Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Inoculation may influence mycorrhizal colonization and provide benefits to plants in restoration projects. However, it is unclear whether inoculation has consistent effects across ecosystem types, if it has long-term effects on colonization, and whether sources of inocula differ in their effectiveness. To address these issues, we performed a meta-analysis of published restoration studies across a variety of ecosystems to examine the effects of mycorrhizal inoculation on mycorrhizal establishment and plant growth under field conditions. Although we included trials from a variety of geographic locations, disturbance types, and ecosystem types, the majority were based in temperate ecosystems in the Northern Hemisphere, and fewer trials were from tropical ecosystems. Across ecosystem types, we found that inoculation consistently increased the abundance of mycorrhizal fungi in degraded ecosystems, and thus improved the establishment of plants. These benefits did not significantly attenuate over time. Moreover, inocula from different sources varied in their effects on mycorrhizal colonization. Inocula sourced from reference ecosystems and inocula with specific fungal species yielded higher increases in mycorrhizal colonization than did inocula from commercial sources. These results suggest that inocula source matters, and that an initial investment into mycorrhizal inoculation could provide lasting benefits for facilitating the establishment of the below-and aboveground components of restored ecosystems.

Fungal community composition often shifts in response to warmer temperatures, which might influence decomposition of recalcitrant carbon (C). We hypothesized that evolutionary trade-offs would enable recalcitrant C-using taxa to respond more positively to warming than would labile C-using taxa. Accordingly, we performed a warming experiment in an Alaskan boreal forest and examined changes in the prevalence of fungal taxa. In a complementary field trial, we characterized the ability of fungal taxa to use labile C (glucose), intermediate C (hemicellulose or cellulose), or recalcitrant C (lignin). We also assigned taxa to functional groups (e.g., free-living filamentous fungi, ectomycorrhizal fungi, and yeasts) based on taxonomic identity. We found that response to warming varied most among taxa at the order level, compared to other taxonomic ranks. Among orders, ability to use lignin was significantly related to increases in prevalence in response to warming. However, the relationship was weak, given that lignin use explained only 9% of the variability in warming responses. Functional groups also differed in warming responses. Specifically, free-living filamentous fungi and ectomycorrhizal fungi responded positively to warming, on average, but yeasts responded negatively. Overall, warming-induced shifts in fungal communities might be accompanied by an increased ability to break down recalcitrant C. This change in potential function may reduce soil C storage under global warming.

Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well-understood. We used high-throughput sequencing to examine the large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.

Few studies have investigated how soil fungal communities respond to elevation, especially within TMCF (tropical montane cloud forests). We used an elevation gradient in a TMCF in Costa Rica to determine how soil properties, processes, and community composition of fungi change in response to elevation and across seasons. As elevation increased, soil temperature and soil pH decreased, while soil moisture and soil C:N ratios increased with elevation. Responses of these properties varied seasonally. Fungal abundance increased with elevation during wet and dry seasons. Fungal community composition shifted in response to elevation, and to a lesser extent by season. These shifts were accompanied by varying responses of important fungal functional groups during the wet season and the relative abundance of certain fungal phyla. We suggest that elevation and the responses of certain fungal functional groups may be structuring fungal communities along this elevation gradient. TMCF are ecosystems that are rapidly changing due to climate change. Our study suggests that these changes may affect how fungal communities are structured.

The generation and transport of mineral dust is strongly related to climate on seasonal, year-to-year, and glacialinterglacial timescales. The modern dust cycle is influenced by soil moisture, which is partly a function of drought duration and severity. The production and transport of dust can therefore be amplified by global and regional droughts, thereby moderating ecosystem vulnerability to disturbance through the influence of dust on nutrient delivery to ecosystems. In this work, we use strontium and neodymium isotopes in combination with trace element concentrations in modern dust samples collected in 2015 to quantify the role of regionally versus globally supplied dust in nutrient delivery to a montane ecosystem. The study sites lie along an elevational transect in the southern Sierra Nevada, USA, with samples spanning the dry seasons of 2014 (Aciego et al., 2017) and 2015 (this study), when the region was experiencing a historic drought. The goal of our research was to quantify the spatial and temporal variability and sensitivity of the dust cycle to short term changes at nutrientlimited sites. We find that, during the dry season of 2015, Asian sources contributed between 10 and 40% of dust to sites located along this elevational transect, and importantly increased in importance during the summer growing season compared to regional dust sources. These changes are likely related to the prolonged drought in Asia in 2015, highlighting both the sensitivity of dust production and transport to drought and the teleconnections of dust transport in terrestrial ecosystems.

The Salton Sea Basin in California suffers from poor air quality, and an expanding dry lakebed (playa) presents a new potential dust source. In 2017−18, depositing dust was collected approximately monthly at five sites in the Salton Sea Basin and analyzed for total elemental and soluble anion content. These data were analyzed with Positive Matrix Factorization (PMF). The PMF method resolved seven dust sources with distinct compositional markers: Playa (Mg, SO 4 2− , Na, Ca, Sr), Colorado Alluvium (U, Ca), Local Alluvium (Al, Fe, Ti), Agricultural Burning (K, PO 4 3− ), Sea Spray (Na, Cl − , Se), Anthropogenic Trace Metals (Sb, As, Zn, Cd, Pb, Na), and Anthropogenic Copper (Cu). All sources except Local Alluvium are influenced or caused by current or historic anthropogenic activities. PMF attributed 55 to 80% of the measured dust flux to these six sources. The dust fluxes at the site where the playa source was dominant (89 g m −2 yr −1 ) were less than, but approaching the scale of, those observed at Owens Lake playas in the late 20th century. Playa emissions in the Salton Sea region were most intense during the late spring to early summer and contain high concentrations of evaporite mineral tracers, particularly Mg, Ca, and SO 4 2− .