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PAH Biodegradation by Sphingomonas and Mycobacterium Spp in Two Different Set Ups

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FACULTEIT LANDBOUWKUNDIGE EN TOEGEPASTE BIOLOGISCHE WETENSCHAPPEN Academiejaar 2003 - 2004 PAH-BIODEGRADATION BY SPHINGOMONAS AND MYCOBACTERIUM : STUDY OF THEIR NATURAL ABUNDANCE, DIVERSITY AND NUTRIENT DEMANDS IN PAH-CONTAMINATED SOILS. PAK-BIODEGRADATIE DOOR SPHINGOMONAS EN MYCOBACTERIUM : STUDIE VAN HUN NATUURLIJKE VERSPREIDING, DIVERSITEIT EN NUTRIËNT EISEN IN PAK-GECONTAMINEERDE BODEMS. door ir. Natalie Leys Thesis submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) in Applied Biological Sciences Proefschrift voorgedragen tot het bekomen van de graad van Doctor in de Toegepaste Biologische Wetenschappen op gezag van Rector: prof. dr. apr. A. DE LEENHEER Decaan: Promotoren: prof. dr. ir. H. VAN LANGENHOVE prof. dr. ir. W. VERSTRAETE prof. dr. ir. E. TOP dr. ir. D. SPRINGAEL dr. ir. L. BASTIAENS ISBN 90-5989-016-7 Auteur en promotoren geven de toelating dit doctoraatswerk voor consultatie beschikbaar te stellen en delen ervan te kopiëren voor persoonlijk gebruik. Elk ander gebruik valt onder de beperkingen van het auteursrecht, in het bijzonder met betrekking tot de verplichting uitdrukkelijk de bron te vermelden bij het aanhalen van de resultaten van dit werk. The author and the promoters give the authorization to consult and to copy parts of this work for personal use only. Every other use is subjected to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. Gent, 28 maart 2004 De auteur: ir. Natalie Leys De promotoren: Prof. dr. ir. Willy Verstraete, Dr. ir. Eva Top, Dr. ir. Dirk Springael, Dr. ir. Leen Bastiaens " Research is what I'm doing when I don't know what I'm doing." - Wernher von Braun – Dankwoord ~ THE END ~ Cast The Doctor…................................................................... Natalie Leys Partners in crime…………..……………………….….........Karolien & Zita Co-stars…....................................Cindy, Barbara, David, Jan & Joke Colleagues.....................................Annemie Ryngaert & the Vito crew Assistants................................................Students Els, Tine & Carlos Supporters...................................................................All my friends! Boyfriend.….............................................................Joachim De Baer Anti-stress ball……........................................................Yazoo the cat Mom & Dad.…........................................Erna Van Hool & Louis Leys Sister & her family.…..................Isabella Leys & Ivan Eulaers & Cato The in-laws..........................................Hilda Ringoot & Hugo De Baer Catherine De Baer & Jeroen Stuur Dankwoord Review comity…..............Prof. H. Van Langenhove, Prof. P. Sorgeloos, Prof. E. Vandamme, Dr. K. Smalla, Prof. M. Höfte, Prof. P. De Vos Producer.............................................................Prof. Willy Verstaete Assistant Producer.........................................................Prof. Eva Top Director..................................................................Dr. Dirk Springael Assistant Director.................................................Dr. Leen Bastiaens Logistics supervisor......................................................Dr. Ludo Diels Production support.……….……………………………………The SCK crew ~ Thank you all very much !!! ~ That's all folks! Summary SUMMARY Polycyclic aromatic hydrocarbons (PAHs) are major soil pollutants in many industrialized countries. Microbial degradation is considered to be the major route through which PAHs are removed from contaminated environments and therefore bioremediation is considered as a feasible remediation technology for cleaning PAH- contaminated soil. Mycobacterium and Sphingomonas strains using polycyclic aromatic hydrocarbons (PAHs) as sole source of carbon and energy could be essential members of such PAH-degrading bacterial communities, as they are often isolated during enrichments of PAH-degrading bacteria from such soil. Therefore, for future optimization of bioremediation process, it is of interest to study more in detail the distribution and diversity and specific nutrient requirements of Mycobacterium and Sphingomonas in PAH-polluted soil. Four new culture-independent PCR-based detection methods targeting the 16S rRNA genes were developed to analyze PAH-degrading Mycobacterium and Sphingomonas communities in PAH-contaminated soils. Genus-specific primers were developed for PCR detection of either Sphingomonas species (Sphingo108f and Sphingo420r), or ‘fast-growing’ Mycobacterium species (Myco66f and Myco600r). The resulting amplicons were separated by Denaturing Gradient Gel Electrophoresis (DGGE) for generating Mycobacterium and Sphingomonas community fingerprints. Both Mycobacterium and Sphingomonas specific primer sets proved to be highly selective for the target group and single-band DGGE profiles were obtained for most strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases but not all, these fingerprints were typical for one species, allowing partial differentiation between species in a Mycobacterium or Sphingomonas population. Inoculated Sphingomonas and Mycobacterium strains could be detected at a cell concentration of 104 respectively 106 cells per gram of soil using the new primer set alone or 102 cells per gram of soil in a nested PCR approach in combination with eubacterial primers. In addition, 2 species specific primer sets were designed to detect bacteria related to Sphingomonas sp. EPA505 (EPAf and EPAr) and M. frederiksbergense (MYCOFf and MYCOFr). Using DNA extracts of a variety of inoculated PAH-contaminated soils, the EPA505 specific primer pair was able to Summary detect EPA505 in concentrations as low as 102 cells per gram of soil. The MYCOF primer set could detect M. frederiksbergense in soil at a cell concentration of 104 cells per g soil via direct PCR and subsequent DNA-DNA hybridization of the PCR products or at a cell concentration of 102 cells per g soil via a nested PCR approach. The new detection methods were used to rapidly asses the Mycobacterium and Sphingomonas population structure of several PAH-contaminated soils of diverse origin and different overall contamination profiles, pollution concentrations and chemical-physical soil characteristics. Using the Mycobacterium genus-specific detection method, fast-growing Mycobacterium species were detected in most uncontaminated soils and PAH-contaminated soils tested. By sequencing of cloned PCR products amplified from DNA from PAH-contaminated soil, well-known PAH- degrading species like M. frederiksbergense and M. austroafricanum were detected. However, in all PAH-contaminated soils bacteria were detected with 16S rRNA gene sequences related to the 16S rRNA gene of M. tusciae, a Mycobacterium species so far not reported in relation to biodegradation of PAHs. Using the species-specific detection method, M. frederiksbergense strains were detected in most PAH- contaminated soils, including soils in which no M. frederiksbergense strains were detected using the Mycobacterium genus-specific detection method. The new Sphingomonas specific PCR-DGGE method revealed the presence of Sphingomonas communities in all tested PAH-contaminated soils, with less diversity in soils containing highest phenanthrene concentrations. Sequence analysis of cloned PCR products revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates. Sequences from environmental clones grouped phylogenetically with other environmental clone sequences available in data bases and possibly originated from several potential new species, not previously detected with culture-dependent detection techniques. In most of the tested PAH-contaminated soils, we detected also 16S rRNA gene fragments from Sphingomonas sp. EPA505 related strains. By adding different inorganic supplements of nitrogen (N) and phosphorus (P) affecting the overall Carbon/Nitrogen/Phosphorus-ratio of soil, we investigated the impact of soil inorganic N and P nutrient conditions on PAH degradation by PAH- degrading Sphingomonas and Mycobacterium strains by means of soil slurry Summary degradation tests. The general theoretical calculated C/N/P-ratio of 120/14/3 [expressed in mg] allowed rapid PAH metabolisation by Sphingomonas and Mycobacterium strains without limitation. In addition, PAH-degradation activity was not affected when circa 10 times lower concentrations of nitrogen and phosphorus were available, indicating that Sphingomonas and Mycobacterium strains are capable of metabolizing PAHs under low nutrient conditions. In addition, PAH-degradation was not affected by an excess of nitrogen and/or phosphorus unbalancing the C/N/P ratio in the soil. Supplements of nitrogen and phosphorus salts increased however the salinity of the soil slurry solutions and seriously limited or even completely blocked biodegradation. The results presented in this thesis suggest an important role for Mycobacterium and Sphingomonas species in the PAH-degrading bacterial communities naturally colonizing PAH-contaminated soils with very different contamination profiles and different origin. Sphingomonas populations seem to dominate in soils contaminated with high concentrations of more bioavailable and more easily degradable PAHs such as phenanthrene, while Mycobacterium populations may be better adapted to flourish in soils enriched in less bioavailable higher molecular weight PAHs. In addition, the results and
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