a target plant at the same time (see Ecology of AM). The identification of the associated fungal symbionts is impossible without the use of molecular methods. Though genetic analysis of AM fungal communities has advanced a great deal in the past decade, the methodology is not yet completely refined. Below is an overview of the methods used in molecular genetic analyses of AM fungi, along with applications to research, future directions and some of their problems. Overview of methods DNA/RNA Genetic analyses of AM fungi from soil and root samples range in their applicability to answer ecological or phylogenetic questions. DNA analyses utilize various nuclear markers to describe AM fungi and represent different regions of the nuclear ribosomal operon (18S rRNA) found in all eukaryotic organisms. The DNA analysis of AM fungi using these markers began in the early 1990s and are continuing to be developed today. The small subunit (SSU) rRNA gene, the internal transcribed spacer (ITS) gene, and the large subunit (LSU) rRNA gene are currently the most common DNA markers used. The SSU region has been used most frequently in ecological studies, while the ITS and LSU regions have been predominantly used in taxonomic constructions of the phylum Glomeromycota. qPCR and qRT-PCR Real-time PCR or quantitative PCR (qPCR), is becoming a well-established method to quickly amplify and simultaneously quantify targeted AM fungal DNA from biological samples (plant roots or soils). Fairly recent developments in qPCR markers allow researchers to explore the relative abundance of AM fungal species within roots in greenhouse experiments as well as in the field to identify local AM fungal communities. qPCR markers for arbuscular mycorrhizal fungi will consist of AM specific primers and fluorescently labeled hydrolysis probes. These AM specific primers (discussed above) can be chosen by the researcher and this decision is typically guided by the question at hand, resources available, and willingness to troubleshoot in the lab. Microarray DNA microarray analysis is currently being used in AM fungal research to simultaneously measure the expression of many genes from target species or experimental samples. The most common tool or method is to use functional gene array (FGA) technology, a specialized microarray that contains probes for genes that are functionally important in microbial processes such as carbon, nitrogen or phosphorus cycling. FGAs have the ability to simultaneously examine many functional genes. This technique is typically used for general analysis of functional microbial genes,