Summary A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.

A growing focus in microbial ecology is understanding of how beneficial microbiome function is created and maintained through both stochastic and deterministic assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species pools in the soil and local communities of an amphibian host. To address this, we compared the microbiomes of over 200 Plethodon cinereus salamanders along a 65km land-use gradient in the greater New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that if soil functions as the main regional species pool to amphibian skin, variation in skin microbial community composition would correlate with changes seen in the soil. We found that salamanders share many microbial taxa with their soil environment but that these two microbiomes exhibit key differences, especially in the relative abundances of the bacteria phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varied with changes in land-use associated factors such as canopy cover, impervious surface, and concentrations of the soil elements Al, Ni, and Hg, creating site-specific compositions. In addition, high dissimilarity among individual amphibian microbiomes across and within sites suggest that both stochastic and deterministic mechanisms guide the assembly of microbes onto amphibian skin, with likely consequences in disease preventative function.

<p><em>Coffea arabica</em> (coffee) is cultivated on ~28-million acres and is essential to local economies in the tropics. Coffee cultivation, however, is threatened by ongoing climate change as its optimal growth occurs in narrow temperature and precipitation ranges. Areas currently growing coffee might become unsuitable leading to increased deforestation and negative effects on coffee quality. These impacts may be especially strong in coffee cultivated in sun-grown monocultures (~75% of all production) versus shade-grown agroforestry systems given relatively higher temperatures in deforested landscapes. As such, shade-grown coffee systems might be one management strategy used to buffer from future climatic shifts. While shade-grown systems provide many ecosystem benefits, the impact of the cultivation system on soil microbiomes is poorly understood. Soil microorganisms perform vital ecosystem functions including aiding plants in nutrient acquisition, buffering against stress, as well as improving nutrient cycling. This is particularly true in shade-grown coffee systems where soil carbon could be increased through increased microbial biomass and soil nitrogen could be increased through increased plant-association with N-fixing bacteria. Therefore, further understanding of the effects of coffee cultivation methods on soil microbial communities may be key to future coffee productivity and local soil biogeochemical function. To explore these themes, we sampled the soil microbial communities at 30 coffee farms in Colombia, Peru, and El Salvador. These farms varied in cultivation system (sun vs. shade) and flavor profiles that separate specialty grade from conventional quality. Our aim was to explore if soil microbiome diversity and composition differ among the three countries, cultivation systems, and coffee quality. We sequenced the DNA of bacterial (16S) and fungal (ITS) communities in coffee soil on an Illumina MiSeq with analysis completed in QIIME2 to identify microbial taxa and composition. Coffee soil microbiomes had similar relative abundance of phyla and similar number of bacterial and fungal taxa, regardless of country of origin or cultivation system. However, coffee soil microbiomes showed pronounced differences in the microbial community composition among the different countries and cultivation systems. We show that biogeography is an important determinant of coffee soil microbiomes and location-specific impacts need to be considered in future coffee management. Further, our data suggests that sun-grown systems can alter microbial community composition compared to more-sustainable shade-grown systems potentially changing soil functionality. As an example, there were increases in taxa punitively classified as mycorrhizal fungi and N-fixing bacteria in shade-grown coffee systems. Our next steps are to link this microbial data to coffee quality and soil characteristics to uncover potential factors influencing the community structure as well as nutrient cycling rates.</p>

Soil fungal communities vary spatially due to factors including variations in plant diversity and soil characteristics; however, the relative influences of these factors on composition and therefore function remain unclear. Small-scale variation in fungal communities may drive local variation in nutrient cycling and decomposition and may respond more to local factors compared with large climatic variations. Clarifying the roles of these factors can improve our predictions of soil fungal community and biogeochemical cycling responses to anthropogenic changes. Therefore, we examined relationships among abiotic and biotic factors and soil fungal communities associated with sapling and mature trees in a mixed-hardwood woodland. We also compared community composition and fungal enzymatic activity. Fungal community composition was most associated with spatial heterogeneity of soil characteristics, while sapling and mature tree species identity were poor predictors of community composition. Further, most of the compositional variation was unexplained by measured variables, suggesting stochasticity and other environmental characteristics may drive spatial variation in these communities. Additionally, enzymatic activity did not clearly correlate with fungal community composition. Overall, soil fungal communities and enzymatic activity adjacent to trees in this woodland are most likely influenced by soil characteristics and not plant species identity.

Soil fungal communities vary spatially due to factors including variations in plant diversity and soil characteristics; however, the relative influences of these factors on composition and therefore function remain unclear. Small-scale variation in fungal communities may drive local variation in nutrient cycling and decomposition and may respond more to local factors compared with large climatic variations. Clarifying the roles of these factors can improve our predictions of soil fungal community and biogeochemical cycling responses to anthropogenic changes. Therefore, we examined relationships among abiotic and biotic factors and soil fungal communities associated with Quercus rubra and Pinus resinosa saplings and mature trees in a mixed-hardwood woodland. We also compared community composition and fungal enzymatic activity. Fungal community composition was associated with spatial heterogeneity of soil characteristics, while host sapling and tree species identity were poor predictors of community composition. Further, most of the compositional variation was unexplained by measured variables, suggesting stochasticity and other environmental characteristics may drive spatial variation in these communities. Additionally, enzymatic activity did not clearly correlate with fungal community composition. Overall, soil fungal communities and enzymatic activity adjacent to saplings in this woodland are influenced primarily by soil characteristics and stochasticity and not plant identity.