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Soil Microbiome Patterns Point to Past Diversity of Native Tallgrass Prairie

NEW YORK (GenomeWeb News) – In a study published online today in Science, researchers from the University of Colorado at Boulder, the University of Kentucky at Lexington, and elsewhere described soil microbiome changes that have accompanied the historical disappearance of native tallgrass prairie biomes from the US Midwest.

"These soils played a huge role in American history because they were so fertile and so incredibly productive," University of Colorado at Boulder ecology and evolutionary biology researcher Noah Fierer, the study's first author, said in a statement.

"They don't exist anymore except in really small parcels," said Fierer, who is also affiliated with the Cooperative Institute for Research in Environmental Sciences. "This is our first glimpse into what might have existed across the whole range."

In an effort to look back at the microbial diversity supported by those tallgrass prairies, Fierer and his colleagues did 16S ribosomal RNA gene sequencing and metagenomic sequencing on soil samples from a few dozen locations containing scraps of previously untilled prairie.

By developing microbe models accounting for historical climate patterns and the like, they were able to get an idea of the microbial diversity that may have existed in the soil in the days when tallgrass carpeted some 150 million acres of land in the US.

The precise makeup of each soil microbiome tested was different, the team found. Even so, microbial communities found in remaining and reconstructed tallgrass prairie soils tended to show particularly pronounced representation by bacteria from a phylum called Verrucomicrobia.

Those microbes are relatively rare in soils where native grass has been turned under to make way for crops and other recently introduced plant and animal types, study authors noted, but may provide information on the metabolic capabilities and composition of native soils.

"Here's a group that's really critical in the functioning of these soils," Fierer said. "So if you're trying to have effective prairie restoration, it may be useful to try and restore the below-ground diversity as well."

For their native tallgrass samples effort, researchers focused on surface soil samples from 31 locales in the Midwest, including cemeteries, nature preserves, and other sites with no documented history of tilling.

By doing 16S rRNA gene sequencing with metagenomic shotgun sequencing on paired cultivated and uncultivated soil samples from such sites, they were able to tease apart soil community members as well as the collection of genes present within each community.

With such present day data in hand, the group used a so-called species distribution modeling method to computationally predict past microbe sequences and relationships in prairie soils with the help of historical climatic data going back more than 150 years.

The composition and functional wherewithal of the existing and reconstructed soil microbiomes varied from one site to the next, the researchers reported, though tallgrass prairie soils were largely marked by a few Verrucomicrobia phylotypes.

The presence of Verrucomicrobia bugs tended to coincide with a boost in representation by carbohydrate metabolism genes in the broader community, they noted, along with a dip in the number of genes involved in nitrogen metabolism or cell division.

By continuing to characterize verrucomicrobial contributions to soil communities, authors of the study hope to better understand features associated with soil degradation in cultivated regions of the Midwest and find clues for those attempting to restore some native prairie sites.

In a perspectives article set to appear in the same issue of Science, the University of Witwatersrand's Mary Scholes and Robert Scholes, with the Council for Scientific and Industrial Research in South Africa, discussed the threat — and potential perils — of soil degradation in the US and other parts of the world.

The pair noted that results from the native tallgrass study point to the importance of both taxonomic and functional diversity in soil microbial communities, supporting the notion that "high diversity is useful rather than redundant."

"An agricultural soil ecosystem that more closely approximates the close and efficient cycling in natural ecosystems, and that also benefits from the yield increases made possible by biotechnology and inorganic fertilizers, is needed to increase agricultural production to the levels that will be required while minimizing its adverse effects," Scholes and Scholes argued.

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