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At least 163 records · Page 9

Leaf traits and canopy structure together explain canopy functional diversity: an airborne remote sensing approach

Plant functional diversity is strongly connected to photosynthetic carbon assimilation in terrestrial ecosystems. However, many of the plant functional traits that regulate photosynthetic capacity, including foliar nitrogen concentration and leaf mass per area, vary significantly between and within plant functional types and vertically through forest canopies, resulting in considerable landscape-scale heterogeneity in three dimensions. Hyperspectral imagery has been used extensively to quantify functional traits across a range of ecosystems but is generally limited to providing information for top-of-canopy leaves only. On the other hand, lidar data can be used to retrieve the vertical structure of forest canopies. Because these data are rarely collected at the same time, there are unanswered questions about the effect of forest structure on the 3-D spatial patterns of functional traits across ecosystems. In the United States, the National Ecological Observatory Network's Airborne Observation Platform (NEON AOP) provides an opportunity to address this structure-function relationship by collecting lidar and hyperspectral data together across a variety of ecoregions. With a fusion of hyperspectral and lidar data from the NEON AOP and field-collected foliar trait data, we assessed the impacts of forest structure on spatial patterns of N. In addition, we examine the influence of abiotic gradients and management regimes on top of canopy %N and total canopy N (i.e. the total amount of N (g/m 2 ) within a forest canopy) at a NEON site consisting of a mosaic of open longleaf pine and dense broadleaf deciduous forests. Here, our resulting maps suggest that in contrast with top-of-canopy values, total canopy N variation is dampened across this landscape resulting in relatively homogeneous spatial patterns. At the same time, we found that leaf functional diversity and canopy structural diversity showed distinct dendritic patterns related to the spatial distribution of plant functional types.

54 ENVIRONMENTAL SCIENCES↗

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss .

59 BASIC BIOLOGICAL SCIENCES↗

Effects of trunk injection with emamectin benzoate on arthropod diversity

Abstract BACKGROUND Pine wood nematode is a major plant quarantine object in the world. Trunk injection is an effective method for controlling pests that cause disease. To evaluate the ecological safety of trunk injection with emamectin benzoates in forests of Pinus massoniana , the community diversity and community composition of soil arthropods and flying insects (Hymenoptera) were studied at different stages of trunk injection. RESULTS The dominant taxonomic groups of soil arthropods were Collembola (30.80%), Insecta (26.42%), and Arachnida (23.84%). The taxonomic groups of flying insects (Hymenoptera) were Ichneumonidae (48.94%), Formicidae (14.10%), and Braconidae (8.44%). Trunk injection with emamectin benzoate has no significant effect on the community diversity indices of total soil arthropods and flying insects (Hymenoptera). However, it has a significant effect on the community diversity indices of detritivores for soil arthropods. It changed the community composition of soil arthropods but did not impact the community composition of flying insects (Hymenoptera). Redundancy analysis of arthropod community structure and environmental variables showed that total potassium, residual of green leaf, and residual of litter leaf have a significant impact on the community structure of soil arthropods, and total phosphorus, total nitrogen, water content, organic matter, and total potassium have a significant impact on the community structure of flying insects (Hymenoptera). CONCLUSION Trunk injection with emamectin benzoate is safe for the ecological environment. This study provides a new insight into the field for the prevention and control of pine wood nematode disease, which is of great significance to forest management and pest control. © 2022 Society of Chemical Industry.

Ouyang, Xianheng↗

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes. It is of interest to understand how perturbations, like the introduction of exogenous chemicals, impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense. These alkaloids are antimicrobial; however, their effect on the frogs’ skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. Further, to better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

59 BASIC BIOLOGICAL SCIENCES↗

The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome

Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. Furthermore, this culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.

CyanoHABs↗

Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor diversity

T cells play a crucial role in combatting SARS-CoV-2 and forming long-term memory responses to this coronavirus. The emergence of SARS-CoV-2 variants that can evade T cell immunity has raised concerns about vaccine efficacy and the risk of reinfection. Some SARS-CoV-2 T cell epitopes elicit clonally restricted CD8 + T cell responses characterized by T cell receptors (TCRs) that lack structural diversity. Mutations in such epitopes can lead to loss of recognition by most T cells specific for that epitope, facilitating viral escape. Here, we studied an HLA-A2–restricted spike protein epitope (RLQ) that elicits CD8 + T cell responses in COVID-19 convalescent patients characterized by highly diverse TCRs. We previously reported the structure of an RLQ-specific TCR (RLQ3) with greatly reduced recognition of the most common natural variant of the RLQ epitope (T1006I). Opposite to RLQ3, TCR RLQ7 recognizes T1006I with even higher functional avidity than the WT epitope. To explain the ability of RLQ7, but not RLQ3, to tolerate the T1006I mutation, we determined structures of RLQ7 bound to RLQ–HLA-A2 and T1006I–HLA-A2. These complexes show that there are multiple structural solutions to recognizing RLQ and thereby generating a clonally diverse T cell response to this epitope that assures protection against viral escape and T cell clonal loss.

60 APPLIED LIFE SCIENCES↗

Internal consistency and diversity scenario development: A comparative framework to evaluate energy model scenarios

Energy modeling frameworks and scenario analysis help us explore the potential impact of our actions and uncertainties in future energy systems. Despite their importance, there is no systematic procedure for evaluating the scenario development process. In a literature review, we identify two core elements of the scenario development process: internal consistency and diversity which are oftentimes missing from scenarios. Here, to address this gap, we create the Internal consistency and Diversity Scenario Development (IDSD) comparative framework which aims to assess the feasibility and diversity of scenarios for a given energy model. With this framework, we review commonly used energy models and demonstrate our framework on their scenarios. The IDSD comparative framework can serve several purposes absent from previous scenario development work by aiding energy modelers and report writers in crafting high-quality scenarios. First, the IDSD is a reflective tool which can improve the quality of the scenario development process, enabling a comparative assessment of energy models and scenarios. Second, the IDSD can provide guidance to modeling frameworks with existing scenarios and those still in development; this feedback will enable modelers to improve the development and the communication of the limitations of their scenarios. Third, this study has highlighted areas for improvement in the scenario development of some commonly used energy model frameworks. Finally, there is a complete lack of explanation regarding the stakeholder selection process. Addressing these identified items could increase opportunities for advanced energy technology uptake and improve our options for achieving a more resilient energy system.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

Abstract The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

59 BASIC BIOLOGICAL SCIENCES↗

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

59 BASIC BIOLOGICAL SCIENCES↗

Viromics approaches for the study of viral diversity and ecology in microbiomes

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

Ecology↗

Diversity-oriented synthesis of polymer membranes with ion solvation cages

Microporous polymers feature shape-persistent free volume elements (FVEs), which are permeated by small molecules and ions when used as membranes for chemical separations, water purification, fuel cells, and batteries. It remains a significant challenge to identify FVEs with analyte specificity, due to difficulties in generating microporous polymer libraries with sufficient diversity for screening their properties. Here, we describe a diversity-oriented synthetic (DOS) strategy for microporous polymer membranes from which we identified those whose FVEs serve as solid solvation cages for lithium ions (Li + ). Furthermore, key elements of our strategy included diversification of bis(catechol)-type monomers via multi-component Mannich reactions to introduce Li+-coordinating functionality within individual FVEs, topology-enforcing polymerizations for generating macromolecular skeletal diversity for networking FVEs into different pore architectures, and several classes of on-polymer reactions for diversifying pore geometries and dielectric properties. Lead candidate polymer membranes featuring explicit ion solvation cages exhibited both higher ionic conductivity and higher cation transference number than control membranes where FVEs were aspecific, which indicates conventional bounds for membrane permeability and selectivity for ion transport can be overcome.4 These advantages are tied to enhanced Li + partitioning from the electrolyte when the cages are present, higher diffusion barriers for anions within the pores, and network-enforced restrictions on the number of solvent molecules bound to Li+ by comparison to the bulk electrolyte, which reduces the effective mass of the working ion. Such membranes show promise as anode-stabilizing interlayers in high-voltage lithium-metal batteries for electric mobility.

42 ENGINEERING↗

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh’s Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R 2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

16S rRNA↗

Constraining the oxygen requirements for modern microbial eukaryote diversity

Eukaryotes originated prior to the establishment of modern marine oxygen (O 2 ) levels. According to the body fossil and lipid biomarker records, modern (crown) microbial eukaryote lineages began diversifying in the ocean no later than ~800 Ma. While it has long been predicted that increasing atmospheric O 2 levels facilitated the early diversification of microbial eukaryotes, the O 2 levels needed to permit this diversification remain unconstrained. Using time-resolved geochemical parameter and gene sequence information from a model marine oxygen minimum zone spanning a range of dissolved O 2 levels and redox states, we show that microbial eukaryote taxonomic richness and phylogenetic diversity remain the same until O 2 declines to around 2 to 3% of present atmospheric levels, below which these diversity metrics become significantly reduced. Our observations suggest that increasing O 2 would have only directly promoted early crown-eukaryote diversity if atmospheric O 2 was below 2 to 3% of modern levels when crown-eukaryotes originated and then later met or surpassed this range as crown-eukaryotes diversified. If atmospheric O 2 was already consistently at or above 2 to 3% of modern levels by the time that crown-eukaryotes originated, then the subsequent diversification of modern microbial eukaryotes was not directly driven by atmospheric oxygenation.

59 BASIC BIOLOGICAL SCIENCES↗

Utilizing a Virtual Sodium-Cooled Fast Reactor Digital Twin to Aid in Diversion Pathway Analysis for International Safeguards Applications

We report digital twin technology has the potential to improve the effectiveness of international safeguards inspectors by providing a tool which can: first, perform an accurate diversion path analysis, identify their indicators, and required sensors to detect them; and second, monitor facilities in real-time using critical data streams that benefit from this safeguards-by-design approach. Safeguards inspectors are required to visit facilities and verify the nuclear material to ensure no diversion has taken place and detect misuse of the facility; however, this analysis and verification effort is time consuming, and with limited funding it is imperative that time spent at a nuclear facility is focused on key areas. A virtual digital twin of three prototypic sodium fast reactors was developed, where diversion and misuse scenarios were explored to determine how a digital twin could provide inspectors with an understanding of how proliferation may occur and where the most likely areas for proliferation would be. For each of the three reactors, an optimization algorithm was able to find core designs which would be difficult to detect via sensors alone; however, the use of a machine learning adapter provided by the digital twin was able to show general trends in where proliferation as likely to take place.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Advancing a toolkit of diverse futures approaches for global environmental assessments

Global Environmental Assessments (GEAs) support national and international policy making for sustainable development. They rely on quantitative scenarios produced by Integrated Assessment Models (IAMs) to assess alternative futures. IAM-based scenarios can provide a coherent assessment framework that integrates different subsystems and their interactions. However, these top-down approaches have limited ability to represent key local dynamics, unexpected events, or the role of diverse actors. Other methods, including participatory scenarios, can help co-create narratives that emphasize diverse contents with clear links to existing decision-making. However, these bottom-up approaches provide only limited insight into global processes and are not constrained by measurable parameters. In our review, we identify four key challenges for current GEA scenarios: surprise, scale, diversity and imagination. We illustrate how these challenges can be overcome by combining top-down and bottom-up scenario approaches and conclude with a call to action for future research to take on this trans-disciplinary challenge.

Pereira, Laura M.↗

Pollinator habitat in solar facilities has potential to support high diversity of bee species

Conversion of agricultural and degraded lands to solar energy production provides opportunities to support diverse bee communities—and their pollination services—by creating habitat at solar facilities. Habitat restoration for bees at solar facilities follows the general principle of installing a diverse flowering plant community and assuming bees will come. However, selecting seed mixes for solar facilities is challenging because selected plants need to establish in the unique abiotic conditions of solar facilities and not interfere with solar energy production (tall plants may shade panels). Recent research tested commercially available and bespoke pollinator mixes for establishment success in Minnesota solar facilities and identified 14 forb species that established successfully over three years of the experiment. We ask an important follow-up question: how many native bee species, and which bee species, are these 14 plant species capable of supporting? We used a plant-bee interaction data set from Minnesota to calculate the number of bee species that would be supported by the 14 plant species for the duration of their flight seasons using a published bee species richness function. We found 122 unique bee species (24% of Minnesota diversity) may be supported for their entire flight seasons by the 14 focal plants.

14 SOLAR ENERGY↗

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗