Soil microbial diversity drops with land-use change in a high mountain temperate forest: a metagenomics survey

Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high-altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high-altitude temperate oak and pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R² = 0.41) with the 10-25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.