Search NASA⌕ Search

SEARCH · Search NASA

Results for “Global ocean”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

INSIGHTS INTO MARINE UNICELLULAR CYANOBACTERIAL AND NON-CYANOBACTERIAL DIAZOTROPHS THROUGH SINGLE-CELL ANALYSES

Nutrient availability affects primary productivity, and nitrogen (N) is the limiting nutrient over large regions of the ocean. Biological N fixation (BNF) is the conversion of atmospheric dinitrogen (N2) to bioavailable forms of N (ammonium and amino acids). A select group of Bacteria and Archaea, known as diazotrophs, are the only organisms capable of this conversion. BNF is a critical source of N in nutrient-depleted (oligotrophic) marine waters. As such, BNF studies are a fundamental component for better understanding primary productivity and carbon cycling, as well as parameterizing predictive future global ocean models. Unicellular diazotrophs are widespread in marine systems and, in some cases, important contributors of BNF. This dissertation investigates unicellular diazotrophs at the single-cell level, including: UCYN-A, a cyanobacterial diazotroph that lives in symbiosis with an algal host, non-cyanobacterial diazotrophs (NCDs), which are putative heterotrophs, as well as a specific NCD known as Gamma A, a commonly occurring organism throughout the tropics and subtropics that belongs to the class Gammaproteobacteria. The single-cell investigations used in these studies can provide high-resolution insights that are not possible from community-level analyses of BNF, such as the N2 fixation rate of individual cells and cell morphology. Singlecell nanoscale secondary ion mass spectrometry (nanoSIMS) analyses were used in chapter 2 and 3 to investigate the cell-specific N2 fixation rates of (2) UCYN-A in the viii cold waters of the Bering and Arctic Seas where N2 fixation was not previously believed to be possible, and (3) NCDs in the North Pacific Subtropical Gyre where we demonstrated the first direct evidence of NCD N2 fixation on open ocean particles. Chapter 4 focused on the uncultivated NCD, Gamma A, using geneFISH to visualize single cells in natural seawater samples. We successfully identified Gamma A by developing a fluorescent in situ hybridization (FISH) probe targeting the diazotrophic functional marker gene nifH, revealing Gamma A cells are most often attached to particles. Together these studies provide new insights into the distributions, activities, and physiologies of geographically widespread, unicellular diazotrophs, thus improving our understanding of their roles as sources of fixed N in the surface ocean.

Harding, K.↗
DOE OSTI2020

Quantifying CanESM5 and EAMv1 sensitivities to Mt. Pinatubo volcanic forcing for the CMIP6 historical experiment

Large volcanic eruptions reaching the stratosphere have caused marked perturbations to the global climate including cooling at the Earth's surface, changes in large-scale circulation and precipitation patterns and marked temporary reductions in global ocean heat content. Many studies have investigated these effects using climate models; however, uncertainties remain in the modelled response to these eruptions. This is due in part to the diversity of forcing datasets that are used to prescribe the distribution of stratospheric aerosols resulting from these volcanic eruptions, as well as uncertainties in optical property derivations from these datasets. To improve this situation for the sixth phase of the Coupled Model Intercomparison Project (CMIP6), a two-step process was undertaken. First, a combined stratospheric aerosol dataset, the Global Space-based Stratospheric Aerosol Climatology (GloSSAC; 1979–2016), was constructed. Next, GloSSAC, along with information from ice cores and Sun photometers, was used to generate aerosol distributions, characteristics and optical properties to construct a more consistent stratospheric aerosol forcing dataset for models participating in CMIP6. This “version 3” of the stratospheric aerosol forcing has been endorsed for use in all contributing CMIP6 simulations. Recent updates to the underlying GloSSAC from version 1 to version 1.1 affected the 1991–1994 period and necessitated an update to the stratospheric aerosol forcing from version 3 to version 4. As version 3 remains the official CMIP6 input, quantification of the impact on radiative forcing and climate is both relevant and timely for interpreting results from experiments such as the CMIP6 historical simulations. This study uses two models, the Canadian Earth System Model version 5 (CanESM5) and the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1), to estimate the difference in instantaneous radiative forcing in simulated post-Pinatubo climate response when using version 4 instead of version 3. Differences in temperature, precipitation and radiative forcings are generally found to be small compared to internal variability. An exception to this is differences in monthly temperature anomalies near 24 km altitude in the tropics, which can be as large as 3 °C following the eruption of Mt. Pinatubo.

58 GEOSCIENCES↗
DOE OSTI2020

Numerical integrators for Lagrangian oceanography

Abstract. A common task in Lagrangian oceanography is to calculate a large number of drifter trajectories from a velocity field precalculated with an ocean model. Mathematically, this is simply numerical integration of an ordinary differential equation (ODE), for which a wide range of different methods exist. However, the discrete nature of the modelled ocean currents requires interpolation of the velocity field in both space and time, and the choice of interpolation scheme has implications for the accuracy and efficiency of the different numerical ODE methods. We investigate trajectory calculation in modelled ocean currents with 800 m, 4 km, and 20 km horizontal resolution, in combination with linear, cubic and quintic spline interpolation. We use fixed-step Runge–Kutta integrators of orders 1–4, as well as three variable-step Runge–Kutta methods (Bogacki–Shampine 3(2), Dormand–Prince 5(4) and 8(7)). Additionally, we design and test modified special-purpose variants of the three variable-step integrators, which are better able to handle discontinuous derivatives in an interpolated velocity field. Our results show that the optimal choice of ODE integrator depends on the resolution of the ocean model, the degree of interpolation, and the desired accuracy. For cubic interpolation, the commonly used Dormand–Prince 5(4) is rarely the most efficient choice. We find that in many cases, our special-purpose integrators can improve accuracy by many orders of magnitude over their standard counterparts, with no increase in computational effort. Equivalently, the special-purpose integrators can provide the same accuracy as standard methods at a reduced computational cost. The best results are seen for coarser resolutions (4 and 20 km), thus the special-purpose integrators are particularly advantageous for research using regional to global ocean models to compute large numbers of trajectories. Our results are also applicable to trajectory computations on data from atmospheric models.

58 GEOSCIENCES↗
DOE OSTI2022

A Statistical Interpolation Code for Ocean Analysis and Forecasting

Abstract We present a data assimilation package for use with ocean circulation models in analysis, forecasting, and system evaluation applications. The basic functionality of the package is centered on a multivariate linear statistical estimation for a given predicted/background ocean state, observations, and error statistics. Novel features of the package include support for multiple covariance models, and the solution of the least squares normal equations either using the covariance matrix or its inverse—the information matrix. The main focus of this paper, however, is on the solution of the analysis equations using the information matrix, which offers several advantages for solving large problems efficiently. Details of the parameterization of the inverse covariance using Markov random fields are provided and its relationship to finite-difference discretizations of diffusion equations are pointed out. The package can assimilate a variety of observation types from both remote sensing and in situ platforms. The performance of the data assimilation methodology implemented in the package is demonstrated with a yearlong global ocean hindcast with a 1/4° ocean model. The code is implemented in modern Fortran, supports distributed memory, shared memory, multicore architectures, and uses climate and forecasts compliant Network Common Data Form for input/output. The package is freely available with an open source license from www.tendral.com/tsis/ .

Srinivasan, Ashwanth↗
DOE OSTI2020

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A High-resolution Regional Wave Resource Characterization For The U.S. West Coast

Objectives/Scope: Wave resource characterization is a critical step for wave energy converter deployment in the coastal ocean and relies on long-term, high-resolution wave datasets. This study presents a detailed modeling study of the wave resource along the U.S. West Coast (Washington, Oregon, and California), a coastal region that was identified with high wave energy potential in earlier studies. Methods, Procedures, Process: The wave hindcast covers a 32-year period from 1979 to 2010 and is based on a multi-resolution, unstructured-grid SWAN model framework. Model configuration closely follows and meets the requirements recommended by the International Electrotechnical Commission Technical Specification (IEC TS) for wave energy resource assessment and characterization (Class 2 - feasibility study). The model domain covers the entire U.S. Exclusive Economic Zone (EEZ) in the West Coast and has a spatial resolution varying from ~300 m in the nearshore region (20 km from the shoreline) to ~2500 m within the EEZ and ~5000 m at the open boundary, which extends beyond the EEZ. The model was forced by hourly 2-D wave spectra produced by a two-way nested WaveWatch III model, which covers the global ocean domain and the broader U.S. West Coast region domain with spatial resolutions of 0.5 degree and 10 arc-minutes, respectively. Both wave models are forced by hourly, 0.5-degree wind forcing obtained from NCEP’s Climate Forecast System Reanalysis (CFSR) product. Results, Observations, Conclusions: The standard model output for the SWAN model includes 3-hourly output for the six IEC wave resource parameters (e.g., omnidirectional wave power) at each grid point and hourly 2-D spectra at more than 50 NDBC buoys. Extensive model validation was achieved by comparing the six model-predicted IEC parameters with those derived from field observations at representative NDBC buoys. The error statistics indicated the model’s satisfactory performance. Further analyses were conducted to systematically evaluate the temporal and spatial distributions of wave energy potential and wave climate along the U.S. West Coast. Results suggest that Washington and Oregon coasts have similar nearshore wave resource, which is significantly higher than resources in Southern California. Strong seasonal variations are also observed, e.g., high wave energy tends to occur in the winter months. In summary, this study produced the first high-resolution, comprehensive dataset on wave energy distribution along the U.S. West Coast. Novel/Additive Information: The results are being used by the National Renewable Energy Laboratory to update the MHK Atlas, which was originally derived from NOAA’s 4-arc-minute WaveWatch III model output. In addition, the monthly averaged wave energy climatology dataset can be readily shared to support a variety of research and application efforts within the EEZ of the U.S. West Coast.

Wang, Taiping↗
DOE OSTI2023

Molybdenum in basalt-hosted seafloor hydrothermal systems: Experimental, theoretical, and field sampling approaches

Here, seafloor hydrothermal vents represent potential sources of Mo and other biologically relevant transition metals to the global ocean, complementing continental runoff. Here, we use a combination of experimental, theoretical, and field-sampling approaches to investigate the behavior of Mo in basalt-hosted seafloor hydrothermal systems to provide insight into the processes controlling Mo concentrations in hydrothermal fluids and to derive estimates of vent fluid Mo concentrations and fluxes. Results of this study demonstrate that reaction fluids generated from 350°C, 500 bar hydrothermal basalt alteration experiments contain 775–801 nmol/kg Mo and are thus comparable to a recently collected time series of natural seafloor vent fluids that contained 200–220 nmol/kg Mo at 302°C and 29–30 nmol/kg at 281–282°C (Evans et al., 2023). Synchrotron-based analyses of experimentally altered basalt produced in this study and additional natural samples of altered oceanic crust originally collected from Pito Deep Rift reveal the presence of Mo-rich particles consistent with trace molybdenite. Comparisons of Mo:Cu ratios in natural vent fluids and near-vent sediment trap samples from Main Endeavour Field indicate that vent fluid Mo is readily incorporated into buoyant plume particles and advected out of the near-vent field, analogous to previous mass balance studies of Cu in this region. Thermodynamic calculations of molybdenite solubility in the context of mineral-buffered hydrothermal fluids and comparisons with natural and experimental hydrothermal fluids suggest that high-temperature vent fluids contain 30–1500 nmol/kg Mo. While a minor component of the modern Mo budget, hydrothermal Mo fluxes are estimated to have constituted 0.3–200× the contemporaneous continental weathering fluxes prior to the ~2.4 Ga ago “Great Oxidation Event” and widespread oxidative continental weathering. Overall, identification of hydrothermal vents as a source of Mo-rich plume particles with potential for dispersal into the wider marine environment has significant implications for hypotheses regarding the co-evolution of Life and Earth’s environments, specifically the form and availability of Mo in anoxic Archean-Eon oceans, where Mo-dependent enzymatic pathways are thought to have emerged and subsequently evolved.

58 GEOSCIENCES↗
DOE OSTI2023

Long-Term Changes in Concentration and Yield of Riverine Dissolved Silicon From the Poles to the Tropics

Riverine exports of silicon (Si) influence global carbon cycling through the growth of marine diatoms, which account for ~25% of global primary production. Climate change will likely alter river Si exports in biome-specific ways due to interacting shifts in chemical weathering rates, hydrologic connectivity, and metabolic processes in aquatic and terrestrial systems. Nonetheless, factors driving long-term changes in Si exports remain unexplored at local, regional, and global scales. We evaluated how concentrations and yields of dissolved Si (DSi) changed over the last several decades of rapid climate warming using long-term data sets from 60 rivers and streams spanning the globe (e.g., Antarctic, tropical, temperate, boreal, alpine, Arctic systems). We show that widespread changes in river DSi concentration and yield have occurred, with the most substantial shifts occurring in alpine and polar regions. The magnitude and direction of trends varied within and among biomes, were most strongly associated with differences in land cover, and were often independent of changes in river discharge. These findings indicate that there are likely diverse mechanisms driving change in river Si biogeochemistry that span the land-water interface, which may include glacial melt, changes in terrestrial vegetation, and river productivity. Finally, trends were often stronger in months outside of the growing season, particularly in temperate and boreal systems, demonstrating a potentially important role of shifting seasonality for the flux of Si from rivers. Our results have implications for the timing and magnitude of silica processing in rivers and its delivery to global oceans.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Impact of Turbulence Representation on the Relationship Between Cloud Feedback and Aerosol‐Cloud Interaction in an E3SMv2 Perturbed Parameter Ensemble

Recent studies reveal an anti‐correlation between global cloud feedback (CF) and effective radiative forcing due to aerosol‐cloud interaction (ERFaci) in Earth system models, but the physical mechanisms underlying it remain uncertain. Here we investigate how different turbulence representations contribute to this relationship over the global ocean using an ensemble of Energy Exascale Earth System Model version 2 simulations with perturbed turbulence parameters. The anti‐correlation appears only in the tropical ascent regime. In the Northern Hemisphere midlatitude and high latitude regimes, there is no significant correlation, and in the tropical marine low cloud and Southern Ocean regimes, the correlation is positive. These opposite correlations are primarily driven by opposing CF responses to perturbed parameters. We find that the mean‐state turbulent mixing strength affects both CF and ERFaci, enabling strong correlations in certain regimes. This study highlights the complex linkages between CF and ERFaci through turbulent processes across diverse cloud regimes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Abstract Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.

Füssy, Zoltán↗
DOE OSTI2020

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dichotomy between freshwater and heat flux effects on oceanic conveyor belt stability and global climate

The Atlantic meridional overturning circulation is an important global-scale oceanic circulation, and its changes may be responsible for past abrupt climate change events. By using two versions of a coupled climate model, here we show that the stability of this circulation depends not only on the background climate, but also on the type of primary external forcing: freshwater vs. greenhouse gases. When freshwater forcing is dominant, hysteresis of this circulation (an abrupt collapse/reactivation) becomes possible only under simulated glacial conditions with closed Bering Strait. Under present day and future conditions, both freshwater and greenhouse gas forcings could collapse this circulation, but only greenhouse gas forcing produced a bi-stable equilibrium state comparable to abrupt climate change. Our results demonstrate that the Bering Strait status (open vs. closed) may facilitate or prohibit the existence of this circulation’s hysteresis, irrespective of the background climate conditions, but is directly related to the primary forcing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Abrupt reduction in shipping emission as an inadvertent geoengineering termination shock produces substantial radiative warming

Abstract Human activities affect the Earth’s climate through modifying the composition of the atmosphere, which then creates radiative forcing that drives climate change. The warming effect of anthropogenic greenhouse gases has been partially balanced by the cooling effect of anthropogenic aerosols. In 2020, fuel regulations abruptly reduced the emission of sulfur dioxide from international shipping by about 80% and created an inadvertent geoengineering termination shock with global impact. Here we estimate the regulation leads to a radiative forcing of $$+0.2\pm 0.11$$ + 0.2 ± 0.11 Wm −2 averaged over the global ocean. The amount of radiative forcing could lead to a doubling (or more) of the warming rate in the 2020 s compared with the rate since 1980 with strong spatiotemporal heterogeneity. The warming effect is consistent with the recent observed strong warming in 2023 and expected to make the 2020 s anomalously warm. The forcing is equivalent in magnitude to 80% of the measured increase in planetary heat uptake since 2020. The radiative forcing also has strong hemispheric contrast, which has important implications for precipitation pattern changes. Our result suggests marine cloud brightening may be a viable geoengineering method in temporarily cooling the climate that has its unique challenges due to inherent spatiotemporal heterogeneity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Effect of viral infection on the ice nucleation efficiency of marine coccolithophores

A marine coccolithophore (Emiliania huxleyi) and coccolithovirus (EhV-207) were grown together in a marine aerosol reference tank (MART) to investigate how the viral lysis of phytoplankton affects the formation of immersion mode ice nucleating particles (INPs) in sea spray aerosol (SSA). The mean ice nucleation temperatures of SSA produced during viral infection were slightly lower (–28.5 °C) than pre-viral infection (–27.5 °C). Ice nucleation temperatures were relatively low, indicating that organic matter from E. huxleyi is less effective as an INP than phytoplankton examined in previous studies. E. huxleyi is covered in calcium carbonate coccoliths and contains high intracellular concentrations of dimethylsulfoniopropionate (DMSP). The ice nucleation efficiencies of purified components were measured to better understand this model system. Purified coccoliths were moderately effective INPs (–25.3 ± 0.4 °C at 5 x 10 2 mg L -1 (mean ±pooled SD)) that showed a concentration effect, with lower freezing temperatures at lower concentrations. Coccoliths and DMSP were both weakly efficient INPs. In comparison, purified phytoplankton viruses (EhV-207 and CtenRNAV-01) infecting coccolithophores and diatoms, respectively, did not affect freezing at temperatures warmer than the procedural blank. Our results suggest that E. huxleyi, in contrast to diatoms and cyanobacteria, is not a significant source of immersion mode INPs to the marine atmosphere, despite its broad distribution in the global ocean and large-scale bloom formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

Abstract Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗