in situ.

El objetivo principal de esta Tesis es contribuir a la elucidación de los procesos microbianos que tienen lugar in situ durante la biodegradación de los HAPs en suelos.

Se seleccionó la comunidad degradadora de HAPs de elevado peso molecular (EPM) de un suelo contaminado mediante un nuevo método de enriquecimiento utilizando un sistema con medio mineral y arena contaminada con creosota previamente degradada. Una vez la comunidad se mantuvo estable, se determinó su potencial degradador. El consorcio UBHP fue capaz de eliminar significativamente los compuestos de 2-6 anillos (90% fluoranteno, 90% pireno, 66% benz(a)antraceno y 59% criseno). Las poblaciones clave de este consorcio fueron identificadas, en base a sus respuestas a sustratos específicos, perfiles filogenéticos, funcionales y de metabolómica, y su recuperación en cultivo puro. Los filotipos clave en la degradación de los HAPs EPM pertenecían a Sphingobium, Sphingomonas, Achromobacter, Pseudomonas y Mycobacterium.

Se investigaron los procesos microbianos para la eliminación de HAP in situ durante la bioestimulación del suelo. Las cinéticas de degradación de los HAPs, oxi-HAPs y N-CAPs, junto con la formación y/o acumulación de posibles productos de oxidación, se correlacionaron con filotipos clave y cambios en la comunidad. A partir del análisis de los cambios en las poblaciones globales (genes) y activas (transcritos), tanto desde el punto de vista filogenético (16S ARNr) como funcional (RHD), se obtuvo una visión real de la dinámica de la comunidad. La adición de nutrientes promovió la biodegradación significativa de los HAPs de 2-5 anillos (93%) y de N-CAPs (85%). Se produjo la acumulación transitoria de oxi-HAPs y de metabolitos ácidos, que posteriormente fueron degradados. La adición de nutrientes también resultó en un aumento en la expresión de genes estructurales y funcionales. Los géneros principales fueron Pseudomonas, Pseudoxanthomons, Achromobacter, Sphingobium, Olivibacter y Mycobacterium.