**5. Assessing fungal biodiversity and functionality in aquatic ecosystems**

Next to classical molecular techniques for assessing *in situ* fungal communities (Bärlocher 2007), massive parallel DNA sequencing in combination with data management systems such as GenBank (Benson et al., 2008), it is now possible to fully explore fungal biodiversity. Amplicon sequencing has been used to explore fungal diversity in soils (Buée et al., 2009; Lim et al., 2010). The approach was recently used in an assessment of estuarine biodiversity (Chariton et al., 2010) and for the first time in two lakes (Monchy et al., 2011), and similar work from a lowland river floodplain has not been published to date (Colloff & Baldwin in prep; Kerr et al., in prep.).

These studies greatly extend our understanding of dimensions and structure of the fungal kingdom. However, in many cases, all we know of newly discovered species is the sequence of a small part of their genome, with no insights regarding morphology, physiology or ecology of the specimen. In the future, a combination of techniques such as transcriptomics (Bhadauria et al., 2007), proteomics (Doyle 2011), metabolomics (Tan et al., 2009) may allow us to evaluate physiological and ecological inferences based on DNA sequences. Classical culture techniques, however, will remain important for studying morphology, preserving voucher specimens, and generally expanding our knowledge of undescribed species associated with novel sequences.

At present, there are a number of biases in the representation of described species in databases such as GenBank. For practical reasons, investigations have focused on the ecology and diversity of macro-fungi and pathogens of plants and animals. In order to use DNA sequence databases to identify fungi in environmental samples, it is at first necessary to fill the database with accurate and appropriate information on fungal sequences with taxonomic descriptions. It is unlikely that this work can keep pace with the potential of current technologies to generate sequence data. Nevertheless, improved sequence analysis techniques are required to link information of the "omics" studies with those of the environment including short- and long-term changes. Although identification of fungi in the environment has been improved a lot throughout the past years, there is an obvious lack in fundamental ecological methods, e.g. methods for differentiating between the biomass of fungal species are still needed. FISH methods, which allow determining fungal biomass have only recently emerged (Mangot et al., 2009) and ergosterol measurements are only applicable to CPOM where algae are not present (e.g. *Chlorella –* a typical fresh water alga - contains ergosterol) and can't detect the presence of many species of lower fungi. To understand the importance of fungi for energy and organic matter cycling in aquatic systems, we need to greatly improve our techniques, e.g. by defining new marker molecules to measure the biomass and activity of fungi in their natural environment.
