**3.2.1 Ectomycorrhizal (ECM) fungal diversity**

As mentioned above, ECM fungi are one of the major functional groups of mycorrhizal fungi. They associate with plant roots by creating a sheath of fungal tissue enclosing short root tips and a net with inward hyphal growth between plant root cells (called a Hartig net). Such anatomy allows for an extensive surface area of plant-fungal contact where fungi exchange soil nutrients for plant-produced cabohydrates. For the most part, ECM fungi belong to the phylum *Basidiomycota* and associate with about 30 plant families, mainly woody perenials (Smith & Read, 2008). These fungi assemble in hyperdiverse, complex and dynamic communities and play a crucial ecological role in most temperate and some tropical habitats.

Unraveling the diversity of ECM fungi is not trivial. Although fruit body inventories provide valuable information, they by no means offer accurate estimates of ectomycorrhizal fungal diversiy. In a pioneer study Gardes & Bruns (1996) surveyed the fungi from pine forests both based on both fruitbody identification and molecular analyses of root samples. They discovered a profound disconnect between the results provided by these different types of data. In fact, the two species producing the majority of fruit bodies were not dominant at the root level, indicating fungal fruiting patterns do not reflect below ground dominances.

Root morphotyping is another approach to study ECM fungal diversity. It has been extensively developed by Agerer (1987-2002) and consists on distinguishing the different fungi based on the morphology and anatomy of ECM root tips. This is a difficult, slow and laborious method that requires extensive training.

As with other areas of mycology, molecular studies have recently revolutionized the study of ECM fungal diversity. In addition to clarifying the discrepancy between above and belowground fungal diversity, molecular surveys also revealed ECM communities as hyperdiverse (particularly when compared to plant host diversity) and composed mostly of rare species (Gehring et al., 1998, Taylor, 2002, Avis et al., 2003, Horton & Bruns, 2005, Walker et al., 2005, Avis et al., 2008, Morris et al., 2008, Branco & Ree, 2010). Figure 5 shows the typical patterns underlying ECM fungal communities: unsaturated species accumulation curves reveal the difficulty in obtaining complete community descriptions and a rank-frequency diagrams illustrate the rarity of most species. These patterns raise interesting questions, particularly from a functional perspective. The most stricking question in ectomycorrhizal

community descriptions (Avis et al., 2009). On the other hand, it is known that there is within species variability in ITS, as the different copies within a genome are not exactly identical. Furthermore, intraspecific variation differs considerably across fungal groups (Karen et al., 1997, O'Donnell & Cigelnik, 1997, Glen et al., 2001, Horton, 2002, Rooney & Ward, 2005, Pawlowska & Taylor, 2004, Avis et al., 2006, Nilsson et al., 2008). These pose challenges in determining meaningful sequence similarity cut-offs (O'Brien et al., 2005). For the most part, OTUs are defined using a 95-97% similarity cut-off with the underlying assumption that resulting units are somewhat equivalent to fungal species. However, different fungal species have been reported to have ITS similarity as high as 99% (Dettman et al., 2001, Johannesson & Stenlid, 2003), while interspecific similarity of 90% or less has been found in other species (Kuniaga et al., 1997, O'Donnell, 2000). Despite these limitations and as mentioned above, ITS is the marker of choice for fungal diversity studies and is likely

As mentioned above, ECM fungi are one of the major functional groups of mycorrhizal fungi. They associate with plant roots by creating a sheath of fungal tissue enclosing short root tips and a net with inward hyphal growth between plant root cells (called a Hartig net). Such anatomy allows for an extensive surface area of plant-fungal contact where fungi exchange soil nutrients for plant-produced cabohydrates. For the most part, ECM fungi belong to the phylum *Basidiomycota* and associate with about 30 plant families, mainly woody perenials (Smith & Read, 2008). These fungi assemble in hyperdiverse, complex and dynamic communities and play a crucial ecological role in most temperate and some

Unraveling the diversity of ECM fungi is not trivial. Although fruit body inventories provide valuable information, they by no means offer accurate estimates of ectomycorrhizal fungal diversiy. In a pioneer study Gardes & Bruns (1996) surveyed the fungi from pine forests both based on both fruitbody identification and molecular analyses of root samples. They discovered a profound disconnect between the results provided by these different types of data. In fact, the two species producing the majority of fruit bodies were not dominant at the root level, indicating fungal fruiting patterns do not reflect below ground

Root morphotyping is another approach to study ECM fungal diversity. It has been extensively developed by Agerer (1987-2002) and consists on distinguishing the different fungi based on the morphology and anatomy of ECM root tips. This is a difficult, slow and

As with other areas of mycology, molecular studies have recently revolutionized the study of ECM fungal diversity. In addition to clarifying the discrepancy between above and belowground fungal diversity, molecular surveys also revealed ECM communities as hyperdiverse (particularly when compared to plant host diversity) and composed mostly of rare species (Gehring et al., 1998, Taylor, 2002, Avis et al., 2003, Horton & Bruns, 2005, Walker et al., 2005, Avis et al., 2008, Morris et al., 2008, Branco & Ree, 2010). Figure 5 shows the typical patterns underlying ECM fungal communities: unsaturated species accumulation curves reveal the difficulty in obtaining complete community descriptions and a rank-frequency diagrams illustrate the rarity of most species. These patterns raise interesting questions, particularly from a functional perspective. The most stricking question in ectomycorrhizal

to remain so in the near future.

tropical habitats.

dominances.

**3.2.1 Ectomycorrhizal (ECM) fungal diversity** 

laborious method that requires extensive training.

ecology has been why are there so many fungal species in a given forest? What are they doing and how do they co-exist? Several explanations have been suggested, such as niche differentiation (Bruns, 1995). These could include vertical niche partitioning, where species have distinct microhabitat preferences that are distributed across a soil vertical gradient (Dickie et al., 2002), or temporal partitioning of ECM fungal communities, where species are active at different times of the year, promoting coexistence by reducing intraspecific competition (Koide et al., 2007). Although the majority of ECM fungal diversity studies are based on root tip data, fungal mycelia also live freely in soil and the community descriptions based on roots and mycelia provide different results (Koide et al., 2005), which adds another layer of complexity to the matter. Host-specificity, where different plant species associate with distinct assemblages of mycorrhizal fungi, has also been suggested as an explanation for the high ECM fungal diversity levels. In general, ECM fungi are known for not having high fidelity to their plant partners and tend to associate with a wide array of plant species. However, there is host preference, which seems to be an important factor in shaping local diversity (Dickie, 2007, Ishida et al., 2007). Inter-specific competition has been another topic of particular interest, given the high numbers of co-existing species. ECM fungi compete for access to the host, more specifically for carbon, as well as soil nutrients, and competition has recently been documented as a major player in ECM community structure (Kennedy, 2010).

Fig. 5. Typical ECM fungal species accumulation curve (top) and species rank-frequency plot (bottom). (Adapted from Branco & Ree, 2010). As more samples are described, new species are discovered at a consistently rate. This indicates that the vast majority of species in the community are rare (see text for details).

Fungal Diversity – An Overview 221

The accessibility of genomics has also enabled the possibility of a dramatic increase in the number of fungal sequenced genomes. Sequencing the genomes of ecologically and taxonomically relevant fungi is and will continue to provide information not only on those specific species, but will also permit the study of genome structure, gene evolution, metabolic and regulatory pathways and life histories (Martin et al., 2011). The sequencing and analysis of fungal genomes is ongoing, mainly through the Fungal Genomics Program (FGP; http://genome.jgi-psf.org/programs/fungi/about-program.jsf), launched by the US Department of Energy Joint Genome Institute (JGI). This program will sequence the genomes of many species, including decomposer and mycorrhizal species enabling comparative studies focused on the pathways and mechanisms involved in being a symbiont or a decomposer across the fungal tree of life. The genomes of species from lineages with no genomic information will also be sequenced, allowing further studies on

Although fungi are cryptic and understudied organisms, there has been increasing concern regarding their conservation. As with many other organisms, fungi are affected by habitat loss, pollution, climate change, and other environmental factors. Overall fungi have no legal protection and the potential decline in fungal diversity, affecting both known and unknown species, has been a major concern among mycologists. The main reason underlying the lack of fungal conservation protocols is the challenge in gathering data on fungal populations and geographic distributions. For the most part, conservation bodies, such as the International Union for the Conservation of Nature (IUCN), rely on data describing distributions, population size and population trends to assign threat categories to species (IUCN Standards and Petitions Subcommittee, 2010). These criteria make it very difficult to

Nevertheless, there have been efforts to gather fungal checklists and flag species of concern with red lists, particularly among European countries. One of the most relevant initiatives has been the European Council for the Conservation of Fungi (ECCF, currently the conservation group at the European Mycological Association), created in 1985 and aimed at promoting awareness about conservation of fungi, stimulating studies and publications on fungal distributions and fungal red lists, as well as promoting international collaborations towards the compilation of a European red list of threatened fungi (http://www.wsl.ch/eccf/). In the early 2000s, ECCF submitted a list of 33 threatened fungi in Europe to be included in the Bern Convention (Dahlberg & Croneborg, 2003). This report referred to rare European macrofungal species and, for the first time, aspired to obtain continental-level legal protection for fungi. This attempt was however unsuccessful, with

More recently, the International Society for the Conservation of Fungi was established specifically with the goal of protecting fungi worldwide (Minter, 2010, Williams, 2010; http://www.fungal-conservation.org). This is the first society devoted exclusively to the conservation of fungi and aims at developing actions on four fronts: infrastructure, science, education, and politics. The political aspect is regarded as a particularly important target, as

Hopefully the recent genomic and metagenomic developments and all the multitude of new possibilities they open for fungal research, will contribute for the development of specific

the society plans to develop and lobby for fungal conservation policies worldwide.

fungal evolution (Martin, 2011).

**4. Fungal conservation** 

apply such categories to fungi.

the Bern Convention rejecting the proposal.
