Threshold effects of air pollution and climate change on understory plant communities at forested sites in the eastern United States

Forest understory plant communities in the eastern United States are often diverse and are potentially sensitive to changes in climate and atmospheric inputs of nitrogen caused by air pollution. In recent years, empirical and processed-based mathematical models have been developed to investigate such changes in plant communities. In the study reported here, a robust set of understory vegetation response functions (expressed as version 2 of the Probability of Occurrence of Plant Species model for the United States [US-PROPS v2]) was developed based on observations of forest understory and grassland plant species presence/absence and associated abiotic characteristics derived from spatial datasets. Improvements to the US-PROPS model, relative to version 1, were mostly focused on inclusion of additional input data, development of custom species-level input datasets, and implementation of methods to address uncertainty. We investigated the application of US-PROPS v2 to evaluate the potential impacts of atmospheric nitrogen (N) and sulfur (S) deposition, and climate change on forest ecosystems at three forested sites located in New Hampshire, Virginia, and Tennessee in the eastern United States. Species-level N and S critical loads (CLs) were determined under ambient deposition at all three modeled sites. The lowest species-level CLs of N deposition at each site were between 2 and 11 kg N/ha/yr. Similarly, the lowest CLs of S deposition, based on the predicted soil pH response, were less than 2 kg S/ha/yr among the three sites. Critical load exceedance was found at all three model sites. The New Hampshire site included the largest percentage of species in exceedance. Simulated warming air temperature typically resulted in lower maximum occurrence probability, which contributed to lower CLs of N and S deposition. The US-PROPS v2 model, together with the PROPS-CLF model to derive CL functions, can be used to develop site-specific CLs for understory plants within broad regions of the United States. This study demonstrates that species-level CLs of N and S deposition are spatially variable according to the climate, light availability, and soil characteristics at a given location. Although the species niche models generally performed well in predicting occurrence probability, there remains uncertainty with respect to the accuracy of reported CLs. As such, the specific CLs reported here should be considered as preliminary estimates. Graphical abstrac

The gold-standard genome of <i>Aspergillus niger</i> NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism.Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source. Key words: Aspergillus, Genomic diversity, Gold standard genome, Sugar catabolis

Harmonization and standardization of nucleus pulposus cell extraction and culture methods

Background In vitro studies using nucleus pulposus (NP) cells are commonly used to investigate disc cell biology and pathogenesis, or to aid in the development of new therapies. However, lab-to-lab variability jeopardizes the much-needed progress in the field. Here, an international group of spine scientists collaborated to standardize extraction and expansion techniques for NP cells to reduce variability, improve comparability between labs and improve utilization of funding and resources. Methods The most commonly applied methods for NP cell extraction, expansion, and re-differentiation were identified using a questionnaire to research groups worldwide. NP cell extraction methods from rat, rabbit, pig, dog, cow, and human NP tissue were experimentally assessed. Expansion and re-differentiation media and techniques were also investigated. Results Recommended protocols are provided for extraction, expansion, and re-differentiation of NP cells from common species utilized for NP cell culture. Conclusions This international, multilab and multispecies study identified cell extraction methods for greater cell yield and fewer gene expression changes by applying species-specific pronase usage, 60–100 U/ml collagenase for shorter durations. Recommendations for NP cell expansion, passage number, and many factors driving successful cell culture in different species are also addressed to support harmonization, rigor, and cross-lab comparisons on NP cells worldwide

Regionalization of soil base cation weathering for evaluating stream water acidification in the Appalachian Mountains, USA

Estimation of base cation supply from mineral weathering (BCw) is useful for watershed research and management. Existing regional approaches for estimating BCw require generalized assumptions and availability of stream chemistry data. We developed an approach for estimating BCw using regionally specific empirical relationships. The dynamic model MAGIC was used to calibrate BCw in 92 watersheds distributed across three ecoregions. Empirical relationships between MAGIC-simulated BCw and watershed characteristics were developed to provide the basis for regionalization of BCw throughout the entire study region. BCw estimates extracted from MAGIC calibrations compared reasonably well with BCw estimated by regression based on landscape characteristics. Approximately one-third of the study region was predicted to exhibit BCw rates less than 100 meq/m2/yr. Estimates were especially low for some locations within national park and wilderness areas. The regional BCw results are discussed in the context of critical loads (CLs) of acidic deposition for aquatic ecosystem protection

Annotator rationales for labeling tasks in crowdsourcing

When collecting item ratings from human judges, it can be difficult to measure and enforce data quality due to task subjectivity and lack of transparency into how judges make each rating decision. To address this, we investigate asking judges to provide a specific form of rationale supporting each rating decision. We evaluate this approach on an information retrieval task in which human judges rate the relevance of Web pages for different search topics. Cost-benefit analysis over 10,000 judgments collected on Amazon’s Mechanical Turk suggests a win-win. Firstly, rationales yield a multitude of benefits: more reliable judgments, greater transparency for evaluating both human raters and their judgments, reduced need for expert gold, the opportunity for dual-supervision from ratings and rationales, and added value from the rationales themselves. Secondly, once experienced in the task, crowd workers provide rationales with almost no increase in task completion time. Consequently, we can realize the above benefits with minimal additional cost

Effects of climate, land management, and sulfur deposition on soil base cation supply in national forests of the Southern Appalachian Mountains

Forest soils having low exchangeable calcium (Ca) and other nutrient base cation (BC) reserves may induce nutrient deficiencies in acid-sensitive plants and impact commercially important tree species. Past and future depletion of soil BC in response to acidic sulfur (S) deposition, forest management, and climate change alter the health and productivity of forest trees. This study used a process model (Model of Acidification of Groundwater in Catchments [MAGIC]) to address a number of questions related to soil BC status for a group of 65 streams and their watersheds in the southern Blue Ridge physiographic province of the southern Appalachian Mountains. Future S deposition to the study watersheds used for the Base Scenario was specified according to proposed reductions in S emissions at the time of this study, representing a reduction of 42 % of ambient S deposition by 2020. Twenty additional simulations were considered, reflecting four alternate S deposition scenarios (6 %, 58 %, 65 %, and 78 % reduction), and various changes in timber harvest, temperature, and precipitation. Base Scenario soil exchangeable Ca and % base saturation showed decreasing trends from 1860 to 2100. Changes in tree harvesting had the largest effect on stream sum of base cations (SBC) and soil BC supply. Each of the scenario projections indicated that median year 2100 soil exchangeable Ca will be at least 20 % lower than pre-industrial values. The simulations suggested that substantial mass loss of soil BC has already occurred since pre-industrial times. Nearly the same magnitude of BC loss is expected to occur over the next 145 years, even under relatively large additional future reductions in S deposition

US-PROPS: Regional Application to Great Smoky Mountains National Park (McDonnell et al. 2022)

This dataset is the data and metadata associated with the application of the US-PROPS model to the Great Smoky Mountains National Park (GSMNP). It is a geodatabase of species and vegetation classes across the GSMNP and describes the distribution of species, critical loads of different vegetation classes, and the changes in the occurrence probabilities for different scenarios explored. Users should start with the "Dataset_Descriptions.docx" file, and read McDonnell et al. (2022) for context (https://www.sciencedirect.com/science/article/pii/S2666765722001065). McDonnell, T.C., Clark, C.M., Reinds, G.J., Sullivan, T.J. and Knees, B., 2022. Modeled vegetation community trajectories: Effects from climate change, atmospheric nitrogen deposition, and soil acidification recovery. Environmental Advances, p.100271

Modeled vegetation community trajectories : Effects from climate change, atmospheric nitrogen deposition, and soil acidification recovery

Forest understory plant communities in the United States harbor most of the vegetation diversity of forests and are often sensitive to changes in climate and atmospheric deposition of nitrogen (N). As temperature increases from human-caused climate change and soils recover from long term atmospheric deposition of N and sulfur (S), it is unclear how these important ecosystem components will respond. We used the newly developed US-PROPS model – based on species response functions for over 1,500 species - to evaluate the potential impacts of atmospheric N deposition and climate change on species occurrence probability for a case study in the forested ecosystems of the Great Smoky Mountains National Park (GRSM), an iconic park in the southeastern United States. We evaluated six future scenarios from various combinations of two potential recoveries of soil pH (no change, +0.5 pH units) and three climate futures (no change, +1.5, +3.0 deg C). Species critical loads (CLs) of N deposition and projected responses for each scenario were determined. Critical loads were estimated to be low (< 2 kg N/ha/yr) to protect all species under current and expected future conditions across broad regions of GRSM and these CLs were exceeded at large spatial extents among scenarios. Northern hardwood, yellow pine, and chestnut oak forests were among the most N-sensitive vegetation map classes found within GRSM. Potential future air temperature conditions generally led to decreases in the maximum occurrence probability for species. Therefore, CLs were considered “unattainable” in these situations because the specified level of protection used for CL determination (i.e., maximum occurrence probability under ambient conditions) was not attainable. Although some species showed decreases in maximum occurrence probability with simulated increases in soil pH, most species were favored by increased pH. The importance of our study is rooted in the methodology described here for establishing regional CLs and for evaluating future conditions, which is transferable to other national parks in the U.S. and in Europe where the original PROPS model was developed

Target loads of atmospheric sulfur and nitrogen deposition for protection of acid-sensitive aquatic resources in the Adirondack Mountains, New York

[1] The dynamic watershed acid-base chemistry model of acidification of groundwater in catchments (MAGIC) was used to calculate target loads (TLs) of atmospheric sulfur and nitrogen deposition expected to be protective of aquatic health in lakes in the Adirondack ecoregion of New York. The TLs were calculated for two future dates (2050 and 2100) and three levels of protection against lake acidification (acid neutralizing capacity (ANC) of 0, 20, and 50 μeq L−1). Regional sulfur and nitrogen deposition estimates were combined with TLs to calculate exceedances. Target load results, and associated exceedances, were extrapolated to the regional population of Adirondack lakes. About 30% of Adirondack lakes had simulated TL of sulfur deposition less than 50 meq m−2 yr to protect lake ANC to 50 μeq L−1. About 600 Adirondack lakes receive ambient sulfur deposition that is above this TL, in some cases by more than a factor of 2. Some critical criteria threshold values were simulated to be unobtainable in some lakes even if sulfur deposition was to be decreased to zero and held at zero until the specified endpoint year. We also summarize important lessons for the use of target loads in the management of acid-impacted aquatic ecosystems, such as those in North America, Europe, and Asia

Feasibility of coupled empirical and dynamic modeling to assess climate change and air pollution impacts on temperate forest vegetation of the eastern United States

Changes in climate and atmospheric nitrogen (N) deposition caused pronounced changes in soil conditions and habitat suitability for many plant species over the latter half of the previous century. Such changes are expected to continue in the future with anticipated further changing air temperature and precipitation that will likely influence the effects of N deposition. To investigate the potential long-term impacts of atmospheric N deposition on hardwood forest ecosystems in the eastern United States in the context of climate change, application of the coupled biogeochemical and vegetation community model VSD+PROPS was explored at three sites in New Hampshire, Virginia, and Tennessee. This represents the first application of VSD+PROPS to forest ecosystems in the United States. Climate change and elevated (above mid-19th century) N deposition were simulated to be important factors for determining habitat suitability. Although simulation results suggested that the suitability of these forests to support the continued presence of their characteristic understory plant species might decline by the year 2100, low data availability for building vegetation response models with PROPS resulted in uncertain results at the extremes of simulated N deposition. Future PROPS model development in the United States should focus on inclusion of additional foundational data or alternate candidate predictor variables to reduce these uncertainties. Climate change and elevated N deposition were simulated to be important factors for determining habitat suitability for plants, and are expected to interact with changes in soil chemistry