Urbanization and fragmentation interact to drive mutualism breakdown and the rise of unstable pathogenic communities in forest soil

Temperate forests are particularly threatened by urbanization and fragmentation, with over 20% (120lJ000 km2) of recently urbanized land in the U.S. subsuming natural forests. We leveraged a unique, well-characterized urban-to-rural and forest edge-to-interior gradient to identify the combined impact of these two land use changes - urbanization and forest fragmentation - on soil microbial community in native, remnant forests. We found evidence of mutualism breakdown between trees and their fungal root mutualists (ectomycorrhizal (ECM) fungi) with urbanization, where ECM fungi colonized fewer tree roots and had less connectivity in soil microbiome networks in urban forests compared to rural forests. However, urbanization did not reduce the relative abundance of ECM fungi in forest soils; instead, forest fragmentation alone led to strong reductions in ECM fungal abundance. At forest edges, ECM fungi were replaced by plant and animal pathogens, as well as copiotrophic, xenobiotics-degrading, and nitrogen-cycling bacteria, including nitrifiers and denitrifiers. Urbanization and fragmentation interacted to generate “suites” of microbes, with urban interior forests harboring highly homogenized microbiomes, while edge forests microbiomes were more heterogeneous and less stable, showing increased vulnerability to low soil moisture. When scaled to the regional level, we found that forest soils are projected to harbor high abundances of fungal pathogens and denitrifying bacteria, even in rural areas, due to extreme, widespread forest fragmentation. Our results highlight the potential for soil microbiome dysfunction - including increased greenhouse gas production - in temperate forest regions that are subsumed by urban expansion, both now and in the future.Significance StatementUrbanization and forest fragmentation are increasingly altering Earth’s ecosystems, yet the effects on soil microbiomes, crucial for plant health and climate regulation, remain unclear. Our data indicate that, in forested land, these two combined, compounding stressors reshape the soil microbiome in ways that could lead to more pathogen infections of plants and animals, higher rates of N loss due to denitrification, and the possibility of tree symbiont extinctions. By identifying the specific environmental stressors that lead to these microbiome shifts, our analysis can be used to inform urban development and forest management plans to mitigate impacts on the soil microbiome to sustain environmental quality and the ecosystem services that remnant native forests provide to society in the coming decades.ClassificationBiological Sciences/Ecology