Projects / Programmes
Metagenomics for bioexploration and biomining of bacterial laccases for a sustainable environment
| Code |
Science |
Field |
Subfield |
| 4.03.03 |
Biotechnical sciences |
Plant production |
Water, rural space, environment |
| Code |
Science |
Field |
| B230 |
Biomedical sciences |
Microbiology, bacteriology, virology, mycology |
| Code |
Science |
Field |
| 4.01 |
Agricultural and Veterinary Sciences |
Agriculture, Forestry and Fisheries |
bacterial laccases, novel enzymes, metagenomics, biomining, diversity, lignin degradation, degradation of pollutants, green biotechnology
Researchers (14)
Organisations (4)
Abstract
Background: Microorganisms comprise the largest resource of metabolic and genetic diversity on Earth. This vast diversity can be explored to better understand links between diversity and ecosystem function and for biotechnological innovation. One important example is a group of environmentally important microbial enzymes, laccases, which are already used in various biotechnological applications (see below). Laccases (benzenediol: oxygen oxidoreductases) are blue multi-copper enzymes with broad substrate specificity towards aromatic compounds and participate in cross-linking of monomers, degradation of polymers and ring cleavage of aromatic compounds. These enzymes oxidise a wide range of important polyphenolic substances in the presence of oxygen, including lignin, antimicrobial agents, and compounds used in personal care products (PCPs) and pharmaceuticals. Microorganisms provide a rich and diverse source of laccases but most microorganisms in natural ecosystems (more than 99.9%) are not cultivable and many interesting targets are accessible only via metagenomics-based tools. Metagenomics allows the cultivation-independent discovery of both the function and diversity of microbial consortia in their natural habitats and is a new and powerful tool for bio-exploration and bio-mining of novel enzymatic functions for sustainable environments.
Problem description: Fungal laccases, that have been studied most, are already used for many industrial applications in the paper, textile, pharmaceutical and petrochemical industries, and have been targeted to improve total hydrolysis of lignocellulosic biomass for energy and chemical production and for bio detection and elimination of environmental pollution. These enzymes are also present in prokaryotes, and bacterial laccases are, importantly, much more robust (tolerant to high pH, temperature) than fungal laccases. We recently developed new tools to detect bacterial laccases and discovered a vast diversity of bacterial laccase genes in peat soils of the Ljubljana marsh (Ausec et al, 2011). We have also developed hidden Markov models to search for two- and three-domain bacterial laccases in bacterial genomes in public databases and identified 1,200 novel putative laccase genes (Ausec et al. in preparation). These advances contrast with the paucity of knowledge of the biology and ecology of bacterial laccases, and show considerable promise, given the great demand by EU industry for novel and more robust biocatalysts and for environmental sustainability.
The aim of the study: The aim of this study is to discover novel bacterial laccase genes with robust properties (e.g. high pH optimum) for potential commercial application in industry, environmental biotechnology and as biosensors for environmental pollutants. This will be achieved by ecological studies on diversity in natural and polluted systems, to target environments for gene mining, by further development and application of bioinformatics and metagenomic tools. Novel genes will be heterologously expressed and at least one of the candidate bacterial laccase will be purified and enzymatically characterized.
Originality of the results: Laccases are industrially and environmentally important enzymes but their study has been restricted mainly to fungi and higher eukaryotes. Few bacterial laccases have been purified and studied in detail, and knowledge of their diversity and ecology is lacking. This project will shift the paradigm and highlight the importance of bacterial laccases by discovering novel molecular patterns and biological functions of bacterial laccases. We are at the forefront of international studies on bacterial laccases and the proposed research will employ novel approaches that we have developed, and will be publishable in high impact journals, with ultimate (though not through this project) patent and industrial applications.
Significance for science
Laccase are oxidoreductase that are highly versatile enzymes and of high interest for many industrial and environmental applications including paper and textile industry, pharmaceutical or food industry but are also of high interest as enzymes added to increase efficiency of biofuel production or removal of toxic chemicals from the environment. The results gained within this project were published in several eminent journals and have brought invitations to present results at foreign universities and international conferences including an invited lecture at the most important EU conference in Europe (FEMS) as well as the request to organize and chair the section on soil metagenomics. The later is the prime subject of this project. This lead to invitations for preparations of several EU project proposals as experts on bacterial laccases. Novel tools and knowledge that we developed enabled us to significantly increase understanding of laccase diversity in the environment, add to the number of bacterial laccases (3) that were previously studied in vitro (less than 10) and find completely novel genes in the environment, some of which are the first time example of laccase in a phylum, like the Acidobacterial laccase is the first ever identified in this large phylum and studied in vitro- the same holds for another two laccases that we addressed- the alkalophilic phenol-oxidoreductase from Thioalcalovibrio or Geobacter. Thus the project yielded a wide array of interesting and novel insights and had therefore an important influence on science. We have already published several papers and we expect that at least two -three more should be published in the future.
Significance for the country
The project had also a positive impact at the level of society as it increased opportunities for international collaborations, especially those that have originated through FP7 Metaexplore were we were the only partner addressing bacterial laccases. Due to additional financing obtained through this project we obtained an opportunity to broaden our expertise number of collaborative projects with other partners. These collaborations had broader impact as enabled exchange of students and knowledge at many levels- also through the BAGECO12 conference that was organized by the project leader during the active period of the project, which brought financial benefits also outside of the science field. As we are dedicated teachers we were able to directly incorporate the acquired knowledge into the education processes in microbiology, biotechnology, biology, chemistry and environmental protection at undergraduate and postgraduate levels (life sciences and biomedicine). This has been evident through 1 PhD and 4 master theses that have been linked to this project. Transfer of knowledge has been achieved also through course lectures and practices and by offering hands-on research work to many students that were interested to perform an individual research project in the labs of the project leader prof. Mandic Mulec and other partners. World demand for enzymes continues to rise and the fundamental objective of this project was to discover and characterize novel enzymes – laccases, which we did but we also we also discovered a novel application for this enzymes in environmental biotechnology , which may have long term benefits in the future. The projt partner was also a biotech company - this means that the knowladge gained in the project has been directly transfered to business sector.
Most important scientific results
Annual report
2011,
2012,
2013,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Annual report
2011,
2012,
2013,
final report,
complete report on dLib.si
