Why Sequence Root-Colonizing Crenarchaeotes and Their Community?

Natural organic matter largely consists of humic substances, a class of biogenic and refractory organic compounds that are prevalent in all terrestrial and aquatic environments. Because these substances are major reservoirs of organic carbon, the global carbon cycle is affected in critical ways by microorganisms that mediate their turnover. Mesophilic crenarchaeotes may be a group of such organisms. Two hypotheses about the carbon and energy utilization pathways in mesophilic crenarchaeotes have been developed to explain results from enrichment culture and environmental studies. Genomic sequence analysis will help determine whether a genetic basis exists to support these hypotheses.

One hypothesis suggests that terrestrial crenarchaeotes indirectly catalyze the oxidization of natural organic matter by a mechanism involving the direct oxidation of Mn(II). While the ability to oxidize Mn(II) is widespread in bacteria and fungi found in diverse fresh and marine waters, sediments, and soils, it has not yet been documented in archaea. If uncovered in mesophilic crenarchaeotes, a major role in global carbon cycling would be potentially implicated for these ubiquitous archaeal organisms. Investigations based on such results could also enhance our understanding of the roles of Mn(II)-oxidizing microorganisms in the biogeochemical cycling of carbon. Furthermore, interest in the nature, roles, and applications of humic substances extends beyond that of microbiologists and soil scientists to geochemists, aquatic biologists, environmental scientists, and medical researchers.

The possibility that mesophilic crenarchaeotes have a role in nitrogen cycling via denitrification is also being explored. Denitrification is one of two major processes of microbial nitrogen transformation (the other being nitrification) and leads to the formation of gaseous nitrogenous compounds by way of the anaerobic reduction of NO₃. Because the major product of denitrification is N₂, the process results in the loss of nitrogen from the biosphere. Uncovering a role for mesophilic crenarchaeotes in denitrification would have major implications for their impact on nutrient cycles in the biosphere.

In addition to the impacts mentioned above, results from this work will contribute to knowledge about archaeal and bacterial genome structures and metabolisms, and interactions of microorganisms in mixed-species assemblages.

CSP project participants: Holly M. Simon (proposer, Oregon Health and Science Univ.), Ross Overbeek (Fellowship for Interpretation of Genomes), and Heidi J.Sofia (Pacific Northwest Natl. Lab.).