Archaea, primarily Crenarchaeota, are common in soil; however, the structure of soil archaeal communities and the factors regulating their diversity and abundance remain poorly understood. Here, we used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe. Relative archaeal abundance, the percentage of all 16S rRNA gene sequences recovered that were archaeal, averaged 2% across all soils and ranged from 0% to 10% in individual soils. Soil C:N ratio was the only factor consistently correlated with archaeal relative abundances, being higher in soils with lower C:N ratios. Soil archaea communities were dominated by just two phylotypes from a constrained clade within the Crenarchaeota, which together accounted for 70% of all archaeal sequences obtained in the survey. As one of these phylotypes was closely related to a previously identified putative ammonia oxidizer, we sampled from two long-term nitrogen (N) addition experiments to determine if this taxon responds to experimental manipulations of N availability. Contrary to expectations, the abundance of this dominant taxon, as well as archaea overall, tended to decline with increasing N. This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
Bibliographical noteFunding Information:
We thank David Tilman, Jay Lennon, Zach Aanderud, and the personnel at Cedar Creek Ecosystem Science Reserve and the Kellogg Biological Station for facilitating sample collection from these sites. We also thank Rebecca McCulley, Diana Wall, and the large number of other collaborators who helped us collect soil samples at the various sites. We acknowledge Dan Arp, Peter Bottomley, Eric Triplett, Ian Clark, Penny Hirsch and Steve McGrath for their collaboration and valuable comments on this paper. Members of the Fierer lab, particularly Chris Lauber, Kathryn Eilers and Kelly Ramirez helped with the laboratory analyses, sample processing and paper preparation. We also appreciated additional comments on the paper by Albert Barberán. Joe Jones, from EnGenCore, supervised the pyrosequencing. This research was funded by grants to RK and NF from the Bill and Melinda Gates Foundation, Crohn’s and Colitis Foundation of America, National Institutes of Health, National Science Foundation and the US Department of Agriculture.
- microbial ecology