Search for: All records

ABSTRACT MotivationHere, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables IncludedThe database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and GrainSampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and GrainThe earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample‐level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of MeasurementThe database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Formatcsv and. SQL. 

Abstract Temporal patterns in chemistry of headwater streams reflect responses of water and elemental cycles to perturbations occurring at local to global scales. We evaluated multi-scale temporal patterns in up to 32 y of monthly observations of stream chemistry (ammonium, calcium, dissolved organic carbon, nitrate, total dissolved phosphorus, and sulfate) in 22 reference catchments within the northern temperate zone of North America. Multivariate autoregressive state-space (MARSS) models were applied to quantify patterns at multi-decadal, seasonal, and shorter intervals during a period that encompassed warming climate, seasonal changes in precipitation, and regional declines in atmospheric deposition. Significant long-term trends in solute concentrations within a subset of the catchments were consistent with recovery from atmospheric deposition (e.g., calcium, nitrate, sulfate) and increased precipitation (e.g., dissolved organic carbon). Lack of evidence for multi-decadal trends in most catchments suggests resilience of northern temperate ecosystems or that subtle net effects of simultaneous changes in climate and disturbance regimes do not result in directional trends. Synchronous seasonal oscillations of solute concentrations occurred across many catchments, reflecting shared climate and biotic drivers of seasonality within the northern temperate zone. Despite shared patterns among catchments at a seasonal scale, multi-scale temporal patterns were statistically distinct among even adjacent headwater catchments, implying that local attributes of headwater catchments modify the signals imparted by atmospheric phenomena and regional disturbances. To effectively characterize hydrologic and biogeochemical responses to changing climate and disturbance regimes, catchment monitoring programs could include multiple streams with contributing areas that encompass regional heterogeneity in vegetation, topography, and elevation. Overall, detection of long-term patterns and trends requires monitoring multiple catchments at a frequency that captures periodic variation (e.g., seasonality) and a duration encompassing the perturbations of interest. 

Abstract Federal and state land agencies lack diversity at the natural resource manager level, in turn limiting the agencies' capacity for creative problem solving needed for complex and wicked environmental problems. Diverse representation is imperative to increase public support and trust in natural resource management.We used an online survey method to examine the relationship and experiences between independent demographic variables (e.g. gender, ethnicity and years worked in natural resources) and two dependent variables: (1) perceived public support and (2) sense of belonging for resource management professionals in the Pacific Northwest, USA.We find in general, that gender is associated with how one progresses through a career in natural resource management. As years in natural resource management increases, sense of belonging decreases for women and remains constant for men. Similarly, as years in natural resource management increases, perceived public support increases for men and remains constant for women.Given that ample past research suggests strong links between sustainable management and diverse perspectives, this study has implications for addressing our current and future natural resource management challenges. Read the freePlain Language Summaryfor this article on the Journal blog. 

Abstract Increasing wildfire activity can impact the global carbon cycle, aquatic ecosystem health, and drinking water treatment through alterations in aquatic dissolved organic matter (DOM) composition. However, uncertainty remains about the spatial and temporal variability in wildfire effects on DOM composition. We sought to improve understanding of how burn severity affects stream DOM and how weather, hydrology, and landscape factors contribute to variability in post‐fire DOM responses across space and time. Following a large 2020 wildfire in Oregon, USA, we collected water samples to quantify dissolved organic carbon and DOM optical properties at 129 stream sites across the fire‐affected stream network. Sampling was repeated across seasonal hydrologic conditions to capture variation in hydrologic pathways and organic matter sources. We developed a PARAFAC model using excitation‐emission matrices (EEMs) and used spatial stream network (SSN) models to determine how DOM composition changed across the stream network with burn severity. The greatest shifts in DOM composition were observed during the dry and wetting seasons, with an increase in aromatic DOM at higher burn severities. In contrast, an increase in protein‐like DOM was observed during the wet season at higher burn severities. Drainage area, 31‐day and 1‐day antecedent precipitation, and baseflow index impacted the relationship between DOM composition and burn severity, which could partially explain the variability in post‐fire DOM responses. Our study contributes a mechanistic understanding of how wildfire impacts DOM sources and composition, which is critical to predicting wildfire effects on aquatic biogeochemical cycling and preserving ecosystem health and source water quality. 

Abstract Riparian zones are a critical terrestrial‐aquatic ecotone. They play important roles in ecosystems including (1) harboring biodiversity, (2) influencing light and carbon fluxes to aquatic food webs, (3) maintaining water quality and streamflow, (4) enhancing aquatic habitat, (5) influencing greenhouse gas production, and (6) sequestering carbon. Defining what qualifies as a riparian zone is a first step to delineation. Many definitions of riparian boundaries focus on static attributes or a subset of potential functions without recognizing that they are spatially continuous, temporally dynamic, and multi‐dimensional. We emphasize that definitions should consider multiple ecological and biogeochemical functions and physical gradients, and explore how this approach influences spatial characterization of riparian zones. One or more of the following properties can guide riparian delineation: (1) distinct species, elevated biodiversity, or species with specific adaptations to flooding and inundation near streams relative to nearby upland areas; (2) unique vegetation structure directly influencing irradiance or organic material inputs to aquatic ecosystems; (3) hydrologic and geomorphic features or processes maintaining floodplains; (4) hydric soil properties that differ from the uplands; and/or (5) elevated retention of dissolved and suspended materials relative to adjacent uplands. Considering these properties for an operational and dynamic definition of riparian zones recognizes that riparian boundaries vary in space (e.g., variation of riparian corridor widths within or among watersheds) and time (e.g., responses to hydrological variance and climate change). Inclusive definitions addressing multiple riparian functions could facilitate attainment of research and management goals by linking properties of interest to specific outcomes. 

Abstract The body size of aquatic vertebrates is declining across populations and ecosystems worldwide owing to warmer water temperature and changing streamflow. In freshwaters, the effects of stream network position and density‐dependent factors on body size are less understood. We used an extensive dataset spanning 41 stream sites over 7 years to evaluate how density‐dependent and density‐independent factors influence the size of two top predators in small watersheds, Coastal Cutthroat TroutOncorhynchus clarkii clarkiiand Coastal Giant SalamandersDicamptodon tenebrosus. We tested three hypotheses of body‐size variation for trout and salamanders, including intraspecific density dependence, interspecific density dependence, and resource availability, using empirical observations in hierarchical linear mixed models in a model‐selection framework. In our best‐supported models, the strongest predictors of size were conspecific negative density dependence, as expected, suggesting greater intraspecific interactions probably owing to conspecific individuals having similar requirements. We reveal a biogeographic pattern in which body size peaks in middle stream‐network positions and plateaus or declines at lower and upper locations, proposing that stream network position also plays a role in determining body size in small watersheds. Salamander density also has a quadratic effect on adult trout size, with salamanders having a greater overall effect on the body size of both species than trout, suggesting that salamanders might be more dominant than trout in some interactions. Collectively, we found that biotic interactions, mainly conspecific but also interspecific, and stream‐network position affect trout and salamander body sizes in small watersheds. 

Abstract An issue of global concern is how climate change forcing is transmitted to ecosystems. Forest ecosystems in mountain landscapes may demonstrate buffering and perhaps decoupling of long‐term rates of temperature change, because vegetation, topography, and local winds (e.g., cold air pooling) influence temperature and potentially create microclimate refugia (areas which are relatively protected from climate change). We tested these ideas by comparing 45‐year regional rates of air temperature change to unique temporal and spatial air temperature records in the understory of regionally representative stable old forest at the H.J. Andrews Experimental Forest, Oregon, USA. The 45‐year seasonal patterns and rates of warming were similar throughout the forested landscape and matched regional rates observed at 88 standard meteorological stations in Oregon and Washington, indicating buffering, but not decoupling of long‐term climate change rates. Consideration of the energy balance explains these results: while shading and airflows produce spatial patterns of temperature, these processes do not counteract global increases in air temperature driven by increased downward, longwave radiation forced by increased anthropogenic greenhouse gases in the atmosphere. In some months, the 45‐year warming in the forest understory equaled or exceeded spatial differences of air temperature between the understory and the canopy or canopy openings and was comparable to temperature change over 1,000 m elevation, while in other months there has been little change. These findings have global implications because they indicate that microclimate refugia are transient, even in this forested mountain landscape. 

Abstract Changing climate conditions are expected to cause increases in the frequency and severity of drought conditions in many areas around the world, including the Pacific Northwest region of North America. While drought impacts manifest across the landscape, headwater streams are particularly susceptible to droughts due to limited deep‐water habitats and low water volumes that allow for substantial increases in water temperature. While low volumes of water and increased stream temperature will likely affect all aquatic species to some degree, the response of different taxa to these impacts is expected to vary with differences in physiological needs and habitat preferences among species. Using a before–after control‐impact (BACI) experimental design, this study investigates how reduced streamflow and increased stream temperature affect the two dominant apex predators in headwater streams of the Pacific Northwest, coastal cutthroat trout (Oncorhynchus clarkii clarkii) and coastal giant salamander (Dicamptodon tenebrosus). In a second‐order stream in the H.J. Andrews Experimental Forest in OR, USA, experimental flow diversions created decoupled drought conditions of reduced streamflow and elevated temperatures. Low‐flow conditions were created by diverting water around a 100‐m stream reach and this diverted water was passively warmed before re‐entering a downstream channel to create an increased temperature reach. We compared fish and salamander abundances and stream habitat in an upstream unmanipulated reference reach to the two experimental reaches. Relative increases in temperature ranged between 0.41 and 0.63°C, reflecting realistic stream warming in this region during drought events. Trout responded positively to increased temperatures, showing an increase in abundance, biomass, condition factor, and growth, whereas salamanders responded negatively in all metrics except condition. The low‐flow reach diverted approximately 50% of the flow, resulting in a relative pool area reduction of about 20%. Relative to the reference reach, salamanders displayed a net positive abundance response while trout declined in the low‐flow reach. The contrasting responses of these populations to decoupled drought conditions suggest that interactions of flow and temperature changes together will influence drought responses of the vertebrate communities of headwater streams. 

Abstract The biodiversity crisis necessitates spatially extensive methods to monitor multiple taxonomic groups for evidence of change in response to evolving environmental conditions. Programs that combine passive acoustic monitoring and machine learning are increasingly used to meet this need. These methods require large, annotated datasets, which are time‐consuming and expensive to produce, creating potential barriers to adoption in data‐ and funding‐poor regions. Recently released pre‐trained avian acoustic classification models provide opportunities to reduce the need for manual labelling and accelerate the development of new acoustic classification algorithms through transfer learning. Transfer learning is a strategy for developing algorithms under data scarcity that uses pre‐trained models from related tasks to adapt to new tasks.Our primary objective was to develop a transfer learning strategy using the feature embeddings of a pre‐trained avian classification model to train custom acoustic classification models in data‐scarce contexts. We used three annotated avian acoustic datasets to test whether transfer learning and soundscape simulation‐based data augmentation could substantially reduce the annotated training data necessary to develop performant custom acoustic classifiers. We also conducted a sensitivity analysis for hyperparameter choice and model architecture. We then assessed the generalizability of our strategy to increasingly novel non‐avian classification tasks.With as few as two training examples per class, our soundscape simulation data augmentation approach consistently yielded new classifiers with improved performance relative to the pre‐trained classification model and transfer learning classifiers trained with other augmentation approaches. Performance increases were evident for three avian test datasets, including single‐class and multi‐label contexts. We observed that the relative performance among our data augmentation approaches varied for the avian datasets and nearly converged for one dataset when we included more training examples.We demonstrate an efficient approach to developing new acoustic classifiers leveraging open‐source sound repositories and pre‐trained networks to reduce manual labelling. With very few examples, our soundscape simulation approach to data augmentation yielded classifiers with performance equivalent to those trained with many more examples, showing it is possible to reduce manual labelling while still achieving high‐performance classifiers and, in turn, expanding the potential for passive acoustic monitoring to address rising biodiversity monitoring needs. 

Abstract Hyporheic exchange is critical to river corridor biogeochemistry, but decameter‐scale flowpaths (∼10‐m long) are understudied due to logistical challenges (e.g., sampling at depth, multi‐day transit times). Some studies suggest that decameter‐scale flowpaths should have initial hot spots followed by transport‐limited conditions, whereas others suggest steady reaction rates and secondary reactions that could make decameter‐scale flowpaths important and unique. We investigated biogeochemistry along a 12‐m hyporheic mesocosm that allowed for controlled testing of seasonal and spatial water quality changes along a flowpath with fixed geometry and constant flow rate. Water quality profiles of oxygen, carbon, and nitrogen were measured at 1‐m intervals along the mesocosm over multiple seasons. The first 6 m of the mesocosm were always oxic and a net nitrogen source to mobile porewater. In winter, oxic conditions persisted to 12 m, whereas the second half of the flowpath became anoxic and a net nitrogen sink in summer. No reactive hot spots were observed in the first meter of the mesocosm. Instead, most reactions were zeroth‐order over 12 m and 54 hr of transit time. Influent chemistry had less impact on hyporheic biogeochemistry than expected due to large amounts of in situ reactant sources compared to stream‐derived reactant sources. Sorbed or buried carbon likely fueled reactions with rates controlled by temperature and redox conditions. Each reactant showed different hyporheic Damköhler numbers, challenging the characterization of flowpaths being intrinsically reaction‐ or transport‐limited. Future research should explore the prevalence and biogeochemical contributions of decameter‐scale flowpaths in diverse field settings.