Earth at risk: An urgent call to end the age of destruction and forge a just and sustainable future.

Human development has ushered in an era of converging crises: climate change, ecological destruction, disease, pollution, and socioeconomic inequality. This review synthesizes the breadth of these interwoven emergencies and underscores the urgent need for comprehensive, integrated action. Propelled by imperialism, extractive capitalism, and a surging population, we are speeding past Earth's material limits, destroying critical ecosystems, and triggering irreversible changes in biophysical systems that underpin the Holocene climatic stability which fostered human civilization. The consequences of these actions are disproportionately borne by vulnerable populations, further entrenching global inequities. Marine and terrestrial biomes face critical tipping points, while escalating challenges to food and water access foreshadow a bleak outlook for global security. Against this backdrop of Earth at risk, we call for a global response centered on urgent decarbonization, fostering reciprocity with nature, and implementing regenerative practices in natural resource management. We call for the elimination of detrimental subsidies, promotion of equitable human development, and transformative financial support for lower income nations. A critical paradigm shift must occur that replaces exploitative, wealth-oriented capitalism with an economic model that prioritizes sustainability, resilience, and justice. We advocate a global cultural shift that elevates kinship with nature and communal well-being, underpinned by the recognition of Earth's finite resources and the interconnectedness of its inhabitants. The imperative is clear: to navigate away from this precipice, we must collectively harness political will, economic resources, and societal values to steer toward a future where human progress does not come at the cost of ecological integrity and social equity.

Opportunities to grow tribal clean energy in the US.

Bold action is needed to address unmanageable time scales, limited access to information, and a need to build capacity.

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.

mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.

MOTIVATION: DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. RESULTS: Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. AVAILABILITY AND IMPLEMENTATION: The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.

Metabolic interaction models recapitulate leaf microbiota ecology.

Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. We mapped the metabolic capabilities of 224 leaf isolates from Arabidopsis thaliana by assessing the growth of each strain on 45 environmentally relevant carbon sources in vitro. We used these data to build curated genome-scale metabolic models for all strains, which we combined to simulate >17,500 interactions. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.

Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.

Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.

The magnitude and pace of photosynthetic recovery after wildfire in California ecosystems.

Wildfire modifies the short- and long-term exchange of carbon between terrestrial ecosystems and the atmosphere, with impacts on ecosystem services such as carbon uptake. Dry western US forests historically experienced low-intensity, frequent fires, with patches across the landscape occupying different points in the fire-recovery trajectory. Contemporary perturbations, such as recent severe fires in California, could shift the historic stand-age distribution and impact the legacy of carbon uptake on the landscape. Here, we combine flux measurements of gross primary production (GPP) and chronosequence analysis using satellite remote sensing to investigate how the last century of fires in California impacted the dynamics of ecosystem carbon uptake on the fire-affected landscape. A GPP recovery trajectory curve of more than five thousand fires in forest ecosystems since 1919 indicated that fire reduced GPP by [Formula: see text] g C m[Formula: see text] y[Formula: see text]([Formula: see text]) in the first year after fire, with average recovery to prefire conditions after [Formula: see text] y. The largest fires in forested ecosystems reduced GPP by [Formula: see text] g C m[Formula: see text] y[Formula: see text] (n = 401) and took more than two decades to recover. Recent increases in fire severity and recovery time have led to nearly [Formula: see text] MMT CO[Formula: see text] (3-y rolling mean) in cumulative forgone carbon uptake due to the legacy of fires on the landscape, complicating the challenge of maintaining California's natural and working lands as a net carbon sink. Understanding these changes is paramount to weighing the costs and benefits associated with fuels management and ecosystem management for climate change mitigation.

Low-elevation conifers in California's Sierra Nevada are out of equilibrium with climate.

Since the 1930s, California's Sierra Nevada has warmed by an average of 1.2 ∘ C. Warming directly primes forests for easier wildfire ignition, but the change in climate also affects vegetation species composition. Different types of vegetation support unique fire regimes with distinct probabilities of catastrophic wildfire, and anticipating vegetation transitions is an important but undervalued component of long-term wildfire management and adaptation. Vegetation transitions are more likely where the climate has become unsuitable but the species composition remains static. This vegetation climate mismatch (VCM) can result in vegetation conversions, particularly after a disturbance like wildfire. Here we produce estimates of VCM within conifer-dominated forests in the Sierra Nevada. Observations from the 1930s Wieslander Survey provide a foundation for characterizing the historical relationship between Sierra Nevada vegetation and climate before the onset of recent, rapid climate change. Based on comparing the historical climatic niche to the modern distribution of conifers and climate, ∼19.5% of modern Sierra Nevada coniferous forests are experiencing VCM, 95% of which is below an elevation of 2356 m. We found that these VCM estimates carry empirical consequences: likelihood of type-conversion increased by 9.2% for every 10% decrease in habitat suitability. Maps of Sierra Nevada VCM can help guide long-term land management decisions by distinguishing areas likely to transition from those expected to remain stable in the near future. This can help direct limited resources to their most effective uses-whether it be protecting land or managing vegetation transitions-in the effort to maintain biodiversity, ecosystem services, and public health in the Sierra Nevada.

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.

BACKGROUND: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. RESULTS: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. CONCLUSIONS: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.

Genome sequences of Rhizopogon roseolus, Mariannaea elegans, Myrothecium verrucaria, and Sphaerostilbella broomeana and the identification of biosynthetic gene clusters for fungal peptide natural products.

In recent years, a variety of fungal cyclic peptides with interesting bioactivities have been discovered. For many of these peptides, the biosynthetic pathways are unknown and their elucidation often holds surprises. The cyclic and backbone N-methylated omphalotins from Omphalotus olearius were recently shown to constitute a novel class (borosins) of ribosomally synthesized and posttranslationally modified peptides, members of which are produced by many fungi, including species of the genus Rhizopogon. Other recently discovered fungal peptide macrocycles include the mariannamides from Mariannaea elegans and the backbone N-methylated verrucamides and broomeanamides from Myrothecium verrucaria and Sphaerostilbella broomeana, respectively. Here, we present draft genome sequences of four fungal species Rhizopogon roseolus, Mariannaea elegans, Myrothecium verrucaria, and Sphaerostilbella broomeana. We screened these genomes for precursor proteins or gene clusters involved in the mariannamide, verrucamide, and broomeanamide biosynthesis including a general screen for borosin-producing precursor proteins. While our genomic screen for potential ribosomally synthesized and posttranslationally modified peptide precursor proteins of mariannamides, verrucamides, broomeanamides, and borosins remained unsuccessful, antiSMASH predicted nonribosomal peptide synthase gene clusters that may be responsible for the biosynthesis of mariannamides, verrucamides, and broomeanamides. In M. verrucaria, our antiSMASH search led to a putative NRPS gene cluster with a predicted peptide product of 20 amino acids, including multiple nonproteinogenic isovalines. This cluster likely encodes a member of the peptaibols, an antimicrobial class of peptides previously isolated primarily from the Genus Trichoderma. The nonribosomal peptide synthase gene clusters discovered in our screenings are promising candidates for future research.

Mercury exposure of tidal marsh songbirds in the northeastern United States and its association with nest survival.

The biogeochemistry of tidal marsh sediments facilitates the transformation of mercury (Hg) into the biologically available form methylmercury (MeHg), resulting in elevated Hg exposures to tidal marsh wildlife. Saltmarsh and Acadian Nelson's sparrows (Ammospiza caudacutua and A. nelsoni subvirgatus, respectively) exclusively inhabit tidal marshes, potentially experiencing elevated risk to Hg exposure, and have experienced range-wide population declines. To characterize spatial and temporal variation of Hg exposure in these species, we sampled total mercury (THg) in blood collected from 9 populations spanning 560 km of coastline, including individuals resampled within and among years. Using concurrent nesting studies, we tested whether THg was correlated with nest survival probabilities, an index of fecundity. Blood THg ranged from 0.074-3.373 µg/g ww across 170 samples from 127 individuals. We detected high spatial variability in Hg exposure, observing differences of more than 45-fold across all individuals and 8-fold in mean blood THg among all study plots, including 4-fold between study plots within 4 km. Intraindividual changes in blood Hg exposure did not vary systematically in time but were considerable, varying by up to 2-fold within and among years. Controlling for both species differences and maximum water level, the dominant driver of fecundity in this system, nest survival probability decreased by 10% across the full range of female blood THg concentrations observed. We conclude that Hg has the potential to impair songbird reproduction, potentially exacerbating known climate-change driven population declines from sea-level rise in saltmarsh and Acadian Nelson's sparrows.

Forest fires and climate-induced tree range shifts in the western US.

Due to climate change, plant populations experience environmental conditions to which they are not adapted. Our understanding of the next century's vegetation geography depends on the distance, direction, and rate at which plant distributions shift in response to a changing climate. In this study we test the sensitivity of tree range shifts (measured as the difference between seedling and mature tree ranges in climate space) to wildfire occurrence, using 74,069 Forest Inventory Analysis plots across nine states in the western United States. Wildfire significantly increased the seedling-only range displacement for 2 of the 8 tree species in which seedling-only plots were displaced from tree-plus-seedling plots in the same direction with and without recent fire. The direction of climatic displacement was consistent with that expected for warmer and drier conditions. The greater seedling-only range displacement observed across burned plots suggests that fire can accelerate climate-related range shifts and that fire and fire management will play a role in the rate of vegetation redistribution in response to climate change.

The limiting factors and regulatory processes that control the environmental responses of C3, C3-C4 intermediate, and C4 photosynthesis.

Here, we describe a model of C3, C3-C4 intermediate, and C4 photosynthesis that is designed to facilitate quantitative analysis of physiological measurements. The model relates the factors limiting electron transport and carbon metabolism, the regulatory processes that coordinate these metabolic domains, and the responses to light, carbon dioxide, and temperature. It has three unique features. First, mechanistic expressions describe how the cytochrome b6f complex controls electron transport in mesophyll and bundle sheath chloroplasts. Second, the coupling between the mesophyll and bundle sheath expressions represents how feedback regulation of Cyt b6f coordinates electron transport and carbon metabolism. Third, the temperature sensitivity of Cyt b6f is differentiated from that of the coupling between NADPH, Fd, and ATP production. Using this model, we present simulations demonstrating that the light dependence of the carbon dioxide compensation point in C3-C4 leaves can be explained by co-occurrence of light saturation in the mesophyll and light limitation in the bundle sheath. We also present inversions demonstrating that population-level variation in the carbon dioxide compensation point in a Type I C3-C4 plant, Flaveria chloraefolia, can be explained by variable allocation of photosynthetic capacity to the bundle sheath. These results suggest that Type I C3-C4 intermediate plants adjust pigment and protein distributions to optimize the glycine shuttle under different light and temperature regimes, and that the malate and aspartate shuttles may have originally functioned to smooth out the energy supply and demand associated with the glycine shuttle. This model has a wide range of potential applications to physiological, ecological, and evolutionary questions.

Routing algorithms as tools for integrating social distancing with emergency evacuation.

One of the lessons from the COVID-19 pandemic is the importance of social distancing, even in challenging circumstances such as pre-hurricane evacuation. To explore the implications of integrating social distancing with evacuation operations, we describe this evacuation process as a Capacitated Vehicle Routing Problem (CVRP) and solve it using a DNN (Deep Neural Network)-based solution (Deep Reinforcement Learning) and a non-DNN solution (Sweep Algorithm). A central question is whether Deep Reinforcement Learning provides sufficient extra routing efficiency to accommodate increased social distancing in a time-constrained evacuation operation. We found that, in comparison to the Sweep Algorithm, Deep Reinforcement Learning can provide decision-makers with more efficient routing. However, the evacuation time saved by Deep Reinforcement Learning does not come close to compensating for the extra time required for social distancing, and its advantage disappears as the emergency vehicle capacity approaches the number of people per household.

Who benefits from urban green spaces during times of crisis? Perception and use of urban green spaces in New York City during the COVID-19 pandemic.

Urban green spaces (UGS) provide health benefits to city dwellers, which may be even more important during times of crisis such as the COVID-19 pandemic. However, lack of access to UGS or important features of UGS, in addition to concerns about UGS safety or maintenance, could prevent people from receiving these benefits. We designed an online survey to understand how people were using and perceiving UGS during the COVID-19 pandemic in New York City during the spring of 2020. The survey included questions about how people's visits to UGS and perceptions of the importance of UGS for their health had changed since the start of the pandemic, as well as the concerns people had and features of UGS they considered important. Of the 1372 people who took the survey, most respondents were concerned about a lack of social distancing and crowded UGS, and respondents with these concerns were less likely to visit UGS and had visited UGS less often during than before the pandemic. In addition, generalized linear models showed differences in some concerns and important features of UGS across gender, race and ethnicity, demonstrating the importance of considering specific community needs in UGS design and management. Although concerns about lack of access were not common in our study population, these also appeared to prevent people from using UGS, and were more common in certain areas of the city that were also hard-hit by COVID-19 in the beginning of the pandemic. To ensure that people can get health benefits from UGS during times of crisis, cities must eliminate barriers by providing equitable access to UGS, considering what amenities communities need from UGS, and provide consistent communication about public health policies.

Using internet search data to understand information seeking behavior for health and conservation topics during the COVID-19 pandemic.

Emerging zoonotic diseases, such as COVID-19, exist at the intersection of human health and the environment. Public interest and support are required to maximize the effectiveness of policies to combat the current pandemic and prevent future outbreaks of zoonoses. Here, we use internet search data from the United States to investigate changes in public information seeking about topics at the intersection of health and the environment during the COVID-19 pandemic. Using breakpoint detection methods, we identify sharp increases in interest for 'wildlife trade', 'bats', and 'pangolins' in the early stages of the pandemic (on Jan. 12, Jan. 19, and Jan. 26, 2020, respectively). Network analyses also revealed increasing connectivity between terms related to human health and the environment, as well as the emergence of novel search terms pointing to a greater interest in wildlife trade and consumption. During the pandemic, the network connectivity between coronavirus keywords and conservation keywords increased, which we measured using the number of unique connections (edge connectivity, k' (G)) and the number of simple paths (Sp) between keywords. Both measures of network connectivity increased between 'coronavirus' and 'bats' or 'pangolins' (Δk' (G) = 1, ΔSp = 37), and between 'coronavirus' and 'conservation' (Δk' (G) = 1, ΔSp = 160). These findings suggest that policy and outreach efforts aimed at engaging public interest in intersectional approaches to pandemic prevention (eg: One Health, Planetary Health), may be able to take advantage of increases in public information seeking following catalyzing events during the pandemic. Further monitoring is needed to determine if these changes persist over time.