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At least 181 records · Page 10

De novo design of tunable, pH-driven conformational changes

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fungal and bacterial growth variation due to drought and nitrogen addition experimental treatments. Loma Ridge Experimental Project. 2010-2012

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities. This data package includes ten csv files (five data files and their corresponding data dictionaries) and one file-level metadata excel file. Data files contains information about which plots were exposed to treatments related to drought and nitrogen, information about litter bags reciprocal transplants manipulation for water input and nitrogen, detail information about water addition, precipitation records, and litter variables collected. Data dictionary files include detail explanation for each column in the data files. The file-level metadata file describes each file mentioned above. All the analyses were done using the R software.

54 ENVIRONMENTAL SCIENCES↗

Final technical report. Can microbial functional traits predict the response and resilience of decomposition to global change?

The role of specific micro-organisms in the carbon cycle, and their responses to environmental change, are unknown in most ecosystems. This knowledge gap limits scientists’ ability to predict how important ecosystem processes, like soil carbon storage and loss, will change with climate and other environmental factors. The investigators addressed this knowledge gap by transplanting microbial communities from different environments into new environments and measuring the response of community composition and carbon cycling over time. Using state-of-the-art sequencing techniques, computational tools, and nanotechnology, the investigators showed that microbial communities on decomposing plant material shift dramatically with natural and experimentally-imposed drought. Microbial communities also shifted in response to added nitrogen, but the effects were smaller. These changes had implications for carbon cycling, with lower rates of carbon loss under drought conditions, and changes in the efficiency of decomposition with nitrogen addition. Even when transplanted into the same conditions, microbial communities from different environments remained distinct in composition and functioning for up to one year. Changes in functioning were related to differences in enzyme gene content across different microbial groups. Computational approaches developed for this project allowed the conclusions to be tested more broadly in other ecosystems, and new computer models will facilitate the prediction of microbial traits and functioning across environments. The data and models resulting from this project benefit the public by improving the ability to predict how microbial communities and carbon cycling functions respond to climate change, nutrient enrichment, and other large-scale environmental changes.

54 ENVIRONMENTAL SCIENCES↗

Aligning theoretical and empirical representations of soil carbon-to-nitrogen stoichiometry with process-based terrestrial biogeochemistry models

Soil carbon-nitrogen (C:N) stoichiometry acts as a control over decomposition and soil organic matter formation and loss, making it a key soil property for understanding ecosystem dynamics and projected ecosystems responses to global environmental change. However, the controls of soil C:N and how they respond to increasing pressures from global change agents are not fully understood. The “foundational” controls on soil C:N, namely plant and microbial C:N, have been used to predict soil C:N, but fail to accurately simulate all ecosystems and may be insufficient for predictions under global environmental change. Here we present an “emerging” representation of controls of soil C:N that includes plant-microbe-mineral feedbacks that have been shown to regulate soil C:N. We argue that including representation of these emerging drivers in process-based terrestrial biogeochemistry models, which include biological N fixation, mycorrhizae, priming, root exudation of organic acids, and mineralogy (including soil texture, mineral composition, and aggregation), will improve mechanistic representation of soil C:N and associated processes. Such improvements will produce models that will better simulate a variety of ecological states and predict soil C:N when global changes modify plant-microbe-mineral interactions. Here, we align our empirical understanding of controls of soil C:N with those controls represented in models, identifying contexts where emerging drivers might be particularly important to represent (e.g., priming and root exudation in nutrient-limited conditions) and areas of future work. Additionally, we show that implementing emerging drivers of soil C:N results in different simulated outcomes at steady state and in response to elevated atmospheric CO2. Our review and preliminary simulations support the need to incorporate emerging drivers of soil C:N into process-based terrestrial biogeochemistry models, allowing for both theoretical exploration of mechanisms and potentially more accurate predictions of land biogeochemical responses to global change.

54 ENVIRONMENTAL SCIENCES↗

Developing Model Benchtop Systems for Microbial Experimental Evolution

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Developing↗

The Study of Environmental Arctic Change (SEARCH) Arctic Futures 2050 Conference. Final Report

The Arctic Futures 2050 Conference was designed as a novel convening of Arctic scientists, Indigenous people, and decision makers, including policy makers at all levels of government. The conference was held 4–6 September 2019 in Washington, D.C. and gathered nearly 400 participants to explore six questions: What do we know, and what do we need to know about the Arctic—and why does it matter? What challenges confront policy makers in the rapidly changing Arctic? What basic research is needed to inform responses to Arctic change? What applied research is needed to inform responses to change? What tools can facilitate informing policy making with science and Indigenous knowledge? What opportunities exist for partnerships between policy makers and scientists? A conference report (see: https://www.searcharcticscience.org/arctic-2050/conference-2019/products) detailed all conference discussions. The main conference conclusion was that holistic understanding and useful adaptation to rapid Arctic change requires bringing together scientists, Indigenous Knowledge holders, and policy makers in all phases of defining the problems, conducting research, and sharing knowledge.

54 ENVIRONMENTAL SCIENCES↗

New Mastcam Multispectral Rock Classes in Sulfate-Bearing Strata, Gale Crater, Mars

Orbital data of Gale Crater, Mars has identified a transition in the stratigraphy of Mt. Sharp indicating an environmental change from a wetter one that accommodated clay mineral formation to a drier environment that led to the precipitation of sulfates. Mt. Sharp is not the only location on Mars for which this transition has been observed which suggests a global environmental change around the Noachian-Hesperian transition. Also visible from orbit is a dark-toned marker band that lies within the sulfate-bearing strata hypothesized to be a volcanic ash deposit. The Mars Science Laboratory (MSL) Curiosity rover is currently exploring this region of Mt. Sharp. In-situ analyses by the rover show changes in morphology and chemistry between the sulfate-bearing layers below and above the marker band and the marker band itself. The MSL instrument payload includes the Mast Camera (Mastcam), which collects multispectral images to provide context for other instruments and broad mineralogic interpretations. In addition to mafic Fe-bearing minerals, Mastcam is sensitive to oxides and some hydrated minerals, important indicators of alteration. In our previous work, we compiled a database of Mastcam spectra through Curiosity’s exploration of Vera Rubin ridge (sols 0-2302), from which 9 spectral classes of rocks were identified (Fig. 1D). Each class has diagnostic spectral features that reflect a common mineralogic interpretation. More recently, as Curiosity traversed through the clay-rich region, Glen Torridon (GT), there was some variation in the rock spectral classes potentially due to nontronite and other phyllosilicates, but not enough to warrant new spectral classes (Fig. 1B). We hypothesize that new classes will appear in accordance with sulfate-bearing strata and the marker band, specifically appearing as a ‘downturn’ in the last two wavelength filters that is inherent, but not unique, to polyhydrated Mg-sulfates. Here, we expand upon our analysis of Mastcam multispectral observations through Curiosity’s second encounter with the marker band (up to sol 3672), comparing the spectral diversity within the sulfate-bearing unit and the marker band to the spectral classes encountered previously in the traverse. These analyses will provide a basis for comparison and aid in selecting targets for in-situ investigations as Curiosity continues its ascent of Mt. Sharp.

A M Eng↗

Systems biology approaches towards predictive microbial ecology

Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N 2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N 2 O production and consumption will respond to future environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Soil moisture drives microbial controls on carbon decomposition in two subtropical forests

Knowledge of microbial mechanisms is critical to understand Earth's biogeochemical cycle under climate and environmental changes. However, large uncertainties remain in model simulations and predictions due to the lack of explicit parameterization of microbial data and few applications beyond the laboratory. In addition, most experimental and modeling studies of warming-induced changes in soil carbon (C) focus on temperature sensitivity, neglecting concomitant effects of changes in soil moisture. Soil microbes are sensitive to moisture, and their responses can dramatically impact soil biogeochemical cycles. Here we represent microbial and enzymatic functions in response to changes in moisture in the Microbial-ENzyme Decomposition (MEND) model. Through modeling with long-term field observations from subtropical forests, we demonstrate that parameterization with microbial data in addition to respiration fluxes greatly increases confidence in model simulations. We further employ the calibrated model to simulate the responses of soil organic C (SOC) under multiple environmental change scenarios. The model shows significant increases in SOC in response to decreasing soil moisture and only minor changes in SOC in response to increasing soil temperature. Increasing litter inputs also cause a significant increase in SOC in the pine forest, whereas an insignificant negative effect is simulated in the broadleaf forest. We also demonstrate the co-metabolism mechanism for the priming effects, i.e., more labile inputs to soil could stimulate microbial and enzymatic growth and activity. Furthermore our study provides strong evidence of microbial control over soil C decomposition and suggests the future trajectory of soil C may be more responsive to changes in soil moisture than temperature, particularly in tropical and subtropical environments.

54 ENVIRONMENTAL SCIENCES↗

Paleobiology, community ecology, and scales of ecological pattern

The fossil record provides a wealth of data on the role of regional processes and historical events in shaping biological communities over a variety of time scales. The Quaternary record with its evidence of repeated climatic change shows that both terrestrial and marine species shifted independently rather than as cohesive assemblages over scales of thousands of years. Larger scale patterns also show a strong individualistic component to taxon dynamics; assemblage stability, when it occurs, is difficult to separate from shared responses to low rates of environmental change. Nevertheless, the fossil record does suggest that some biotic interactions influence large-scale ecological and evolutionary patterns, albeit in more diffuse and protracted fashions than those generally studied by community ecologists. These include: (1) the resistance by incumbents to the establishment of new or invading taxa, with episodes of explosive diversification often appearing contingent on the removal of incumbents at extinction events; (2) steady states of within-habitat and global diversity at longer time scales (10(7)-l0(8) yr), despite enormous turnover of taxa; and (3) morphological and biogeographic responses to increased intensities of predation and substratum disturbance over similarly long time scales. The behavior of species and communities over the array of temporal and spatial scales in the fossil record takes on additional significance for framing conservation strategies, and for understanding recovery of species, lineages, and communities from environmental changes.

NASA Discipline Exobiology↗

Survival Strategies in the Aquatic and Terrestrial World: The Impact of Second Messengers on Cyanobacterial Processes

Second messengers are intracellular substances regulated by specific external stimuli globally known as first messengers. Cells rely on second messengers to generate rapid responses to environmental changes and the importance of their roles is becoming increasingly realized in cellular signaling research. Cyanobacteria are photooxygenic bacteria that inhabit most of Earth’s environments. The ability of cyanobacteria to survive in ecologically diverse habitats is due to their capacity to adapt and respond to environmental changes. This article reviews known second messenger-controlled physiological processes in cyanobacteria. Second messengers used in these systems include the element calcium (Ca 2+ ), nucleotide-based guanosine tetraphosphate or pentaphosphate (ppGpp or pppGpp, represented as (p)ppGpp), cyclic adenosine 3’,5’-monophosphate (cAMP), cyclic dimeric GMP (c-di-GMP), cyclic guanosine 3’,5’-monophosphate (cGMP), and cyclic dimeric AMP (c-di-AMP), and the gaseous nitric oxide (NO). The discussion focuses on processes central to cyanobacteria, such as nitrogen fixation, light perception, photosynthesis-related processes, and gliding motility. In addition, we address future research trajectories needed to better understand the signaling networks and cross talk in the signaling pathways of these molecules in cyanobacteria. Second messengers have significant potential to be adapted as technological tools and we highlight possible novel and practical applications based on our understanding of these molecules and the signaling networks that they control.

59 BASIC BIOLOGICAL SCIENCES↗

NASA Tools for Climate Impacts on Water Resources

Climate and environmental change are expected to fundamentally alter the nation's hydrological cycle and water availability. Satellites provide global or near-global coverage using instruments, allowing for consistent, well-calibrated, and equivalent-quality data of the Earth system. A major goal for NASA climate and environmental change research is to create multi-instrument data sets to span the multi-decadal time scales of climate change and to combine these data with those from modeling and surface-based observing systems to improve process understanding and predictions. NASA and Earth science data and analyses will ultimately enable more accurate climate prediction, and characterization of uncertainties. NASA's Applied Sciences Program works with other groups, including other federal agencies, to transition demonstrated observational capabilities to operational capabilities. A summary of some of NASA tools for improved water resources management will be presented.

Toll, David↗

A decreasing carbon allocation to belowground autotrophic respiration in global forest ecosystems

Belowground autotrophic respiration (RAsoil) depends on carbohydrates from photosynthesis flowing to roots and rhizospheres, and is one of the most important but least understood components in forest carbon cycling. Carbon allocation plays an important role in forest carbon cycling and reflects forest adaptation to changing environmental conditions. However, carbon allocation to RAsoil has not been fully examined at the global scale. To fill this knowledge gap, first, the spatio-temporal patterns of RAsoil from 1981 to 2017 were predicted by a Random Forest (RF) algorithm using the most updated Global Soil Respiration Database (v5) with global environmental variables; second, carbon allocation from photosynthesis to RAsoil (CAB), was calculated as the ratio of RAsoil to gross primary production; and its temporal and spatial patterns were assessed in global forest ecosystems. . Globally, mean RAsoil from forests was 8.9 ± 0.08 Pg C yr-1 (mean ± standard deviation) from 1981 to 2017 with strong spatial variabilities. Temporally, RAsoil increased at a rate of 0.0059 Pg C yr-2, paralleling broader soil respiration changes and indicating increasing carbon respired by roots. Mean CAB was 0.243 ± 0.016 and decreased over time. The temporal trend of CAB varied greatly in space, reflecting uneven responses of CAB to environmental changes. This study is the first attempt to predict global CAB and analyze its temporal and spatial patterns. With the linkage of carbon use efficiency, the developed CAB offers an completely independent approach to quantify global aboveground autotropic respiration spatially and temporally, which could provide crucial insights into carbon flux partition and global carbon cycling under climate change.

Tang, Xiaolu↗

Histological Findings in Wild Rodents of the Great Basin

In the western United States, significant environmental change is expected through the combined effects of climate change, tree mortality, drought, and invasive species. Wild animals can be used as indicators of threats to populations and even entire communities by looking for histopathological changes in their tissues. This method may identify threats to wild populations quickly and more accurately than waiting to observe population declines; however, baseline data are needed for comparisons. In this work, rodents are surveyed at 5 sites in the Great Basin to record histopathological changes. Additionally, one site is next to a copper mine that was in operation for nearly 100 years. This site is compared to the other more pristine sites. Liver, lung, heart, and kidney tissues of 143 rodents from 10 species were processed and examined using standard histological methods. Thirty percent of rodents had histopathological changes. The most common histopathological changes were extramedullary hematopoiesis (11.9%), hyperplastic BALT (6.3%), and pyelitis (4.9%). Two pathogens were found: the nematode Capillaria hepatica (0.7%) and the fungus Emmonsia crescens (2.8%). The most common rodent captured, Peromyscus maniculatus (n = 116), was used to determine whether sex and mass predict histopathological changes. Body mass, not sex, was the best predictor, suggesting that heavier, older individuals should be selectively sampled if the goal is to assess potential threats to rodent populations. Data such as these can be compared to future data to assess populations and communities for effects of environmental change.

59 BASIC BIOLOGICAL SCIENCES↗

Uranium Attenuated by a Wetland 50 Years after Release into a Stream

: Wetlands have several important roles in the hydrological cycle, including maintaining water quality by removing surface and groundwater contaminants. Over time, the wetlands themselves can become contaminated, posing a secondary environmental threat. The objective of this study was to calculate the inventory of uranium (U) remaining in a wetland 50 years after the Fuel Fabrication Facility on the Savannah River Site located in South Carolina released 43.5 Mg of U into the nearby environment. Over 232 700 gamma spectra and their associated global positioning system (GPS) coordinates were collected and collated into a map of the contaminated land area. Five core samples were also collected that contained U concentrations as high as 14 099 mg/kg (background levels are about 2.7 mg/kg U). The contaminated area was 278 000 m2 , and it contained 36.2 Mg U, about 83% of the U released. About 80% of the U in the wetland was concentrated in a former beaver pond, a 73 000 m2 area (26% of the contaminated area). This contaminated wetland area was almost 2 km from the source, indicating that it comprised unique hydro-biogeochemical properties for immobilizing the released U. To the best of our knowledge, this is the first data-rich study to quantify the long-term effectiveness of a wetland to immobilize inorganic contaminants. Significant environmental changes to the system, such as those associated with hydrology, forest fires, or anthropogenic land use, may alter the complex hydro-biogeochemical interactions necessary for the long-term immobilization of the U.

Contaminant inventory↗

Experimental testing of hypotheses for temperature‐ and pH ‐based niche specialization of ammonia oxidizing archaea and bacteria

Summary Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Using research networks to create the comprehensive datasets needed to assess nutrient availability as a key determinant of terrestrial carbon cycling

A wide range of research shows that nutrient availability strongly influences terrestrial carbon (C) cycling and shapes ecosystem responses to environmental changes and hence terrestrial feedbacks to climate. Nonetheless, our understanding of nutrient controls remains far from complete and poorly quantified, at least partly due to a lack of informative, comparable, and accessible datasets at regional-to-global scales. A growing research infrastructure of multi-site networks are providing valuable data on C fluxes and stocks and are monitoring their responses to global environmental change and measuring responses to experimental treatments. These networks thus provide an opportunity for improving our understanding of C-nutrient cycle interactions and our ability to model them. However, coherent information on how nutrient cycling interacts with observed C cycle patterns is still generally lacking. Here, we argue that complementing available C-cycle measurements from monitoring and experimental sites with data characterizing nutrient availability will greatly enhance their power and will improve our capacity to forecast future trajectories of terrestrial C cycling and climate. Therefore, we propose a set of complementary measurements that are relatively easy to conduct routinely at any site or experiment and that, in combination with C cycle observations, can provide a robust characterization of the effects of nutrient availability across sites. In addition, we discuss the power of different observable variables for informing the formulation of models and constraining their predictions. Most widely available measurements of nutrient availability often do not align well with current modelling needs. This highlights the importance to foster the interaction between the empirical and modelling communities for setting future research priorities.

54 ENVIRONMENTAL SCIENCES↗

Intraspecific Trait Variation and Phenotypic Plasticity Mediate Alpine Plant Species Response to Climate Change

In a rapidly changing climate, alpine plants may persist by adapting to new conditions. However, the rate at which the climate is changing might exceed the rate of adaptation through evolutionary processes in long-lived plants. Persistence may depend on phenotypic plasticity in morphology and physiology. Here we investigated patterns of leaf trait variation including leaf area, leaf thickness, specific leaf area, leaf dry matter content, leaf nutrients (C, N, P) and isotopes (δ 13C and δ 15N) across an elevation gradient on Gongga Mountain, Sichuan Province, China. We quantified inter- and intra-specific trait variation and the plasticity in leaf traits of selected species to experimental warming and cooling by using a reciprocal transplantation approach. We found substantial phenotypic plasticity in most functional traits where δ 15N, leaf area, and leaf P showed greatest plasticity. These traits did not correspond with traits with the largest amount of intraspecific variation. Plasticity in leaf functional traits tended to enable plant populations to shift their trait values toward the mean values of a transplanted plants’ destination community, but only if that population started with very different trait values. These results suggest that leaf trait plasticity is an important mechanism for enabling plants to persist within communities and to better tolerate changing environmental conditions under climate change.

54 ENVIRONMENTAL SCIENCES↗