Hypoliths, microbial assemblages found below translucent rocks, provide important
ecosystem services in deserts. While several studies have assessed microbial diversity
of hot desert hypoliths and whether these communities are metabolically active, the
interactions among taxa remain unclear. Here, we assessed the structure, diversity, and
co-occurrence patterns of hypolithic communities from the hyperarid Namib Desert
by comparing total (DNA) and potentially active (RNA) communities. The potentially
active and total hypolithic communities differed in their composition and diversity, with
significantly higher levels of Cyanobacteria and Alphaproteobacteria in potentially active
hypoliths. Several phyla known to be abundant in total hypolithic communities were
metabolically inactive, indicating that some hypolithic taxa may be dormant or dead.
The potentially active hypolith network was highly modular in structure with almost
exclusively positive co-occurrences (>95% of the total) between taxa. Members of the
Cyanobacteria and Alphaproteobacteria were identified as potential keystone taxa, and
exhibited numerous positive co-occurrences with other microbes, suggesting that these
groups might have important roles in maintaining network topological structure despite
their low abundance.