With human activity transforming nearly all of Earth's natural systems and the population now exceeding 7 billion people, humanity's growing ecological footprint is altering the planet's land cover, rivers and oceans, climate system, biological cycles, and the functioning of its ecosystems. So far, terrestrial ecosystems have been good to us by providing 'services' including nutrition, purification of water, protection from natural hazards, and reduction of some infectious diseases. However, there is widespread debate about the ability of an altered terrestrial ecosystem to meet the needs of a growing and prospering human population. Here, we describe how climate change will affect terrestrial ecosystems and their capacity to reduce infectious diseases. Rhizosphere and bulk soil was collected from grassland and forest ecosystems at the Hawkesbury and EUC-FACE climate change field experiments in Western Sydney (Australia). Real-time PCR approaches targeting toxins-encoding genes revealed that elevated CO2 and rainfall patterns intensified the effect of warming by significantly increasing the virulence of soil-borne human pathogens associated with grassland and forest rhizosphere and bulk soils. As opposed to simply increasing the biomass of soil-borne pathogens at ambient CO2 under changes in rainfall patterns and temperature, elevated atmospheric CO2 strongly selected for virulent human pathogens and effected shifts in pathogens composition. Bacterial metagenomic analysis revealed the dominance of several opportunistic and true human pathogens in the rhizosphere microbiome, including Staphylococcus, Salmonella, Clostridium and Vibrio species. The potential mechanisms involved in the interplay between the good, the bad and the ugly in the rhizosphere microbiome are presented in a bioclimatic model of relative microbial abundance that specifically incorporates interactions between biological units.