The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.

Plant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, “generalist” pathogens are likely segregated, while hosting more abundant unique, “specialist” ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal “fingerprinting” into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.

Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity vary between the vegetated canopy and gap soils. The specific aim of this study was to characterize canopy versus gap microsite effect on soil microbial diversity, the capacity of gap soils to serve as a canopy soil microbial reservoir, nitrogen (N)-mineralization genetic potential (ureC gene abundance) and urease enzyme activity, and microbial-nutrient pool associations in four arid-hyperarid geolocations of the western Sonoran Desert, Arizona, United States. Microsite combined with geolocation explained 57% and 45.8% of the observed variation in bacterial/archaeal and fungal community composition, respectively. A core microbiome of amplicon sequence variants was shared between the canopy and gap soil communities; however, canopy soils included abundant taxa that were not present in associated gap communities, thereby suggesting that these taxa cannot be sourced from the associated gap soils. Linear mixed-effects models showed that canopy soils have significantly higher microbial richness, nutrient content, and organic N-mineralization genetic and functional capacity. Furthermore, ureC gene abundance was detected in all samples, suggesting that ureC is a relevant indicator of N mineralization in deserts. Additionally, novel phylogenetic associations were observed for ureC, with the majority belonging to Actinobacteria and uncharacterized bacteria. Thus, key N-mineralization functional capacity is associated with a dominant desert phylum. Overall, these results suggest that lower microbial diversity and functional capacity in gap soils may impact ecosystem sustainability as aridity drives open-space expansion in deserts. IMPORTANCE Increasing aridity will drive a shift in desert vegetation and interspace gap (microsite) structure toward gap expansion. To evaluate the impact of gap expansion, we assess microsite effects on soil nutrients, microbiome community composition and functional capacity, and the potential of gap soils to serve as microbial reservoirs for plant root-associated microbiomes in an arid ecosystem. Results indicate that gap soils have significantly lower bioavailable nutrients, microbial richness, and N-mineralization functional capacity. Further, abundance of the bacterial urease gene (ureC) correlates strongly with N availability, and its major phylogenetic association is with Actinobacteria, the dominant phylum found in deserts. This finding is relevant because it identifies an important N-mineralization capacity indicator in the arid soil microbiome. Such indicators are needed to understand the relationships between interplant gap expansion and microbial diversity and functional potential associated with plant sustainability. This will be a critical step in recovery of land degraded by aridity stress.