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Biocrust science and global change

Global environmental changes such as climate and land‐use change affect ecosystems worldwide, and this New Phytologist Virtual Issue brings together fundamental research questions and novel approaches associated with the study of biological soil crusts in the context of such shifts. In a changing world, organisms can display a limited set of responses that will determine their persistence over varied spatial and temporal scales. Specifically, organisms might tolerate the change – for example, via phenotypic plasticity – and remain present in local communities. Alternatively, organisms might shift or retract their range to match their historical niche, they may adapt to the directional selection pressures imposed by change, or they could be driven to local (and possibly global) extinction. Efforts to understand which of these responses particular plant species or assemblages will exhibit are necessary for predicting changes in ecosystem functioning and trophic interactions under global change scenarios, and for managing and supporting sustainable terrestrial ecosystems. Accordingly, the assessment of plant responses to global change has become a significant research focus. Despite this impressive effort, our understanding and combined work to measure the responses to global change for species and communities of nonvascular autotrophs, such as the cyanobacteria, lichens, and bryophytes that form biological soil crusts (Fig. 1), remain rare compared with the large focus on vascular plants (Fig. 2; Reed et al., 2016). Nevertheless, these nonvascular photosynthetic communities and their responses to change could have critical implications for determining ecosystem structure and function at the global‐scale (Elbert et al., 2012; Ferrenberg et al., 2017; Rodriguez‐Caballero et al., 2018).

New Phytologist↗

Statistical analysis of water-quality data containing multiple detection limits II: S-language software for nonparametric distribution modeling and hypothesis testing

Analysis of low concentrations of trace contaminants in environmental media often results in left-censored data that are below some limit of analytical precision. Interpretation of values becomes complicated when there are multiple detection limits in the data-perhaps as a result of changing analytical precision over time. Parametric and semi-parametric methods, such as maximum likelihood estimation and robust regression on order statistics, can be employed to model distributions of multiply censored data and provide estimates of summary statistics. However, these methods are based on assumptions about the underlying distribution of data. Nonparametric methods provide an alternative that does not require such assumptions. A standard nonparametric method for estimating summary statistics of multiply-censored data is the Kaplan-Meier (K-M) method. This method has seen widespread usage in the medical sciences within a general framework termed "survival analysis" where it is employed with right-censored time-to-failure data. However, K-M methods are equally valid for the left-censored data common in the geosciences. Our S-language software provides an analytical framework based on K-M methods that is tailored to the needs of the earth and environmental sciences community. This includes routines for the generation of empirical cumulative distribution functions, prediction or exceedance probabilities, and related confidence limits computation. Additionally, our software contains K-M-based routines for nonparametric hypothesis testing among an unlimited number of grouping variables. A primary characteristic of K-M methods is that they do not perform extrapolation and interpolation. Thus, these routines cannot be used to model statistics beyond the observed data range or when linear interpolation is desired. For such applications, the aforementioned parametric and semi-parametric methods must be used.

Computers & Geosciences↗

Becoming an actionable scientist: Challenges, competency, and the development of expertise

Demand has grown for actionable science to support real-world decision-making around climate change and related environmental management challenges. Producing actionable science requires scientists to hold a distinct set of competencies, yet relatively little is known about what these competencies are or how to train scientists to develop them. We conducted interviews with mid- and late-career scientists to empirically identify competencies they used when producing actionable science and to understand how they developed those competencies. We describe expertise in terms of 18 competencies—categorised as cognitive, interpersonal, or intrapersonal—that scientists integrated and applied to address the challenges associated with actionable science. We argue that scientists must engage in the social process of producing actionable science (i.e., learning by doing) to become an expert. Expert actionable scientists discussed the importance of learning through different contexts, processes, interactions, and relationships. By naming the competencies that constitute expertise, as well as methods for expertise development, our findings facilitate greater conscious awareness of the process of becoming an actionable scientist, a gradual process that starts during graduate training and continues as a career proceeds. Our results can inform the development of formal learning opportunities as well as the informal learning process that occurs whereby scientists take charge of their own learning.

Environmental Management↗

Strategic Science for Coral Ecosystems 2007-2011

Shallow and deep coral ecosystems are being imperiled by a combination of stressors. Climate change, unsustainable fishing practices, and disease are transforming coral communities at regional to global scales. At local levels, excessive amounts of sediments, nutrients, and contaminants are also impacting the many benefits that healthy coral ecosystems provide. This Plan, Strategic Science for Coral Ecosystems, describes the information needs of resource managers and summarizes current research being conducted by U.S. Geological Survey (USGS) scientists and partners. It outlines important research actions that need to be undertaken over the next five years to achieve more accurate forecasting of future conditions and develop more effective decision-support tools to adaptively manage coral ecosystems. The overarching outcome of this Plan, if fully implemented, would be in transferring relevant knowledge to decision-makers, enabling them to better protect and sustain coral ecosystem services. These services include sources of food, essential habitat for fisheries and protected species, protection of coastlines from wave damage and erosion, recreation, and cultural values for indigenous communities. The USGS has a long history of research and monitoring experience in studying ancient and living coral communities and serving many stakeholders. The research actions in this Plan build on the USGS legacy of conducting integrated multidisciplinary science to address complex environmental issues. This Plan is responsive to Federal legislation and authorities and a variety of external and internal drivers that include the President's Ocean Action Plan, the recommendations of the Coral Reef Task Force, the information needs of Bureaus in the Department of Interior, the USGS Bureau Science Strategy (USGS 2007) and the formal plans of several USGS Programs. To achieve this Plan's desired outcomes will require increased funding and more effective coordination and collaboration among USGS managers and scientists within a national and international framework of partnerships in coral ecosystem science.

Circular↗

Considering science needs to deliver actionable science

Conservation practitioners, natural resource managers, and environmental stewards often seek out scientific contributions to inform decision-making. This body of science only becomes actionable when motivated by decision makers considering alternative courses of action. Many in the science community equate addressing stakeholder science needs with delivering actionable science. However, not all efforts to address science needs deliver actionable science, suggesting that the synonymous use of these two constructs (delivering actionable science and addressing science needs) is not trivial. This can be the case when such needs are conveyed by people who neglect decision makers responsible for articulating a priority management concern and for specifying how the anticipated scientific information will aid the decision-making process. We argue that the actors responsible for articulating these science needs and the process used to identify them are decisive factors in the ability to deliver actionable science, stressing the importance of examining the provenance and the determination of science needs. Guided by a desire to enhance communication and cross-literacy between scientists and decision makers, we identified categories of actors who may inappropriately declare science needs (e.g., applied scientists with and without regulatory affiliation, external influencers, reluctant decision makers, agents in place of decision makers, and boundary organization representatives). We also emphasize the importance of, and general approach to, undertaking needs assessments or gap analyses as a means to identify priority science needs. We conclude that basic stipulations to legitimize actionable science, such as the declaration of decisions of interest that motivate science needs and using a robust process to identify priority information gaps, are not always satisfied and require verification. To alleviate these shortcomings, we formulated practical suggestions for consideration by applied scientists, decision makers, research funding entities, and boundary organizations to help foster conditions that lead to science output being truly actionable.

Conservation Biology↗

Improving ecological data science with workflow management software

Pressing environmental research questions demand the integration of increasingly diverse and large-scale ecological datasets as well as complex analytical methods, which require specialized tools and resources. Computational training for ecological and evolutionary sciences has become more abundant and accessible over the past decade, but tool development has outpaced the availability of specialized training. Most training for scripted analyses focuses on individual analysis steps in one script rather than creating a scripted pipeline, where modular functions comprise an ecosystem of interdependent steps. Although current computational training creates an excellent starting place, linear styles of scripting can risk becoming labor- and time-intensive and less reproducible by often requiring manual execution. Pipelines, however, can be easily automated or tracked by software to increase efficiency and reduce potential errors. Ecology and evolution would benefit from techniques that reduce these risks by managing analytical pipelines in a modular, readily parallelizable format with clear documentation of dependencies. Workflow management software (WMS) can aid in the reproducibility, intelligibility and computational efficiency of complex pipelines. To date, WMS adoption in ecology and evolutionary research has been slow. We discuss the benefits and challenges of implementing WMS and illustrate its use through a case study with the targets r package to further highlight WMS benefits through workflow automation, dependency tracking and improved clarity for reviewers. Although WMS requires familiarity with function-oriented programming and careful planning for more advanced applications and pipeline sharing, investment in training will enable access to the benefits of WMS and impart transferable computing skills that can facilitate ecological and evolutionary data science at large scales.

Methods in Ecology and Evolution↗

Climate consideration in environmental effects analyses on federal public lands in the United States

Effects of a changing climate, including drought, wildfire, and invasive species encroachment, are evident on public lands across the United States. Decision making on Federal public lands requires analyses under the National Environmental Policy Act (NEPA), and there are guidelines for considering climate in NEPA analyses. To better understand how climate most recently has been considered, we analyzed a stratified random sample of 130 environmental assessments (EAs) completed by the Bureau of Land Management (BLM) from 2021 to 2023 across the contiguous United States. We assessed whether EAs considered (1) potential effects of the proposed action on climate (2) potential climate effects on the proposed action, and (3) potential climate effects on resources of concern. We also identified whether EAs included data and science about climate or greenhouse gas emissions, and which datasets and documents were cited. We used two approaches: automated keyword searches and document analysis. Thirty-seven percent of EAs considered the potential effects of the proposed action on climate, 8% considered the potential effects of climate on the proposed action, and 4% of individual resource analyses considered the potential effects of climate on the resource. EAs in the ‘oil and gas development,’ ‘renewable energy,’ and ‘forestry and timber management’ proposed action categories most frequently considered the potential effects of climate and used climate data and science. Our findings suggest an opportunity for scientists to work more closely with public land managers to identify available data and science for considering climate in environmental effects analyses and to provide science delivery mechanisms that can facilitate the consideration and use of climate science in decision making.

Environmental Management↗

Evaluation of Indoor PM2.5 concentrations in a Native American community: A pilot study

Background Indoor air pollution is associated with adverse health effects; however, few studies exist studying indoor air pollution on the Navajo Nation in the southwest U.S., a community with high rates of respiratory disease. Methods Indoor PM 2.5 concentration was evaluated in 26 homes on the Navajo Nation using real-time PM 2.5 monitors. Household risk factors and daily activities were evaluated with three metrics of indoor PM 2.5 : time-weighted average (TWA), 90th percentile of concentration, and daily minutes exceeding 100 μg/m 3 . A questionnaire and recall sheet were used to record baseline household characteristics and daily activities. Results The median TWA, 90th percentile, and daily minutes exceeding 100 μg/m 3 were 7.9 μg/m 3 , 14.0 μg/m 3 , and 17 min, respectively. TWAs tended to be higher in autumn and in houses that used fuel the previous day. Other characteristics associated with elevated PM exposure in all metrics included overcrowded houses, nonmobile houses, and houses with current smokers, pets, and longer cooking time. Conclusions Some residents of the Navajo Nation have higher risk of exposure to indoor air pollution by Environmental Protection Agency (EPA) standards. Efforts to identify the causes and associations with adverse health effects are needed to ensure that exposure to risks and possible health impacts are mitigated.

Journal of Exposure Science and Environmental Epid↗

Use of land surface remotely sensed satellite and airborne data for environmental exposure assessment in cancer research

In recent years, geographic information systems (GIS) have increasingly been used for reconstructing individual-level exposures to environmental contaminants in epidemiological research. Remotely sensed data can be useful in creating space-time models of environmental measures. The primary advantage of using remotely sensed data is that it allows for study at the local scale (e.g., residential level) without requiring expensive, time-consuming monitoring campaigns. The purpose of our study was to identify how land surface remotely sensed data are currently being used to study the relationship between cancer and environmental contaminants, focusing primarily on agricultural chemical exposure assessment applications. We present the results of a comprehensive literature review of epidemiological research where remotely sensed imagery or land cover maps derived from remotely sensed imagery were applied. We also discuss the strengths and limitations of the most commonly used imagery data (aerial photographs and Landsat satellite imagery) and land cover maps.

Journal of Exposure Science and Environmental Epid↗

Limnogeology, news in brief

We've invited Michael R. Rosen, water quality specialist within the USGS Water Science Field Team in Carson City and Elizabeth Gierlowski-Kordesch, professor of geology at Ohio University, to take a look at the intriguing new developments that are emerging in limnogeologic studies. These studies are increasing our understanding of how climate and movements of the Earth's surface influence terrestrial environments, as well as how contaminants are distributed and retained in the environment. They present a selection of recent significant research on sediments, rock, and biota that have been preserved in modern and ancient lake basins.

Environmental Earth Sciences↗

Sustaining Rocky Mountain landscapes: Science, policy and management for the Crown of the Continent ecosystem

Prato and Fagre offer the first systematic, multi-disciplinary assessment of the challenges involved in managing the Crown of the Continent Ecosystem ( CCE), an area of the Rocky Mountains that includes northwestern Montana, southwestern Alberta, and southeastern British Columbia. The spectacular landscapes, extensive recreational options, and broad employment opportunities of the CCE have made it one of the fastest growing regions in the United States and Canada, and have lead to a shift in its economic base from extractive resource industries to service-oriented recreation and tourism industries. In the process, however, the amenities and attributes that draw people to this “New West” are under threat. Pastoral scenes are disappearing as agricultural lands and other open spaces are converted to residential uses, biodiversity is endangered by the fragmentation of fish and wildlife habitats, and many areas are experiencing a decline in air and water quality. Sustaining Rocky Mountain Landscapes provides a scientific basis for communities to develop policies for managing the growth and economic transformation of the CCE without sacrificing the quality of life and environment for which the land is renowned. This forthcoming edited volume focuses on five aspects of sustaining mountain landscapes in the CCE and similar regions in the Rocky Mountains. The five aspects are: 1) how social, economic, demo graphic and environmental forces are transforming ecosystem structure and function, 2) trends in use and conditions for human and environmental resources, 3) activating science, policy and education to enhance sustainable landscape management, 4) challenges to sustainable management of public and private lands, and 5) future prospects for achieving sustainable landscapes.

Idaho, Montana↗

Operational Group Sandy technical progress report

Hurricane Sandy made US landfall near Atlantic City, NJ on 29 October 2012, causing 72 direct deaths, displacing thousands of individuals from damaged or destroyed dwellings, and leaving over 8.5 million homes without power across the northeast and mid-Atlantic. To coordinate federal rebuilding activities in the affected region, the President established the cabinet-level Hurricane Sandy Rebuilding Task Force (Task Force). The Task Force was charged with identifying opportunities for achieving rebuilding success while supporting economic vitality, improving public health and safety, protecting and enhancing natural and manmade infrastructure, bolstering resilience, and ensuring appropriate accountability. The Department of the Interior (DOI) Strategic Sciences Group (SSG) was established in 2012 to provide interdisciplinary science-based scenarios for environmental crises affecting Departmental resources. In January 2013, the Secretary of the Interior directed the SSG to support the Department’s participation in the Task Force. The SSG assembled a team of experts from government, academia, and non-governmental organizations – Operational Group Sandy (OGS) – to develop scenarios for the impacts of Hurricane Sandy and future major storms on coastal communities and urban systems in the New York/New Jersey region. This report documents results from the March 2013 deployment of the OGS. It includes background information on Hurricane Sandy and the federal response; the OGS methodology; scenarios for Hurricane Sandy’s impact on coastal communities and urban ecosystems; potential interventions to improve regional resilience to future major storms; a discussion of scenario results; and lessons learned about the OGS process.

Report↗

Counterfactuals to assess effects to species and systems from renewable energy development

Renewable energy production, mostly via wind, solar, and biofuels, is central to goals worldwide to reduce carbon emissions and mitigate anthropogenic climate change (IPCC, 2014; Pörtner et al., 2021). Nevertheless, adverse impacts to natural systems, especially fatalities of wildlife and alteration of habitat, are key challenges for renewable energy production (Allison et al., 2019; Katzner et al., 2019). Because of the magnitude of these challenges, extensive effort has been invested in surveys and science to understand the environmental effects of renewable energy on species and systems. Nevertheless, these impacts have not been formally compared relative to counterfactual conditions (Bull et al., 2021; Coetzee and Gaston, 2021), i.e., those occurring in the absence of renewable energy. As such, cumulative ecological impact assessments required by many regulating agencies typically only consider the adverse impacts of renewables, without evaluating whether mitigative effects of current and planned build-out (e.g., Larson et al., 2020) will offset their adverse impacts to species and natural systems (Allison et al., 2014). Accordingly, these critical decision processes have an insufficient perspective to foster fully informed decisions, and, for some species or systems, renewable energy could lead to more profound impacts than those it is intended to prevent. Furthermore, because of this approach and, despite the well-studied benefits to society of renewable energy development (IPCC, 2014), the ecological value of renewable energy is often premised on the plausible but untested assumption that its negative effects to natural populations and systems are less consequential than the negative effects in alternative scenarios with less renewable energy and greater climate change. A more comprehensive framing of the counterfactual in cumulative ecological impact assessments would evaluate, for each species or system, the incremental effects of renewables over their full life cycle against the incremental effects they provide by mitigating climate change. This framing is important because a given species or system may see net positive or net negative effects from either renewables or climate change. Furthermore, cumulative impact assessments could identify optimized tradeoffs that balance, for each species or system, the effects of both climate change and renewable energy.

Frontiers in Conservation Science↗

Too much and not enough data: Challenges and solutions for generating information in freshwater research and monitoring

Evaluating progress toward achieving freshwater conservation and sustainability goals requires transforming diverse types of data into useful information for scientists, managers, and other interest groups. Despite substantial increases in the volume of freshwater data collected worldwide, many regions and ecosystems still lack sufficient data collection and/or data access. We illustrate how these data challenges result from a diverse set of underlying mechanisms and propose solutions that can be applied by individuals or organizations. We discuss creative approaches to address data scarcity, including the use of community science, remote-sensing, environmental sensors, and legacy datasets. We highlight the importance of coordinated data collection efforts among groups and training programs to improve data access. At the institutional level, we emphasize the power of prioritizing data curation, incentivizing data publication, and promoting research that enhances data coverage and representativeness. Some of these strategies involve technological and analytical approaches, but many necessitate shifting the priorities and incentives of organizations such as academic and government research institutions, monitoring groups, journals, and funding agencies. Our overarching goal is to stimulate discussion to narrow the data disparities hindering the understanding of freshwater processes and their change across spatial scales.

Nahuel Huapi Lake, Lake Tahoe↗

Response of oxidative enzyme activities to nitrogen deposition affects soil concentrations of dissolved organic carbon

Recent evidence suggests that atmospheric nitrate (NO3- ) deposition can alter soil carbon (C) storage by directly affecting the activity of lignin-degrading soil fungi. In a laboratory experiment, we studied the direct influence of increasing soil NO 3- concentration on microbial C cycling in three different ecosystems: black oak-white oak (BOWO), sugar maple-red oak (SMRO), and sugar maple-basswood (SMBW). These ecosystems span a broad range of litter biochemistry and recalcitrance; the BOWO ecosystem contains the highest litter lignin content, SMRO had intermediate lignin content, and SMBW leaf litter has the lowest lignin content. We hypothesized that increasing soil solution NO 3- would reduce lignolytic activity in the BOWO ecosystem, due to a high abundance of white-rot fungi and lignin-rich leaf litter. Due to the low lignin content of litter in the SMBW, we further reasoned that the NO3- repression of lignolytic activity would be less dramatic due to a lower relative abundance of white-rot basidiomycetes; the response in the SMRO ecosystem should be intermediate. We increased soil solution NO3- concentrations in a 73-day laboratory incubation and measured microbial respiration and soil solution dissolved organic carbon (DOC) and phenolics concentrations. At the end of the incubation, we measured the activity of ??-glucosidase, N-acetyl-glucosaminidase, phenol oxidase, and peroxidase, which are extracellular enzymes involved with cellulose and lignin degradation. We quantified the fungal biomass, and we also used fungal ribosomal intergenic spacer analysis (RISA) to gain insight into fungal community composition. In the BOWO ecosystem, increasing NO 3- significantly decreased oxidative enzyme activities (-30% to -54%) and increased DOC (+32% upper limit) and phenolic (+77% upper limit) concentrations. In the SMRO ecosystem, we observed a significant decrease in phenol oxidase activity (-73% lower limit) and an increase in soluble phenolic concentrations (+57% upper limit) in response to increasing NO 3- in soil solution, but there was no significant change in DOC concentration. In contrast to these patterns, increasing soil solution NO3- in the SMBW soil resulted in significantly greater phenol oxidase activity (+700% upper limit) and a trend toward lower DOC production (-52% lower limit). Nitrate concentration had no effect on microbial respiration or ??-glucosidase or N-acetyl-glucosaminidase activities. Fungal abundance and basidiomycete diversity tended to be highest in the BOWO soil and lowest in the SMBW, but neither displayed a consistent response to NO 3- additions. Taken together, our results demonstrate that oxidative enzyme production by microbial communities responds directly to NO3- deposition, controlling extracellular enzyme activity and DOC flux. The regulation of oxidative enzymes by different microbial communities in response to NO3- deposition highlights the fact that the composition and function of soil microbial communities directly control ecosystem-level responses to environmental change. ?? 2006 Springer Science+Business Media, Inc.

Ecosystems↗

Measurement of field-saturated hydraulic conductivity on fractured rock outcrops near Altamura (Southern Italy) with an adjustable large ring infiltrometer

Up to now, field studies set up to measure field-saturated hydraulic conductivity to evaluate contamination risks, have employed small cylinders that may not be representative of the scale of measurements in heterogeneous media. In this study, a large adjustable ring infiltrometer was designed to be installed on-site directly on rock to measure its field-saturated hydraulic conductivity. The proposed device is inexpensive and simple to implement, yet also very versatile, due to its large adjustable diameter that can be fixed on-site. It thus allows an improved representation of the natural system's heterogeneity, while also taking into consideration irregularities in the soil/rock surface. The new apparatus was tested on an outcrop of karstic fractured limestone overlying the deep Murge aquifer in the South of Italy, which has recently been affected by untreated sludge disposal, derived from municipal and industrial wastewater treatment plants. The quasi-steady vertical flow into the unsaturated fractures was investigated by measuring water levels during infiltrometer tests. Simultaneously, subsurface electrical resistivity measurements were used to visualize the infiltration of water in the subsoil, due to unsaturated water flow in the fractures. The proposed experimental apparatus works well on rock outcrops, and allows the repetition of infiltration tests at many locations in order to reduce model uncertainties in heterogeneous media. ?? 2009 Springer-Verlag.

Environmental Earth Sciences↗

Evaluating remediation alternatives for mine drainage, Little Cottonwood Creek, Utah, USA

The vast occurrence of mine drainage worldwide, documented in descriptive studies, presents a staggering challenge for remediation. Any tool that can move beyond descriptive study and helps to evaluate options for remediation in a way that maximizes improvements to the water quality of streams and minimizes cost of remediation could save valuable resources and time. A reactive solute transport model, calibrated from two detailed mass-loading studies in Little Cottonwood Creek (LCC), Utah, provides a tool to evaluate remediation options. Metal loading to LCC is dominated by discharge from two mine drainage tunnels. Discharge from an upstream tunnel has been treated by a fen to reduce metal loading. Discharge from the downstream tunnel (WDT) can be controlled because of a bulkhead that creates a mine pool. Simulations of remedial options for three compliance locations suggest that the water-quality standards for Cu and Zn at upstream and downstream compliance locations are met using various combinations of fen treatment and WDT regulation, but the complete compliance at the middle compliance location requires the highest level of fen treatment and the greatest regulation of WDT discharge. Reactive transport modeling is an useful tool for the evaluation of remedial alternatives in complex natural systems, where multiple hydrologic and geochemical processes determine metal fate.

Utah↗