Molecular Genetics, Genomics and Evolution of AMF Nuclear Genomes
Arbuscular mycorrhizal fungi (AMF) are asexual root-inhabiting symbionts organisms, and among the most common soil fungi. AMF form symbioses with the roots of approximately 80% of all vascular plant species. These fungi offer a variety of services, in particular, improved capacity for P uptake and drought tolerance. From a genetic point of view, AMF are extremely complex when compared to most other eukaryotes. AMF are coenocytic organisms that contain thousands of nuclei throughout their life cycle. There is much evidence that these nuclei are genetically divergent, and fungal isolates show extensive intracellular genetic polymorphism. Therefore, many fundamental questions bearing on AMF biology remain difficult to investigate. An international consortium of nuclear genome sequencing of the model species Glomus irregulare (formerly G. intraradices), has encountered many difficulties due to sequence assembly problems and contamination. Gene sequences are so divergent within these populations of nuclei that nuclear genome sequencing is not a simple matter in AMF. The goal of this research is to understand AMF genome structure and genome evolution using comparative genomic analyzes, and to define the extent of genetic variation in AMF with a particular focus on the way polymorphism is maintained and lost by processes such as mutation, recombination, anastomoses, horizontal gene transfers and genetic drift. Using a high-throughput genomic and cellular imaging approaches, we will improve our understanding of fungal symbionts. Specific aims are: (1) To sequence, assemble and annotate AMF partial genomes; (2) To investigate how processes such as recombination, and transposition are responsible for genomic variability and study congruence of AMF gene phylogenies to estimate the extent of horizontal gene transfer between AMF and its symbiotic partners; (3) To study gene exchange between individuals.
This research will generate new knowledge on AMF genetics and will also yield fundamental insights into genomic mutation and recombination rates and the importance of horizontal gene transfer in AMF.
This project focuses, more specifically, on Arbuscular Mycorrhizal Fungi (AMF). As symbionts, AMF are highly effective in mobilizing, taking up and transferring mineral nutrients from soil to plants, and readily colonize many plants, including most agriculturally important species. The objective of this project is to develop basic knowledge of AMF mitochondrial genomics.
Environmental genomics, Biodiversity of soil bacteria and fungi and their use in bioremediation
During the past 100 years, industrial production and human population have expanded exponentially resulting in increased soil, water and air pollution – raising serious concerns about the future availability of clean air, water and land resources, as well as our quality of life in terms of health and environment. The time has come for seriously practicing proper (sustainable) exploitation and management of natural resources, and remediation of existing pollution. Bioremediation is a new and most promising approach to decontamination. It uses living organisms for this purpose, i.e. to degrade organic environmental pollutants, prevent the formation of toxic waste during the production processes themselves, avoid accumulation of toxic inorganic compounds in the soil, and ultimately, remove remaining pollutants by uptake into plant material followed by harvesting and disposal. Bioremediation makes use of and optimizes biodegradation and selective uptake processes that occur in nature. In comparison to alternative remediation procedures such as excavation, and ‘vitrification’, or chemical treatment of contaminated soil, biology-based procedures are far less expensive. The objective of this research is to develop the use of microorganisms (bacteria, mycorrhizal and other fungi) and plants to stabilize or remove contamination in soil. The project will develop an understanding of how plants, in concert with microbial communities respond to natural environments that contain a broad variety of toxic inorganic and organic compounds. The project will not only substantially expand knowledge of bioremediation processes at the genetic and genomic levels, but also test newly developed techniques in field studies at sites with various types and extents of contamination.