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At least 127 records · Page 7

A taxogenomic view of the genus Torulaspora : an expansion from ten to twenty-two species

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species, T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how the complex relationship between key genes and the physiological traits they control both between and within species. This remarkable increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomic approaches can foster the assessment of species circumscriptions in fungi.

59 BASIC BIOLOGICAL SCIENCES↗

The Coupled Influence of Thermal Physiology and Biotic Interactions on the Distribution and Density of Ant Species along an Elevational Gradient

A fundamental tenet of biogeography is that abiotic and biotic factors interact to shape the distributions of species and the organization of communities, with interactions being more important in benign environments, and environmental filtering more important in stressful environments. This pattern is often inferred using large databases or phylogenetic signal, but physiological mechanisms underlying such patterns are rarely examined. We focused on 18 ant species at 29 sites along an extensive elevational gradient, coupling experimental data on critical thermal limits, null model analyses, and observational data of density and abundance to elucidate factors governing species’ elevational range limits. Thermal tolerance data showed that environmental conditions were likely to be more important in colder, more stressful environments, where physiology was the most important constraint on the distribution and density of ant species. Conversely, the evidence for species interactions was strongest in warmer, more benign conditions, as indicated by our observational data and null model analyses. Our results provide a strong test that biotic interactions drive the distributions and density of species in warm climates, but that environmental filtering predominates at colder, high-elevation sites. Such a pattern suggests that the responses of species to climate change are likely to be context-dependent and more specifically, geographically-dependent.

54 ENVIRONMENTAL SCIENCES↗

Major Ion Toxicity to Glochidia of Common and Imperiled Freshwater Mussel Species

Freshwater mussel taxa are severely imperiled and among the most sensitive to several contaminants, including chloride. Relatively little is known of the toxicity of major ions to glochidia (larvae), particularly for rare species, or the effects of hardness on major ion toxicity to glochidia. Therefore, the primary objectives of this work were to: (1) determine the acute toxicity of major ion salts to glochidia, (2) compare chloride sensitivity of glochidia from common and rare species, and (3) evaluate the relationship between water hardness and chloride toxicity to glochidia. We assessed 24 h EC50s for fatmucket (Lampsilis siliquoidea) glochidia exposed to NaCl, KCl, MgCl 2 , CaCl 2 , Na 2 SO4, MgSO 4 , CaSO 4 , and NaHCO 3 in moderately hard water. We determined NaCl EC50s for four species and KCl EC50s for glochidia of three species. Toxicity of chloride was generally consistent among the various chloride salts except for KCl, which was more toxic than all others by 1–2 orders of magnitude. Our results suggest that commonly tested species may be generally representative of rare species. Water hardness ameliorated the toxicity of chloride for all species to varying degrees. Results of this work indicate that some existing water quality criteria that do not include mussel toxicity data may not be protective of freshwater mussels.

59 BASIC BIOLOGICAL SCIENCES↗

The behaviour of minor species in the solar wind

The flow of minor species in the solar wind is considered on the basis of a model in which all species are heated in an arbitrary manner as they leave the sun and the minor species interact with the background proton-electron plasma through the radial electric field associated with the latter and by means of Coulomb collisions. In order to produce satisfactory results in which the ions all move at more or less the same speed at the orbit of the earth, it is necessary to introduce heating functions such that each species is given energy in proportion to its mass. Coulomb collisions are found to be important as a means of removing energy from the heavier species close to the sun and bringing all species closer to thermal equilibrium at great distances from the sun. Substantial velocity differences can occur between species, especially close to the sun. Furthermore it is not difficult to construct solutions in which the bulk velocity of the helium ions exceeds that of the solar wind, as is often observed.

Ryan, J. M.↗

Cumulative frequency distribution of past species extinctions

Analysis of Sepkoski's compendium of the time ranges of 30,000+ taxa yields a mean duration of 28.4 ma for genera of fossil invertebrates. This converts to an average extinction rate of 3.5 percent per million years or about one percent every 286,000 years. Using survivorship techniques, these estimates can be converted to the species level, yielding a Phanerozoic average of one percent species extinction every 40,000 years. Variation in extinction rates through time is far greater than the null expectation of a homogeneous birth-death model and this reflects the well-known episodicity of extinction ranging from a few large mass extinctions to so-called background extinction. The observed variation in rates can be used to construct a cumulative frequency distribution of extinction intensity, and this distribution, in the form of a kill curve for species, shows the expected waiting times between extinction events of a given intensity. The kill curve is an average description of the extinction events of a given intensity. The kill curve is an average description of the extinction record and does not imply any cause or causes of extinction. The kill curve shows, among other things, that only about five percent of total species extinctions in the Phanerozoic were involved in the five largest mass extinctions. The other 95 percent were distributed among large and small events not normally called mass extinctions. As an exploration of the possibly absurd proposition that most past extinctions were produced by the effects of large-body impact, the kill curve for species was mapped on the comparable distribution for comet and asteroid impacts. The result is a curve predicting the species kill for a given size of impacting object (expressed as crater size). The results are reasonable in that impacts producing craters less than 30 km (diameter) cause negligible extinction but those producing craters 100-150 km (diameter) cause extinction of species in the range of 45-60 percent.

Raup, D. M.↗

DSMC analysis of species separation in rarefied nozzle flows

The direct-simulation Monte Carlo method has been used to investigate the behavior of a small amount of a harmful species in the plume and the backflow region of nuclear thermal propulsion rockets. Species separation due to pressure diffusion and nonequilibrium effects due to rapid expansion into a surrounding low-density environment are the most important factors in this type of flow. It is shown that a relatively large amount of the lighter species is scattered into the backflow region and the heavier species becomes negligible in this region due to the extreme separation between species. It is also shown that the type of molecular interaction between the species can have a substantial effect on separation of the species.

Chung, Chan-Hong↗

Novel Species of Non-Spore-Forming Bacteria

While cataloging cultivatable microbes from the airborne biological diversity of the atmosphere of the Regenerative Enclosed life-support Module Simulator (REMS) system at Marshall Space Flight Center, two strains that belong to one novel bacterial species were isolated. Based on 16S rRNA gene sequencing and the unique morphology and the taxonomic characteristics of these strains, it is shown that they belong to the family Intrasporangiaceae, related to the genus Tetrasphaera, with phylogenetic distances from any validly described species of the genus Tetrasphaera ranging from 96.71 to 97.76 percent. The fatty acid profile supported the affiliation of these novel strains to the genus Tetrasphaera except for the presence of higher concentrations of octadecenoic acid (C18:0) and cis-9-octadecenoic acid (C18:1), which discriminates these strains from other valid species. In addition, DNA-DNA hybridization studies indicate that these strains belong to a novel species that could be readily distinguished from its nearest neighbor, Tetrasphaera japonica AMC 5116T, with less than 20 percent DNA relatedness. Physiological and biochemical tests show few phenotypic dissimilarities, but genotypic analysis allowed the differentiation of these gelatin-liquefying strains from previously reported strains. The name Tetrasphaera remsis sp. Nov. is proposed with the type strain 3-M5-R-4(sup T) (=ATCC BAA-1496(sup T)=CIP 109413(sup T). The cells are Gram-positive, nonmotile, cocci, in tetrad arrangement and clusters. Spore formation is not observed. No species of Tetrashpaera has ever been isolated from airborne samples. Previous discoveries have come from soil and activated sludge samples. As other species of this genus have demonstrated enhanced biological phosphorus removal activity, further tests are required to determine if this newly discovered species would have bioremediation applications.

Briegel, Ariane↗

Biotic predictors improve species distribution models for invasive plants in Western U.S. Forests at high but not low spatial resolutions

Invasions by non-native plants threaten forest health and sustainability. The ability to predict areas at greatest risk to invasion is essential for informing both monitoring and management of invasive species. Species distribution models (SDMs) are often used to identify environmental correlates of a species’ occurrence and predict geographic areas that may be suitable for its presence and are commonly constructed using solely abiotic predictors. However, mounting evidence implies that not including biotic predictors in SDMs may yield less accurate models at some resolutions typical of landscape-scale models, although this possibility has rarely been evaluated in invasive plants. In this study, we determined whether including descriptors of the biotic environment improved the accuracy of SDMs built at five decreasing spatial resolutions for infestations of five common invasive plants in forests of California, Oregon, and Washington, USA and described environmental correlates of each species’ presence. Predictors of occurrence often echoed those identified in previous studies of the focal species, indicating that our models accurately identified important environmental drivers of occurrence. Including biotic predictors in the SDMs consistently improved model accuracy only at the highest resolution we examined, which may be due to the spatial scale at which biotic interactions primarily act to constrain species’ distributions, the particular biotic predictors we used in our models, or correlations between attributes of the abiotic and biotic environment. This finding suggests that, while the practice of building SDMs using abiotic predictors alone may generally yield models whose accuracy does not differ substantially from those that also include biotic predictors, the effects of biotic interactions on the distribution of invasive plants in forests may be detectable at larger scales than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗

Litter Production and Foliar Nutrient Resorption in Pioneer and Non-Pioneer Species in a Selective Logging Experiment in the Central Amazon, BIONTE, ZF-2, Manaus, 2022-23

This dataset was collected near the city of Manaus, Brazil, at the Experimental Station of Tropical Forestry (EEST, aka “ZF2”), inside the BIONTE (BIOmass and NuTrient Experiment). The experiment included three levels of increasing selective logging intensity, along with control, with 1-hectare permanent plots (12 total) located at the center of 4-hectare treatment plots. The vegetation has a high floristic diversity, the soils of the region are poor in nutrients, and the topography is characterized by plateaus (where BIONTE is located), and also valley bottoms and slopes. Three treatments of differing logging intensities were applied in the BIONTE experiment (T1, T2 and T3). The study was conducted in Treatment 3 (Block I – permanent plot), which represents the most intensive logging treatment, with 69% of the basal area (m²∙ha⁻¹) removed in 1988. The present dataset spans the period from May 1, 2022, to May 1, 2023. The data package includes leaf_nutrient_data, litterfall_total_data, leaf_litterfall_species_specific_data, and species_info, all provided in .csv format. These formats allow users to process and analyze the data in various software applications and programming languages, such as Python and R. This dataset was collected to advance knowledge on nutrient cycling in Amazonian forests, specifically distinguishing between species with two distinct functional traits: fast-growing and slow-growing. It also aims to improve Earth System Models, such as the E3SM Functionally Assembled Terrestrial Ecosystem Simulator (FATES). Additionally, it was used in a paper currently in preparation (Carvalho et al., in prep.), which aims to quantify seasonal litter production and foliar nutrient resorption in pioneer (fast-growing) and non-pioneer (slow-growing) tree species in the central Amazon. Specifically, it seeks to answer two key questions: 1) Is there a difference in leaf litter production, leaf nutrient flux and leaf nutrient concentration between pioneers and non-pioneers species? Is there a difference in the efficiency of foliar nutrient resorption between pioneers and non-pioneers species?

54 ENVIRONMENTAL SCIENCES↗

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species

This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. Herein, a total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.

59 BASIC BIOLOGICAL SCIENCES↗

Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446T (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

59 BASIC BIOLOGICAL SCIENCES↗

Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. “desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata , supported by a high-quality genome assembly

Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. “desiccata” UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. “desiccata” UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.

59 BASIC BIOLOGICAL SCIENCES↗

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Evolutionary Biology↗

Boundary spanning increases knowledge and action on invasive species in a changing climate

Abstract Challenges associated with global change stressors on ecosystems have prompted calls to improve actionable science, including through boundary‐spanning activities, which aim to build connections and communication between researchers and natural resource practitioners. By synthesizing and translating research and practitioner knowledge, boundary‐spanning activities could support proactive, research‐informed conservation practice, but the success of these efforts is rarely evaluated. Using repeat survey data from the Northeast Regional Invasive Species and Climate Change (NE RISCC) Management Network, a boundary‐spanning organization, we evaluate whether participating in NE RISCC affected practitioners' knowledge, actions and priorities related to invasive species management under a changing climate. Our survey results suggest that practitioners who participate in NE RISCC have greater knowledge about invasive species and climate change and are incorporating climate change in more ways into their invasive species management. We also found NE RISCC membership affected the perceived usefulness of informational resources, with NE RISCC members more frequently identifying research syntheses and targeted workshops (both are common products used by NE RISCC to translate science into practice and share manager knowledge) as useful compared to non‐members. Practitioners who participate in NE RISCC also identified somewhat different research priorities, with non‐members and short‐term members more frequently identifying range‐shifting neonative species and their impacts on native communities as higher priorities compared to long‐term NE RISCC members. NE RISCC research activities and outreach materials have consistently framed range‐shifting neonative species as comparatively low risk, suggesting that this information has influenced practitioner's perception of risk. Practical implication : Although real‐world impacts of applied ecology are notoriously difficult to quantify, this analysis illustrates that if research results are actively translated, they can affect the knowledge and actions of natural resource practitioners. These impacts illustrate the potential for boundary‐spanning efforts to address other global change challenges to conservation.

Evans, Annette E.↗

Effects of surface species and homogeneous reactions on rates and selectivity in ethane oxidation on oxide catalysts

Selective alkane oxidations on metal oxide catalysts involve complex mechanisms with multiple reactions in series and parallel, different types of reduced and oxidized surface species, and potential contributions from gas-phase reactions. We report kinetics and thermodynamics of elementary steps involved in C 2 H 6 -O 2 reactions on SiO 2 -supported small vanadium oxide domains are determined using density functional theory. These surface reactions together with gas-phase mechanisms are incorporated in kinetic simulations to determine how surface and gaseous reactions interact and contribute to rates and selectivity. The results show that gas-phase reactions within pore volumes in contact with the catalyst contribute significantly to C 2 H 6 activation rates, even at conditions where gas-phase reactions in empty volumes without catalyst are negligible. The majority of C 2 H 6 activations occur on the surface, via H abstraction by vanadium oxo species present at terminal lattice oxygens. The gas-phase activations via H-abstraction by OH radicals also exhibit significant contributions. The reduced centers formed by reactions at vanadium oxo species are re-oxidized rapidly and, therefore, are present in very small concentrations at reaction conditions. The re-oxidation steps lead to the formation of HO 2 radicals and surface peroxo species that are also rapidly consumed and are present in small concentrations. The peroxo species preferentially convert C 2 H 4 to its epoxide product and influence selectivity even at low concentrations. The gas-phase reactions decrease the concentrations of peroxo species and improve selectivity slightly. The effects of reaction conditions and catalyst site density provide further insights into how factors beyond conversions at lattice oxygens influence rates and selectivity in alkane oxidation reactions of significant industrial importance.

42 ENGINEERING↗

Interactions Between Climate and Species Drive Future Forest Carbon and Water Balances

Global change is altering forest carbon and water balances; however, the extent to which tree species shape ecosystem‐scale responses to climate, particularly in biodiverse forests, remains unclear. To address this, we simulated the effects of an envelope of future climate conditions on watershed carbon and water balances and quantified the contributions of tree species based on their xylem anatomy. We accomplished this by incorporating species‐level transpiration calculations into a landscape‐scale ecosystem process model. Our revised model linked the effects of forest succession, species composition, and climate change on water and carbon. Calibration of forest water fluxes using sap flux measurements and catchment water balances captured variability in species transpiration and interannual ET in biodiverse, humid temperate forest catchments in the southern Blue Ridge Mountains, USA. Across wet and dry future climate projections, ET increased, and streamflow and net carbon uptake decreased, particularly under a scenario of increasing drought. Despite accounting for just 30% of current biomass, diffuse‐porous tree species were the main driver of carbon and water flux responses now and in the future, thus intensifying the increase in ET and decline in streamflow. As diffuse‐porous biomass continues to increase, these forests will be increasingly sensitive to drought, amplifying losses of carbon sequestration and freshwater delivery.

54 ENVIRONMENTAL SCIENCES↗

Spatial Bayesian models project shifts in suitable habitat for Pacific Northwest tree species under climate change

Abstract We developed spatial Bayesian hierarchical models to assess potential climate change impacts on suitable habitat for five important tree species in the Pacific northwestern United States (California, Oregon, and Washington). Individual‐species models were fit with presence–absence data from forest inventory field plots and spatial relationships were specified through a conditional autoregressive model. This modeling approach allowed us to visualize uncertainty in response curves, map current and future prediction uncertainty, and provide interval estimates for change. Upward elevational or northward latitudinal shifts in climatically suitable habitat were projected for all species. Climate change impacts were the most damaging for noble fir ( Abies procera ), for which 79%–100% of the current range was projected to become climatically unsuitable by the 2080s. Although coastal Douglas‐fir ( Pseudotsuga menziesii var. menziesii ) has been projected by others to gain habitat in Canada, within our study area we projected a net loss of climatically suitable habitat (ca. 8000–31,400 km 2 ) under three of four future climate scenarios. A net loss in habitat was also projected for Oregon white oak ( Quercus garryana ) under three of four scenarios, with 40%–60% of the current range becoming unsuitable. Although there was no net loss of habitat for forest land blue oak under any scenario, other factors like competition may inhibit blue oak ( Quercus douglasii ) and white oak from occupying areas projected to increase in climatic suitability. Additionally, between 13% and 32% of blue oak's current range was projected to become unsuitable; some of these areas aligned with dieback following the 2012–2015 California drought, which our data set predates. Unlike the other four species, we projected a 17%–25% increase in climatically suitable habitat for California black oak ( Quercus kelloggii ), although 1%–20% of the current range was still projected to become unsuitable. Our findings indicate that, although some species will face more pressure in tracking climatically suitable habitat than others, climate change will impact the location of suitable habitat for many species.

Kralicek, Karin↗

Detection of non‐native species formed during fibrillization of the myocilin olfactomedin domain

Abstract Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin‐associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C‐terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid‐like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X‐ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non‐native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo‐EM imaging shows two‐dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X‐ray crystallography. In summary, after incubating OLF under fibrillization‐promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid‐like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non‐model amyloidogenic proteins.

Scelsi, Hailee F. [School of Chemistry and Biochem↗