Urbanization Alters Soil Microbial Functioning in the Sonoran Desert

Microbial communities in terrestrial surface soils are not widely limited by carbon

Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid- to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid- to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.

Soil biogeochemical responses to multiple co-occurring forms of human-induced environmental change

Human activities cause a multitude of environmental issues, including increased temperatures and altered precipitation patterns associated with climate change, air pollution, and other impacts of urbanization. One area highly affected by these issues is the Sonoran Desert, specifically the Phoenix metropolitan area where urbanization is among the most rapid in the United States. Most studies investigate these multiple environmental change factors independently or sometimes in pairs, but rarely all together as co-occurring forms of change. We examined how the simultaneous manipulation of increasing temperatures, altered precipitation patterns, nitrogen deposition, and urbanization influenced soil respiration and mineral N pools in the Sonoran Desert. Soil was collected from urban and exurban sites, from both nitrogen-fertilized and control plots. To simulate projected climate change, the soils were incubated in microcosm at the annual average Phoenix temperature as well a 2 ℃ increase under a factorial precipitation treatment of decreased frequency and increased pulse size. Our results show that C and N dynamics were altered by all four forms of environmental change. However, the dominance of significant 3- and 4-way interactions among the four environmental factors for both respiration and mineral N pools demonstrates that the impact of any given form of environmental change will depend on the levels of the other environmental factors. In other words, the cumulative effect of altered precipitation, fertilization, temperature, and urbanization on soil biogeochemical processes is not necessarily predictable from their individual impact.

Spatial cover and carbon fluxes of urbanized Sonoran Desert biological soil crusts

Biological soil crusts (BSC) are important contributors to nutrient cycling in arid environments such as the Sonoran Desert. BSC at an urban (University Indian Ruins) and at a non-urban site (Santa Rita Experimental Range) were compared to determine if their structure or function was influenced by proximity to an urban environment. The Step Point method was used in the field to determine ground cover; which was found to be similar between sites. However, the spatial distribution of the BSCs was significantly different, such that more BSCs were found under plants at the non-urban site (P < 0.05). Relative gross photosynthesis was measured in the lab by addition of a watering event. Gross photosynthesis was found to be higher in the non-urban BSCs (P < 0.001), indicating lowered productivity in urban BSCs due to effects caused by proximity to urban environments. This study provides evidence that BSCs at urbanized sites are affected functionally, and therefore may be contributing differently to carbon and nitrogen cycling in these ecosystems.

Changes in Soil Microbial Communities across an Urbanization Gradient: A Local-Scale Temporal Study in the Arid Southwestern USA

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.

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.

Nature-based approaches to managing climate change impacts in cities

Managing and adapting to climate change in urban areas will become increasingly important as urban populations grow, especially because unique features of cities amplify climate change impacts. High impervious cover exacerbates impacts of climate warming through urban heat island effects and of heavy rainfall by magnifying runoff and flooding. Concentration of human settlements along rivers and coastal zones increases exposure of people and infrastructure to climate change hazards, often disproportionately affecting those who are least prepared. Nature-based strategies (NBS), which use living organisms, soils and sediments, and/or landscape features to reduce climate change hazards, hold promise as being more flexible, multi-functional and adaptable to an uncertain and non-stationary climate future than traditional approaches. Nevertheless, future research should address the effectiveness of NBS for reducing climate change impacts and whether they can be implemented at scales appropriate to climate change hazards and impacts. Further, there is a need for accurate and comprehensive cost-benefit analyses that consider disservices and co-benefits, relative to grey alternatives, and how costs and benefits are distributed across different communities. NBS are most likely to be effective and fair when they match the scale of the challenge, are implemented with input from diverse voices and are appropriate to specific social, cultural, ecological and technological contexts. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Nematode Community Response to Green Infrastructure Design in a Semiarid City

Urbanization affects ecosystem function and environmental quality through shifts in ecosystem fluxes that are brought on by features of the built environment. Green infrastructure (GI) has been suggested as a best management practice (BMP) to address urban hydrologic and ecological impacts of the built environment, but GI practice has only been studied from a limited set of climatic conditions and disciplinary approaches. Here, we evaluate GI features in a semiarid city from the perspective of soil ecology through the application of soil nematode community analysis. This study was conducted to investigate soil ecological interactions in small-scale GI as a means of assessing curb-cut rain garden basin design in a semiarid city. We looked at the choice of mulching approaches (organic vs. rock) and how this design choice affects the soil ecology of rain basins in Tucson, AZ. We sampled soils during the monsoon rain season and assessed the soil nematode community as a bioindicator of soil quality and biogeochemical processes. We found that the use of organic mulch in GI basins promotes enhanced soil organic matter contents and larger nematode populations. Nematode community indices point to enhanced food web structure in streetscape rain garden basins that are mulched with organic material. Results from this study suggest that soil management practices for GI can help promote ecological interactions and ecosystem services in urban ecosystems.

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods

In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

Connecting carbon and nitrogen storage in rural wetland soil to groundwater abstraction for urban water supply

We investigated whether groundwater abstraction for urban water supply diminishes the storage of carbon (C), nitrogen (N), and organic matter in the soil of rural wetlands. Wetland soil organic matter (SOM) benefits air and water quality by sequestering large masses of C and N. Yet, the accumulation of wetland SOM depends on soil inundation, so we hypothesized that groundwater abstraction would diminish stocks of SOM, C, and N in wetland soils. Predictions of this hypothesis were tested in two types of subtropical, depressional-basin wetland: forested swamps and herbaceous-vegetation marshes. In west-central Florida, >650 ML groundwater day(-1) are abstracted for use primarily in the Tampa Bay metropolis. At higher abstraction volumes, water tables were lower and wetlands had shorter hydroperiods (less time inundated). In turn, wetlands with shorter hydroperiods had 50-60% less SOM, C, and N per kg soil. In swamps, SOM loss caused soil bulk density to double, so areal soil C and N storage per m(2) through 30.5 cm depth was diminished by 25-30% in short-hydroperiod swamps. In herbaceous-vegetation marshes, short hydroperiods caused a sharper decline in N than in C. Soil organic matter, C, and N pools were not correlated with soil texture or with wetland draining-reflooding frequency. Many years of shortened hydroperiod were probably required to diminish soil organic matter, C, and N pools by the magnitudes we observed. This diminution might have occurred decades ago, but could be maintained contemporarily by the failure each year of chronically drained soils to retain new organic matter inputs. In sum, our study attributes the contraction of hydroperiod and loss of soil organic matter, C, and N from rural wetlands to groundwater abstraction performed largely for urban water supply, revealing teleconnections between rural ecosystem change and urban resource demand.

Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils

In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.

Sources and transport of nitrogen in arid urban watersheds

Urban watersheds are often sources of nitrogen (N) to downstream systems, contributing to poor water quality. However, it is unknown which components (e.g., land cover and stormwater infrastructure type) of urban watersheds contribute to N export and which may be sites of retention. In this study we investigated which watershed characteristics control N sourcing, biogeochemical processing of nitrate (NO3-) during storms, and the amount of rainfall N that is retained within urban watersheds. We used triple isotopes of NO3- (δ15N, δ18O, and Δ17O) to identify sources and transformations of NO3- during storms from 10 nested arid urban watersheds that varied in stormwater infrastructure type and drainage area. Stormwater infrastructure and land cover--retention basins, pipes, and grass cover--dictated the sourcing of NO3- in runoff. Urban watersheds were strong sinks or sources of N to stormwater depending on runoff, which in turn was inversely related to retention basin density and positively related to imperviousness and precipitation. Our results suggest that watershed characteristics control the sources and transport of inorganic N in urban stormwater but that retention of inorganic N at the time scale of individual runoff events is controlled by hydrologic, rather than biogeochemical, mechanisms.

Trace metal contamination in urban soils of China

The contamination of urban soils can affect the health of people living in urban areas, and the surrounding ecosystems. Urbanization in China has taken place at an unprecedented pace in the last three decades. This paper provides an overview of studies on the quality of urban soils in China with special reference to trace metal contamination. It summarizes the characteristics of accumulation, spatial and temporal distribution, and major sources of various toxic or potentially toxic trace metals in urban soils as reported in recent literature. Levels of pollution in urban soil and road dust were discussed using the concentrations, enrichment factors, pollution indexes, and chemical fractionation of trace metals in major cities of China, and compared with other countries. In future studies, more pollutants in urban environments need to be included in multi-compartmental environmental surveillance for potential risk assessments. In addition to routine urban soil surveys by a harmonized methodology, a comprehensive assessment of soil quality is needed for the control and management of many urban brownfield sites. Taking into consideration pathways of exposure and site characteristics, risk assessment frameworks for major pollutants in urban soils, which integrate land use type and environmental availability, may be developed in the future.

Ecosystem response to nutrient enrichment across an urban airshed in the Sonoran Desert

Rates of nitrogen (N) deposition have increased in arid and semiarid ecosystems, but few studies have examined the impacts of long-term N enrichment on ecological processes in deserts. We conducted a multiyear, nutrient-addition study within 15 Sonoran Desert sites across the rapidly growing metropolitan area of Phoenix, Arizona (USA). We hypothesized that desert plants and soils would be sensitive to N enrichment, but that these effects would vary among functional groups that differ in terms of physiological responsiveness, proximity to surface N sources, and magnitude of carbon (C) or water limitation. Inorganic N additions augmented net potential nitrification in soils, moreso than net potential N mineralization, highlighting the important role of nitrifying microorganisms in the nitrate economy of drylands. Winter annual plants were also responsive to nutrient additions, exhibiting a climate-driven cascade of resource limitation, from little to no production in seasons of low rainfall (winter 2006 and 2007), to moderate N limitation with average precipitation (winter 2009), to limitation by both N and P in a season of above-normal rainfall (winter 2008). Herbaceous production is a potentially important mechanism of N retention in arid ecosystems, capable of immobilizing an amount equal to or greater than that deposited annually to soils in this urban airshed. However, interannual variability in precipitation and abiotic processes that limit the incorporation of detrital organic matter into soil pools may limit this role over the long term. In contrast, despite large experimental additions of N and P over four years, growth of Larrea tridentata, the dominant perennial plant of the Sonoran Desert, was unresponsive to nutrient enrichment, even during wet years. Finally, there did not appear to be strong ecological interactions between nutrient addition and location relative to the city, despite the nearby activity of nearly four million people, perhaps due to loss or transfer pathways that limit long-term N enrichment of ecosystems by the urban atmosphere.

The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion

A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory. Second, using quantitative real-time PCR, we investigated whether microbial nitrogen functional gene (NFG) abundance was altered with soil nutrient enrichment, livestock exclusion, and exotic grass invasion. The target genes were chiA (decomposition-ammonification), nifH (nitrogen fixation), nirK and narG (denitrification), and bacterial amoA (nitrification). Woodland soils were enriched in phosphorus and nitrogen compared to reference condition sites, but soil nutrients were not lower following livestock exclusion. Total nitrogen and nifH were negatively correlated in grazed woodlands, suggesting that aboveground herbivory reduces the capacity for belowground nitrogen fixation. Woodlands dominated by exotic grasses had higher levels of nitrate, narG, and nirK than those dominated by native grasses. We hypothesize that the increase in potential for denitrification was due to increases in soil nitrate, rather than changes in plant composition. Overall, soil physicochemistry explained more variation in NFG abundance than livestock presence or plant invasion, particularly for chiA and bacterial amoA, with significant relationships between the abundance of all five NFGs and total nitrogen or nitrate. All woodlands investigated had a history of anthropogenic disturbance and nutrification, and soil nutrient levels and the abundance of NFGs are likely to be related to long-term land management practices.