Leafcutter ants enhance microbial drought resilience in tropical forest soil.

We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

Bacterial denitrification drives elevated N2O emissions in arid southern California drylands.

Soils are the largest source of atmospheric nitrous oxide (N2O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N2O-producing process, yet, among the largest N2O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N2O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N2O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ15Nbulk = 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N2O emissions by 59%. Our results suggest that despite extreme environmental conditions-months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%-bacterial denitrifiers can account for most of the N2O emitted when dry soils are wetted.

Leaf-cutter ants - mycorrhizal fungi: observations and research questions from an unexpected mutualism.

Leaf-cutter ants (LCAs) are widely distributed and alter the physical and biotic architecture above and below ground. In neotropical rainforests, they create aboveground and belowground disturbance gaps that facilitate oxygen and carbon dioxide exchange. Within the hyperdiverse neotropical rainforests, arbuscular mycorrhizal (AM) fungi occupy nearly all of the forest floor. Nearly every cubic centimeter of soil contains a network of hyphae of Glomeromycotina, fungi that form arbuscular mycorrhizae. Our broad question is as follows: how can alternative mycorrhizae, which are-especially ectomycorrhizae-essential for the survival of some plant species, become established? Specifically, is there an ant-mycorrhizal fungus interaction that facilitates their establishment in these hyperdiverse ecosystems? In one lowland Costa Rican rainforest, nests of the LCA Atta cephalotes cover approximately 1.2% of the land surface that is broadly scattered throughout the forest. On sequencing the DNA from soil organisms, we found the inocula of many AM fungi in their nests, but the nests also contained the inocula of ectomycorrhizal, orchid mycorrhizal, and ericoid mycorrhizal fungi, including Scleroderma sinnamariense, a fungus critical to Gnetum leyboldii, an obligate ectomycorrhizal plant. When the nests were abandoned, new root growth into the nest offered opportunities for new mycorrhizal associations to develop. Thus, the patches created by LCAs appear to be crucial sites for the establishment and survival of shifting mycorrhizal plant-fungal associations, in turn facilitating the high diversity of these communities. A better understanding of the interactions of organisms, including cross-kingdom and ant-mycorrhizal fungal interactions, would improve our understanding of how these ecosystems might tolerate environmental change.

Root endophytic bacterial and fungal communities in a natural hot desert are differentially regulated in dry and wet seasons by stochastic processes and functional traits.

Dryland ecosystems experience seasonal cycles of severe drought and moderate precipitation. Desert plants may develop symbiotic relationships with root endophytic microbes to survive under the repeated wet and extremely dry conditions. Although community coalescence has been found in many systems, the colonization by functional microbes and its relationship to seasonal transitions in arid regions are not well understood. Here we examined root endophytic microbial taxa, and their traits in relation to their root colonization, during the dry and wet seasons in a hot desert of the southwestern United States. We used high-throughput DNA sequencing of 16S rRNA and internal transcribed spacer gene profiling of five desert shrubs, and analyzed the seasonal change in endophytic microbial lineages. Goodness of fit to the neutral community model in relationship to microbial traits was evaluated. In summer, Actinobacteria and Bacteroidia increased, although this was not genus-specific. For fungi, Glomeraceae selectively increased in summer. In winter, Gram-negative bacterial genera, including those capable of nitrogen fixation and plant growth promotion, increased. Neutral model analysis revealed a strong stochastic influence on endophytic bacteria but a weak effect for fungi, especially in summer. The taxa with higher frequency than that predicted by neutral model shared environmental adaptability and symbiotic traits, whereas the frequency of pathogenic fungi was at or under the predicted value. These results suggest that community assembly of bacteria and fungi is regulated differently. The bacterial community was affected by stochastic and deterministic processes via bacterial response to drought (response trait), beneficial effect on plants (effect trait), and likely stable mutualistic interactions with plants suggested by the frequency of nodule bacteria. For fungi, mycorrhizal fungi were selected by plants in summer. The regulation of beneficial microbes by plants in both dry and wet seasons suggests the presence of plant-soil positive feedback in this natural desert ecosystem.

Wetting-induced soil CO2 emission pulses are driven by interactions among soil temperature, carbon, and nitrogen limitation in the Colorado Desert.

Warming-induced changes in precipitation regimes, coupled with anthropogenically enhanced nitrogen (N) deposition, are likely to increase the prevalence, duration, and magnitude of soil respiration pulses following wetting via interactions among temperature and carbon (C) and N availability. Quantifying the importance of these interactive controls on soil respiration is a key challenge as pulses can be large terrestrial sources of atmospheric carbon dioxide (CO2 ) over comparatively short timescales. Using an automated sensor system, we measured soil CO2 flux dynamics in the Colorado Desert-a system characterized by pronounced transitions from dry-to-wet soil conditions-through a multi-year series of experimental wetting campaigns. Experimental manipulations included combinations of C and N additions across a range of ambient temperatures and across five sites varying in atmospheric N deposition. We found soil CO2 pulses following wetting were highly predictable from peak instantaneous CO2 flux measurements. CO2 pulses consistently increased with temperature, and temperature at time of wetting positively correlated to CO2 pulse magnitude. Experimentally adding N along the N deposition gradient generated contrasting pulse responses: adding N increased CO2 pulses in low N deposition sites, whereas adding N decreased CO2 pulses in high N deposition sites. At a low N deposition site, simultaneous additions of C and N during wetting led to the highest observed soil CO2 fluxes reported globally at 299.5 µmol CO2  m-2  s-1 . Our results suggest that soils have the capacity to emit high amounts of CO2 within small timeframes following infrequent wetting, and pulse sizes reflect a non-linear combination of soil resource and temperature interactions. Importantly, the largest soil CO2 emissions occurred when multiple resources were amended simultaneously in historically resource-limited desert soils, pointing to regions experiencing simultaneous effects of desertification and urbanization as key locations in future global C balance.

Effects of experimental nitrogen deposition on soil organic carbon storage in Southern California drylands.

Atmospheric nitrogen (N) deposition is enriching soils with N across biomes. Soil N enrichment can increase plant productivity and affect microbial activity, thereby increasing soil organic carbon (SOC), but such responses vary across biomes. Drylands cover ~45% of Earth's land area and store ~33% of global SOC contained in the top 1 m of soil. Nitrogen fertilization could, therefore, disproportionately impact carbon (C) cycling, yet whether dryland SOC storage increases with N remains unclear. To understand how N enrichment may change SOC storage, we separated SOC into plant-derived, particulate organic C (POC), and largely microbially derived, mineral-associated organic C (MAOC) at four N deposition experimental sites in Southern California. Theory suggests that N enrichment increases the efficiency by which microbes build MAOC (C stabilization efficiency) if soil pH stays constant. But if soils acidify, a common response to N enrichment, then microbial biomass and enzymatic organic matter decay may decrease, increasing POC but not MAOC. We found that N enrichment had no effect on C fractions except for a decrease in MAOC at one site. Specifically, despite reported increases in plant biomass in three sites and decreases in microbial biomass and extracellular enzyme activities in two sites that acidified, POC did not increase. Furthermore, microbial C use and stabilization efficiency increased in a non-acidified site, but without increasing MAOC. Instead, MAOC decreased by 16% at one of the sites that acidified, likely because it lost 47% of the exchangeable calcium (Ca) relative to controls. Indeed, MAOC was strongly and positively affected by Ca, which directly and, through its positive effect on microbial biomass, explained 58% of variation in MAOC. Long-term effects of N fertilization on dryland SOC storage appear abiotic in nature, such that drylands where Ca-stabilization of SOC is prevalent and soils acidify, are most at risk for significant C loss.

Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California.

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions.

Global climate and land use change are causing woody plant encroachment in arctic, alpine, and arid/semi-arid ecosystems around the world, yet our understanding of the belowground impacts of this phenomenon is limited. We conducted a globally distributed field study of 13 alpine sites across four continents undergoing woody plant encroachment and sampled soils from both woody encroached and nearby herbaceous plant community types. We found that woody plant encroachment influenced soil microbial richness and community composition across sites based on multiple factors including woody plant traits, site level climate, and abiotic soil conditions. In particular, root symbiont type was a key determinant of belowground effects, as Nitrogen-fixing woody plants had higher soil fungal richness, while Ecto/Ericoid mycorrhizal species had higher soil bacterial richness and symbiont types had distinct soil microbial community composition. Woody plant leaf traits indirectly influenced soil microbes through their impact on soil abiotic conditions, primarily soil pH and C:N ratios. Finally, site-level climate affected the overall magnitude and direction of woody plant influence, as soil fungal and bacterial richness were either higher or lower in woody encroached versus herbaceous soils depending on mean annual temperature and precipitation. All together, these results document global impacts of woody plant encroachment on soil microbial communities, but highlight that multiple biotic and abiotic pathways must be considered to scale up globally from site- and species-level patterns. Considering both the aboveground and belowground effects of woody encroachment will be critical to predict future changes in alpine ecosystem structure and function and subsequent feedbacks to the global climate system.

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next-generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0-5 cm) beneath giant sequoia and co-occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove-dependent.

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

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.

Establishment and characterization of a multi-purpose large animal exposure chamber for investigating health effects.

Air pollution poses a significant threat to the environment and human health. Most in vivo health studies conducted regarding air pollutants, including particulate matter (PM) and gas phase pollutants, have been either through traditional medical intranasal treatment or using a tiny chamber, which limit animal activities. In this study, we designed and tested a large, whole-body, multiple animal exposure chamber with uniform dispersion and exposure stability for animal studies. The chamber simultaneously controls particle size distribution and PM mass concentration. Two different methods were used to generate aerosol suspension through either soluble material (Alternaria extract), liquid particle suspension (nanosilica solution), or dry powder (silica powder). We demonstrate that the chamber system provides well controlled and characterized whole animal exposures, where dosage is by inhalation of particulate matter.

Environmental impacts on the diversity of methane-cycling microbes and their resultant function.

Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5-15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters.

Meta-analysis of environmental impacts on nitrous oxide release in response to N amendment.

Atmospheric nitrous oxide (N(2)O) accounts for approximately 5% of the global greenhouse effect and destroys stratospheric ozone. Soils are the most important source of N(2)O, which is produced during nitrification and denitrification. To assess the impact of environmental variables and ecosystems on N(2)O flux, we performed a meta-analysis comparing N(2)O flux in N amended and matched control plots in non-agricultural soils. We found that N(2)O release increased with N amendment in the short term. Although there were few studies in shrubland, this ecosystem showed the greatest response. The N(2)O response to N amendment was greater in year-round studies and in studies with more measurements, but lower in longer studies. The N(2)O response was greater at higher latitudes and precipitation rates. We also observed an unexpected 55% decline in the N(2)O response to N amendment over the 23 years covered by the studies. This pattern may reflect a suppression of the N(2)O response from long-term N deposition accumulation, particularly in temperate regions. Although short term increases in reactive N entering natural systems may cause positive feedbacks to the release of N(2)O, this effect may diminish over time in locations with high rates of N deposition.