In Australia, the historical loss of native digging mammals has profoundly changed ecosystems and their functioning. However, little is known about how the decline in digging mammal presence alters microbes and their functional potential, and how these relationships are affected by aridity. Using a metagenomics approach we surveyed the soil metagenomes from five reserves with reintroduced digging mammals and adjacent un-manipulated areas over an aridity gradient ranging from 0.077 to 0.88 (1-aridity index; 166 to 900 mm average annual rainfall), with site ranging over 3300 km of the Australian continent.