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DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Drylands cover one-third of the Earth’s surface and are one of the largest terrestrial sinks for methane. Understanding the structure–function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors—water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m 2 h −1 , peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum , two Methylobacter , and uncultivated Methylococcaceae ). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum . Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1976

Apollo-Soyuz Test Project: Preliminary Science Report

This document summarizes the experimental concepts and preliminary analyses (as of December 1975) for each of the 28 scientific experiments conducted during the Apollo-Soyuz Test Project from July 15 to 24, 1975. The scientific topics are X- ray and extreme ultraviolet astronomy, solar astronomy, gamma- ray detectors, Earth studies (including the upper atmosphere, meteorological phenomena, hydrology, oceanography, geology, desert studies, and gravity field studies), microbiology, heavy cosmic particle interaction with live cells, vestibular system studies, and materials processing (including high-temperature and ambient-temperature processing of industrial materials and electrophoretic processing of biological materials) .

Orbital science↗

DOE OSTI2024

Visualisation and outlier detection for probability density function ensembles

Abstract Exploratory data analysis (EDA) for functional data—data objects where observations are entire functions—is a difficult problem that has seen significant attention in recent literature. This surge in interest is motivated by the ubiquitous nature of functional data, which are prevalent in applications across fields such as meteorology, biology, medicine and engineering. Empirical probability density functions (PDFs) can be viewed as constrained functional data objects that must integrate to one and be nonnegative. They show up in contexts such as yearly income distributions, zooplankton size structure in oceanography and in connectivity patterns in the brain, among others. While PDF data are certainly common in modern research, little attention has been given to EDA specifically for PDFs. In this paper, we extend several methods for EDA on functional data for PDFs and compare them on simulated data that exhibit different types of variation, designed to mimic that seen in real‐world applications. We then use our new methods to perform EDA on the breakthrough curves observed in gas transport simulations for underground fracture networks.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1974

An interdisciplinary study of the estuarine and coastal oceanography of Block Island Sound and adjacent New York coastal waters

The author has identified the following significant results. Photo-optical additive color quantitative measurements were made of ERTS-1 reprocessed positives of New York Bight and Block Island Sound. Regression of these data on almost simultaneous ship sample data of water's physical, chemical, biological, and optical properties showed that ERTS bands 5 and 6 can be used to predict the absolute value of the total number of particles and bands 4 and 5 to predict the relative extinction coefficient in New York Bight. Water masses and mixing patterns in Block Island Sound heretofore considered transient were found to be persistent phenomena requiring revision of existing mathematical and hydraulic models.

Yost, E. F.↗

DOE OSTI2025

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1996

(abstract) Seasonal Variability in Coastal Upwelling: A Comparison of Four Coastal Upwelling Sites from Space

Coastal upwelling of subsurface nutrient-rich water occurs along the eastern boundary of the ocean basins and leads to high primary production and fish catches. In this study satellite observations are used to compare the seasonal cycle in wind forcing and in the oceanic and biological response of the major coastal upwelling regions associated with the Canary, Benguela, California, and Humboldt Currents.

Current California Current Canary Current Benguela↗

NASA NTRS1984

The analysis of ocean optical data

A new oceanographic instrument to measure underwater optical, biological and physical properties simultaneously has been built and used extensively at sea. The Bio-Optical Profiling System (BOPS) was designed for the rapid acquisition of data to accommodate shipboard 'synoptic' sampling strategies, often in conjunction with concurrent aircraft and satellite sensors. The data rates and associated quantity of data from the BOPS are some orders of magnitude larger than those traditionally encountered in optical oceanography. The rapid acquisition of optical data in a wide range of environmental conditions requires new methodologies in ocean optical data analysis.

Smith, R. C.↗

NASA NTRS2001

Ocean Drifters Get the Facts

With the help of Small Business Innovation Research (SBIR) funding from NASA's Goddard Space Flight Center, of Greenbelt, Maryland, Clearwater Instrumentation, of Watertown, Massachusetts, created the ClearSat-Autonomous Drifting Ocean Station (ADOS). The multi-sensor array ocean drifting station was developed to support observations of Earth by NASA satellites. It is a low-cost device for gathering an assortment of data necessary to the integration of present and future satellite measurements of biological and physical processes. Clearwater Instrumentation developed its ADOS technology based on Goddard's Sea-viewing Wide Field-of-view Sensor (SeaWiFS) project, but on a scale that is practical for commercial use. ADOS is used for the in situ measuring of ocean surface layer properties such as ocean color, surface thermal structure, and surface winds. Thus far, multiple ADOS units have been sold to The Scripps Institution of Oceanography, where they are being applied in the field of academic science research. Fisheries can also benefit, because ADOS can locate prime cultivation conditions for this fast-growing industry.

Source record↗

NASA NTRS2018

Satellite Remote Sensing: Ocean Color

Satellite ocean color instruments routinely provide global, synoptic views of the Earth's marine biosphere. These spaceborne radiometers measure light exiting the top of the atmosphere at discrete wavelengths in the ultraviolet to shortwave infrared region of the spectrum. This includes measurements of the color of the ocean - information used to infer the contents of the sunlit upper ocean, such as concentrations of phytoplankton, suspended sediments, and dissolved organic carbon. Continuous marine biological, ecological, and biogeochemical data records from satellite ocean color instruments now span over twenty years. This time-series not only supports Earth system and climate research, but also ecosystem and watershed management activities, including detection of nuisance and harmful algal blooms.

Biosphere↗

NASA NTRS1975

In situ spectroradiometric calibration of EREP imagery and estuarine and coastal oceanography of Block Island sound and adjacent New York coastal waters

The author has identified the following significant results. The first part of the study resulted in photographic procedures for making multispectral positive images which greatly enhance the color differences in land detail using an additive color viewer. An additive color analysis of the geologic features near Willcox, Arizona using enhanced black and white multispectral positives allowed compilation of a significant number of unmapped geologic units which do not appear on geologic maps of the area. The second part demonstrated the feasibility of utilizing Skylab remote sensor data to monitor and manage the coastal environment by relating physical, chemical, and biological ship sampled data to S190A, S190B, and S192 image characteristics. Photographic reprocessing techniques were developed which greatly enhanced subtle low brightness water detail. Using these photographic contrast-stretch techniques, two water masses having an extinction coefficient difference of only 0.07 measured simultaneously with the acquisition of S190A data were readily differentiated.

Yost, E. F.↗

NASA NTRS2020

Exploring the human-nature dynamics of Hunga Tonga Hunga Ha'apai, Earth's newest landmass

This paper examines the human-nature dynamics of volcanic eruptions through a multidisciplinary exploration of the recently-formed Hunga Tonga Hunga Ha‘apai (HTHH) landmass in the Kingdom of Tonga. HTHH was formed in early 2015 in the Ha‘apai island group in southwestern Tonga. This landmass has persisted longer than expected, providing a rare opportunity to examine pathways of erosion and biological colonization, and offering a glimpse into the cultural dynamics of a continuously changing Polynesian seascape. In 2018 and 2019, a collaborative partnership between the Kingdomof Tonga, Sea Education Association (SEA), and the United States National Aeronautics and Space Administration (NASA) ran expeditions to HTHH to calibrate satellite observations via field, ship, and drone-based measurements. In accessing HTHH via SEA's sailing school vessel (SSV) the Robert C. Seamans, a team of scientists and students combined fieldwork in anthropology, oceanography, and physical volcanology to study micro- and macro-scale dynamics of this classical surtseyan eruption site. In this pathfinding paper, we discuss the value of involving students in the process of real-time scientific discovery with on-the-fly adaptive hypothesis testing; this collaborative project provided mutual benefit to initiatives in science and education by offering robust data collection, while expanding environmental and cultural literacy. Additionally, we integrate collaborative research on HTHH with ethnographic research to understand how this ever changing “sea of islands” or intimately interconnected island spaces impact social-cultural relations within Oceania. We emphasize the importance of such multidisciplinary research in understanding the complexity of human-nature relations in a rapidly changing world.

Emily B. Hite↗

NASA NTRS2023

Assessment of Oceanographic Conditions during the North Atlantic EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) Field Campaign

This manuscript presents an overview of NASA’s EXport Processes in the Ocean from Remote Sensing 2021 Field Campaign in the North Atlantic (EXPORTS NA) and provides quantitative and dynamical descriptions of the physical processes modulating water transformations during the study. A major programmatic goal was to conduct the sampling in a Lagrangian mode so that ocean ecological and biogeochemical changes can be observed independent from physical advective processes. To accomplish this goal, EXPORTS NA conducted a multi-ship, multi-asset field sampling program within a retentive, anticyclonic mode water eddy. Beneath depths of ∼100 m, Lagrangian sampling assets remained within the eddy core waters (ECWs) throughout the experiment, demonstrating that the ECWs within the mode water eddy were retentive. However, strong westerly winds from four storm events deepened the mixed layer (ML) of the surface core waters (SCWs) above the eddy’s mode water core by 25-40 m and exchanged some of the SCWs with surface waters outside of the eddy via Ekman transport. Estimates of flushing times ranged from 5-8 days, with surface exchange fractions ranging from 20-75% and were consistent with particle tracking advected by combined geostrophic and Ekman velocities. The relative contributions of horizontal and vertical advection on changes in ECW tracers depended on the horizontal and vertical gradients of that tracer. For example, horizontal advection played a large role in ECW salinity fluxes, while vertical entrainment played a larger role in the fluxes of nutrients into SCW ML. Each storm injected nutrients and low oxygen waters into the ML, after which the surface ocean ecosystem responded by reducing nutrient concentrations and increasing %O2 saturation levels. Overall, ECW values of chlorophyll and POC were the largest at the onset of the field program and decreased throughout the campaign. The analysis presented provides a physical oceanographic context for the many measurements made during the EXPORTS NA field campaign while illustrating the many challenges of conducting a production-flux experiment, even in a Lagrangian frame, and the inherent uncertainties of interpreting biological carbon pump observations that were collected in a Eulerian frame of reference.

oceanography↗

NASA NTRS1992

Atmospheric correction of AVIRIS data in ocean waters

Hyperspectral data offers unique capabilities for characterizing the ocean environment. The spectral characterization of the composition of ocean waters can be organized into biological and terrigenous components. Biological photosynthetic pigments in ocean waters have unique spectral ocean color signatures which can be associated with different biological species. Additionally, suspended sediment has different scattering coefficients which result in ocean color signatures. Measuring the spatial distributions of these components in the maritime environments provides important tools for understanding and monitoring the ocean environment. These tools have significant applications in pollution, carbon cycle, current and water mass detection, location of fronts and eddies, sewage discharge and fate etc. Ocean color was used from satellite for describing the spatial variability of chlorophyll, water clarity (K(sub 490)), suspended sediment concentration, currents etc. Additionally, with improved atmospheric correction methods, ocean color results produced global products of spectral water leaving radiance (L(sub W)). Ocean color results clearly indicated strong applications for characterizing the spatial and temporal variability of bio-optical oceanography. These studies were largely the results of advanced atmospheric correction techniques applied to multispectral imagery. The atmosphere contributes approximately 80 percent - 90 percent of the satellite received radiance in the blue-green portion of the spectrum. In deep ocean waters, maximum transmission of visible radiance is achieved at 490nm. Conversely, nearly all of the light is absorbed by the water at wavelengths greater than about 650nm and thus appears black. These spectral ocean properties are exploited by algorithms developed for the atmospheric correction used in satellite ocean color processing. The objective was to apply atmospheric correction techniques that were used for procesing satellite Coastal Zone Color Scanner (CZCS) data to AVIRIS data. Quantitative measures of L(sub W) from AVIRIS are compared with ship ground truth data and input into bio-optical models.

Terrie, Gregory↗

NASA NTRS2014

SWIM: A Semi-Analytical Ocean Color Inversion Algorithm for Optically Shallow Waters

Ocean color remote sensing provides synoptic-scale, near-daily observations of marine inherent optical properties (IOPs). Whilst contemporary ocean color algorithms are known to perform well in deep oceanic waters, they have difficulty operating in optically clear, shallow marine environments where light reflected from the seafloor contributes to the water-leaving radiance. The effect of benthic reflectance in optically shallow waters is known to adversely affect algorithms developed for optically deep waters [1, 2]. Whilst adapted versions of optically deep ocean color algorithms have been applied to optically shallow regions with reasonable success [3], there is presently no approach that directly corrects for bottom reflectance using existing knowledge of bathymetry and benthic albedo.To address the issue of optically shallow waters, we have developed a semi-analytical ocean color inversion algorithm: the Shallow Water Inversion Model (SWIM). SWIM uses existing bathymetry and a derived benthic albedo map to correct for bottom reflectance using the semi-analytical model of Lee et al [4]. The algorithm was incorporated into the NASA Ocean Biology Processing Groups L2GEN program and tested in optically shallow waters of the Great Barrier Reef, Australia. In-lieu of readily available in situ matchup data, we present a comparison between SWIM and two contemporary ocean color algorithms, the Generalized Inherent Optical Property Algorithm (GIOP) and the Quasi-Analytical Algorithm (QAA).

QAA↗

DOE OSTI2021

Interdisciplinary Research Collaborative Trains Students to See Through Turbulent Systems

Despite the availability of interdisciplinary academic training programs, the practice of environmental science is often hampered by a lack of convergence across diverse disciplines. This gap is particularly salient in settings characterized by complex environmental issues, such as multiple-use coastal ecosystems. In response, we developed and implemented a training, research, and communication framework to provide undergraduates with an authentic operative experience working at the interface of interdisciplinary science and public decision-making within a case study of marine renewable energy. In our program, students gained hands-on experience with the scientific process and learned how to make information relevant, useful, and accessible to diverse stakeholder groups. Application of this framework demonstrates that the process of integrating data from biological (visual and acoustic monitoring of fish and marine mammals), physical (hydrodynamics), and social (local ecological knowledge) sciences can provide a more complete understanding of complex and turbulent ecosystems for better informed decision-making. We offer several recommendations to facilitate the adaptation and implementation of our interdisciplinary framework to diverse research contexts, with a focus on interdisciplinary training for the next generation of marine scientists.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Adaptable Monitoring Package Development and Deployment: Lessons Learned for Integrated Instrumentation at Marine Energy Sites

Integrated instrumentation packages are an attractive option for environmental and ecological monitoring at marine energy sites, as they can support a range of sensors in a form factor compact enough for the operational constraints posed by energetic waves and currents. Here we present details of the architecture and performance for one such system—the Adaptable Monitoring Package—which supports active acoustic, passive acoustic, and optical sensing to quantify the physical environment and animal presence at marine energy sites. we describe cabled and autonomous deployments and contrast the relatively limited system capabilities in an autonomous operating mode with more expansive capabilities, including real-time data processing, afforded by shore power or in situ power harvesting from waves. Across these deployments, we describe sensor performance, outcomes for biological target classification algorithms using data from multibeam sonars and optical cameras, and the effectiveness of measures to limit biofouling and corrosion. On the basis of these experiences, we discuss the demonstrated requirements for integrated instrumentation, possible operational concepts for monitoring the environmental and ecological effects of marine energy converters using such systems, and the engineering trade-offs inherent in their development. Overall, we find that integrated instrumentation can provide powerful capabilities for observing rare events, managing the volume of data collected, and mitigating potential bias to marine animal behavior. These capabilities may be as relevant to the broader oceanographic community as they are to the emerging marine energy sector.

16 TIDAL AND WAVE POWER↗