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DOE OSTI2015

The Ocean Sampling Day Consortium

In this study, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.

This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Chemical Insights into the Molecular Composition of Organic Aerosols in the Urban Region of Houston, Texas

Molecular functional groups, such as organosulfates (CHOS) and organonitrates (CHNO) are important tracers for field observations of secondary organic aerosols (SOA). While CHOS and CHNO are prevalent in the atmosphere, there is a lack of knowledge regarding daily and day- and night-time variations in these species in the urban atmosphere. Meteorological factors such as wind speed/direction, relative humidity (RH), and temperature can influence the formation of CHOS/CHNO. To investigate these trends, we utilized multimodal chemical imaging and advanced high resolution mass spectrometry techniques to acquire particle speciation and molecular formulas (MFs) associated with day and night sampling periods. Back trajectory analyses revealed the oceanic influence of southern wind airmasses in later June sampling periods with organic fractions <10%. Conversely, northern winds in early June sampling periods contributed to the episodic emergence of extremely low volatile organics (ELVOCs) and organic factions up to 41%. The observed unique MFs to June 3 (223 MFs) and to June 4 (144 MFs) were largely found to be of biogenic rather than anthropogenic origin. Finally, our findings reveal episodic prevalence and temporal distribution of SOA constituents across the urban region of Houston, Texas.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Diel Redox Cycle of Manganese in the Surface Arctic Ocean

Knowledge of the chemical speciation of particulate manganese (pMn) is important for understanding the biogeochemical cycling of Mn and other particle-reactive elements. Here, in this work, we present the synchrotron-based X-ray spectroscopy-derived average oxidation state (AOS) of pMn in the surface Arctic Ocean collected during the United States GEOTRACES Arctic cruise (GN01) in 2015. We show that the pMn AOS is <2.4 when sampled during the day and more than ~3.0 when sampled at night. We hypothesize that an active light-dependent redox cycle between dissolved Mn and particulate Mn(III/IV) exists during the day-night cycle in the surface Arctic Ocean, which occurs on the timescale of hours. The magnitude of observed pMn AOS is likely determined by the net effect of the length of the previous night and integrated light level before the end of pMn sampling.

58 GEOSCIENCES↗

DOE OSTI2018

Advances in the Recovery of Uranium from Seawater: Studies Under Real Ocean Conditions

The objective of this project was to move the testing of uranium adsorbents from the laboratory to the field. We were successfully able to test fibers in both a flume and ocean environment under varying conditions to quantify the adsorptive properties and uranium uptake of adsorbents under coastal ocean conditions. Through this testing we have identified numerous challenges to be overcome prior to large-scale deployment of these fibers This project began in Phase I with laboratory experiments examining the effects of flow rates and water filtration on the absorption of uranium to fibers in flowthrough columns. In this experiment we found that fibers adsorb most efficiently at a flow rate of 250 ml/min, on a per liter basis. However faster flow rates increase exposure volume and allowed for slightly greater total U absorption. Therefore a balance between current speeds that are too fast and potentially break down fibers and those that are slower will be important to consider, alongside bio-fouling and exposure time, when deciding which current regimes are best to place fibers in the ocean. Phase II examined biofouling, comparing exposure of fibers in filtered flume water to that in a coastal ocean environment. Results from the dock and flume parallel experiment indicate a strong effect of biofouling on the capacity of the adsorbent fibers to adsorb uranium towards the very end of the experiment. Dock and flume samples showed comparable adsorption rates with the flume maximum achieved at day 49 with an adsorbance of 3.4 g U/kg-ads while the dock maximum was reached at day 42 with an adsorbance of 2.7 g U/kg-ads. Biofouling mitigation techniques were also examined. A comparison of 5 m and 12 m samples showed less growth at 12 meters where there is less light as well as less growth on the copper cages, which are toxic to many marine organisms. Overall despite biofouling, particles and other elements present, the fibers adsorbed uranium up to 2.7 g U/kg-ads in our open water dock experiments. This is lower than the maximum achieved in the flume of 3.4 g U/kg-ads and much lower than rates observed with synthetic seawater in laboratory experiments. Phase III involved two parts: working at Woods Hole Oceanographic Institution (WHOI) we examined the feasibility of reusing fibers after ocean deployment. Fiber reuse is an important consideration for operational costs associated with deployment. At present our data implies that reuse after open ocean exposure may not be significantly more effective than a single long deployment of fibers. The second part of Phase III involved collaboration with A. Slocum and M. Haji at MIT to examine the effects of various enclosures for fibers. This also involved testing a rotating system, designed to be deployed as part of an offshore wind turbine.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2019

Stochastic Parameterization of Subgrid-Scale Velocity Enhancement of Sea Surface Fluxes

Abstract Subgrid-scale (SGS) velocity variations result in gridscale sea surface flux enhancements that must be parameterized in weather and climate models. Traditional parameterizations are deterministic in that they assign a unique value of the SGS velocity flux enhancement to any given configuration of the resolved state. In this study, we assess the statistics of SGS velocity flux enhancement over a range of averaging scales (as a proxy for varying model resolution) through systematic coarse-graining of a convection-permitting atmospheric model simulation over the Indian Ocean and west Pacific warm pool. Conditioning the statistics of the SGS velocity flux enhancement on 1) the fluxes associated with the resolved winds and 2) the precipitation rate, we find that the lack of a separation between “resolved” and “unresolved” scales results in a distribution of flux enhancements for each configuration of the resolved state. That is, the SGS velocity flux enhancement should be represented stochastically rather than deterministically. The spatial and temporal statistics of the SGS velocity flux enhancement are investigated by using basic descriptive statistics and through a fit to an anisotropic space–time covariance structure. Potential spatial inhomogeneities of the statistics of the SGS velocity flux enhancement are investigated through regional analysis, although because of the relatively short duration of the simulation (9 days) distinguishing true inhomogeneity from sampling variability is difficult. Perspectives for the implementation of such a stochastic parameterization in weather and climate models are discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Cloud condensation nuclei activity of internally mixed particle populations at a remote marine free troposphere site in the North Atlantic Ocean

Here, this study reports results from research conducted at the Observatory of Mount Pico (OMP), 2225 m above mean sea level on Pico Island in the Azores archipelago in June and July 2017. We investigated the chemical composition, mixing state, and cloud condensation nuclei (CCN) activities of long-range transported free tropospheric (FT) particles. FLEXible PARTicle Lagrangian particle dispersion model (FLEXPART) simulations reveal that most air masses that arrived at the OMP during the sampling period originated in North America and were highly aged (average plume age > 10 days). We probed size-resolved chemical composition, mixing state, and hygroscopicity parameter ($\mathcal{κ}$) of individual particles using computer-controlled scanning electron microscopy with an energy-dispersive X-ray spectrometer (CCSEM-EDX). Based on the estimated individual particle mass from elemental composition, we calculated the mixing state index, $χ$. During our study, FT particle populations were internally mixed ($χ$ of samples are between 53% and 87%), owing to the long atmospheric aging time. We used data from a miniature Cloud Condensation Nucleus Counter (miniCCNC) to derive the hygroscopicity parameter, $\mathcal{κ}$ CCNC . Combining $\mathcal{κ}$ CCNC and FLEXPART, we found that air masses recirculated above the North Atlantic Ocean with lower mean altitude had higher $\mathcal{κ}$ CCNC due to the higher contribution of sea salt particles. We used CCSEM-EDX and phase state measurements to predict single-particle $\mathcal{κ}$ ($\mathcal{κ}$ CCSEM-EDX ) values, which overlap with the lower range of $\mathcal{κ}$ CCNC measured below 0.15 % SS. Therefore, CCSEM-EDX measurements can be useful in predicting the lower bound of $\mathcal{κ}$, which can be used in climate models to predict CCN activities, especially in remote locations where online CCN measurements are unavailable.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

The Two-Column Aerosol Project: Phase I-Overview and impact of elevated aerosol layers on aerosol optical depth

The Two-Column Aerosol Project (TCAP), conducted from June 2012 through June 2013, was a unique study designed to provide a comprehensive data set that can be used to investigate a number of important climate science questions, including those related to aerosol mixing state and aerosol radiative forcing. The study was designed to sample the atmosphere between and within two atmospheric columns; one fixed near the coast of North America (over Cape Cod, MA) and a second moveable column over the Atlantic Ocean several hundred kilometers from the coast. The U.S. Department of Energy's (DOE) Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF) was deployed at the base of the Cape Cod column, and the ARM Aerial Facility was utilized for the summer and winter intensive observation periods. One important finding from TCAP is that four of six nearly cloud-free flight days had aerosol layers aloft in both the Cape Cod and maritime columns that were detected using the nadir pointing second-generation NASA high-spectral resolution lidar (HSRL-2). In addition, these layers contributed up to 60% of the total observed aerosol optical depth (AOD). Many of these layers were also intercepted by the aircraft configured for in situ sampling, and the aerosol in the layers was found to have increased amounts of biomass burning material and nitrate compared to aerosol found near the surface. Lastly, while there was a great deal of spatial and day-to-day variability in the aerosol chemical composition and optical properties, no systematic differences between the two columns were observed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 C and 1 2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

Onstott, T. C.↗

DOE OSTI2018

Historical separation and present-day structure of common dolphinfish (Coryphaena hippurus) populations in the Atlantic Ocean and Mediterranean Sea

Abstract The common dolphinfish (Coryphaena hippurus) is an epipelagic, mid-trophic level, highly migratory species distributed throughout the world’s tropical and subtropical oceans in waters greater than 20°C. Life-history variables, migratory behaviour, and genetic markers have been used to define major stocks in the central Atlantic Ocean and Mediterranean Sea. Here, we used the mitochondrial DNA gene NADH subunit 1 (688 bp) to test for differences between population groups. A total of 103 haplotypes were detected among 203 fish. Gene diversities in samples were large and similar among populations (mean h = 0.932; range 0.894–0.987), but nucleotide diversities varied widely among samples (range π = 0.004–0.034) and appear to reflect population histories. Principal component analysis revealed two large populations groups, and the analysis of molecular variation and pairwise values of ΦST resolved population structure within these groups. Populations in the eastern Atlantic and Mediterranean showed the largest amounts of divergence from one another (ΦCT = 0.331). Adult movement and biophysical barriers to larval dispersal may explain contemporary differences between stocks, but the divergent populations in the Mediterranean Sea are likely due to isolations by cold temperature barriers during Pleistocene glaciations. The geographically large stock groupings require international cooperation in the harvest management and conservation of local dolphinfish populations.

Maggio, Teresa↗

DOE OSTI2025

The Imprint of Southern Ocean Storms on Modeled Surface Chlorophyll, Their Drivers and Satellite Biases

Southern Ocean (SO) phytoplankton chlorophyll is highly variable on sub-seasonal time scales. Although the SO is the windiest ocean basin globally, it is not conclusively understood how storms impact SO phytoplankton dynamics. Much of our existing knowledge stems from satellites, but biases due to data gaps from cloud cover and low solar angles remain unquantified. Here, we use ocean–sea-ice simulations with the Community Earth System Model to quantify the climatological 1997–2018 imprint of storms on chlorophyll and phytoplankton dynamics in the ice-free SO. Additionally, by comparing the full-field model output to synthetic satellite observations, we quantify sampling biases in satellite-derived estimates. We find that both the sign and the magnitude of the average surface chlorophyll imprint vary substantially across storms but last for at least 4 days after the storm passing. Based on our analysis, more than one third of the storms explain the majority of local non-seasonal chlorophyll variability, but satellite-derived storm imprints are often too large in magnitude. On the day of the storm passing, changes in vertical mixing predominantly cause surface chlorophyll anomalies, and reduced light availability due to enhanced cloud cover outweighs the enhanced nutrient availability due to entrainment. Interestingly, storms imprint differently on total net primary production than on surface chlorophyll, demonstrating the difficulty to derive carbon-cycle impacts from a surface-chlorophyll assessment. With SO future storm activity projected to increase, complementing satellite observations with other observing technologies, for example, profiling floats, is necessary to better constrain how storms impact biological carbon cycling in the SO.

Nissen, Cara [University of Colorado, Boulder, CO ↗

DOE OSTI2016

Aboard the R/V Oceanus: Carbon Flux Explorers

Jim Bishop, senior scientist at Berkeley Lab and professor at UC Berkeley, is leading a project to deploy robotic floats that provide data on how microorganisms sequester carbon in the ocean. He recently led a research team on a 10-day voyage, funded by the National Science Foundation, to put the Carbon Flux Explorers to the test. Read more at http://oceanbots.lbl.gov (Video edited by Roxanne Makasdjian and Stephen McNally/UC Berkeley. Video shot by Jessica Kendall-Bar. Drone footage provided by Mark Booher.)

47 OTHER INSTRUMENTATION↗

DOE OSTI2017

Cross-polar transport and scavenging of Siberian aerosols containing black carbon during the 2012 ACCESS summer campaign

During the ACCESS airborne campaign in July 2012, extensive boreal forest fires resulted in significant aerosol transport to the Arctic. A 10-day episode combining intense biomass burning over Siberia and low-pressure systems over the Arctic Ocean resulted in efficient transport of plumes containing black carbon (BC) towards the Arctic, mostly in the upper troposphere (6–8 km). Here, a combination of in situ observations (DLR Falcon aircraft), satellite analysis and WRF-Chem simulations is used to understand the vertical and horizontal transport mechanisms of BC with a focus on the role of wet removal. Between the northwestern Norwegian coast and the Svalbard archipelago, the Falcon aircraft sampled plumes with enhanced CO concentrations up to 200 ppbv and BC mixing ratios up to 25 ng kg –1 . During transport to the Arctic region, a large fraction of BC particles are scavenged by two wet deposition processes, namely wet removal by large-scale precipitation and removal in wet convective updrafts, with both processes contributing almost equally to the total accumulated deposition of BC. Our results underline that applying a finer horizontal resolution (40 instead of 100 km) improves the model performance, as it significantly reduces the overestimation of BC levels observed at a coarser resolution in the mid-troposphere. According to the simulations at 40 km, the transport efficiency of BC (TE BC ) in biomass burning plumes was larger (60 %), because it was impacted by small accumulated precipitation along trajectory (1 mm). In contrast TE BC was small (< 30 %) and accumulated precipitation amounts were larger (5–10 mm) in plumes influenced by urban anthropogenic sources and flaring activities in northern Russia, resulting in transport to lower altitudes. TE BC due to large-scale precipitation is responsible for a sharp meridional gradient in the distribution of BC concentrations. Wet removal in cumulus clouds is the cause of modeled vertical gradient of TE BC , especially in the mid-latitudes, reflecting the distribution of convective precipitation, but is dominated in the Arctic region by the large-scale wet removal associated with the formation of stratocumulus clouds in the planetary boundary layer (PBL) that produce frequent drizzle.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2011

Underwater Application of Quantitative PCR on an Ocean Mooring

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Origin of 182 W Anomalies in Ocean Island Basalts

Ocean island basalts (OIB) show variable 182 W deficits that have been attributed to either early differentiation of the mantle or core-mantle interaction. However, 182 W variations may also reflect nucleosynthetic isotope heterogeneity inherited from Earth's building material, which would be evident from correlated 182 W and 183 W anomalies. Some datasets for OIB indeed show hints for such correlated variations, meaning that a nucleosynthetic origin of W isotope anomalies in OIB cannot be excluded. We report high-precision W isotope data for OIB from Samoa and Hawaii, which confirm previously reported 182 W deficits for these samples, but also demonstrate that none of these samples have resolvable 183 W anomalies. These data therefore rule out a nucleosynthetic origin of the 182 W deficits in OIB, which most likely reflect the entrainment of either core material or an overabundance of late-accreted materials within OIB mantle sources. If these processes occurred over Earth's history, they may have also been responsible for shifting the 182 W composition of the bulk mantle to its modern-day value. We also report Mo isotope data for some Hawaiian OIB, which reveal no resolved nucleosynthetic Mo isotopic anomalies. This is consistent with inheritance of 182 W deficits in OIB from the addition of either core or late-accreted material, but only if these materials have a non-carbonaceous (NC) meteorite-like heritage. As such, these data rule out significant contributions of carbonaceous chondrite (CC)-like materials to either Earth's core or late accretion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A population of free-living highland wild dogs in Indonesian Papua

A 10-day rapid assessment has confirmed a small population of indigenous wild-living dogs in the highlands of Papua Province, Indonesia. The goal of the assessment was to observe, census, assess health and reproductive status, and collect biological samples or other data for this understudied canid. Trail cameras and DNA hair traps were deployed and baited with scent attractants, and game calls were used to elicit vocal responses or lure the dogs within observation range. Adults and pups of both sexes as well as a den were documented in 149 photographs. DNA testing of scat samples confirmed a canid origin with a close relationship to other oceanic canids including NGSD (New Guinea Singing Dog) and dingoes.

Zoology↗

DOE OSTI2017

Methods for using argon-39 to age-date groundwater using ultra-low-background proportional counting

Argon-39 can be used as a tracer for age-dating glaciers, oceans, and more recently, groundwater. With a half-life of 269 years, 39Ar fills an intermediate age range gap (50-1,000 years) not currently covered by other common groundwater tracers. Therefore, adding this tracer to the data suite for groundwater studies provides an important tool for improving our understanding of groundwater systems. We present the methods employed for arriving at an age-date for a given sample of argon degassed from groundwater.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2017

Collaborative Research: Cloudiness transitions within shallow marine clouds near the Azores

Marine stratocumulus clouds are low, persistent, liquid phase clouds that cover large areas and play a significant role in moderating the climate by reflecting large quantities of incoming solar radiation. The deficiencies in simulating these clouds in global climate models are widely recognized. Much of the uncertainty arises from sub-grid scale variability in the cloud albedo that is not accurately parameterized in climate models. The Clouds, Aerosol and Precipitation in the Marine Boundary Layer (CAP–MBL) observational campaign and the ongoing ARM site measurements on Graciosa Island in the Azores aim to sample the Northeast Atlantic low cloud regime. These data represent, the longest continuous research quality cloud radar/lidar/radiometer/aerosol data set of open-ocean shallow marine clouds in existence. Data coverage from CAP–MBL and the series of cruises to the southeast Pacific culminating in VOCALS will both be of sufficient length to contrast the two low cloud regimes and explore the joint variability of clouds in response to several environmental factors implicated in cloudiness transitions. Our research seeks to better understand cloud system processes in an underexplored but climatologically important maritime region. Our primary goal is an improved physical understanding of low marine clouds on temporal scales of hours to days. It is well understood that aerosols, synoptic-scale forcing, surface fluxes, mesoscale dynamics, and cloud microphysics all play a role in cloudiness transitions. However, the relative importance of each mechanism as a function of different environmental conditions is unknown. To better understand cloud forcing and response, we are documenting the joint variability of observed environmental factors and associated cloud characteristics. In order to narrow the realm of likely parameter ranges, we assess the relative importance of parameter conditions based primarily on two criteria: how often the condition occurs (frequency) and to what degree varying that condition within its typically observed range affects cloud characteristics (magnitude of impact given the condition). In this manner we will be able to address the relative importance of individual factors within a multivariate range of environmental conditions. We will determine the relative roles of the thermodynamic, aerosol, and synoptic environmental factors on low cloud and drizzle formation and lifetime.

54 ENVIRONMENTAL SCIENCES↗