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The Great Salt Lake (GSL) is a unique hypersaline system with an understudied phytoplankton assemblage supporting a productive open water ecosystem in the largest embayment of the lake, Gilbert Bay. Determination of phytoplankton by microscopy has practical limitations that can constrain the scope of a study, but DNA metabarcoding may improve upon this through higher taxonomic resolution and the capacity to generate a large volume of assemblage data in comparatively little time. To determine if metabarcoding could replicate microscopy and expand the assessment of GSL phytoplankton, a 23S SSU rRNA metabarcoding and microscopy survey of Gilbert Bay was conducted in 2017 and 2018. Assemblage composition and relative abundances from each method were compared, and spatial and temporal assemblage changes from metabarcoding data were investigated using non-metric multidimensional scaling. Metabarcoding differed from microscopy in multiple taxonomic assignments and relative abundances, with poor correlation for most categories. Diatoms were overrepresented by metabarcoding relative to microscopy, and chlorophytes underrepresented. However, metabarcoding revealed seasonal and spatial patterns in assemblage, detected seasonal patterns within phytoplankton sequences of very low abundance, and detected potential cryptic speciation within the lake’s dominant Dunaliella viridis. Phylogenetic analysis revealed greater phytoplankton diversity than observed before in GSL, but demonstrated the need to improve taxonomic assignment of the resulting sequences, particularly within the diatoms. The expansion of detectable diversity and isolation of DNA sequences that can be traced through time and analyzed against environmental variables make metabarcoding a potentially effective tool for parallel use with microscopy in future GSL research.

The productivity of ecosystems and their capacity to support life depends on access to reactive nitrogen (N). Over the past century, humans have more than doubled the global supply of reactive N through industrial and agricultural activities. However, long-term records demonstrate that N availability is declining in many regions of the world. Reactive N inputs are not evenly distributed, and global changes—including elevated atmospheric carbon dioxide (CO 2 ) levels and rising temperatures—are affecting ecosystem N supply relative to demand. Declining N availability is constraining primary productivity, contributing to lower leaf N concentrations, and reducing the quality of herbivore diets in many ecosystems. We outline the current state of knowledge about declining N availability and propose actions aimed at characterizing and responding to this emerging challenge.

Background Nutrition is a key determinant of North American plains bison (Bison bison) weight gain and reproduction, yet little is known about what bison eat and the pattern of nutritional stress across their distribution. Aims In order to better understand patterns of bison nutrition across broad climatic gradients, bison fecal material was sampled from 50 sites across the United States in June and September of 2018. Materials and Methods For each sample, dietary composition and microbial composition were assessed with DNA metabarcoding, along with dietary quality via near‐infrared spectroscopy and elemental composition. Results Herds in cool, wet sites typically had diets with high crude protein but not necessarily higher or lower digestible organic matter than in hot, dry sites. Independent of climate and season, on average, 57% and 48% of protein intake was derived from non‐graminoids in June and September, respectively. Cool‐season grass abundance in the diet was greater in cooler climates in June and September, while N2‐fixing plant abundance in the diet was greater in warmer climates in June. Among multivariate patterns, bison eating a high‐quality diet had fecal material with higher concentrations of P, Mg, Mn, and Ca, and a higher relative abundances of cellulose‐digesting Ruminococcus. Discussion By sampling across broad geographic gradients and across seasons, the drivers of different components of bison diet are becoming clear. Our results show that climate is integral to structuring bison diet quality, diet composition, elemental intake, and their gut microbiomes. Conclusions Although future work remains to better understand seasonal patterns and inter‐annual variation in diet, North American plains bison should no longer be considered strict grazers. Also, given current geographic dietary patterns, bison in a warmer climate are likely to suffer increased nutritional stress unless actions are taken to increase protein availability.

Plant functional traits can predict community assembly and ecosystem functioning and are thus widely used in global models of vegetation dynamics and land–climate feedbacks. Still, we lack a global understanding of how land and climate affect plant traits. A previous global analysis of six traits observed two main axes of variation: (1) size variation at the organ and plant level and (2) leaf economics balancing leaf persistence against plant growth potential. The orthogonality of these two axes suggests they are differently influenced by environmental drivers. We find that these axes persist in a global dataset of 17 traits across more than 20,000 species. We find a dominant joint effect of climate and soil on trait variation. Additional independent climate effects are also observed across most traits, whereas independent soil effects are almost exclusively observed for economics traits. Variation in size traits correlates well with a latitudinal gradient related to water or energy limitation. In contrast, variation in economics traits is better explained by interactions of climate with soil fertility. These findings have the potential to improve our understanding of biodiversity patterns and our predictions of climate change impacts on biogeochemical cycles., Nature Ecology & Evolution, 6 (1), ISSN:2397-334X

In the United States, bioassessment is a key component of clean water assessment for each state and territory under federal guidelines. Yet, there is a patchwork of approaches implemented by different states that restricts geographic comparisons of water condition. At Jonah Ventures, we have reviewed approaches to implementation of bioassessment for each state and have recommendations for the adoption of aquatic eDNA metabarcoding to complement or replace current practices. States sample different organisms and assess biotic condition differently. For example, only 38 of 55 U.S. states and territories use or have developed methods for using fish assemblages in bioassessments of wadeable streams and rivers. States also differ in the analytical methods used to determine impairment. For benthic macroinvertebrate-based assessments, 2 states apply biotic indices, 35 multimetric indices, 2 predictive models, 2 no standard, and 9 a combination of approaches. Additionally, states vary in ecological values assigned to species, a result of geographic and methodological discrepancies. For instance, the common carp is considered tolerant of disturbance in most states, but not in Arkansas, Georgia, or Maryland. Adoption of eDNA-based bioassessments has the benefits of being cheaper and faster while providing higher taxon detection and resolution than traditional techniques. A single sample can be used to detect the presence or relative abundances of multiple biotic groups. As a result, sample collection can be democratized, and larger, more frequent datasets can be generated that cover a greater range of environments. As a first effort, in 2020, we collected over 100 filtered water samples from streams across the conterminous states. We sequenced multiple PCR replicates of each sample for a hypervariable region of the 12S rRNA gene using the MiFish-U primer set targeting bony fish. ESVs were then assigned to morphospecies taxonomy, and we calculated morphospecies trait-based and compositional metrics for each sample. Up to 18 species of fish were identified at a single site. We also began the process of developing de novo sequence-based ecological values and indices. Given recent advances in sample collection and processing, the path to adoption of eDNA-based assessment in the U.S. is clear: (1) Primer sets for benthic macroinvertebrates need to be improved. (2) Reference sequence libraries need to be expanded. As an example, only about one-third of the freshwater fish species in the U.S. have been sequenced to date. Although taxonomy-free assessments are viable, empirically managers will require taxon-specific information prior to adoption. Genome skimming is recommended for constructing full mitochondrial and chloroplast genome sequence libraries. (3) eDNA must be sampled across a broad gradient of sites that vary in their biogeography and stressors. We estimate about 10,000 samples across the U.S. should be sufficient to generate high-performing indices across the various ecoregions. (4) Analytical techniques must be rigorously tested, regionally calibrated, and consistently implemented across states. We favor an approach in which indices are calculated from gradients of ESV or taxon presence or relative abundances that can secondarily be interpreted based on specific ecological conditions - as opposed to a generalized stress gradient. The transition to eDNA-based bioassessments in the U.S. can likely be accomplished for

International audience; The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities after draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macroinvertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, United States) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150-200 mu S/cm that are substantially below the current U.S. Environmental Protection Agency aquatic life benchmark of 300 mu S/cm for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.

[Motivation]: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready to use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks., [Main types of variables contained]: GRooT contains 114,222 trait records on 38 continuous root traits.Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies., [Time period and grain]: Data were recorded between 1911 and 2019., [Major taxa and level of measurement]: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values., [Software format]: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database., The study has been supported by the TRY initiative on plant traits (http://www.try-db.org). The TRY initiative and database are hosted, developed and maintained at the Max Planck Institute for Biogeochemistry, Jena, Germany. TRY is currently supported by DIVERSITAS/Future Earth and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. Open access funding enabled and organized by Projekt DEAL.

This is a commentary on Brookshire et al. 26, 5404-5413 For the Northern Great Plains, Brookshire, Stoy, Currey, and Finney (Global Change Biology, 2020) analyze satellite-based reconstructions of greenness and foliar nutrition and isotopic composition from herbarium samples. Their results of greater productivity coupled with reduced N availability are part of an inflection in our understanding of the global N cycle as much of the terrestrial biosphere appears to be experiencing reduced N availability.

The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world., It is unclear whether plant trait relationships found at the global scale extend to climatic extremes. Here the authors analyse six major aboveground traits to show that known plant trait relationships extend to the tundra biomes and exhibit the same two dimensions of variation detected at the global scale.

Aim: Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We identified the direct and indirect connections across plant traits relevant to competition, resource acquisition and reproductive strategies using a global database and explored whether connections within and between traits from different tissue types vary across climates and growth forms. Location: Global. Major taxa studied: Plants. Time period: Present. Methods: We used probabilistic graphical models and a database of 10 plant traits (leaf area, specific leaf area, mass- and area-based leaf nitrogen and phosphorous content, leaf life span, plant height, stem specific density and seed mass) with 16,281 records to describe direct and indirect connections across woody and non-woody plants across tropical, temperate, arid, cold and polar regions. Results: Trait networks based on direct connections are sparser than those based on correlations. Land plants had high connectivity across traits within and between tissue types; leaf life span and stem specific density shared direct connections with all other traits. For both growth forms, two groups of traits form modules of more highly connected traits; one related to resource acquisition, the other to plant architecture and reproduction. Woody species had higher trait network modularity in polar compared to temperate and tropical climates, while non-woody species did not show significant differences in modularity across climate regions. Main conclusions: Plant traits are highly connected both within and across tissue types, yet traits segregate into persistent modules of traits. Variation in the modularity of trait networks suggests that trait connectivity is shaped by prevailing environmental conditions and demonstrates that plants of different growth forms use alternative strategies to cope with local conditions. © 2019 John Wiley and Sons Ltd

Although a number of different factors influence C and N isotopic fractionation of organic matter, the δ13C and δ15N values of soil organic matter both tend to increase with soil depth, following similar trajectories. This similarity has not been investigated at the global scale. As microbial decomposition increases organic matter δ13C and δ15N values, soil isotopic values are hypothesized to generally increase with depth across local and global scales. Soil δ13C and δ15N values for 16 soil depth-profile sites were used for local-scale investigation, and 5447 global single-depth sites were used for global-scale investigation of the correspondence between δ13C and δ15N. Correlative and boosted regression tree analyses were used to determine the main drivers of the variance in soil δ15N globally and also the environmental association of variability in the correlation with depth between δ13C and δ15N at a number of sites. Strong positive correlations between δ13C and δ15N values through soil profiles were found at a number of sites and were found to be independent of vegetation type. Globally, soil δ13C and δ15N values were also found to be significantly positively correlated across a wide range of climates and biomes. The global correspondences between δ13C and δ15N values may suggest a mechanistic link between δ13C and δ15N through the process of SOM decomposition and microbial processing and highlight the importance of soil-related processes in determining isotopic signals in soils. The variability in these soil processes should be considered when interpreting soil isotopic values of δ13C and δ15N as indicators of ecosystem sources of soil C and N and inferring vegetation inputs.

Ecologists traditionally use environmental parameters to predict successional shifts in compositional characteristics of local species assemblages (environmental control). Another important focus in ecology is to understand functional roles of species assemblages in determining local environmental properties (diversity control). Then, the question emerges: which is the cause, and which is the consequence? To clarify the causal relationships between species assemblages and environmental properties, we focused on seral changes in species/functional diversity of vascular plants in tundra ecosystems of the High Arctic. We found that, although species richness was influenced by soil properties in the earlier stages of primary succession, the causalities were reversed in the later stages. We also found functional differentiation among coexisting species in the later stage, suggesting that the 'complementarity effect' of diversity on ecosystem functions likely increased with ecosystem development through time. By contrast, particular species had little disproportional influence on soil properties, suggesting that the 'selection effect' as an alternative mechanism was less important. This result was likely attributed to the importance of facilitation in the marginal High Arctic environment. Plant-microsite associations are shaped by feedback mechanisms and therefore, neither plant nor microsite is a single absolute predictor of the other. Although our observational study has limitations, we demonstrates a possibility that the relative magnitude of the influence of one on the other can change in the process of succession, emphasizing that the causalities underlying biodiversity-ecosystem function relationships change through succession.

How climate and rising carbon dioxide concentrations (pCO2) have influenced competition between C3 and C4 plants over the last 50 years is a critical uncertainty in climate change research. Here, we used carbon isotope (δ13C) values of the saprotrophic lawn fungus Amanita thiersii to integrate the signal of C3 and C4 carbon in samples collected between 1982 and 2009 from the Midwestern USA. We then calculated 13C fractionation (Δ) to assess the balance between C3 and C4 photosynthesis as influenced by mean annual temperature (MAT), mean annual precipitation over a 30-year period (MAP-30), and pCO2. Sporocarp Δ correlated negatively with MAT (-1.74‰ °C-1, 79% of variance) and positively with MAP (9.52‰ m-1, 15% of variance), reflecting the relative productivity of C3 and C4 grasses in lawns. In addition, Δ values correlated positively with pCO2 (0.072‰ ppm-1, 5% of variance). Reduced photorespiration with rising pCO2 accounted for 20% of this increased Δ, but the remaining 80% is consistent with increased assimilation of C3-derived carbon by Amanita thiersii resulting from increased productivity of C3 grasses with rising pCO2. Between 1982 and 2009, pCO2 rose by 47 ppm and the relative contribution of C3 photosynthesis to Amanita thiersii carbon increased 18.5%. The δ13C value of Amanita thiersii may integrate both lawn maintenance practices and the physiological responses of turf grasses to rising CO2 concentrations.

Geremia et al. (1) analyze a range of data on bison movement, remotely sensed Normalized Difference Vegetation Index, and plant dietary quality at Yellowstone National Park to test tenets of the Green Wave Hypothesis (GWH). The authors conclude that bison migrate in concert with plant phenological development along elevational gradients in the spring and then slow their migration to consume high-quality forage on previously grazed areas. To this point, the authors state that, “While most bison surfed during early spring, they eventually slowed and let the green wave pass them by” (ref. 1, p. 25707). Likewise, they state that, “Across their migratory paths, bison … surfed by matching their date of use with the date of peak IRG … but mainly in early spring…. [B]ison exhibited a consistent pattern … [↵][1]1Email: josephmcraine{at}gmail.com. [1]: #xref-corresp-1-1

Questions: What is the functional trait variation of European temperate grasslands and how does this reflect global patterns of plant form and function? Do habitat specialists show trait differentiation across habitat types?. Location: Europe. Methods: We compiled 18 regeneration and non-regeneration traits for a continental species pool consisting of 645 species frequent in five grassland types. These grassland types are widely distributed in Europe but differentiated by altitude, soil bedrock and traditional long-term management and disturbance regimes. We evaluated the multivariate trait space of this entire species pool and compared multi-trait variation and mean trait values of habitat specialists grouped by grassland type. Results: The first dimension of the trait space accounted for 23% of variation and reflected a gradient between fast-growing and slow-growing plants. Plant height and SLA contributed to both the first and second ordination axes. Regeneration traits mainly contributed to the second and following dimensions to explain 56% of variation across the first five axes. Habitat specialists showed functional differences between grassland types mainly through non-regeneration traits. Conclusions: The trait spectrum of plants dominating European temperate grasslands is primarily explained by growth strategies which are analogous to the trait variation observed at the global scale, and secondly by regeneration strategies. Functional differentiation of habitat specialists across grassland types is mainly related to environmental filtering linked with altitude and disturbance. This filtering pattern is mainly observed in non-regeneration traits, while most regeneration traits demonstrate multiple strategies within the same habitat type., EL, BJA, MTI, AM, PI and CB acknowledge the research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013 under REA grant agreement no. 607785, as a part of the NAtive Seed Science TEchnology and Conservation (NASSTEC) Initial Training Network (ITN). BJA was further funded by the Marie Curie Clarín‐COFUND program of the Principality of Asturias and the European Union (ACB17‐26). BJA and HB acknowledge support from the German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig funded by the German Research Foundation (DFTG FZT 118) through the sPlot research platform. PI acknowledges support from the Rural & Environment Science & Analytical Services Division of the Scottish Government. KÖ thanks RO1567‐IBB03/2018 for financial support.

Despite the prevalence and costs of allergic diseases caused by pollen, we know little about the distributions of allergenic and non-allergenic pollen inside and outside homes at the continental scale. To better understand patterns in potential pollen diversity across the United States, we used DNA sequencing of a chloroplast marker gene to identify the plant DNA found in settled dust collected on indoor and outdoor surfaces across 459 homes. House location was the best predictor of the relative abundance of plant taxa found in outdoor dust samples. Urban, southern houses in hotter climates that were further from the coast were more likely to have more DNA from grass and moss species, while rural houses in northern, cooler climates closer to the coast were more likely to have higher relative abundances of DNA from Pinus and Cedrus species. In general, those plant taxa that were more abundant outdoors were also more abundant indoors, but indoor dust had uniquely high abundances of DNA from food plants and plants associated with lawns. Approximately 14 % of the plant DNA sequences found outside were from plant taxa that are known to have allergenic pollen compared to just 8 % inside. There was little geographic pattern in the total relative abundance of these allergens highlighting the difficulties associated with trying to predict allergen exposures based on geographic location alone. Together, this work demonstrates the utility of using environmental DNA sequencing to reconstruct the distributions of plant DNA inside and outside buildings, an approach that could prove useful for better understanding and predicting plant allergen exposures.

The pace and degree of nutrient limitation are among the most critical uncertainties in predicting terrestrial ecosystem responses to global change. In the northeastern United States, forest growth has recently declined along with decreased soil calcium (Ca) availability, suggesting that acid rain has depleted soil Ca to the point where it may be a limiting nutrient. However, it is unknown whether the past 60 y of changes in Ca availability are strictly anthropogenic or partly a natural consequence of long-term ecosystem development. Here, we report a high-resolution millennial-scale record of Ca and 16 other elements from the sediments of Mirror Lake, a 15-ha lake in the White Mountains of New Hampshire surrounded by northern hardwood forest. We found that sedimentary Ca concentrations had been declining steadily for 900 y before regional Euro-American settlement. This Ca decline was not a result of serial episodic disturbances but instead the gradual weathering of soils and soil Ca availability. As Ca availability was declining, nitrogen availability concurrently was increasing. These data indicate that nutrient availability on base-poor, parent materials is sensitive to acidifying processes on millennial timescales. Forest harvesting and acid rain in the postsettlement period mobilized significant amounts of Ca from watershed soils, but these effects were exacerbated by the long-term pattern. Shifting nutrient limitation can potentially occur within 10,000 y of ecosystem development, which alters our assessments of the speed and trajectory of nutrient limitation in forests, and could require reformulation of global models of forest productivity.

The physical and biotic environment is often considered the primary driver of functional variation in plant communities. Here, we examine the hypothesis that spatial isolation may also be an important driver of functional variation in plant communities where disturbance and dispersal limitation may prevent species from occupying all suitable habitats. To test this hypothesis, we surveyed the vascular plant composition of 30 islands in the Gulf of Maine, USA, and used available functional trait and growth form data to quantify the functional composition of these islands. We categorized species based on dispersal mode and used a landscape metric of isolation to assess the potential role of dispersal limitation as a mechanism of isolation-driven assembly. We tested for island and species level effects on functional composition using a hierarchical Bayesian framework to better assess the causal link between isolation and functional variation. Growth form composition and the community mean value of functional traits related to growth rate, stress tolerance, and nutrient use varied significantly with island isolation. Functional traits and growth forms were significantly associated with dispersal mode, and spatial isolation was the strongest driver of primary trait variation, while island properties associated with environmental drivers in our system were not strong predictors of trait variation. Despite the species-level association of dispersal mode and functional traits, dispersal mode only accounted for a small proportion of the overall isolation effect on community-level trait variation. Our study suggests that spatial isolation can be a key driver of functional assembly in plant communities on islands, though the role of particular dispersal processes remains unclear.