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Soil Sequencing Uncovers 500 Common, Abundant Bacterial Species

NEW YORK (GenomeWeb) – Only a small percentage of bacterial species are both common and abundant in soils around the world, a new sequencing analysis has found.

A University of Colorado, Boulder-led team of researchers sequenced hundreds of soil samples obtained from six continents to create an atlas of soil bacteria. As the team reported in Science today, it found that though soil microbes are tremendously diverse, there are about 500 bacterial species that account for about half of worldwide soil bacterial communities.

"With this research, we have started to open the black box and are gaining a better understanding of what microbes are living in our soils," first author Manuel Delgado-Baquerizo from CU Boulder said in a statement.

Delgado-Baquerizo and his colleagues collected soil samples from 237 sites around the globe, spanning 18 countries and a range of climate and ecosystem types. They amassed samples from forests and shrublands as well as from arid and tropical regions. Using 16S rRNA gene amplicon sequencing, the researchers identified the dominant — both the most abundant and most ubiquitous — bacterial species, or phylotypes among the samples.

The samples were highly variable, the researchers reported. Some samples contained hundreds of phylotypes, while others harbored thousands.

Still, they found that 2 percent of the bacterial phylotypes — or 511 of the 25,224 phylotypes — were dominant. These phylotypes accounted for 41 percent of 16S rRNA gene sequences across all samples and were found at sites across the six continents studied.

About 85 percent of the phylotypes identified by the researchers were also uncovered by a previous shotgun metagenomic study of 123 soils, and the majority of the dominant phylotypes found by the Earth Microbiome Project were also on the researchers' list from this study, which provides some validation of their findings, they said.

These dominant phylotypes include species belonging to Alphaproteobacteria, Betaproteobacteria, and Actinobacteria, among others.

Using random forest modeling, Delgado-Baquerizo and his colleagues sought to uncover whether the phylotypes had specific habitat preferences. Their model took 15 environmental variables, such as aridity, ultraviolent radiation levels, and soil pH, into account. They found that slightly more than half of the 511 dominant phylotypes had predictable habitat preferences. Variables such as soil pH, climatic factors like soil pH and seasonal rainfall levels, and plant productivity were the best predictors of the bacterial abundance, the researchers noted.

Two hundred of these 270 phylotypes could also then be clustered into five groups with similar habitat preferences: high pH, low pH, drylands, low plant productivity, and dry-forest environment. Each cluster included phylotypes from a range of phyla, suggesting to the researchers that habitat preference wasn't linked to phylogeny.

They did, though, examine the genomes of the members of each cluster to see whether they shared any particular characteristics. While they had a limited sample size for four of the five clusters, the researchers could still tease out that the drylands cluster had an increased relative abundance of 18 genes. This gene set includes Mnh and Mrp genes, which both encode membrane transport proteins, and have been linked to bacterial tolerance to alkaline or saline conditions.

Co-author Noah Fierer noted that this list and groupings of soil bacteria could help focus research efforts to understand the roles of the bacteria. Further study of these dominant soil bacteria could have agricultural applications, he and his colleagues said.

"Eventually, knowing more about these bacteria might allow us to improve soil health and fertility," Delgado-Baquerizo added. "There's a lot that we can do now that we have some tractable information."