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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

2019 Results for Avian Monitoring at the Technical Area 36 Minie Site, Technical Area 39 Point 6, and Technical Area 16 Burn Ground at the Los Alamos National Laboratory

Los Alamos National Laboratory biologists in the Environmental Compliance and Protection Division at Los Alamos National Laboratory (LANL) initiated a multi-year program in 2013 to monitor avifauna (birds) at two open detonation sites and one open burn site on LANL property. Monitoring results from these efforts were compared among years to monitor trends. The objectives of this study were to 1) determine whether LANL operations impact bird species richness, diversity, or abundance 2) evaluate trends in species abundance by feeding guild, and 3) examine occupancy and nest success of secondary-cavity nesting birds using nestboxes. LANL biologists completed the seventh year of this effort in 2019. Three bird point count surveys were completed at each of the treatment sites at the Technical Area (TA) 36 Minie site, the TA-39 point 6, and the TA-16 burn ground between May and July 2019. A total of 853 birds representing 53 species were recorded at the three treatment sites and compared to their associated controls. Occupancy and nest success data from nestboxes at treatment sites were compared with the overall avian nestbox monitoring network. In 2019 the species richness and diversity at the treatment sites were not statistically different from their associated controls. Rarefaction and extrapolation plots for all years through 2018 suggest that over time the species diversity was statistically different between treatments and controls, although the diversity was higher at the treatment sites than the control sites. Avian abundance showed more variability but treatment and controls were trending together year to year. The mean number of granivores, insectivores, and omnivores varies from year to year, but there is not a significant trend at any of the treatment sites. The dominant feeding guild at the treatment sites continues to be insectivores. The overall results from 2019 continue to indicate that operations at the three treatment sites are not negatively affecting bird populations. This long-term monitoring will continue to monitor for any changes over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. Furthermore, these findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
DOE OSTI2020

Distinctiveness of genes contributing to growth of Pseudomonas syringae in diverse host plant species

A variety of traits are necessary for bacterial colonization of the interior of plant hosts, including well-studied virulence effectors as well as other phenotypes contributing to bacterial growth and survival within the apoplast. High-throughput methods such as transposon sequencing (TnSeq) are powerful tools to identify such genes in bacterial pathogens. However, there is little information as to the distinctiveness of traits required for bacterial colonization of different hosts. Here, we utilize randomly barcoded TnSeq (RB-TnSeq) to identify the genes that contribute to the ability of Pseudomonas syringae strain B728a to grow within common bean (Phaseolus vulgaris), lima bean (Phaseolus lunatus), and pepper (Capsicum annuum); species representing two different plant families. The magnitude of contribution of most genes to apoplastic fitness in each of the plant hosts was similar. However, 50 genes significantly differed in their fitness contributions to growth within these species. These genes encoded proteins in various functional categories including polysaccharide synthesis and transport, amino acid metabolism and transport, cofactor metabolism, and phytotoxin synthesis and transport. Six genes that encoded unannotated, hypothetical proteins also contributed differentially to growth in these hosts. The genetic repertoire of a relatively promiscuous pathogen such as P. syringae may thus be shaped, at least in part, by the conditional contribution of some fitness determinants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Including biodiversity in life cycle assessment – State of the art, gaps and research needs

Purpose: For over 20 years the feasibility of including man-made impacts on biodiversity in the context of Life Cycle Assessment (LCA) has been explored. However, a comprehensive biodiversity impact assessment has so far not been performed. The aim of this study is to analyse how biodiversity is currently viewed in LCA, to highlight limitations and gaps and to provide recommendations for further research. Method: Firstly, biodiversity indicators are examined according to the level of biodiversity they assess (genetic, species, ecosystem) and to their usefulness for LCA. Secondly, relevant pressures on biodiversity that should be included in LCA are identified and available models (in and outside of an LCA context) for their assessment are discussed. Thirdly, existing impact assessment models are analysed in order to determine whether and how well pressures are already integrated into LCA. Finally, suggestions on how to include relevant pressures and impacts on biodiversity in LCA are provided and the necessary changes in each LCA phase that must follow are discussed. Results: The analysis of 119 indicators shows that 4% of indicators represent genetic diversity, 40% species diversity and 35% ecosystem diversity. 21% of the indicators consider further biodiversity-related topics. Out of the indicator sample, 42 indicators are deemed useful as impact indicators in LCA. Even though some identified pressures are already included in LCA with regard to their impacts on biodiversity (e.g. land use, carbon dioxide emissions etc.), other proven pressures on biodiversity have not yet been considered (e.g. noise, artificial light). Conclusion: Further research is required to devise new options (e.g. impact assessment models) for integrating biodiversity into LCA. The final goal is to cover all levels of biodiversity and include all missing pressures in LCA. Tentative approaches to achieve this goal are outlined. - Highlights: •Calculating man-made impacts highlights possible biodiversity protection strategies. •An appropriate method to match this objective is Life Cycle Assessment. •Majority of impact assessment methods refer to habitat loss and assess impacts specific to surrogate species and regions. •Several pressures on biodiversity are not considered.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Abiotic proxies for predictive mapping of nearshore benthic assemblages: implications for marine spatial planning

Marine spatial planning (MSP) should assist managers in guiding human activities toward sustainable practices and in minimizing user conflicts in our oceans. A necessary first step is to quantify spatial patterns of marine assemblages in order to understand the ecosystem's structure, function, and services. However, the large spatial scale, high economic value, and density of human activities in nearshore habitats often makes quantifying this component of marine ecosystems especially daunting. To address this challenge, we developed an assessment method that employs abiotic proxies to rapidly characterize marine assemblages in nearshore benthic environments with relatively high resolution. We evaluated this assessment method along 300 km of the State of Maine's coastal shelf (<100 m depth), a zone where high densities of buoyed lobster traps typically preclude extensive surveys by towed sampling gear (i.e., otter trawls). During the summer months of 2010–2013, we implemented a stratified-random survey using a small remotely operated vehicle that allowed us to work around lobster buoys and to quantify all benthic megafauna to species. Stratifying by substrate, depth, and coastal water masses, we found that abiotic variables explained a significant portion of variance (37–59%) in benthic species composition, diversity, biomass, and economic value. Generally, the density, diversity, and biomass of assemblages significantly increased with the substrate complexity (i.e., from sand-mud to ledge). The diversity, biomass, and economic value of assemblages also decreased significantly with increasing depth. Last, demersal fish densities, sessile invertebrate densities, species diversity, and assemblage biomass increased from east to west, while the abundance of mobile invertebrates and economic value decreased, corresponding mainly to the contrasting water mass characteristics of the Maine Coastal Current system (i.e., summertime current direction, speed, and temperature). Integrating modeled predictions with existing GIS layers for abiotic conditions allowed us to scale up important assemblage attributes to define key foundational ecological principles of MSP and to find priority regions where some bottom-disturbing activities would have minimal impact to benthic assemblages. We conclude that abiotic proxies can be strong forcing functions for the assembly of marine communities and therefore useful tools for spatial extrapolations of marine assemblages in congested (heavily used) nearshore habitats.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Effects of EMF Emissions from Cables and Junction Boxes on Marine Species

Studies have shown that diverse aquatic species are electrosensitive. Many fishes, and marine mammals, can either detect, navigate by, or are affected by electromagnetic fields (EMF) with various sensitivities, and their behavior may be impacted by unnatural EMF emissions in the water column. Sharks, rays and skates are known to have the highest sensitivity to electric fields. Electric field emissions in the range 0.5–100 micro volt/m appear to attract them, and emissions over 100 micro volt/m to repulse them. A marine hydrokinetic MHK device will have multiple components and associated multiple submarine cables on the seafloor and running through the water column and would potentially increase the level of EMF emissions to which the marine species at the site may be exposed to. There are therefore concerns amongst stakeholders that EMF emissions associated with MHK devices and their components may act as barriers to species migration, cause disorientation, change community compositions and ecosystems, and that they may attract sharks, leading to a local increase in the risk of shark attacks. However, field data to validate and model potential relationships between observed responses and the EMF emissions in situ are sparse. A program of experimental field surveys were conducted off the coast of South Florida, USA to characterize the electromagnetic field (EMF) emissions in the water column from a submarine cable, and to monitor for responses of local aquatic species. The field surveys were conducted at the South Florida Ocean Measurement Facility (SFOMF) off Fort Lauderdale, which is a cabled offshore in-water navy range. It consists of multiple active submarine power cables and a number of junction boxes, with the capability to transmit AC/DC power at a range of strength and frequencies. The site includes significant marine life activities and community structure, including highly mobile species, such as sharks, stingrays, mammals and turtles. SFOMF therefore typifies a setting representative of an offshore location where a MHK device may be sited. Background electromagnetic field (EMF) levels and EMF emissions due to submarine cables were measured using a custom E-field sensor and a commercial magnetometer deployed from an autonomous underwater vehicle (AUV) at various fixed altitudes above the seafloor. EMF signatures detected from power cables and junction boxes are contrasted against ambient background levels and other EMF sources. The potential responses of local marine species were observed at selected representative locations using divers on SCUBA, complemented with fixed cameras on the sea bottom and by a set of video cameras mounted on the AUV. The objectives of the study were: 1) to characterize the EMF emission levels associated with submarine cables 2) to monitor potential responses of aquatic animals to the emissions and 3) to develop an associated database of field observations. As control, observations of EMF levels and in situ marine species were conducted with power in the cable turned off. Good quality measurements of EMF emissions were obtained using the mobile AUV platform and the data from the surveys were used to develop contour maps of the EMF levels in the water column above the live cable as well as to provide information about how the field decays away from the cable. The measurements show good agreement with theoretical models of the how EMF levels decay away from the cable in deep and shallow water environment. Electric fields in excess of 200µV/m were measured in the vicinity of the cable during the power on state. Quarterly surveys by SCUBA divers were conducted, using point and transect count methods, over a period of one year at three locations, one at a shallow site where the water depth is approximately 5m, and the other at the Barracuda Reef where the water depth is approximately 10m. The sampling results were analyzed to determine if the presence of an SFOMF generated EMF alters: (1) abundance, species richness, and assemblage structure of coral reef fishes, (2) the behavior of fishes including elasmobranchs, and (3) the distribution of marine turtles and mammals. Diver observations were also used in attempt to discern if there were any noticeable organismal responses during the transitional period between ambient OFF to energized AC or DC power states, and video footage was intended to augment the in-situ visual survey data and aid in interpretation of the results. Comparisons are provided between observation datasets between the three sites and between the point and transect count methods. Presence of several individual elasmobranch species, including sharks and stingrays, were recorded during the surveys. No apparent effect on richness could be discerned between the power on and off states. No apparent sudden animal movements were observed during transitions between power states.

16 TIDAL AND WAVE POWER↗
DOE OSTI2019

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity

Species-rich plant communities have been shown to be more productive and to ­exhibit increased long-term soil organic carbon (SOC) storage. Soil microorganisms are central to the conversion of plant organic matter into SOC, yet the relationship between plant diversity, soil microbial growth, turnover as well as carbon use efficiency (CUE) and SOC accumulation is unknown. As heterotrophic soil microbes are primarily carbon limited, it is important to understand how they respond to increased plant-derived carbon inputs at higher plant species richness (PSR). We used the long-term grassland biodiversity experiment in Jena, Germany, to examine how microbial physiology responds to changes in plant diversity and how this affects SOC content. The Jena Experiment considers different numbers of species (1–60), functional groups (1–4) as well as functional identity (small herbs, tall herbs, grasses, and legumes). We found that PSR accelerated microbial growth and turnover and increased microbial biomass and necromass. PSR also accelerated microbial respiration, but this effect was less strong than for microbial growth. In contrast, PSR did not affect microbial CUE or biomass-specific respiration. Structural equation models revealed that PSR had direct positive effects on root biomass, and thereby on microbial growth and microbial biomass carbon. Finally, PSR increased SOC content via its positive influence on microbial biomass carbon. We suggest that PSR favors faster rates of microbial growth and turnover, likely due to greater plant productivity, resulting in higher amounts of microbial biomass and necromass that translate into the observed increase in SOC. We thus identify the microbial mechanism linking species-rich plant communities to a carbon cycle process of importance to Earth's climate system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Disturbance differentially affects alpha and beta diversity of ants in tallgrass prairies

Abstract Biodiversity conservation requires understanding how disturbance influences biodiversity patterns at multiple spatial scales. Because the total diversity of species within a given region (γ diversity) is influenced by both local diversity (α diversity) and dissimilarity in community composition (β diversity), understanding disturbance effects on both components of diversity is essential, especially if disturbance impacts α and β diversities differently. In this three‐year study, we examined how a disturbance (annual harvesting of grasslands) and environmental gradients in the proportion of sand locally, habitat size, and landscape diversity influenced the abundance and α and β diversities of ants within tallgrass prairie habitat in Wisconsin. We used a null‐model approach to examine how harvest and environmental factors influence β diversity. Following three years of treatments, we found that ant abundance was greater in harvested sites compared to control sites and ant abundance was positively correlated with soil sandiness. We also found that α diversity was lower in harvested sites compared to control sites and none of the measured environmental gradients influenced α diversity. The effects of harvest on α‐diversity patterns may have been mediated through the competitive interactions of the two dominant ant species ( Formica montana and Lasius neoniger ). In contrast, β diversity (after adjusting for random effects and changes to α diversity) was higher in harvest sites compared to control sites, and variability in community composition was largely driven by the occurrence of rare species. The proportion of sand in the local habitat and habitat size positively influenced β diversity suggesting that community dissimilarity was due in part to environmental filtering and the size of species pools. Because biomass harvest had contrasting effects on ant α and β diversities, trade‐offs in maintaining α vs. β diversity might need to be considered in land management and conservation efforts.

Kim, Tania N.↗
DOE OSTI2019

Short-term response to season of burn by amphibians and reptiles in a Florida longleaf pine – wiregrass sandhill

We investigated how herpetofauna respond to burning and burn season in longleaf pine (Pinus palustris Mill.) sandhills by contrasting preburn species richness, diversity, and evenness and captures of six reptile and six amphibian species to the first (Y+1) or second (Y+2) year after burn or between dormant-season burns (DSB) and growing-season burns (GSB). Responses to burning overall or burn season were inconsistent among species; several showed no response, whereas others responded positively or negatively. Most responses were evident only in Y+1. Reptile species richness, diversity, and evenness responses were not detected. Amphibian richness increased after burning overall; diversity and evenness decreased more in GSB than in DSB in Y+1. Southern toad (Anaxyrus terrestris (Bonnaterre, 1789)) captures increased and Florida crowned snake (Tantilla relicta Telford, 1966) captures decreased following burns overall in Y+1. Ground skink (Scincella lateralis (Say in James, 1823)) captures increased more in DSB than GSB in Y+1. Florida gopher frog (Lithobates capito (LeConte, 1855)) and southeastern five-lined skink (Plestiodon inexpectatus; Taylor, 1932) captures increased, and oak toad (Anaxyrus quercicus (Holbrook, 1840)) decreased more in GSB than DSB in Y+2. Responses were likely due to changes in aboveground activity affecting captures or (for amphibians especially) annual variability in captures unrelated to burns. Our results indicated that reptiles and amphibians of sandhills are resilient to short-term effects of burning overall and burn season.

Forestry↗
DOE OSTI2022

Genetic diversity loss in the Anthropocene

Anthropogenic habitat loss and climate change are reducing species’ geographic ranges, increasing extinction risk and losses of species’ genetic diversity. Although preserving genetic diversity is key to maintaining species’ adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations’ post-2020 targets for genetic preservation.

Science & Technology - Other Topics↗
DOE OSTI2015

Can the Results of Biodiversity-Ecosystem Productivity Studies Be Translated to Bioenergy Production?

Biodiversity experiments show that increases in plant diversity can lead to greater biomass production, and some researchers suggest that high diversity plantings should be used for bioenergy production. However, many methods used in past biodiversity experiments are impractical for bioenergy plantings. For example, biodiversity experiments often use intensive management such as hand weeding to maintain low diversity plantings and exclude unplanted species, but this would not be done for bioenergy plantings. Also, biodiversity experiments generally use high seeding densities that would be too expensive for bioenergy plantings. Here we report the effects of biodiversity on biomass production from two studies of more realistic bioenergy crop plantings in southern Michigan, USA. One study involved comparing production between switchgrass (Panicum virgatum) monocultures and species-rich prairie plantings on private farm fields that were managed similarly to bioenergy plantings. The other study was an experiment where switchgrass was planted in monoculture and in combination with increasingly species-rich native prairie mixtures. Overall, we found that bioenergy plantings with higher species richness did not produce more biomass than switchgrass monocultures. The lack of a positive relationship between planted species richness and production in our studies may be due to several factors. Non-planted species (weeds) were not removed from our studies and these non-planted species may have competed with planted species and also prevented realized species richness from equaling planted species richness. Also, we found that low seeding density of individual species limited the biomass production of these individual species. Finally, production in future bioenergy plantings with high species richness may be increased by using a high density of inexpensive seed from switchgrass and other highly productive species, and future efforts to translate the results of biodiversity experiments to bioenergy plantings should consider the role of seeding density.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium— Arthrospira platensis . Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.

horizontal gene transfer↗