Archaea, one of three Domains of Life, are microorganisms that have only recently been discovered as ubiquitous soil residents. However, their diversity and function in the complex soil environment is still not fully understood. This work reports on diversity and potential function of Archaea using soils displaying a range of physiochemical characteristics collected from the rhizosphere of Arabidopsis thaliana(Arabidopsis), geographic locations around the world, and tropical soils that have direct anthropogenic effects on the community structure through land-use changes for agricultural purposes.

To better understand the diversity of Archaea in these soils, molecular fingerprinting techniques using the 16S rRNA gene and the 16S-23S internal transcribed spacer regions of DNA were employed. In an experimental design using Arabidopsis , an important plant model, four genotype accessions of the plant were grown and the rhizosphere soil was collected. Based on the molecular techniques used, differences in the community diversity were not detected. A subsequent study with genetically engineered Arabidopsis plants phenotypically producing varying levels of glucosinolate, a phytochemical exuded by the root, showed statistically significant differences in the archaeal community suggesting that there is a dynamic relationship between the plant and archaeal community in the rhizosphere.

A primer used for molecular fingerprinting was designed as part of this study and tested in soils displaying a range of physio-chemical characteristics. With this, high levels of archaeal (specifically Thaumarchaeota) diversity were detected allowing its use as a novel tool to assess diversity.

DNA fingerprinting results from soils collected in this study revealed that human land-use has an impact on thaumarchaeal communities in Costa Rican rainforests. Specifically, the gene coding for a subunit of ammonia monoxygenase (amoA), an enzyme used by microorganisms to oxidize NH ₃, can be detected in thaumarchaea and used as a marker to link this group to nitrification in soils. Phylogenetic analysis revealed that the thaumarchaeaota community present in these soils are closely related to thaumarchaea occurring in seawater, sediments, and soil. Changes in the thaumarchaeal communities observed are of larger significance because of the role these organisms play in the nitrogen cycle by providing nutrient turnover for tropical plants.