Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities

Fungi play fundamental roles in the nutrient cycling process in most terrestrial ecosystems, notably through forming symbiotic associations such as mycorrhiza with plants and through decomposition of wood and plant debris (Stajich et al., 2009). The fact that fungi spend most of their life cycle below ground or within substrates has left the scientific community with a fragmentary understanding of fungal diversity, and a modest c. 7% of the estimated 1.5 million extant species of fungi have been described (Kirk et al., 2008). The poor correlation between the presence of fungal fruiting bodies or other macroscopic structures and the full diversity of the mycobiome at any sample site has shifted the focus in fungal ecology from fruiting bodies to molecular (DNA sequence) data, and nearly all recent attempts to characterize fungal communities are based on sequence data (Taylor, 2008). Such studies have hitherto been limited in sequence depth by the high cost and investment of effort associated with traditional Sanger sequencing of large numbers of samples, but recent methodological progress in the form of next-generation sequencing (NGS) technologies (Shendure & Ji, 2008) offers a remedy to these problems. One of these NGS technologies – massively parallel (‘454’) pyrosequencing (Margulies et al., 2005) – has the capacity to generate more than a million sequences of c. 500 base-pairs (bp) length in the course of a day, making it a groundbreaking tool for environmental sequencing of fungi.