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Soil drying and wetting cycles can produce pulses of nitric oxide (NO) and nitrous oxide (N2O) emissions with substantial effects on both regional air quality and Earth’s climate. While pulsed production of N emissions is ubiquitous across ecosystems, the processes governing pulse magnitude and timing remain unclear. We studied the processes producing pulsed NO and N2O emissions at two contrasting drylands, desert and chaparral, where despite the hot and dry conditions known to limit biological processes, some of the highest NO and N2O flux rates have been measured. We measured N2O and NO emissions every 30 min for 24 h after wetting soils with isotopically-enriched nitrate and ammonium solutions to determine production pathways and their timing. Nitrate was reduced to N2O within 15 min of wetting, with emissions exceeding 1000 ng N–N2O m−2 s−1 and returning to background levels within four hours, but the pulse magnitude did not increase in proportion to the amount of ammonium or nitrate added. In contrast to N2O, NO was emitted over 24 h and increased in proportion to ammonium addition, exceeding 600 ng N–NO m−2 s−1 in desert and chaparral soils. Isotope tracers suggest that both ammonia oxidation and nitrate reduction produced NO. Taken together, our measurements demonstrate that nitrate can be reduced within minutes of wetting summer-dry desert soils to produce large N2O emission pulses and that multiple processes contribute to long-lasting NO emissions. These mechanisms represent substantial pathways of ecosystem N loss that also contribute to regional air quality and global climate dynamics.

Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions., Funding was provided from USDA NIFA in Seed Grant CA-R-PPA-5101-CG and Hatch Grant CA-R-PPA-5093-H to EA, and Spanish Ministry of Science Grants CGL2016-79790-P and PID2019-108195GB-I00 and Spanish Aragon Government and European Social Found Bioflora A01-20R Grant to PC.

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.

Nitrogen enrichment due to atmospheric nitrogen deposition has affected plant growth and microbial activity globally, leading to an increase in soil organic carbon in many ecosystems. Drylands cover ~45% of the global land area and constitute ~32% of the global carbon stocks, but the response of dryland carbon storage to atmospheric nitrogen deposition remains unclear and understudied relative to mesic systems. Observations from mesic systems suggest that nitrogen enrichment can increase the efficiency by which microbes incorporate carbon into mineral-associated forms if pH stays constant. Under acidification, a common response to nitrogen deposition, microbial biomass and enzymatic organic matter decay often decrease, leading to a build-up in plant-derived particulate organic carbon. However, in drylands, where organic carbon often associates with mineral surfaces via Ca-bridging, acidification may also abiotically decrease mineral-associated organic carbon if Ca is leached. In this study we tested how experimental nitrogen deposition affects different soil organic carbon fractions in drylands through microbial and abiotic effects.We used four long-running nitrogen deposition experiments in Mediterranean shrub- and grassland ecosystems in Southern California, where two of the sites showed strong nitrogen-induced acidification (pH drop by ~1.5 units). We studied changes in soil organic carbon fractions, soil extracellular enzyme activity, microbial carbon stabilization efficiency and exchangeable Ca. Experimental nitrogen deposition had relatively small effects on soil organic carbon storage, which appeared to be mostly driven by soil physicochemical changes. Particulate organic carbon did not increase despite previously reported increases in plant biomass and decreases in microbial biomass and extracellular enzyme activity in acidified sites. Furthermore, microbial carbon stabilization efficiency was unaffected by N fertilization in non-acidified sites and decreased in short-term but not long-term incubations in acidified sites. Importantly, mineral-associated organic carbon decreased significantly by 20% in response to N fertilization at one of the acidified sites, likely as result of pH-induced loss of Ca, which dropped by 48%. Our measurements suggest that long-term effects of nitrogen fertilization on dryland carbon storage might be primarily abiotic in nature, such that drylands, which may undergo acidification and where Ca-stabilization of soil organic carbon is prevalent, may be most at risk for loss of mineral-associated organic carbon.

Human activities accelerate acidification, particularly as acid rain, which may have lasting impacts on soil abiotic and biotic parameters. However, the effects of acidification on aboveground vegetation, belowground communities, and carbon cycling remains unresolved. We examined the effects of long-term acidic treatments and Pisolithus inoculation on plants, soils, and microbial communities in pine plantations and found that exposure to severely-acidic treatments diminished plant performance, altered microbial communities, and decreased organic matter, nitrate, and available phosphorus. Although we did not detect any benefits of Pisolithus inoculation for Pinus seedlings impacted by severely-acidic treatments, when these severe treatments were inoculated with Pisolithus, both soil properties and microbial community composition shifted. We posit that inoculation with Pisolithus may alleviate stressful environmental conditions, and change the structure of mycorrhizal fungal communities. Although acidification may alter biogeochemical cycles and constrain aboveground and belowground communities, Pisolithus inoculation may provide benefits to some components of forested ecosystems.

Abstract Fungal community composition in the Anthropocene is driven by rapid changes in environmental conditions caused by human activities. This study examines the relative importance of two global change drivers – atmospheric nitrogen (N) deposition and annual grass invasion – on structuring fungal communities in a California chaparral ecosystem, with emphasis on arbuscular mycorrhizal fungi. We used molecular markers, functional groupings, generalized linear statistics and joint distribution modeling, to examine how environmental variables structure taxonomic and functional composition of fungal communities. Invasion of a chaparral ecosystem decreased richness and relative abundance of non-AMF symbionts and rhizophilic AMF (e.g. Glomeraceae) as well as the proportion of edaphophilic AMF (e.g. Gigasporaceae). We found increased richness and the proportion of rhizophilic and edaphophilic AMF with increasing soil NO3. Our findings suggest that invasive persistence may decrease the presence of multiple soil symbionts that native species depend on for pathogen protection and increased access to soil resources.

A significant challenge for understanding how fungal communities may change in the Anthropocene are the multiple aspects of simultaneous environmental change. To address this challenge, we used a seven-year multi-factorial field experiment in southern California to examine how root-associated fungi respond to aridity, nitrogen deposition, and plant invasions. We hypothesized that all three global change drivers reduce the abundance of arbuscular mycorrhizal fungi responsible for nutrient uptake (edaphophilic AMF), while increasing the abundance of AMF that colonize roots at high rates (rhizophilic AMF). We found that invasive grasses hosted lower abundances of edaphophilic AMF, and higher abundances of rhizophilic AMF and opportunistically parasitic fungi. Aridity reduced overall AMF abundance while N addition altered the allocation of AMF biomass, increasing root colonization while reducing the density of extraradical hyphae. Overall, these results imply that ongoing global change will alter both the composition of AMF and how these fungi interact with plants.

Although many studies have reported the negative effects of elevated O3 on plant physiological characteristics, the influence of elevated O3 on below-ground processes and soil microbial functioning is less studied. In this study, we examined the effects of elevated O3 on soil properties, soil microbial biomass, as well as microbial community composition using high-throughput sequencing. Throughout one growing season, one-year old seedlings of two important endemic trees in subtropical China: Taxus chinensis (Pilger) Rehd. var. chinensis, and Machilus ichangensis Rehd. Et Wils, were exposed to charcoal-filtered air (CF as control), 100 nl l−1 (E100) or 150 nl l−1 (E150) O3-enriched air, in open top chambers (OTCs). We found that only higher O3 exposure (E150) significantly decreased soil microbial biomass carbon and nitrogen in M. ichangensis, and the contents of organic matter were significantly decreased by E150 in both tree species. Although both levels of O3 exposure decreased NO3-N in T. chinensis, only E150 increased NO3-N in M. ichangensis, and there were no effects of O3 on NH4-N. Moreover, elevated O3 elicited changes in soil microbial community structure and decreased fungal diversity in both M. ichangensis and T. chinensis. However, even though O3 exposure reduced bacterial diversity in M. ichangensis, no effect of O3 exposure on bacterial diversity was detected in soil grown with T. chinensis. Our results showed that elevated O3 altered the abundance of bacteria and fungi in general, and in particular reduced nitrifiers and increased the relative abundance of some fungal taxa capable of denitrification, which may stimulate N2O emissions. Overall, our findings indicate that elevated O3 not only impacts the soil microbial community structure, but may also exert an influence on the functioning of microbial communities.

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, SO42-, Na, Ca, Sr), Colorado Alluvium (U, Ca), Local Alluvium (Al, Fe, Ti), Agricultural Burning (K, PO43-), 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 SO42-.

Climate and regional air quality models predict that Southern California will experience longer and more severe droughts, and possibly wetter, more intense storms and changing nitrogen (N) deposition. We investigated how the three major soil greenhouse gas (GHG) fluxes respond to 4–6 years of exposure to a full-factorial experiment of reduced and augmented precipitation crossed with increased N in a semi-arid grassland in Irvine, CA, USA. The mean emission fluxes across all treatments were 249.8 mg CO2 m−2 h−1, -16.41 μg CH4 m−2 h−1, and 2.24 μg N2O m−2 h−1. Added N plots released 3.5 times more N2O than ambient N plots, and N treatment and soil moisture interacted, such that volumetric soil moisture in added N plots correlated positively with N2O release. Soil moisture, which was higher in the added water plots, correlated positively with respiration. CH4 consumption increased with soil moisture in the drought treatment, an opposite trend to that observed in most other studies. Our data suggest that CH4 consumption, N2O production, and soil respiration will decline if Southern California grasslands experience more frequent and extreme droughts. However, when drought is followed by high rainfall, the additional moisture will likely increase CH4 consumption and N2O release in periodic pulses. Overall, climatic shifts in this ecosystem may lead to a decrease in overall soil GHG emissions to the atmosphere. However, increased N deposition to Southern California will likely lead to increased N2O release and a shift in the dominant N loss pathway toward gaseous release of N. If N deposition continues to increase along with severity and duration of drought, our data predict a decrease in global warming potential (GWP) of 17.2% from this ecosystem.

1. Leaf‐cutter ants are a prominent feature in Neotropical ecosystems, but a comprehensive assessment of their effects on ecosystem functions is lacking. We reviewed the literature and used our own recent findings to identify knowledge gaps and develop a framework to quantify the effects of leaf‐cutter ants on ecosystem processes. 2. Leaf‐cutter ants disturb the soil structure during nest excavation changing soil aeration and temperature. They mix relatively nutrient‐poor soil from deeper layers with the upper organic‐rich layers increasing the heterogeneity of carbon and nutrients within nest soils. 3. Leaf‐cutter ants account for about 25% of all herbivory in Neotropical forest ecosystems, moving 10%-15% of leaves in their foraging range to their nests. Fungal symbionts transform the fresh, nutrient‐rich vegetative material to produce hyphal nodules to feed the ants. Organic material from roots and arbuscular mycorrhizal fungi enhances carbon and nutrient turnover in nest soils and creates biogeochemical hot spots. Breakdown of organic matter, microbial and ant respiration, and nest waste material decomposition result in increased CO2, CH4, and N2O production, but the build‐up of gases and heat within the nest is mitigated by the tunnel network ventilation system. Nest ventilation dynamics are challenging to measure without bias, and improved sensor systems would likely solve this problem. 4. Canopy gaps above leaf‐cutter ant nests change the light, wind and temperature regimes, which affects ecosystem processes. Nests differ in density and size depending on colony age, forest type and disturbance level and change over time resulting in spatial and temporal changes of ecosystem processes. These characteristics remain a challenge to evaluate rapidly and non‐destructively. 5. Addressing the knowledge gaps identified in this synthesis will bring insights into physical and biological processes driving biogeochemical cycles at the nest and ecosystem scale and will improve our understanding of ecosystem biogeochemical heterogeneity and larger scale ecological phenomena. National Science Foundation/[DEB-1442568]/NSF/Estados Unidos National Science Foundation/[DEB-1442537]/NSF/Estados Unidos National Science Foundation/[DEB-1442622]/NSF/Estados Unidos Universidad de Costa Rica/[801-B4-527]/UCR/Costa Rica UCR::Vicerrectoría de Docencia::Salud::Facultad de Medicina::Escuela de Medicina UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM) UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC)

In California, invasive grasses have displaced native plants, transforming much of the endemic coastal sage scrub (CSS) to nonnative grasslands. This has occurred for several reasons, including increased competitive ability of invasive grasses and long-term alterations to the soil environment, called legacy effects. Despite the magnitude of this problem, however, it is not well understood how these legacy effects have altered the soil microbial community and, indirectly, native plant restoration. We assessed the microbial composition of soils collected from an uninvaded CSS community (uninvaded soil) and a nearby 10-ha site from which the invasive grass Harding grass (Phalaris aquaticaL.) was removed after 11 yr of growth (postinvasive soil). We also measured the survival rate, biomass, and length of three CSS species andP. aquaticagrown in both soil types (uninvaded and postinvasive). Our findings indicate thatP. aquaticamay create microbial legacy effects in the soil that likely cause soil conditions inhibitory to the survival rate, biomass, and length of coastal sagebrush, but not the other two native plant species. Specifically, coastal sagebrush growth was lower in the postinvasive soil, which had more Bacteroidetes, Proteobacteria,Agrobacterium,Bradyrhizobium,Rhizobium(R. leguminosarum),Candidatus koribacter,Candidatus solibacter, and rhizophilic arbuscular mycorrhizal fungi, and fewer Planctomycetes, Acidobacteria,Nitrospira, andRubrobactercompared with the uninvaded soil. Shifts in soil microbial community composition such as these can have important implications for restoration strategies in postinvasive sites.

Ambigolimax valentianus is an invasive European terrestrial gastropod distributed throughout California. It is a serious pest of gardens, plant nurseries, and greenhouses. We evaluated the bacterial microbiome of whole slugs to capture a more detailed picture of bacterial diversity and composition in this host. We concentrated on the influences of diet and environment on the Ambigolimax valentianus core bacterial microbiome as a starting point for obtaining valuable information to aid in future slug microbiome studies. Ambigolimax valentianus were collected from two environments (gardens or reared from eggs in a laboratory). DNA from whole slugs were extracted and next-generation 16S rRNA gene sequencing was performed. Slug microbiomes differed between environmental sources (garden- vs. lab-reared) and were influenced by a sterile diet. Lab-reared slugs fed an unsterile diet harbored greater bacterial species than garden-reared slugs. A small core microbiome was present that was shared across all slug treatments. This is consistent with our hypothesis that a core microbiome is present and will not change due to these treatments. Findings from this study will help elucidate the impacts of slug-assisted bacterial dispersal on soils and plants, while providing valuable information about the slug microbiome for potential integrated pest research applications.

Abigail C Burr,1,* Jalene V Velazquez,1,* Arzu Ulu,1 Rohan Kamath,1 Sang Yong Kim,1 Amanpreet K Bilg,1 Aileen Najera,1 Iman Sultan,1 Jon K Botthoff,2 Emma Aronson,3 Meera G Nair,1 Tara M Nordgren1 1Division of Biomedical Sciences, University of California Riverside, Riverside, CA, 92521, USA; 2Center for Conservation Biology, University of California Riverside, Riverside, CA, 92521, USA; 3Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, 92521, USA*These authors contributed equally to this workCorrespondence: Tara M NordgrenDivision of Biomedical Sciences, University of California Riverside, 92521 University Avenue, Riverside, CA, 92521, USATel +1 951 827 3148Email tmnordgren@gmail.comPurpose: The Salton Sea, California’s largest lake, is designated as an agricultural drainage reservoir. In recent years, the lake has experienced shrinkage due to reduced water sources, increasing levels of aerosolized dusts in surrounding regions. Communities surrounding the Salton Sea have increased asthma prevalence versus the rest of California; however, a connection between dust inhalation and lung health impacts has not been defined.Methods: We used an established intranasal dust exposure murine model to study the lung inflammatory response following single or repetitive (7-day) exposure to extracts of dusts collected in regions surrounding the Salton Sea (SSDE), complemented with in vitro investigations assessing SSDE impacts on the airway epithelium.Results: In these investigations, single or repetitive SSDE exposure induced significant lung inflammatory cytokine release concomitant with neutrophil influx. Repetitive SSDE exposure led to significant lung eosinophil recruitment and altered expression of genes associated with allergen-mediated immune response, including Clec4e. SSDE treatment of human bronchial epithelial cells (BEAS-2B) induced inflammatory cytokine production at 5- and 24-hours post-treatment. When BEAS-2B were exposed to protease activity-depleted SSDE (PDSSDE) or treated with SSDE in the context of protease-activated receptor-1 and − 2 antagonism, inflammatory cytokine release was decreased. Furthermore, repetitive exposure to PDSSDE led to decreased neutrophil and eosinophilic influx and IL-6 release in mice compared to SSDE-challenged mice.Conclusion: These investigations demonstrate potent lung inflammatory responses and tissue remodeling in response to SSDE, in part due to environmental proteases found within the dusts. These studies provide the first evidence supporting a link between environmental dust exposure, protease-mediated immune activation, and respiratory disease in the Salton Sea region.Keywords: Salton Sea, dust exposure, lung inflammation, asthma, proteases, protease-activated receptors

Nitrogen (N) trace gas emission pulses produced after wetting dry soils may be important pathways of ecosystem N loss. However, the rates and mechanisms controlling these emissions remain unclear. We tested whether changes in microbial community structure and increased rates of atmospheric N deposition could explain N emissions at two desert sites differing in atmospheric N deposition by ~ six fold. We measured peak NOₓ (sum of nitric oxide and nitrogen dioxide) emissions 12h post-wetting. NOₓ emissions remained elevated over 24h and increased after adding N. In contrast, we measured the highest nitrous oxide (N₂O) emissions within only 15min post-wetting. N₂O emissions decreased within 12h, were insensitive to adding N, and were among the highest reported globally. Microbial communities at the high N deposition site were less diverse with higher 16Snitrifier and bacterial amoA gene abundances relative to the low N deposition site, suggesting an increased capacity for nitrification. Nevertheless, N emissions were lower at the high N deposition site. While microbial communities changed after wetting, these changes were not correlated with N emissions. We conclude that desert soils can produce substantial NOₓ and N₂O emission pulses, but that these emissions do not appear directly governed by changing microbial community characteristics or higher atmospheric N inputs. These findings highlight the importance of gaseous N loss pathways from dryland ecosystems that may contribute to sustained N limitation, with implications for atmospheric chemistry and Earth’s climate.

Although aboveground metrics remain the standard, restoring functional ecosystems should promote both aboveground and belowground biotic communities. Restoration using salvaged soil&mdash, removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites&mdash, is an alternative to traditional methods. Salvaged soil contains both seed and spore banks, which may holistically augment restoration. Salvaged soil methods may reduce non-native germination by burying non-native seeds, increase native diversity by adding native seeds, or transfer soil microbiomes, including arbuscular mycorrhizal fungi (AMF), to recipient sites. We transferred soil to three degraded recipient sites and monitored soil microbes, using flow cytometry and molecular analyses, and characterized the plant community composition. Our findings suggest that salvaged soil at depths &ge, 5 cm reduced non-native grass cover and increased native plant density and species richness. Bacterial abundance at recipient sites were statistically equivalent to donor sites in abundance. Overall, topsoil additions affected AMF alpha diversity and community composition and increased rhizophilic AMF richness. Because salvaged soil restoration combines multiple soil components, including native plant and microbial propagules, it may promote both aboveground and belowground qualities of the donor site, when applying this method for restoring invaded and degraded ecosystems.

Nitrogen deposition into arid ecosystems is increasingly shaping biogeochemical dynamics worldwide. We propose a framework to investigate the role of pulsed soil N emission as a mechanism that relays the influences of atmospheric anthropogenic N deposition to areas that otherwise would be minimally affected. We use nutrient spiraling theory, developed in lotic ecosystems, to quantify how regeneration of N by soils influences N deposition downwind of an urban plume. Our hierarchical framework of landscape functioning thereby connects ecosystem processes occurring from microbial (100km and inter-annual) scales through reciprocal interactions among soils and microbes, pollution sources, and the atmosphere. We use southern California, USA as a case study for evaluation where we test the terrestrial nitrogen spiraling framework using a combination of field experiments, isotopic measurements, theoretical models, and atmospheric transport and chemistry model outputs. Initial results from field wetting experiments, isotope measurements and contrasting modeling approaches all support a spiraling framework and the increasing importance of soil regeneration of nitrogen to deposition farther from the urban source. Soil microbiome communities associated with nitrogen cycling vary both spatially across the deposition gradient and temporally in response to wetting events. From these results we derive terrestrial spiraling metrics that can identify consequences of both soil and anthropogenic inputs to regional nitrogen cycling. New landscape frameworks for evaluating the role of transport and transformations on N cycling can help understand and predict spatial variation in ecosystems connected across multiple scales.

Soils form the skin of the Earth’s surface, regulating water and biogeochemical cycles and generating production of food, timber, and textiles around the world. Changes in soil and its ability to perform a range of processes have important implications for Earth system function, especially in the critical zone (CZ)—the area that extends from the top of the canopy to the bottom of groundwater and that harbors most of Earth’s biosphere. A key aspect of the way soil functions results from its structure, defined as the size, shape, and arrangement of soil particles and pores. The network of pores provides storage space for at least a quarter of Earth’s biodiversity, while the abundance, size and connectivity of the pore space regulates fluxes of heat, water, nutrients and gases that define the physical and chemical environment. Here we review the nature of soil structure, focusing on its co-evolution with the plants and microbes that live within the soil, and the degree to which these processes have been incorporated into flow and transport models. Though it is well known that soil structure can change with wetting and drying events, often oscillating seasonally, the dynamic nature of soil structure that we discuss is a systematic shift that results in changes in its hydro-bio-geochemical function over decades to centuries, timescales over which major changes in carbon and nutrient cycles have been observed in the Anthropocene. We argue that the variable nature of soil structure, and its dynamics, need to be better understood and captured by land surface and ecosystem models, which currently describe soil structure as static. We further argue that modelers and empiricists both are well-poised to quantify and incorporate these dynamics into their studies. From these efforts, four fundamental questions emerge: 1) How do rates of soil aggregate formation and collapse, and their overall arrangements, interact in the Anthropocene to regulate CZ functioning from soil particle to continental scales? 2) How do alterations in rooting-depth distributions in the Anthropocene influence pore structure to control hydrological partitioning, biogeochemical transformations and fluxes, exchanges of energy and carbon with the atmosphere and climate, regolith weathering, and thus regulation of CZ functioning? 3) How does changing microbial functioning in a high CO2, warmer world with shifting precipitation patterns influence soil organic carbon dynamics and void-aggregate profile dynamics? 4) How deeply does human influence in the Anthropocene propagate into the subsurface, how does this depth relate to profile structure, and how does this alter the rate at which the CZ develops? The United Nations has recently recognized that 33% of the Earth's soils are already degraded and over 90% could become degraded by 2050. This recognition highlights the importance of addressing these proposed questions, which will promote a predictive understanding of soil structure.

Data sharing benefits the researcher, the scientific community, and the public by allowing the impact of data to be generalized beyond one project and by making science more transparent. However, many scientific communities have not developed protocols or standards for publishing, citing, and versioning datasets. One community that lags in data management is that of low-temperature geochemistry (LTG). This paper resulted from an initiative from 2018 through 2020 to convene LTG and data scientists in the U.S. to strategize future management of LTG data. Through webinars, a workshop, a preprint, a townhall, and a community survey, the group of U.S. scientists discussed the landscape of data management for LTG – the data-scape. Currently this data-scape includes a “street bazaar” of data repositories. This was deemed appropriate in the same way that LTG scientists publish articles in many journals. The variety of data repositories and journals reflect that LTG scientists target many different scientific questions, produce data with extremely different structures and volumes, and utilize copious and complex metadata. Nonetheless, the group agreed that publication of LTG science must be accompanied by sharing of data in publicly accessible repositories, and, for sample-based data, registration of samples with globally unique persistent identifiers. LTG scientists should use certified data repositories that are either highly structured databases designed for specialized types of data, or unstructured generalized data systems. Recognizing the need for tools to enable search and cross-referencing across the proliferating data repositories, the group proposed that the overall data informatics paradigm in LTG should shift from “build data repository, data will come” to “publish data online, cybertools will find”. Funding agencies could also provide portals for LTG scientists to register funded projects and datasets, and forge approaches that cross national boundaries. The needed transformation of the LTG data culture requires emphasis in student education on science and management of data.

International audience; 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. © 2020 John Wiley & Sons Ltd

The generation and transport of mineral dust is strongly related to climate on seasonal, year-to-year, and glacial-interglacial 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 nutrient-limited 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.

Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic 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 extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question we characterized microbiomes associated with giant sequoia and co-occurring sugar pine (Pinus lambertiana) by sequencing 16S and ITS1 of the bulk soil community at two groves with distinct parent material. 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 unique core community that was 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 ofHygrocybespecies beneath giant sequoia. Compositional differences between host trees correlated with soil pH, calcium availability, 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.

Author(s): Burr, A.C.; Kamath, R; Velazquez, J; Peng, X; Maltz, M; Botthoff, J; Cocker, D; Aronson, E; Carson, M; Lo, D; Nordgren, T.M.

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.

ABSTRCT Mounting evidence suggests that Earth's cryosphere harbors diverse and active microbial communities. However, our understanding of microbial composition and diversity in seasonal snowpack of montane ecosystems remains limited. We sequenced the 16S rRNA gene to determine microbial structure (composition and diversity) of snow at two depths (0–15 and 15–30 cm) of a subalpine site in the Southern Sierra Critical Zone Observatory, California, U.S.A. Proteobacteria dominated both depths (~72% of sequences), and this phylum was composed mostly of bacteria within the Rhodospirillales order. Cyanobacteria were almost exclusively present in the upper snow layer, while Actinobacteria and Firmicutes were more abundant in the deep snow layer. Many of the most abundant phylotypes were Acetobacteraceae. Phylotype NCR4874, which comprised 22%–32% of the sequences, was most closely related to the N2-fixing bacteria Asaia siamensis, suggesting that N2 fixation may be an important process within the Sierra snowpack...

Summary Analogous to the spread of non-native species, shifts in native species’ ranges resulting from climate and land use change are also creating new combinations of species in many ecosystems. These native range shifts may be facilitated by similar mechanisms that provide advantages for non-native species and may also have comparable impacts on the ecosystems they invade. Soil biota, in particular bacteria and fungi, are important regulators of plant community composition and below-ground ecosystem function. Compared to non-native plant invasions, there have been relatively few studies examining how soil biota influence – or are influenced by – native species range shifts. Here, we examined how a native range-expanding sagebrush species (Artemisia rothrockii) affects below-ground abiotic conditions and microbial community structure and function using next-generation sequencing coupled with other biotic and abiotic soil analyses. We utilized a range-expansion gradient, together with a shrub removal experiment and structural equation models, to determine the direct and indirect drivers of these interconnected processes. Sagebrush colonization increased bacterial and archaeal richness and diversity and altered community composition across the expansion gradient. Soil organic C and N and soil moisture increased with sagebrush presence; however, results varied across the expansion gradient. We found no relationship between sagebrush and soil pH; however, pH strongly influenced microbial richness and diversity. Microbial (substrate-induced) respiration was influenced by soil organic N, as well as microbial diversity and functional group relative abundances, highlighting direct and indirect effects of sagebrush on microbial community structure and function. Microbial community composition of soils after 4 years of sagebrush removal was more similar to communities in shrub interspaces than underneath shrubs, suggesting microbial community resilience. Synthesis. Our results suggest that native range expansions can have important impacts on soil biological communities, soil chemistry and hydrology which can further impact below-ground ecosystem processes such as nutrient cycling and litter decomposition. The combination of high-throughput sequencing and structural equation modelling used here offers an exciting yet underutilized approach to understanding how both native and non-native species’ range expansions may affect the structure and function of soil ecosystems.

Shifts in microbial communities driven by anthropogenic nitrogen (N) addition have broad-scale ecological consequences. However, responses of microbial groups to exogenous N supply vary considerably across studies, hindering efforts to predict community changes. We used meta-analytical techniques to explore how amoA gene abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) respond to N addition, and found that N addition increased AOA and AOB abundances by an average of 27% and 326%, respectively. Responses of AOB varied by study type, ecosystem, fertilizer type, and soil pH, and were strongest in unmanaged wildland soils and soils fertilized with inorganic N sources. Increases in nitrification potential with N addition significantly correlated with only AOB. Our analyses suggest that elevated N supply enhances soil nitrification potential by increasing AOB populations, and that this effect may be most pronounced in unmanaged wildland soils.

Chemical stabilization of microbial-derived products such as extracellular enzymes (EE) onto mineral surfaces has gained attention as a possibly important mechanism leading to the persistence of soil organic carbon (SOC). While the controls on EE activities and their stabilization in the surface soil are reasonably well-understood, how these activities change with soil depth and possibly diverge from those at the soil surface due to distinct physical, chemical, and biotic conditions remains unclear. We assessed EE activity to a depth of 1 m (10 cm increments) in 19 soil profiles across the Critical Zone Observatory Network, which represents a wide range of climates, soil orders, and vegetation types. For all EEs, activities per mass of soil correlated positively with microbial biomass (MB) and SOC, and all three of these variables decreased logarithmically with depth (p < 0.05). Across all sites, over half of the potential EE activities per mass soil consistently occurred below 20 cm for all measured EEs. Activities per unit MB or SOC were substantially higher at depth (soils below 20 cm accounted for 80% of whole-profile EE activity), suggesting an accumulation of stabilized (i.e. mineral sorbed) EEs in subsoil horizons. The pronounced enzyme stabilization in subsurface horizons was corroborated by mixed-effects models that showed a significant, positive relationship between clay concentration and MB-normalized EE activities in the subsoil. Furthermore, the negative relationships between soil C, N, and P and C-, N-, and P-acquiring EEs found in the surface soil decoupled below 20 cm, which could have also been caused by EE stabilization. This finding suggests that EEs may not reflect soil nutrient availabilities deeper in the soil profile. Taken together, our results suggest that deeper soil horizons hold a significant reservoir of EEs, and that the controls of subsoil EEs differ from their surface soil counterparts.

Global change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring California’s biodiversity through environmental DNA (eDNA)—DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.

Global atmospheric methane growth rates have wildly fluctuated over the past three decades, which may be driven by the proportion of tropical land surface saturated by water. The El Niño/Southern Oscillation Event (ENSO) cycle drives large‐scale climatic trends globally, with El Niño events typically bringing drier weather than La Niña. In a lowland tropical wet forest in Costa Rica, we measured methane flux bimonthly from March 2016 to June 2017 and using an automated chamber system. We observed a strong drying trend for several weeks during the El Niño in 2016, reducing soil moisture below normal levels. In contrast, soil conditions had high water content prior to the drought and during the moderate La Niña that followed. Soil moisture varied across the period studied and significantly impacted methane flux. Methane consumption was greater during the driest part of the El Niño period, while during La Niña and other time periods, soils had lower methane consumption. The mean methane flux observed was −0.022 mg CH4‐C m−2 hr−1, and methane was consumed at all timepoints, with lower consumption in saturated soils. Our data show that month studied, and the correlation between soil type and month significantly drove methane flux trends. Our data indicate that ENSO cycles may impact biogenic methane fluxes, mediated by soil moisture conditions. Climate projections for Central America show dryer conditions and increased El Niño frequency, further exacerbating predicted drought. These trends may lead to negative climate feedbacks, with drier conditions increasing soil methane consumption from the atmosphere. National Science Foundation/[DEB‐1624623]/NSF/Estados Unidos National Science Foundation/[DEB‐1442537]/NSF/Estados Unidos National Science Foundation/[DEB‐1624658]/NSF/Estados Unidos National Science Foundation/[DEB‐1442714]/NSF/Estados Unidos United States Department of Agriculture-National Institute of Food and Agriculture/[CA‐R‐PPA‐5093‐H/1005159]/USDA NIFA/Estados Unidos UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM) UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC)

Dust provides ecosystem-sustaining nutrients to landscapes underlain by intensively weathered soils. Here we show that dust may also be crucial in montane forest ecosystems, dominating nutrient budgets despite continuous replacement of depleted soils with fresh bedrock via erosion. Strontium and neodymium isotopes in modern dust show that Asian sources contribute 18–45% of dust deposition across our Sierra Nevada, California study sites. The remaining dust originates regionally from the nearby Central Valley. Measured dust fluxes are greater than or equal to modern erosional outputs from hillslopes to channels, and account for 10–20% of estimated millennial-average inputs of bedrock P. Our results demonstrate that exogenic dust can drive the evolution of nutrient budgets in montane ecosystems, with implications for predicting forest response to changes in climate and land use., Dust is an important nutrient source to landscapes, but often the source of dust is poorly constrained. Here, the authors quantify the origin of different dust sources in the Sierra Nevada by analysing dust composition and suggest exogenic dust may drive nutrient budgets in montane ecosystems.

Microorganisms inhabit almost every environment, comprise the majority of diversity on Earth, are important in biogeochemical cycling, and may be vital to ecosystem responses to large-scale climatic change. In recent years, ecologists have begun to use rapidly advancing molecular techniques to address questions about microbial diversity, biogeography, and responses to environmental change. Studies of microbes in the environment generally focus on three broad objectives: determining which organisms are present, what their functional capabilities are, and which are active at any given time. However, comprehending the range of methodologies currently in use can be daunting. To provide an overview of environmental microbial sequence data collection and analysis approaches, we include case studies of microbiomes ranging from the human mouth to geothermal springs. We also suggest contexts in which each technique can be applied and highlight insights that result from their use.

The controls on methane (CH4) flux into and out of soils are not well understood. Environmental variables including temperature, precipitation, and nitrogen (N) status can have strong effects on the magnitude and direction (e.g., uptake vs. release) of CH4 flux. To better understand the interactions between CH4-cycling microorganisms and N in the non-wetland soil system, a meta-analysis was performed on published literature comparing CH4 flux in N amended and matched control plots. An appropriate study index was developed for this purpose. It was found that smaller amounts of N tended to stimulate CH4 uptake while larger amounts tended to inhibit uptake by the soil. When all other variables were accounted for, the switch occurred at 100 kg N x ha(-1) x yr(-1). Managed land and land with a longer duration of fertilization showed greater inhibition of CH4 uptake with added N. These results support the hypotheses that large amounts of available N can inhibit methanotrophy, but also that methanotrophs in upland soils can be N limited in their consumption of CH4 from the atmosphere. There were interactions between other variables and N addition on the CH4 flux response: lower temperature and, to a lesser extent, higher precipitation magnified the inhibition of CH4 uptake due to N addition. Several mechanisms that may cause these trends are discussed, but none could be conclusively supported with this approach. Further controlled and in situ study should be undertaken to isolate the correct mechanism(s) responsible and to model upland CH4 flux.

[1] Methane (CH4) is an important anthropogenic greenhouse gas, up to 15% of which is consumed by terrestrial soils. In this field study of the CH4cycle of a pine forest, 18 plots were established at each of two sites, located 40 m apart. The upper site was well-drained and the lower site was poorly drained, but they shared similar overstory tree composition. Nitrogen was added as NH4NO3 incrementally across the 2009 growing season in a high (67 kg NH4NO3 ha−1 yr−1) and a low (5 kg NH4NO3 ha−1 yr−1) concentration. The sites were monitored for soil and air temperature, soil moisture, precipitation, air pressure, and NH4 and NO2+NO3 concentrations throughout the growing season. Across all treatments for the duration of the field season, average CH4 flux showed consumption of −0.84 kg CH4 ha−1 yr−1, but CH4 flux differed between the upper and lower sites. Across all treatments, upper site CH4 flux averaged −5.38 kg CH4 ha−1 yr−1, while lower site flux averaged 3.72 kg CH4 ha−1 yr−1, with greater variance than was observed at the upper site. High N treatments caused greater CH4 release than the control in the lower, but not the upper, site. The main correlated variable with CH4 flux was soil moisture; however, it accounted for