Urbanization, an extreme form of land use change, has increasingly caused shifts in the diversity and the functioning of surrounding ecosystems. Its effects are amplified in the soil environment, which contains a diverse community of microorganisms whose characteristics and functionality change as the environment is disturbed. This can have important consequences for larger vertebrate organisms, such as amphibians, which obtain their skin microbes from soil. Environmental gradients, such as soil pH, moisture, and distance from a stream, are useful for studying how abiotic factors associated with urbanization may alter soil microbial diversity indirectly affecting which microbes are available to colonize amphibians. Soil samples were collected from nine amphibian habitats across an urban-to-rural gradient originated in New York City, USA. Bacterial DNA was extracted and amplified using the 515F/806R primer pair and sequenced on an Illumina MiSeq. Sequences were analyzed in QIIME2 and alpha and beta diversity was calculated using Shannon index and UniFraq, respectively. We hypothesized that diversity would be positively correlated with pH and moisture, with urban areas being the most diverse.
Results/Conclusions
In agreement with other studies in temperate forest habitats, our soils were dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Soil pH was more important in driving variation in diversity than either moisture or distance from stream. In agreement with our hypothesis, urban soils were the most diverse, but were uneven—dominated by a few highly abundant taxa. Using NMDS and PERMANOVA, we noted that soils clustered both by site and level of urbanization showing distinct differences in community composition across our gradient. Studying microbial diversity differences along land-use gradients will help to elucidate the effects of urbanization on soil, microbial, and other ecosystems, providing us with a framework for how to approach problems of conservation and responsible land use change in the future. Results of this study may inform further research on the impact of the soil reservoir on disease prevention in amphibian communities affected by urbanization.