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DOE OSTI2024

Adaptation strategies of giant viruses to low-temperature marine ecosystems

Abstract Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.

Environmental Sciences & Ecology↗

DOE OSTI2022

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep

We report Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (“Candidatus Methanocomedenaceae”) and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages

Very little is known about sea ice microbes despite the significant role played by sea ice in the global oceans as well as microbial input into biogeochemical cycling. Studies on the sea ice viruses have been typically limited to -omics-based approaches and microscopic examinations of sea ice samples.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Forecasting Remote Atmospheric Responses to Decadal Kuroshio Stability Transitions

Based on observational estimates and global ocean eddy-resolving coupled retrospective initialized predictions, we show that Kuroshio Extension variability affects rainfall variability along the west coast of North America. We show that the teleconnection between the current undulations and downstream rainfall can lead to improved subseasonal to seasonal predictions of precipitation over California, and we demonstrate that capturing these teleconnections requires coupled systems with sufficient ocean resolution (i.e., eddy-resolving), especially over time scales longer than one season. The improved forecast skill is diagnosed in terms of 35 years of retrospective initialized ensemble forecasts with an ocean eddy-resolving and an ocean eddy-parameterized coupled model. Not only does the ocean eddy-resolving model show sensitivity to Kuroshio Extension variability in terms of western North America precipitation, but the ocean eddy-resolving forecasts also show improved forecast skill compared to the ocean eddy-parameterized model. Additionally, the ocean eddy-parameterized coupled model shows no sensitivity to Kuroshio Extension variability. We also find near-decadal variability associated with a progression of a lower-tropospheric height dipole around the North Pacific and how these height anomalies lead to wind-driven Rossby waves that affect the eddy activity in the Kuroshio Extension with a time lag on the order of four years. This decadal-scale variability (~10 years) opens the possibility of multiyear predictability of western North American rainfall.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Krinos, Arianna I. (ORCID:0000000197678392)↗

DOE OSTI2022

KBase Narrative - Viral Analysis End-to-End

This pipeline processes a single metagenomic dataset (downloaded from NCBI SRA) from the Global Ocean Viromes dataset, identifies the viral sequences using VirSorter, and subsequently classifies them with vConTACT2. Along the way there are several intermediary steps to convert files from one KBase object to another - and though some of these can be skipped for this particular dataset - we're explicitly doing them here as to be more easily generalized to other datasets.

Bolduc, Benjamin↗

DOE OSTI2021

Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems

Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Cloud water adjustments to aerosol perturbations are buffered by solar heating in non-precipitating marine stratocumuli

Abstract. Marine low-level clouds are key to the Earth's energy budget due to their expansive coverage over global oceans and their high reflectance of incoming solar radiation. Their responses to anthropogenic aerosol perturbations remain the largest source of uncertainty in estimating the anthropogenic radiative forcing of climate. A major challenge is the quantification of the cloud water response to aerosol perturbations. In particular, the presence of feedbacks through microphysical, dynamical, and thermodynamical pathways at various spatial and temporal scales could augment or weaken the response. Central to this problem is the temporal evolution in cloud adjustment, governed by entangled feedback mechanisms. We apply an innovative conditional Monte Carlo subsampling approach to a large ensemble of diurnal large-eddy simulation of non-precipitating marine stratocumulus to study the role of solar heating in governing the evolution in the relationship between droplet number and cloud water. We find a persistent negative trend in this relationship at night, confirming that the role of microphysically enhanced cloud-top entrainment. After sunrise, the evolution in this relationship appears buffered and converges to ∼-0.2 in the late afternoon. This buffering effect is attributed to a strong dependence of cloud-layer shortwave absorption on cloud liquid water path. These diurnal cycle characteristics further demonstrate a tight connection between cloud brightening potential and the relationship between cloud water and droplet number at sunrise, which has implications for the impact of the timing of advertent aerosol perturbations.

Zhang, Jianhao (ORCID:0000000169882935)↗

DOE OSTI2023

Understanding the compound flood risk along the coast of the contiguous United States

Abstract. Compound flooding is a type of flood event caused by multiple flood drivers. The associated risk has usually been assessed using statistics-based analyses or hydrodynamics-based numerical models. This study proposes a compound flood (CF) risk assessment (CFRA) framework for coastal regions in the contiguous United States (CONUS). In this framework, a large-scale river model is coupled with a global ocean reanalysis dataset to (a) evaluate the CF exposure related to the coastal backwater effects on river basins, and (b) generate spatially distributed data for analyzing the CF hazard using a bivariate statistical model of river discharge and storm surge. The two kinds of risk are also combined to achieve a holistic understanding of the continental-scale CF risk. The estimated CF risk shows remarkable inter- and intra-basin variabilities along the CONUS coast with more variabilities in the CF hazard over the US west and Gulf coastal basins. Different risk assessment methods present significantly different patterns in a few key regions such as the San Francisco Bay area, the lower Mississippi River, and Puget Sound. Our results highlight the need to weigh different CF risk measures and avoid using single statistics-based or hydrodynamics-based CFRAs. Uncertainty sources in these CFRAs include the use of gauge observations, which cannot account for the flow physics or resolve the spatial variability of risks, and underestimations of the flood extremes and the dependence of CF drivers in large-scale models, highlighting the importance of understanding the CF risks for developing a more robust CFRA.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway

Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum . Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Distinctive Pattern of Global Warming in Ocean Heat Content

Abstract Huge heat anomalies in the atmosphere and ocean in recent years are not yet explained. Strong characteristic patterns in temperatures for upper layers of the ocean occurred from 2000 to 2023 in the presence of global warming from increasing atmospheric greenhouse gases. Here, we show that the deep tropics are warming, although sharply modulated by El Niño–Southern Oscillation events, with strong heating in the extratropics near 40°N and 40°–45°S but little heating near 20°N and 25°–30°S. The heating is most clearly manifested in zonal-mean ocean heat content and is evident in sea surface temperatures. The strongest heating is in the Southern Hemisphere, where aerosol effects are small. Estimates are made of the contributions to heating of top-of-atmosphere (TOA) radiation, atmospheric energy transports, surface fluxes of energy, and redistribution of energy by surface winds and ocean currents. The patterns of change are not directly related to TOA radiation but are evident in net surface energy fluxes and inferred ocean heat transports, underscoring their coupled origin. Changes in the atmospheric circulation through a poleward shift in ocean jet streams and storm tracks are reflected in surface wind-driven ocean Ekman transports. As well as human-induced climate change, internal natural variability is likely in play. Hence, the atmosphere and ocean currents are systematically redistributing heat from global warming, profoundly affecting local climates. Significance Statement As the climate changes, it has been difficult to discern meaningful patterns. Distinctive patterns of change have occurred in the ocean when examined as zonal averages around latitude bands. Most excess heat from global warming resides in the ocean and, since 2005, has become focused into bands near 40°N and 40°S, with little net warming in the subtropics. The strongest warming is in the Southern Hemisphere, although sea surface temperatures have increased more in the Northern Hemisphere. Changes in the atmospheric circulation through a poleward shift in the jet stream and storm tracks are primarily responsible along with corresponding changes in ocean currents. These changes are linked through surface exchanges of energy via heat, moisture, and wind stress.

Trenberth, Kevin E. [National Center for Atmospher↗

DOE OSTI2022

Global decline in ocean memory over the 21st century

Ocean memory, the persistence of ocean conditions, is a major source of predictability in the climate system beyond weather time scales. We show that ocean memory, as measured by the year-to-year persistence of sea surface temperature anomalies, is projected to steadily decline in the coming decades over much of the globe. This global decline in ocean memory is predominantly driven by shoaling of the upper-ocean mixed layer depth in response to global surface warming, while thermodynamic and dynamic feedbacks can contribute substantially regionally. As the mixed layer depth shoals, stochastic forcing becomes more effective in driving sea surface temperature anomalies, increasing high-frequency noise at the expense of persistent signals. Reduced ocean memory results in shorter lead times of skillful persistence-based predictions of sea surface thermal conditions, which may present previously unknown challenges for predicting climate extremes and managing marine biological resources under climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Ocean Model for E3SM Global Applications (OMEGA)

This ocean model is the next generation version of the previous LANL developed MPAS-Ocean (Model for Prediction Across Scales) Ocean model. It is specifically designed to be used effectively on high performance computing, in particular GPU enabled architectures.

Van Roekel, Luke↗

DOE OSTI2021

Observed Global Increases in Tropical Cyclone-Induced Ocean Cooling and Primary Production

Tropical cyclones (TC) provide an important source of mixing for the upper ocean, bringing cold, nutrient-rich water to the surface and triggering phytoplankton blooms. TCs are changing in response to global warming, yet the impacts of those changes on the upper ocean are poorly known. Here we show a significant increasing trend in global TC-induced sea surface temperature (SST) cooling of 0.054oC per decade since 1982. The enhanced cooling has been driven primarily by an increase in the intensity of strong TCs (maximum wind speed > 33 m s-1) and associated strengthening of TC-induced mixing. Consistent with the enhanced mixing and SST cooling, we find a significant increase in TC-induced surface chlorophyll-a concentration of 3.7 x 10-3 mg m-3 per decade in oligotrophic areas. This enhancement of oceanic primary production by TCs is expected to partially offset its projected global decline under climate change.

Dac Da, Nguyen↗

DOE OSTI2020

A global ensemble of ocean wave climate projections from CMIP5-driven models

This dataset, produced through the Coordinated Ocean Wave Climate Project (COWCLIP) phase 2, represents the first coordinated multivariate ensemble of 21st Century global wind-wave climate projections available (henceforth COWCLIP2.0). COWCLIP2.0 comprises general and extreme statistics of significant wave height (H S ), mean wave period (T m ), and mean wave direction (θ m ) computed over time-slices 1979–2004 and 2081–2100, at different frequency resolutions (monthly, seasonally and annually). The full ensemble comprising 155 global wave climate simulations is obtained from ten CMIP5-based state-of-the-art wave climate studies and provides data derived from alternative wind-wave downscaling methods, and different climate-model forcing and future emissions scenarios. The data has been produced, and processed, under a specific framework for consistency and quality, and follows CMIP5 Data Reference Syntax, Directory structures, and Metadata requirements. Technical comparison of model skill against 26 years of global satellite measurements of significant wave height has been undertaken at global and regional scales. This new dataset provides support for future broad scale coastal hazard and vulnerability assessments and climate adaptation studies in many offshore and coastal engineering applications.

Science & Technology - Other Topics↗

DOE OSTI2023

Global cascade of kinetic energy in the ocean and the atmospheric imprint

Here, we present an estimate for the ocean's global scale transfer of kinetic energy (KE), across scales from 10 to 40,000 km. Oceanic KE transfer between gyre scales and mesoscales is induced by the atmosphere’s Hadley, Ferrel, and polar cells, and the intertropical convergence zone induces an intense downscale KE transfer. Upscale transfer peaks at 300 gigawatts across mesoscales of 120 km in size, roughly one-third the energy input by winds into the oceanic general circulation. Nearly three quarters of this “cascade” occurs south of 15°S and penetrates almost the entire water column. The mesoscale cascade has a self-similar seasonal cycle with characteristic lag time of ≈27 days per octave of length scales; transfer across 50 km peaks in spring, while transfer across 500 km peaks in summer. KE of those mesoscales follows the same cycle but peaks ≈40 days after the peak cascade, suggesting that energy transferred across a scale is primarily deposited at a scale four times larger.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Improved Time-Stepping Methods in Global to Regional Ocean Modeling (Annual Status Report 2020)

Time stepping algorithms are an important part of ocean models, and strongly influence both the accuracy of solution and performance. There have been a number of projects investigating various improvements for ocean time-stepping schemes in the Model for Prediction Across Scales-Ocean (MPAS-Ocean), a component of the DOE Energy Exascale Earth System Model. Ocean dynamics include fast surface gravity waves, which are two-dimensional, and slower internal waves, which are three-dimensional, so ocean models use a split time-stepping scheme that separates these barotropic and baroclinic modes for efficiency. MPAS-Ocean runs on variable-resolution horizontal meshes, and must scale to tens of thousands of cores and millions of horizontal gridcells. Ocean models require time stepping algorithms that are customized to these needs, and which are tuned for performance on various resolutions and architectures.

58 GEOSCIENCES↗

DOE OSTI2022

Improved Time-Stepping Methods in Global to Regional Ocean Modeling (Annual Status Report)

58 GEOSCIENCES↗