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At least 109 records · Page 6

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliate Zoothamnium niveum and its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup, Z. niveum holds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.

59 BASIC BIOLOGICAL SCIENCES↗

Optimising response to an introduction of African swine fever in wild pigs

African swine fever virus (ASFv) is a virulent pathogen that threatens domestic swine industries globally and persists in wild boar populations in some countries. Persistence in wild boar can challenge elimination and prevent disease-free status, making it necessary to address wild swine in proactive response plans. In the United States, invasive wild pigs are abundant and found across a wide range of ecological conditions that could drive different epidemiological dynamics among populations. Information on the size of the control areas required to rapidly eliminate the ASFv in wild pigs and how this area should change with management constraints and local ecology is needed to optimize response planning. We developed a spatially explicit disease transmission model contrasting wild pig movement and contact ecology in two ecosystems in Southeastern United States. We simulated ASFv spread and determined the optimal response area (reported as the radius of a circle) for eliminating ASFv rapidly over a range of detection times (when ASFv was detected relative to the true date of introduction), culling capacities (proportion of wild pigs in the culling zone removed weekly) and wild pig densities. Large radii for response areas (14 km) were needed under most conditions but could be shortened with early detection (≤ 8 weeks) and high culling capacities (≥ 15% weekly). Under most conditions, the ASFv was eliminated in less than 22 weeks using optimal control radii, although ecological conditions with high rates of wild pig movement required higher culling capacities (≥ 10% weekly) for elimination within 1 year. The results highlight the importance of adjusting response plans based on local ecology and show that wild pig movement is a better predictor of the optimal response area than the number of ASFv cases early in the outbreak trajectory. Furthermore, our framework provides a tool for determining optimal control plans in different areas, guiding expectations of response impacts, and planning resources needed for rapid elimination.

59 BASIC BIOLOGICAL SCIENCES↗

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping the Path Forward to Next Generation Algal Technologies: Workshop on Understanding the Rules of Life and Complexity in Algal Systems

Algal technology offers enormous potential as a source of renewable biomass and bioproducts for fuels, biochemicals, nutrients, and numerous other applications. While tremendous opportunities exist, significant challenges are also present in harnessing and utilizing this valuable and potentially sustainable bioproduction platform. Funded by a joint partnership between the Bioenergy Technologies Office (BETO) at the Department of Energy (DOE) and the National Science Foundation (NSF), the recent virtual workshop, "Understanding the Rules of Life: Complexity in Algal Systems Workshop," was organized to bring together thought leaders from academia, national laboratories and other government agencies, and industry to identify key challenges and propose research strategies to overcome these barriers. Two parallel sessions were undertaken: 1) algae strain and toolkit development and 2) algal ecosystem and microbiome dynamics, in order to advance algae engineering and cultivation efforts. In each session, attendees discussed the most pressing challenges from the perspective of model systems and omics analysis. Themes such as genetic engineering toolboxes, translation from the laboratory to outdoor cultivation, functional genomics, metabolomics, algal ecology, consortial design, microbiome dynamics, mathematical models, and data analytics emerged from the discussion. Overall, this workshop has served to elucidate the key hurdles and many opportunities present as we continue to advance algal science and technology from the laboratory and into the commercial realm.

09 BIOMASS FUELS↗

Linking Community‐Climate Disequilibrium to Ecosystem Function

Turnover in species composition often lags behind the pace of climate change, resulting in mismatches between climate and communities. However, the impact of these community‐climate disequilibria on ecosystem functions is rarely considered, and current methods for measuring disequilibria assume that species ranges were, until recently, in equilibrium with climate. Here, in this work, we develop a simple theoretical model to address both of these problems by linking community‐climate disequilibrium with ecosystem functioning. We show how disequilibrium can impair functioning in the near‐term even when climate change is expected to enhance functioning in the long‐term. Responses are most likely to change over time in communities where turnover is slow, the impact of disequilibrium counteracts the direct effects of climate on ecosystem function, and pre‐existing disequilibrium is large. These findings emphasise the importance of precise and unbiased estimates of community‐climate disequilibria for improving ecological forecasts. By fitting our model to time series of both climate and ecosystem function from a metacommunity simulation, we show the potential for community‐climate disequilibrium to be inferred without direct knowledge about species' distributions or climatic tolerances. We end by outlining a research agenda to apply dynamic disequilibrium concepts and test novel hypotheses across diverse ecosystems.

climate change↗

Predicting spring phenology in deciduous broadleaf forests: NEON phenology forecasting community challenge

Accurate models are important to predict how global climate change will continue to alter plant phenology and near-term ecological forecasts can be used to iteratively improve models and evaluate predictions that are made a priori. The Ecological Forecasting Initiative's National Ecological Observatory Network (NEON) Forecasting Challenge, is an open challenge to the community to forecast daily greenness values, measured through digital images collected by the PhenoCam Network at NEON sites before the data are collected. For the first round of the challenge, which is presented here, we forecasted canopy greenness throughout the spring at eight deciduous broadleaf sites to investigate when, where, and for what model type phenology forecast skill is highest. A total of 192,536 predictions were submitted, representing eighteen models, including a persistence and a day of year mean null models. We found that overall forecast skill was highest when forecasting earlier in the greenup curve compared to the end, for shorter lead times, for sites that greened up earlier, and when submitting forecasts during times other than near budburst. The models based on day of year historical mean had the highest predictive skill across the challenge period. In this first round of the challenge, by synthesizing across forecasts, we started to elucidate what factors affect the predictive skill of near-term phenology forecasts.

54 ENVIRONMENTAL SCIENCES↗

A New Ecosystem Model for Arctic Phytoplankton Phenology From Ice‐Covered to Open‐Water Periods: Implications for Future Sea Ice Retreat Scenarios

Abstract To predict ecosystem change in the Arctic Ocean, understanding Arctic phytoplankton phenology is essential. We develop a marine ecosystem model focusing on phytoplankton dynamics and the competition for multiple resources based on knowledge from in situ data obtained in the Chukchi Sea. The model is designed to include the unique ecological characteristics of the Arctic Ocean. To the best of our knowledge, this is the first model successfully simulating the current paradigm for Arctic phytoplankton phenology, including both under‐ice blooms and succession of phytoplankton groups. Sensitivity experiments show that the dominance of diatoms can be sustained by lateral transport of a high‐silicate water mass (Pacific Winter Water). Experiments for future scenarios show that sea ice retreat drives a decrease in large diatoms and an increase in the other relatively small non‐diatom groups. These results suggest that dominant phytoplankton groups can be shifted from diatoms to non‐diatoms under ongoing Arctic Ocean sea ice retreat.

Choi, Jang‐Geun↗

Unveiling the transferability of PLSR models for leaf trait estimation: lessons from a comprehensive analysis with a novel global dataset

Leaf traits are essential for understanding many physiological and ecological processes. Partial least squares regression (PLSR) models with leaf spectroscopy are widely applied for trait estimation, but their transferability across space, time, and plant functional types (PFTs) remains unclear. We compiled a novel dataset of paired leaf traits and spectra, with 47 393 records for >700 species and eight PFTs at 101 globally distributed locations across multiple seasons. Using this dataset, we conducted an unprecedented comprehensive analysis to assess the transferability of PLSR models in estimating leaf traits. While PLSR models demonstrate commendable performance in predicting chlorophyll content, carotenoid, leaf water, and leaf mass per area prediction within their training data space, their efficacy diminishes when extrapolating to new contexts. Specifically, extrapolating to locations, seasons, and PFTs beyond the training data leads to reduced R 2 (0.12–0.49, 0.15–0.42, and 0.25–0.56) and increased NRMSE (3.58–18.24%, 6.27–11.55%, and 7.0–33.12%) compared with nonspatial random cross-validation. The results underscore the importance of incorporating greater spectral diversity in model training to boost its transferability. These findings highlight potential errors in estimating leaf traits across large spatial domains, diverse PFTs, and time due to biased validation schemes, and provide guidance for future field sampling strategies and remote sensing applications.

59 BASIC BIOLOGICAL SCIENCES↗

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

Abstract In studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

54 ENVIRONMENTAL SCIENCES↗

Evidence for a genetic basis in functional trait tradeoffs with microbial growth rate but not growth yield

Tradeoffs in microbial functional traits have been a focus of recently described ecological frameworks and of mathematical models of microbial community functioning. Tradeoffs in key traits such as growth rate, growth yield, resource acquisition, and stress tolerance may have either a genetic basis or a physiological basis, and the type of tradeoff can inform how traits are modeled and measured. Here we provide evidence that growth rate/decomposition and growth rate/stress tolerance tradeoffs have a primarily genetic basis in a phylogenetically diverse suite of ten leaf litter-inhabiting fungi. In contrast, growth yield tradeoffs with functional traits are more likely to have a physiological basis. Consideration of the type of tradeoff, genetic or physiological, should help to inform efforts to model microbial contributions to ecosystem processes, especially when considering different scales. Consideration of physiological tradeoffs may be important for understanding short-term variability (e.g., pulse events) and fine spatial scales, whereas genetic tradeoffs are likely to be useful for understanding regional- to continental-scale and medium- to long-term contributions of microbes to ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗

Global gridded crop harvested area, production, yield, and monthly physical area data circa 2015

Abstract Here we provide an update to global gridded annual and monthly crop datasets. This new dataset uses the crop categories established by the Global Agro-Ecological Zones (GAEZ) Version 3 model, which is based on the Food and Agricultural Organization of the United Nations (FAO) crop production data. We used publicly available data from the FAOSTAT database as well as GAEZ Version 4 global gridded dataset to generate circa 2015 annual crop harvested area, production, and yields by crop production system (irrigated and rainfed) for 26 crops and crop categories globally at 5-minute resolution. We additionally used available data on crop rotations, cropping intensity, and planting and harvest dates to generate monthly gridded cropland data for physical areas for the 26 crops by production system. These data are in standard georeferenced gridded format, and can be used by any global hydrology, land surface, or other earth system model that requires gridded annual or monthly crop data inputs.

54 ENVIRONMENTAL SCIENCES↗

The time since land-use transition drives changes in fire activity in the Amazon-Cerrado region

Abstract Deforestation and climate change are expected to alter fire regimes along the Cerrado-Amazon transition, one of the world’s most active agricultural frontiers. Here we tested the hypothesis that the time since land-use transition (age of frontier) and agricultural intensification also drive changes in the region’s fire regimes by reducing fire probability in both drought and non-drought years. We modeled fire probability as a function of the time since land-use transitions based on MapBiomas Project datasets from 1986 to 2020. We find that, while burned area declined as pasturelands aged and croplands advanced, deforestation abruptly increased fire activity before (Amazon: 4 years; Cerrado: 3 years) and after (Amazon: 8 years; Cerrado: 7 years) land clearing for pasture, especially in the Amazon. Additionally, the combination of ignition risk, drought, and air-dryness increased the likelihood of large extents of burned areas associated with deforestation. Incorporating frontier age as a proxy for governance in fire modeling is crucial, given the ecological implications of changing fire regimes despite declining rates of fire probability. Most importantly, protecting against deforestation and preserving native vegetation are vital.

Environmental Sciences & Ecology↗

Fine-scale landscape characteristics, vegetation composition, and snowmelt timing control phenological heterogeneity across low-Arctic tundra landscapes in Western Alaska

The Arctic is warming at over twice the rate of the rest of the Earth, resulting in significant changes in vegetation seasonality that regulates annual carbon, water, and energy fluxes. However, a crucial knowledge gap exists regarding the intricate interplay among climate, permafrost, and vegetation that generates high phenology variability across extensive tundra landscapes. This oversight has led to significant discrepancies in phenological patterns observed across warming experiments, long-term ecological observations, and satellite and modeling studies, undermining our ability to understand and forecast plant responses to climate change in the Arctic. To address this problem, we assessed plant phenology across three low-Arctic tundra landscapes on the Seward Peninsula, Alaska, using a combination of in-situ phenocam observations and high-resolution PlanetScope CubeSat data. We examined the patterns and drivers of phenological diversity across the landscape by (1) quantifying phenological diversity among dominant plant function types (PFTs) and (2) modeling the interrelations between plant phenology and fine-scale landscape features, such as topography, snowmelt, and vegetation. Our findings reveal that both spring and fall phenology varied significantly across Arctic PFTs, accounting for about 25%–44% and 34%–59% of the landscape-scale variation in the start of spring [SOS] and start of fall [SOF], respectively. Deciduous tall shrubs (e.g. alder and willow) had a later SOS (~7 d behind the mean of other PFTs), but completed leaf expansion (within 2 weeks) considerably faster compared to other PFTs. We modeled the landscape-scale variation in SOS and SOF using Random Forest, which showed that plant phenology can be accurately captured by a suite of variables related to vegetation composition, topographic characteristics, and snowmelt timing (variance explained: 53%–68% for SOS and 59%–82% for SOF). Notably, snowmelt timing was a crucial determinant of SOS, a factor often neglected in most spring phenology models. Our study highlights the impact of fine-scale vegetation composition, snow seasonality, and landscape features on tundra phenological heterogeneity. Improved understanding of such considerable intra-site phenological variability and associated proximate controls across extensive Arctic landscapes offers critical insights for representation of tundra phenology in process models and associated impact assessments with climate change.

54 ENVIRONMENTAL SCIENCES↗

CRISPR/Cas9-based gene activation and base editing in Populus

The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone “717-1B4” (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone “717-1B4” and poplar clone “WV94” (P. deltoides “WV94”), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%–14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone “717-1B4”. Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.

59 BASIC BIOLOGICAL SCIENCES↗

Designing Iowa Agricultural Landscapes to Improve Environmental Co-Benefits of Bioenergy Production

Cellulosic bioenergy feedstocks are needed to improve carbon (C) management while provisioning biomass for bioproducts and biofuel. The transition to increased cellulosic biomass production can be guided by land management plans designed to improve economic, environmental, and ecological performance. We constructed a sustainability model to compare landscape designs for biofuel production from corn (Zea mays L.) stover and switchgrass (Panicum virgatum L.) in central Iowa, USA. We used the model to compare environmental and socioeconomic outcomes associated with four landscape management strategies, with and without cellulosic biomass markets. We evaluated (1) a fuelshed area containing over 1.2 million ha (3 million acres) of corn and soybean (Glycine max (L.) Merr.) within 80 km (50 miles) of a commercial-scale cellulosic biorefinery in Nevada, Iowa, and (2) the South Fork watershed containing over 72,000 ha (178,000 acres) of these row crops within eight north central Iowa HUC-12 (hydrologic unit code) watersheds. At both landscape scales, we found that it is possible to achieve multiple environmental and socioeconomic benefits concomitantly with cellulosic biomass production by strategically collecting corn stover and converting the 10% of the lowest-profitability row crop land to perennial switchgrass. Potential benefits from landscape design include increased biodiversity, soil and water quality improvements, increased soil carbon sequestration for climate change mitigation, and reduced fertilizer use and cost. Our model results showed that increasing benefits can accrue when complementary conservation practices (e.g., reduced tillage, use of a rye cover crop) are combined and integrated throughout a fuelshed or watershed area. We conclude that ecologically based landscape designs offer valuable insights about costs and benefits of land management alternatives, with relevance for achieving stakeholder goals.

54 ENVIRONMENTAL SCIENCES↗

Catching up with the trees: empirical advancements to improve herbaceous representation in models

Ecosystems dominated by herbaceous vegetation (i.e. nonwoody species) represent c. 40% of the terrestrial land surface on Earth (White et al., 2000), facilitate large quantities of carbon sequestration (reviewed by Bai & Cotrufo, 2022), and provide much of the food production for humans (O'Mara, 2012). Many of these ecosystems are currently in danger of being lost due to global change drivers, shrub encroachment, and calls for afforestation (Bond et al., 2019). Furthermore, our predictive understanding of these systems is limited, which can be seen from high levels of uncertainty in modeled future carbon (C) storage of these systems (e.g. fig. 3 in McGuire et al., 2018).

59 BASIC BIOLOGICAL SCIENCES↗

Growth rate as a link between microbial diversity and soil biogeochemistry

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Estimating dermal contact soil exposure for amphibians

Abstract Chemical exposure estimation through the dermal route is an underemphasized area of ecological risk assessment for terrestrial animals. Currently, there are efforts to create exposure models to estimate doses from this pathway for use in ecological risk assessment. One significant limitation has been insufficient published data to characterize exposure and to support the selection and parameterization of appropriate models, particularly for amphibians in terrestrial habitats. Recent publications measuring pesticide doses to terrestrial‐phase amphibians have begun to rectify this situation. We collated and summarized available measurements of terrestrial amphibian dermal exposure to pesticides from 11 studies in which researchers measured tissue concentrations associated with known pesticide experimental application rates. This data set included tissue concentrations in 11 amphibian species and 14 different pesticides. We then compared the results of two screening exposure models that differed based on surface area scaling approaches as a function of body weight (one based on birds as surrogates for amphibians and another amphibian‐specific) to the measured tissue residue concentrations. We define a false‐negative rate for each screening model as the proportion of amphibians for which the predicted concentration is less than the observed concentration (i.e., underestimate), contrary to the intent of screening models, which are intended to have a bias for higher exposure concentrations. The screening model that uses birds as surrogates did not have any instances where estimated expected avian doses were less than measured amphibian body burdens. When using the amphibian‐specific exposure model that corrected for differences between avian and amphibian surface area, measured concentrations were greater than model estimates for 11.3% of the 1158 comparisons. The database of measured pesticide concentrations in terrestrial amphibians is provided for use in calculating bioconcentration factors and for future amphibian dermal exposure model development. Integr Environ Assess Manag 2023;19:9–16. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Environmental Sciences & Ecology↗