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Team Profiles Microbial Communities in Soils Spanning Several Environments

NEW YORK (GenomeWeb News) – In a study appearing in the early, online edition of the Proceedings of the National Academy of Sciences this week, researchers reported on results from a comparison of soil microbial communities across a range of natural biomes.

An international team led by investigators from the University of Colorado at Boulder, Argonne National Laboratory, and Northern Arizona University used 16S ribosomal RNA sequencing and metagenomic sequencing to profile the functional, taxonomic, and phylogenetic features of soil microbe communities from more than a dozen sites. These included hot and cold deserts as well as forest, tundra, and grassland locations.

"As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes," University of Colorado, Boulder, ecology and evolutionary biology researcher Noah Fierer, the study's corresponding author, and his colleagues wrote.

Together, results of the analyses highlight the distinctiveness of microbe communities in desert soils. For instance, soil from cold desert environments housed microbial communities with low overall diversity, the researchers reported. In both the hot and cold desert samples, meanwhile, investigators saw microbial communities rich in genes needed for dormancy and osmotic regulation, but lacking in antibiotic resistance genes or genes to cycle nutrients or break down plant matter.

A good deal of effort has gone into defining plant and animal interactions within terrestrial biomes, the authors of the study noted. But, research on the collections of microorganisms that inhabit soils from these environments is at an earlier stage. Even so, they said, "we are beginning to understand how soil microbial diversity varies across the globe and how this diversity is related to the physical, chemical, and biological characteristics of an ecosystem."

In an effort to explore relationships between soil properties, microbe community diversity, and the functional capabilities of these communities, the team assessed samples from 16 locales.

Nine of these were deserts — three hot and six cold — as the researchers were especially keen to compare the taxonomy and function of desert soil microbiomes with those from other environments. The seven remaining samples represented temperate, tropical, or boreal forests and prairie grasslands or tundra sites.

To take a peek at the collection of genes present in each sample, researchers performed metagenomic paired-end sequencing with the Illumina GAIIx, generating between 688,000 and 1.9 million reads per sample. Most of those reads came from bacteria or archaea, they noted, though some represented genes from fungi or other eukaryotes.

On top of that, the team used 16S rRNA amplicon sequencing on Illumina's HiSeq 2000 to take a closer look at community composition and taxonomic diversity.

As researchers suspected from the low water levels, high pH, and dearth of plant material characterizing most desert sites, soils from both hot and cold deserts had microbial communities that were taxonomically and functionally distinct from those in the other biomes.

The team's metagenomic analyses uncovered genes from almost three dozen functional categories that showed distinguishable patterns in these desert biomes. For instance, desert soil microbiomes tended to contain distinct metabolic pathways, more stress response or dormancy-related genes, and fewer genes contributing to antibiotic resistance.

Samples from cold desert sites also contained microbial communities with especially low diversity, they reported, both in terms of microorganism taxonomy and phylogeny.

Soils at the other pH extreme — such as highly acidic soils from the Peruvian rainforest or Arctic tundra — showed a dip in microbial diversity, too, the team said, while a neutral soil pH seemed to foster more diverse communities of soil microbes.

Despite what they've learned so far, though, those involved in the study cautioned that even deeper sequencing will likely be needed to reveal the full range of taxonomic, phylogenetic, and functional features in each soil sample.

"As sequencing capacities continue to increase and tools for analyzing the resulting data become more effective," the researchers concluded, "we will soon be able to expand upon the work presented here and gain a more comprehensive understanding of how soil microbial communities vary across time and space."