Protecting the unseen majority: Land cover and environmental factors linked with soil bacterial communities and functions in New Zealand

The biodiversity in soil ecosystems is simultaneously incredibly rich and poorly described. In countries such as New Zealand, where high endemism in plant species emerged following extended geographical isolation, it is likely similar evolutionary pressures extended to soil microbial communities (our biodiversity ‘dark matter’). However, we have little understanding of the extent of microbial life in New Zealand soils, let alone estimates of endemism, rates of species loss or gain, or implications for systems where plants and their microbiomes have co-evolved. In this study, we tested for the impacts of land-cover type (native forest, planted forest with exotic conifers, and pastoral agriculture) on soil bacterial communities and their functional potential, using environmental microarrays (PhyloChip and GeoChip, respectively). This evaluation was conducted across four environmentally different locations (Hokitika, Banks Peninsula, Craigieburn, and Eyrewell). The environment from which samples were collected was the largest and most significant factor associated with variation in bacterial community assemblage and function. As such, novel pockets of bacterial biodiversity, with discrete ecosystem function, may be present in New Zealand. There was some evidence to suggest that change in land cover affected soil bacterial species, but not their functions. Secondary testing found this effect was restricted to differences between native forest and agricultural land use. Bacterial communities and functions between native and planted forests were similar. Analysis of soil environmental properties among samples found that land cover effects were underpinned by changes in soil pH that typically accompanies application of lime in agricultural systems, but is uncommon in planted forests. When compared with other studies conducted in New Zealand, we conclude that: (1) different locations can harbour distinct communities of soil microbial diversity, and (2) land-use intensification, not land cover change per se, shifts microbial biodiversity through alteration of primary habitat conditions, particularly soil pH.