In dryland ecosystems species richness for all domains decreases with increasing aridity. Several environmental stressors (desiccation, thermal and radiation stress) in hyper-arid drylands limit the complex life forms, thus microorganisms comprise most of the standing biomass and diversity in this particular ecosystem. Interestingly, these microorganisms colonize cryptic habitats that provide shelter from harsh environmental conditions. They form unique hypolithic, cryptoendolithic and chasmoendolithic communities beneath and within rocks and soil.

The microbial diversity and community structure in refugia of the McMurdo Dry Valleys, the coldest and driest dryland on Earth, has been extensively studied using 16S rRNA gene surveys. These have revealed photoautotrophic cyanobacteria dominate hypoliths and endoliths whereas Actinobacteria dominate soil communities. Despite this, very little is known about the functionality of these communities and how they respond to environmental stress. In the first part of this study, the GeoChip DNA microarray was used to interrogate carbon and nitrogen transformation pathways of asmoendoliths, hypoliths and soil communities in a maritime-influenced location, Miers Valley. The chasmoendoliths, and hypoliths were identified as the potential primary production sites since cyanobacterial rubisco signatures were not commonly recovered from soils. Other forms of rubisco originated from Proteobacteria and archaea were identified, suggesting that chemoautotrophic pathways also contributed to carbon fixation. All communities supported diverse carbohydrate transformation pathways. However, soil communities supported significantly greater aromatic carbon utilization genes than hypoliths and chasmoendoliths, and this was related to the recalcitrant ‘legacy’ carbon stored in Antarctic soils.

For nitrogen fixation, all communities displayed the full suite of genes involved in nitrogen transformations. Soil communities generally supported slightly higher abundance of proteobacterial nitrogenase than chasmoendoliths and hypoliths, and so soil may be more important than rock as a site for microbial nitrogen fixation. Stress response pathways were also identified, and soil communities displayed higher diversity and abundance of environmental stress response pathways compared to more cryptic rock communities. The high throughput 16S rRNA gene sequencing showed Cyanobacteria (46%), Actinobacteria (31%), Proteobacteria (25%) and were relatively dominant in hypolithic and soil communities, and these phyla also displayed the greatest functional diversity. This suggests that the metabolic plasticity for these taxa may be an important factor in their role as keystone species in these communities.

In addition, GeoChip analyses also identified possible sources of community regulation in the Dry Valleys where grazing and predation are minimal or non-existent. Widespread occurrence of antibiotic resistance genes indicated that inter-specific competition may be important among these diverse communities, and phage signatures indicated a potential bottom-up control via phage lysis of microbial cells.

In a metagenomic study, protein sequences involved in extracellular polymer substances (EPS) synthesis (Wzy-dependent pathway) of dryland cyanobacteria were identified by de novo sequencing on the Miseq platform, since EPS played important roles in bio-weathering, nutrient repositories and stress response. Together with other cyanobacterial EPS synthesis protein sequences, phylogenetic analyses showed that these proteins derived different environments were not correlated to their habitats, indicating these genes were highly conserved and that EPS production might be induced and regulated under specific conditions and mechanisms.