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Barcode Sequencing Study Describes Fungal Diversity at Sites Around the Globe

NEW YORK (GenomeWeb) – Through targeted gene sequencing on soil samples from hundreds of sites around the world, an team led by Estonian researchers has started documenting the fungal diversity found in various environments and geographic regions.

As they reported in the current issue of Science, the researchers collected 40 soil samples apiece in 365 different places around the globe. By figuring out the sorts of fungi present at each site, as well as their diversity, they were then able to begin tying such patterns to determinants such as soil composition, the global location of a sampling site, and the type of biome samples.

For instance, the team's results suggest fungal species richness can be distinct from the diversity of plant communities at the same sites, with that richness increasing relative to plant diversity at increasing distances from the equator.

"Climatic variables explained the greatest proportion of richness and community composition in fungal groups by exhibiting both direct and indirect effects through altered soil and floristic variables," senior author Kessy Abarenkov, with the University of Tartu's Natural History Museum, and colleagues wrote.

The team used the Roche 454 GS FLX+ Titanium platform to do pyrosequencing on amplicon libraries produced by targeting internal transcribed spacer sequences in fungal DNA from pooled core soil samples taken at each of the 365 sites considered.

When they compared the resulting barcodes to sequence databases, the researchers identified more than 94,000 species-level operational taxonomic units, including 80,486 fungal OTUs.

After tossing out the nearly 36,000 fungal OTUs represented by just one sequence read, they were left with OTUs that corresponded with roughly half of the known fungal species and represented the main fungal phyla and classes.

More than half of the sequences came from fungi in the Basidiomycota phylum, though the Ascomycota phylum was the best represented when it came to OTU richness, the team reported.

Based on information from fungal reads that did not fit neatly into any of the known fungal groups, the researchers speculated that several fungal classes remain to be described.

Just 4 percent or so of the OTUs came from fungi that have been described as potential plant pathogens, while fungi known for forming mutually beneficial relationships with bacteria and/or plants were far more common.

By folding in a range of other variables at each site — from plant diversity and soil carbon concentrations to annual temperature and precipitation measurements — the team started looking into factors that affect fungal distribution and diversity.

Across 11 different biomes spanning the Arctic tundra through moist, dry, and montane tropical forests, for instance, the study's authors typically saw representation from many of the same main phylogenetic and functional fungi groups.

The proportion of these groups varied depending on the ecosystem considered, they reported, noting that "[t]he ratio of Ascomycota to Basidiomycota OTUs was highest in grasslands and shrublands and tropical dry forests but lowest in the temperate deciduous forests."

Similarly, representation by possible pathogens and fungi prone to forming mutualistic relationships varied depending on the type of environment at hand.

While both plant and fungal diversity varied in response to climate, meanwhile, the team saw differences in the precise effects of precipitation, soil minerals, soil pH, and other variables depending on fungal phylogeny and function. And overall, the mean annual precipitation at each site seemed to have the most pronounced impact on the number of different fungal representatives present at a given site.

When they compared sites around the globe, researchers detected a dip in fungal diversity at sites sampled from farther from the equator. This pattern was not quite as clear-cut as has been described for plants and fungi growing above the ground. And a few fungal groups showed opposing patterns, becoming more common at high latitude, contributing to a shift in the relationship between fungal and plant diversity in different parts of the world.

"Our results highlight how little insight we still have into natural microbial distribution patterns, and this undermines our ability to appraise the actual role of humans in shaping these biogeographical processes," the researchers concluded.

"Even larger-scale sampling campaigns are needed to provide data for establishing natural distributions and building species distribution models," they noted, "which will enable us to predict the spread and habitat suitability of non-native microorganisms."

In a related perspectives article in Science, Swedish University of Agricultural Sciences researchers David Wardle and Bjorn Lindahl discussed key findings from the fungal diversity analysis, noting that such studies "may serve as benchmarks against which we can assess rearrangement of species assemblages caused by human activity."

The duo pointed out that further research is required to more fully delineate features of the fungal communities identified and to understand their interactions with living and non-living features of their ecosystems.