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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Assessing biogeographic survey gaps in bacterial diversity knowledge: A global synthesis of freshwaters

Freshwaters account for 0.8% of Earth's surface area, yet support >10% of known plant and animal species making them disproportionately biodiverse. Modern molecular techniques have begun to reveal microbial diversity, but application of these approaches to address global microbial biogeography is relatively unknown in freshwaters. Our aim was to identify gaps in microbial data coverage along climatic and landscape disturbance gradients and among terrestrial biomes and hydrographic regions for all freshwater ecosystems and three freshwater habitat types: lakes and reservoirs (lentic); streams and rivers (lotic); and wetlands. We reviewed literature on microbial diversity in freshwaters surveyed using 16S ribosomal RNA sequencing which identify microbial taxa. We georeferenced survey locations and used a geographic information system to identify and map gaps in survey coverage using open-source data for climate, landscape disturbance, terrestrial biomes, and freshwater ecoregions. In our study, we compiled 3,425 georeferenced survey locations reported from 963 studies. Streams were surveyed most frequently (60.8% of survey locations), followed by lakes (33.5%) and wetlands (5.6%). Surveys were concentrated in North America, central and western Europe, and Southeast Asia; 35% of freshwater ecoregions were surveyed at least once across freshwater habitat types, whereas 23%, 23%, and 12% were surveyed at least once for lentic, lotic, and wetland habitat types, respectively. The climatic gap analysis indicated coverage is high for temperate regions but lacking in the tropics and Arctic, particularly for wetland ecosystems. Our assessment revealed high climatic coverage of freshwater microbial diversity knowledge, but expansive ecoregional gaps attributable to biased sampling near research institutions in North America, western Europe, and China. Future surveys should target ecoregions in Africa, South America, Central Asia, Australia, and Antarctica. An essential next step will be to curate and disseminate sequencing efforts to facilitate the study of processes driving global diversity patterns.

16S rRNA↗
DOE OSTI2024

Biomass yields, reproductive fertility, compositional analysis, and genetic diversity of newly developed triploid giant miscanthus hybrids

Abstract Miscanthus × giganteus (giant miscanthus), first found as a naturally occurring hybrid, has shown promise as a bioenergy/biomass crop throughout much of the temperate world. This allotriploid (2 n = 3 x = 57) hybrid resulted from a cross between tetraploid Miscanthus sacchariflorus (2 n = 4 x = 76) and diploid Miscanthus sinensis (2 n = 2 x = 38) and is particularly desirable due to its low fertility that minimizes reseeding and potential invasiveness. However, there is limited genetic diversity in commonly grown cultivars of triploid M. × giganteus and breeding and development efforts to improve and domesticate this crop have been minimal. Here, we report on newly developed M. × giganteus hybrids compared with the industry standard M. × giganteus '1993‐1780'. Dry biomass yields of new hybrids ranged from 19.5 to 32.4 Mg/ha/year for the fourth growing season, compared with 21.0 Mg/ha/year for M. × giganteus '1993‐1780'. Plant reproductive fertility remained low for all accessions with overall fertility [(seed set × seed germination)/100] ranging from 0.3% to 4.5% for new hybrids compared to 0.4% for M. × giganteus '1993‐1780'. Culm density and height varied among accessions and were positively correlated with increased biomass. Based on compositional analyses, theoretical ethanol yields ranged from 9, 740 to 16,278 L/ha/year for new hybrids compared to 10,406 L/ha/year for M. × giganteus '1993‐1780'. Relative feed value indices were low overall and ranged between 66.0 and 72.8 for new hybrids compared to M. × giganteus '1993‐1780' with 71.3. The genetic diversity of new hybrids, compared with existing cultivars, was characterized using whole genome sequences. Based on pair‐wise distances, cluster analysis clearly showed increased diversity of new hybrids compared with earlier selections. These results document new triploid hybrids of M. × giganteus with enhanced biomass and theoretical ethanol yields in combination with broader genetic diversity and lowreproductive fertility.

Touchell, Darren H.↗
DOE OSTI2025

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity

ABSTRACT Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon. Suillus are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three Suillus species ( Suillus hirtellus EM16, Suillus decipiens EM49, and Suillus cothurnatus VC1858), core members of the pine microbiome. After 28 days of growth on solid media, liquid chromatography–tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between Suillus co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 41 putative prenol lipids (includes 37 putative terpenes) were identified across the three Suillus species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and Suillus spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication. IMPORTANCE Using a combination of genomics and metabolomics, this study’s findings offer new insights into the chemical diversity of Suillus fungi, which serve a critical role in forest ecosystems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Single-shot, phase-diversity phase retrieval for high-energy beam focal-spot diagnostics

A single-shot, phase-diversity phase-retrieval method is demonstrated for directly characterizing the on-target focal spot at kilojoule energy in the OMEGA 60-beam laser. A 2D holographic grating that introduces diversity focal spots is installed in an existing on-target focal-spot diagnostic to obtain a single-shot diversity focal-spot image. A nonlinear optimization phase-retrieval algorithm with four diversity focal spots is employed to determine modal coefficients for the incident wavefront. The agreement between the measured and calculated focal spots is excellent. Furthermore, this approach can be easily adapted for other high-energy focal-spot diagnostics.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering

Microbial biotechnologies are key to addressing grand challenges to promote human health, reverse carbon emissions, recycle mixed plastic waste, remediate contaminated soils, and achieve sustainable economies. Synthetic biology has enabled design of diverse microbes and their proteins for useful purposes, but the narrowness of the natural genetic code limits functional diversity (e.g., biosynthesis) of engineered microbes. The natural genetic code defines the fundamental rules of translating genetic information into proteins comprised of 22 ‘canonical’ amino acids. However, using a technique called genetic code expansion (GCE), the chemical properties and therefore functions of proteins can be transformed by incorporation of one or more of ~200 chemically diverse ‘non-canonical’ amino acids. The effective application of genetic code expansion in diverse microbes has the potential to revolutionize biotechnology. However, despite over 50 years of research and its transformative potential, the application of genetic code expansion has been limited to a handful of bacterial species. In this project, we will perform three tasks to both overcome the barriers that prevent wide spread adoption of GCE as molecular tool and demonstrate its potential for biotechnological applications. Specifically, we will (1) develop a genetic engineering methodology that will enable use of GCE in a broad range of bacterial hosts, (2) use high-throughput functional genomics methods to identify physiological responses to both genetic code expansion and exposure to non-canonical amino acids in three different bacteria, and (3) demonstrate an application of GCE by selectively incorporate non-canonical amino acids into surface displayed peptides such as those used for biomining.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass ( Panicum virgatum ), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine-learning based approach to examine ecological processes influencing the diversity of riverine dissolved organic matter composition

Dissolved organic matter (DOM) assemblages in freshwater rivers are formed from mixtures of simple to complex compounds that are highly variable across time and space. These mixtures largely form due to the environmental heterogeneity of river networks and the contribution of diverse allochthonous and autochthonous DOM sources. Most studies are, however, confined to local and regional scales, which precludes an understanding of how these mixtures arise at large, e.g., continental, spatial scales. The processes contributing to these mixtures are also difficult to study because of the complex interactions between various environmental factors and DOM. Here we propose the use of machine learning (ML) approaches to identify ecological processes contributing toward mixtures of DOM at a continental-scale. We related a dataset that characterized the molecular composition of DOM from river water and sediment with Fourier-transform ion cyclotron resonance mass spectrometry to explanatory physicochemical variables such as nutrient concentrations and stable water isotopes ( 2 H and 18 O). Using unsupervised ML, distinctive clusters for sediment and water samples were identified, with unique molecular compositions influenced by environmental factors like terrestrial input and microbial activity. Sediment clusters showed a higher proportion of protein-like and unclassified compounds than water clusters, while water clusters exhibited a more diversified chemical composition. We then applied a supervised ML approach, involving a two-stage use of SHapley Additive exPlanations (SHAP) values. In the first stage, SHAP values were obtained and used to identify key physicochemical variables. These parameters were employed to train models using both the default and subsequently tuned hyperparameters of the Histogram-based Gradient Boosting (HGB) algorithm. The supervised ML approach, using HGB and SHAP values, highlighted complex relationships between environmental factors and DOM diversity, in particular the existence of dams upstream, precipitation events, and other watershed characteristics were important in predicting higher chemical diversity in DOM. Our data-driven approach can now be used more generally to reveal the interplay between physical, chemical, and biological factors in determining the diversity of DOM in other ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean.

Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Soil carbon accrual and biopore formation across a plant diversity gradient

Plant diversity promotes soil organic carbon (SOC) gains through intricate changes in root-soil interactions and their subsequent influence on soil physical and biological processes. We assessed SOC and pore characteristics of soils under a range of switchgrass-based plant systems 12 years after their establishment. The systems represented a gradient of plant diversity with species richness ranging from 1 to 30 species. We focused on soil biopores as indicators of the legacy of root activity and explored biopore relationships with SOC accumulation. Biopores were measured using X-ray computed micro-tomography. Plant functional richness explained 29 % of bioporosity and 36 % of SOC variation, while bioporosity itself explained 36 % of the variation in SOC. The most diverse plant system (30 species) had the highest SOC, while long-term bare soil fallow and monoculture switchgrass had the lowest. Of particular note was a 2-species mixture of switchgrass (Panicum virgatum L.) and ryegrass (Elymus canadensis), which exhibited the highest bioporosity and achieved SOC levels comparable to those of the systems with 6 and 10 plant species, and were inferior only to the system with 30 species. We conclude that plant diversity may enhance SOC through biopore-mediated mechanisms and suggest a potential for identifying specific plant combinations that may be particularly efficient for fostering biopore formation and, subsequently, SOC sequestration.

Kim, Kyungmin [Seoul National Univ. (Korea, Republ↗
DOE OSTI2020

Data-Driven Load Diversity and Variability Modeling for Quasi-Static Time-Series Simulation on Distribution Feeders

This paper presents a data-driven load modeling methodology for distribution system quasi-static time-series (QSTS) simulation considering both diversity and variability characteristics of distribution loads. Based on our previous work in [1]-[2], a variability library and diversity library have been established based on the realistic high-resolution data collected from actual utility feeders. Given the load profile for the start-of-circuit load of a feeder, the loads on the feeder nodes can be modeled with both diversity and variability instead of being directly scaled from the substation load profile according to the distribution allocation factors. With diversified load models, the load-induced impact on the feeder operation characteristics, such as voltage ramp and regulator operations, can be better considered in QSTS simulation. The proposed modeling methodology has been tested on both the IEEE 123-bus feeder and an actual utility feeder model, and the simulation results have demonstrated the merits of deploying the proposed load modeling methodology.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Soil disturbance and invasion magnify CO 2 effects on grassland productivity, reducing diversity

Climate change, disturbance, and plant invasion threaten grassland ecosystems, but their combined and interactive effects are poorly understood. Here, in this study, we examine how the combination of disturbance and plant invasion influences the sensitivity of mixed-grass prairie to elevated carbon dioxide (eCO 2 ) and warming. We established subplots of intact prairie and disturbed/invaded prairie within a free-air CO 2 enrichment (to 600 ppmv) by infrared warming (+1.5°C day, 3°C night) experiment and followed plant and soil responses for 5 years. Elevated CO 2 initially led to moderate increases in biomass and plant diversity in both intact and disturbed/invaded prairie, but these effects shifted due to strong eCO 2 responses of the invasive forb Centaurea diffusa. In the final 3 years, biomass responses to eCO 2 in disturbed/invaded prairie were 10 times as large as those in intact prairie (+186% vs. +18%), resulting in reduced rather than increased plant diversity (-17% vs. +10%). At the same time, warming interacted with disturbance/invasion and year, reducing the rate of topsoil carbon recovery following disturbance. The strength of these interactions demonstrates the need to incorporate disturbance into predictions of climate change effects. In contrast to expectations from studies in intact ecosystems, eCO 2 may threaten plant diversity in ecosystems subject to soil disturbance and invasion.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America, and Europe

Abstract Miscanthus is a high‐yielding bioenergy crop that is broadly adapted to temperate and tropical environments. Commercial cultivation of Miscanthus is predominantly limited to a single sterile triploid clone of Miscanthus × giganteus , a hybrid between Miscanthus sacchariflorus and M. sinensis. To expand the genetic base of M. × giganteus , the substantial diversity within its progenitor species should be used for cultivar improvement and diversification. Here, we phenotyped a diversity panel of 605 M. sacchariflorus from six previously described genetic groups and 27 M. × giganteus genotypes for dry biomass yield and 16 yield‐component traits, in field trials grown over 3 years at one subtropical location (Zhuji, China) and four temperate locations (Foulum, Denmark; Sapporo, Japan; Urbana, Illinois; and Chuncheon, South Korea). There was considerable diversity in yield and yield‐component traits among and within genetic groups of M. sacchariflorus , and across the five locations. Biomass yield of M. sacchariflorus ranged from 0.003 to 34.0 Mg ha −1 in year 3. Variation among the genetic groups was typically greater than within, so selection of genetic group should be an important first step for breeding with M. sacchariflorus . The Yangtze 2x genetic group (=ssp. lutarioriparius ) of M. sacchariflorus had the tallest and thickest culms at all locations tested. Notably, the Yangtze 2x genetic group's exceptional culm length and yield potential were driven primarily by a large number of nodes (>29 nodes culm −1 average over all locations), which was consistent with the especially late flowering of this group. The S Japan 4x, the N China/Korea/Russia 4x, and the N China 2x genetic groups were also promising genetic resources for biomass yield, culm length, and culm thickness, especially for temperate environments. Culm length was the best indicator of yield potential in M. sacchariflorus . These results will inform breeders' selection of M. sacchariflorus genotypes for population improvement and adaptation to target production environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Long-Term and Low-Level Envelope C2V3 Stimulation by Highly Diverse Virus Isolates Leads to Frequent Development of Broad and Elite Antibody Neutralization in HIV-1-Infected Individuals

A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemics in the world. Three hundred twenty-two HIV-1-infected adults from Angola were included in this retrospective study. Phylogenetic analysis of C2V3C3 env gene sequences was used for virus subtyping. Env-binding antibody reactivity was tested against polypeptides comprising the C2, V3, and C3 regions. Neutralizing-antibody responses were determined against a reference panel of tier 2 Env pseudoviruses in TZM-bl cells; neutralizing epitope specificities were predicted using ClustVis. All subtypes were found, along with untypeable strains and recombinant forms. Notably, 56% of the patients developed cross neutralizing, broadly neutralizing, or elite neutralizing responses. Broad and elite neutralization was associated with longer infection time, subtype C, lower CD4 + T cell counts, higher age, and higher titer of C2V3C3-specific antibodies relative to failure to develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients. V3 and C3 regions were significantly less variable in elite neutralizers than in weak neutralizers and nonneutralizers, suggesting an active role of V3C3-directed bNAbs in controlling HIV-1 replication and diversification. In conclusion, prolonged and low-level envelope V3C3 stimulation by highly diverse and ancestral HIV-1 isolates promotes the frequent elicitation of bNAbs. These results provide important clues for the development of an effective HIV-1 vaccine. Studies on neutralization by antibodies and their determinants in HIV-1-infected individuals have mostly been conducted in relatively recent epidemics caused by subtype B and C viruses. Results have suggested that elicitation of broadly neutralizing antibodies (bNAbs) is uncommon. The mechanisms underlying the elicitation of bNAbs are still largely unknown. We performed the first characterization of the plasma neutralizing response in a cohort of HIV-1-infected patients from Angola. Angola is characterized by an old and dynamic epidemic caused by highly diverse HIV-1 variants. Remarkably, more than half of the patients produced bNAbs, mostly targeting the V3-glycan supersite in HIV-1. This was associated with higher age, longer infection time, lower CD4 + T cell counts, subtype C infection, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. These results may help develop the next generation of vaccine candidates for HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ENSO Diversity Simulated in a Revised Cane-Zebiak Model

The El Niño-Southern Oscillation (ENSO) phenomenon features rich sea surface temperature (SST) spatial pattern variations dominated by the Central Pacific (CP) and Eastern Pacific (EP) patterns during its warm phase. Understanding such ENSO pattern diversity has been a subject under extensive research activity. To provide a framework for unveiling the fundamental dynamics of ENSO diversity, an intermediate coupled model based on the Cane-Zebiak-type framework, named RCZ, is established in this study. Compared with the original Cane-Zebiak model, RCZ consists of revised model formulation and well-tuned parameterization schemes. All model components are carefully validated against the observations via the standalone mode, in which the observed anomalous SST (wind stress) forcing is prescribed to drive the atmospheric (oceanic) component. The superiority of RCZ’s model components over those in the original Cane-Zebiak model is evidenced by their better performance in simulating the observations. Coupled simulation with RCZ satisfactorily reproduces aspects of the observed ENSO characteristics, including the spatial pattern, phase-locking, amplitude asymmetry, and, particularly, ENSO diversity/bi-modality. RCZ serves as a promising tool for studying dynamics of ENSO diversity as it resolves most of the relevant processes proposed in the literature, including atmospheric nonlinear convective heating, oceanic nonlinear dynamical heating, and the ENSO/westerly wind burst interaction.

54 ENVIRONMENTAL SCIENCES↗