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DOE OSTI2024

Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling

Abstract. Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales.

58 GEOSCIENCES↗

NASA NTRS1984

Geographic Distribution of Wetland Parameters: the Foundation of a Data Base

Few quantitative estimates exist concerning the large fluxes of various materials between wetlands and adjacent bodies of water and the atmosphere. Three areas research were identified which will aid in the quantitative assessment of wetland biogeochemical processes: (1) geographic distribution of wetland parameters, (2) the processes involved in wetland material fluxes, and (3) the extrapolation of local measurements of material fluxes and storage to large geographic areas.

Source record↗

NASA NTRS1986

Distribution and geochemistry of aerosols in the tropical North Atlantic troposphere - Relationship to Saharan dust

Estimates of global aerosol production suggest that mobilization of natural eolian material greatly exceeds anthropogenic-related emissions, and it appears that soil material transported from arid regions by wind might be mainly responsible for the distribution of certain clay materials in oceanic sediments. In connection with studies related to an investigation of these possibilities, the present paper provides a discussion of the aerosol spatial distribution and its water-soluble chemical composition in the tropical North Atlantic troposphere during the ABLE-Barbados mission. Particular attention is given to the composition of the water-soluble fraction, since its chemical reactivity is important with respect to various atmospheric and biogeochemical processes. On the basis of the obtained results, it is suggested that Saharan dust has also a significant impact on the aerosol chemistry over the tropical North Atlantic.

Talbot, R. W.↗

NASA NTRS1987

N-15/N-14 variations in Cretaceous Atlantic sedimentary sequences - Implication for past changes in marine nitrogen biogeochemistry

Unusually low delta N-15 found in early to middle Cretaceous beds rich in marine organic matter from two separate eastern Atlantic Ocean basins is reported. These findings constitute unambiguous evidence that the N contained in these strata is the end result of biogeochemical processes that differed substantially from those that operated on the N contained in intervening organic carbon-poor strata and younger marine sediments. The data indicate that the low N-15 relative abundance is the consequence of pelagic rather than postdepositional processes. Reduced ocean circulation, increased denitrification, and hence, reduced euphotic zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of the sedimentary N-15 depletion.

Rau, Greg H.↗

NASA NTRS1987

Biogeochemistry of dimethylsulfide in a seasonally stratified coastal salt pond

Dimethylsulfide (DMS) is the major volatile reduced organic sulfur compound in the water column of coastal Salt Pond, Cape Cod, MA. DMS concentration and vertical distributions vary seasonally in response to changing biogeochemical processes in the pond. When the pond is thermally stratified in summer, maximum DMS concentrations of up to 60 nmol/l were found in the oxygen-deficient metalimnion. DMS concentrations in the epilimnion (typically 5-10 nmol/l) were always an order of magnitude higher than in the hypolimnion (less than 0.2 nmol/l). The most likely precursor for DMS is algal dimethylsulfoniopropionate (DMSP), which showed vertical profiles similar to those of DMS. Laboratory experiments show that microorganisms in the pond, especially in the metalimnion, are capable of decomposing DMSP to DMS, while photosynthetic sulfur bacteria in the hypolimnion can consume DMS. Estimates of DMS production and consumption in Salt Pond have been made, considering production of DMS in the epilimnion and metalimnion and removal of DMS via gas exchange to the atmosphere, tidal exchange, and microbial consumption in the hypolimnion.

Wakeham, S. G.↗

NASA NTRS1987

The high resolution imaging spectrometer (HIRIS) for EOS

The HIRIS is designed to acquire images in 196 spectral bands simultaneously in the 0.4-2.5 micron wavelength region. HIRIS is a targeting rather than a continuous acquisition instrument and obtains high spatial and spectral resolution images in a 23 km swath with a 30 m GIFOV in vertical viewing. Gimbal pointing is proposed which will allow image acquisition at -30 + 60 deg down-track and + or - 25 deg cross-track. The raw data rate of the instrument is 393 Mbs. The high spectral resolution will make it possible to directly identify surficial materials such as rocks, soils, and suspended matter in water, and HIRIS opens up the possibility of studying biogeochemical processes in vegetation canopies. HIRIS will be used in conjunction with MODIS as a multistage sampling system.

Goetz, Alexander F. H.↗

NASA NTRS1989

Estimating biogeochemical fluxes across sagebrush-steppe landscapes with Thematic Mapper imagery

Thematic Mapper (TM) satellite data were coupled to an ecosystem simulation model to simulate variation in nitrogen mineralization over time and space in a sagebrush steppe. This system of data inputs and calculations provides estimates of ecosystem properties including rates of biogeochemical processes over extensive and complex landscapes, and under changing management and climatic conditions. The landscape surface was divided into three sagebrush ecosystem types plus one other class consisting of nonsagebrush vegetation. This classification presented a complex mosaic of ecosystem types that shifted markedly in composition from one end of the 933-sq km study area to the other. Annual N-mineralization rates ranged from 5 to 25 kg N/ha among the three sagebrush types. The most active type comprised 42 percent of the entire area but contributed 60 percent to the nitrogen mineralization throughout the landscape.

Reiners, W. A.↗

NASA NTRS1991

Examining several Southern Ocean data sets

Several datasets regarding the ocean in the Southern Hemisphere are combined into a coregistered format to analyze the use of the data in multidisciplinary research. The datasets are described detailing bathymetric climatological data on surface pigment concentration, eddy-kinetic-energy measurements, surface wind-stress magnitudes, sea-surface temperatures, surface densities, and nitrate concentrations. The data are combined in a common projection which facilitates the comparison of the fields, and the combined data yield insights regarding such phenomena as bottom topography, surface heat and moisture fluxes, and divergences in flow. The number of available datasets is shown to be good, and the data can be used to develop working hypotheses on the relationships between physical and biogeochemical processes.

Mcclain, Charles R.↗

NASA NTRS1992

Atmospheric sounding with the Lidar In-Space Technology Experiment (LITE)

The Lidar In-Space Technology Experiment (LITE) is being developed by NASA Langley Research Center for a series of flights on the Space Shuttle. Using a three-wavelength Nd:YAG laser and a 1-meter-diameter telescope, the system will be used to study clouds, aerosols in the troposphere and stratosphere, density and temperature perturbations of the stratosphere, and characteristics of the planetary boundary layer. Data collected from the system will be used in studies of atmospheric dynamics, meteorology, climate, the radiation budget, biogeochemical processes, and the hydrologic cycle. Additionally, the data will be used to develop retrieval techniques optimized for a spaceborne configuration and to develop requirements for future operational spaceborne lidar systems.

Winker, D. M.↗

NASA NTRS1992

Sulfate reduction and other sedimentary biogeochemistry in a northern New England salt marsh

Sulfate reduction rates, dissolved iron and sulfide concentrations, and titration alkalinity were measured in salt marsh soils along a transect that included areas inhabited by both the tall and short forms of Spartina alterniflora and by Spartina patens. Pore waters were collected with in situ 'sippers' to acquire temporal data from the same location without disturbing plant roots. During 1984, data collected at weekly intervals showed rapid temporal changes in belowground biogeochemical processes that coincided with changes in S. alterniflora physiology. Rates of SO4(-2) reduction increased fivefold (to greater than 2.5 micromol ml(sup -1)d(sup -1)) when plants began elongating aboveground yet decreased fourfold upon plant flowering. This rapid increase in rates of SO4(-2) reduction must have been fueled by dissolved organic matter released from roots only during active growth. Once plants flowered, the supply of oxidants to the soil decreased and sulfide and alkalinity concentrations increased despite decreases in SO4(-2) reduction and increases in SO4(-2):Cl(-) ratios. Sulfide concentrations were highest in soils inhabited by tallest plants. During 1985, S. alterniflora became infested with fly larvae (Chaetopsis apicalis John) and aboveground growth ceased in late June. This cessation was accompanied by decreased rates of SO4(-2) reduction similar to those noted during the previous year when flowering occurred. After the fly infestation, the pore-water chemical profiles of these soils resembled profiles of soils inhabited by the short form of S. alterniflora. The SO4(-2) reduction rates in S. patens soils are the first reported. Rates were similar to those in S. alterniflora except that they did not increase greatly when S. patens was elongating. Tidal and rainfall events produced desiccation-saturation cycles that altered redox conditions in the S. patens soils, resulting in rapid changes in the dissolution and precipitation of iron and in the magnitude and spatial distribution of SO4(-2) reduction.

Hines, Mark E.↗

NASA NTRS1995

Effect of the nonlinearity of the carbonate system on partial pressure of carbon dioxide in the oceans

Partial pressure of CO2 is a nonlinear function of several seawater properties. Due to the nonlinearity in this relationship, the partial pressure of a uniform ocean would be different from that of a nonuniform ocean with the same bulk seawater properties. Assuming uniformity of seawater properties at some temporal and spatial scales in carbon models leads to systematic errors in partial pressure of CO2. In this paper we evaluate the magnitude of these errors. We partition the Geochemical Ocean Sections Study and Transient Tracers in the Oceans data according to the horizontal structure of several box models from the literature. Our results suggest that assumption of uniformity at large scales leads to understanding of underestimation of global surface ocean partial pressure of CO2 by at least 3 - 12 microatm. Nonlinear effects also introduce systematic errors in the buffer factor estimated from bulk seawater properties. We find the standard deviation of partial pressure of CO2 to be an indicator of the magnitude of the nonlinear effects. We discuss the implications of these errors for some conclusions drawn from carbon models. Biogeochemical processes, such as mixing, gas exchange, or biological activity, influence the distribution of the seawater properties. A shift in spatial or temporal patterns of these processes can modify the nonuniformity of the seawater properties and thus alter the partial pressure of the surface waters, even if the mean intensities of the processes remain constant.

Trela, Piotr↗

NASA NTRS1998

SeaWiFS Postlaunch Technical Report Series: AMT-5 Cruise Report - Volume 2

This report documents the scientific activities on board the Royal Research Ship (RRS) James Clark Ross (JCR) during the fifth Atlantic Meridional Transect (AMT-5), 14 September to 17 October 1997. There are three objectives of the AMT Program. The first is to derive an improved understanding of the links between biogeochemical processes, biogenic gas exchange, air-sea interactions, and the effects on, and responses of, oceanic ecosystems to climate change. The second is to investigate the functional roles of biological particles and processes that influence ocean color in ecosystem dynamics. The Program relates directly to algorithm development and the validation of remotely-sensed observations of ocean color. Because the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) instrument achieved operational status during the cruise (on 18 September), AMT-5 was designated the SeaWiFS Atlantic Characterization Experiment (SeaACE) and was the only major research cruise involved in the validation of SeaWiFS data during the first 100 days of operations. The third objective involved the near-real time reporting of in situ light and pigment observations to the SeaWiFS Project, so the performance of the satellite sensor could be determined.

Hooker, Stanford B.↗

NASA NTRS1998

Laser Induced Fluorescence (LIF) as a Remote Sensing Tool: A Review

Vegetational changes are primary indicators of the present and future ecological status of the globe. These are changes which not only impact upon the primary productivity, but the total of the biogeochemical processes occurring on the planet. The impacts of global climatic and other environmental changes on vegetation must be monitored by some means in order to develop models which will allow us to predict long term effects. Large scale monitoring is now possible only with remote sensing systems, primarily passive reflectance, obtained by the use of satellite and aircraft platforms. However, passive reflectance techniques at this time are limited in their ability to detect subtle changes in the concentration and oxidation states of the many compounds involved in the light reactions of photosynthesis. Knowledge of these changes we consider to be fundamental in the remote assessment of both the rate and efficiency of photosynthesis and also the early detection of stress damage. The above factors pointed to the desirability of a sensing technique with the sensitivity and specificity necessary for detecting and quantifying those biological entities involved in photosynthesis. Another optical technique for vegetation monitoring is fluorescence. Previously, the lack of adequate excitation light sources and detector technologies have limited the use of fluorescence on intact plant leaves in the field. It is only recently with the advent of lasers with short pulse duration and advanced detector technologies that fluorescence measurements in the remote mode have become possible in the presence of ambient light.

Chappelle, E. W.↗

NASA NTRS1997

Biogeochemistry of DMS in Surface Waters

Dimethylsulfide (DMS) is important in influencing the formation of aerosols in the troposphere over large areas of the world's oceans. Understanding the dynamics of aerosols is important to understanding the earth's radiation balance. In evaluating the factors controlling DMS in the troposphere it is vital to understand the dynamics of DMS in the surface ocean. The biogeochemical processes controlling DMS concentration in seawater are myriad; modeling and theoretical estimation are problematic. At the beginning of this project we believed that we were on the verge of simplifying the ship-track measurement of DMS, and we proposed to deploy such a system to develop a database relating high frequency DMS measurements to biological and physicochemical and optical properties of surface water that can be quantified by remote sensing techniques. We designed a system to measure DMS concomitantly with other basic chemical and biological data in a flow-through system. The project was collaborative between Woods Hole Oceanographic Institution (WHOI) and Bermuda Biological Station for Research (BBSR). The project on which we are reporting was budgeted for only one year with a one year no-cost extension. At WHOI our effort was directed towards designing traps which would be used to concentrate DMS from seawater and allow storage for subsequent analysis. At that time, GC systems were too large for easy long-term deployment on a research vessel like R/V Weatherbird, so we focused on simplifying the shipboard sampling procedure. Initial studies of sample recovery with high levels of DMS suggested that Carboxen 1000, a relatively new carbon molecular sieve, could be used as a stable storage medium. The affinity of Carboxen for DMS is several orders of magnitude higher than gold wool (another adsorbent used for DMS collection) on a weight or volume basis. Furthermore, Carboxen's affinity for DMS is also far less susceptible to humidity than gold wool. Unfortunately, further experiments with low level DMS indicated that recovery of DMS after storage was not quantitative. The material has proven to be completely acceptable for short term storage and has been incorporated into a micro-GC system. Since working on this project, we have collaborated with RVM Scientific in Santa Barbara in the design and construction of small portable micro-GC's that will make feasible at-sea measurement in moving ships, making rapid gas analysis and quantification feasible in a ship-track mode. Throughout this period at both WHOI and BBSR, we continued to analyze field data to understand that patterns of time and space variability in DMS and the processes that govern it. These insights will be crucial to determining the specifications for our automated sampling program. The data from this, the longest continuous sampling program for ocean DMS, provided insights into year to year and short-term variability.

Dacey, J. W. H.↗

NASA NTRS1999

Seasonal Distributions of Global Ocean Chlorophyll and Nutrients: Analysis with a Coupled Ocean General Circulation Biogeochemical, and Radiative Model

A coupled general ocean circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. The model is driven by climatological meteorological conditions, cloud cover, and sea surface temperature. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability, and the interactions among three functional phytoplankton groups (diatoms, chorophytes, and picoplankton) and three nutrient groups (nitrate, ammonium, and silicate). Phytoplankton groups are initialized as homogeneous fields horizontally and vertically, and allowed to distribute themselves according to the prevailing conditions. Basin-scale model chlorophyll results are in very good agreement with CZCS pigments in virtually every global region. Seasonal variability observed in the CZCS is also well represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are also in good conformance, although occasional departures are apparent. Agreement of nitrate distributions with in situ data is even better, including seasonal dynamics, except for the equatorial Atlantic. The good agreement of the model with satellite and in situ data sources indicates that the model dynamics realistically simulate phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization, and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

Gregg, Watson W.↗

NASA NTRS2000

A Coupled Ocean General Circulation, Biogeochemical, and Radiative Model of the Global Oceans: Seasonal Distributions of Ocean Chlorophyll and Nutrients

A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability. and the interactions among three functional phytoplankton groups (diatoms. chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (greater than 1000 km) model chlorophyll results are in overall agreement with CZCS pigments in many global regions. Seasonal variability observed in the CZCS is also represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are generally in conformance although occasional departures are apparent. Model nitrate distributions agree with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicates that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent many aspects of the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

Gregg, Watson W.↗

NASA NTRS2000

Significant Findings: Seasonal Distributions of Global Ocean Chlorophyll and Nutrients With a Coupled Ocean General Circulation, Biogeochemical, and Radiative Model: Comparisons With Satellite and In Situ Data - 2

A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model were determined from the influences of circulation and turbulence dynamics, irradiance availability, and the interactions among three functional phytoplankton groups (diatoms, chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (>1000 km) model chlorophyll seasonal distributions were statistically positively correlated with CZCS chlorophyll in 10 of 12 major oceanographic regions, and with SeaWiFS in all 12. Notable disparities in magnitudes occurred, however, in the tropical Pacific, the spring/summer bloom in the Antarctic, autumn in the northern high latitudes, and during the southwest monsoon in the North Indian Ocean. Synoptic scale (100-1000 km) comparisons of satellite and in situ data exhibited broad agreement, although occasional departures were apparent. Model nitrate distributions agreed with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicated that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on basin and synoptic scales.

Gregg, Watson W.↗

NASA NTRS2000

The Northeast Monsoon's Impact on Mixing, Phytoplankton Biomass and Nutrient Cycling in the Arabian Sea

In the northern Arabian Sea, atmospheric conditions during the Northeast (winter) Monsoon lead to deep convective mixing. Due to the proximity of the permanent pyncnocline to the sea surface, this mixing does not penetrate below 125 m. However, a strong nitracline is also present and the deep convection results in significant nitrate flux into the surface waters. This leads to nitrate concentrations over the upper 100 m that exceed 4 micrometers toward the end of the Monsoon. During the 1994/1995 US JGOFS/Arabian Sea expedition, the mean areal gross primary production over two successive Northeast Monsoons was determined to be 1.35gC/sq m/d. Thus, despite the deep penetrative convection, high rates of primary productivity were maintained. An interdisciplinary model was developed to elucidate the biogeochemical processes involved in supporting the elevated productivity. This model consists of a 1-D mixed-layer model coupled to a set of equations that tracked phytoplankton growth and the concentration of the two major nutrients (nitrate and ammonium). Zooplankton grazing was parameterized by rate constant determined by shipboard experiments. Model boundary conditions consist of meteorological time-series measured from the surface buoy that was part of the ONR Arabian Sea Experiment's central mooring. Our numerical experiments show that elevated surface evaporation, and the associated salinization of the mixed layer, strongly contributes to the frequency and penetration depth of the observed convective mixing. Cooler surface temperatures, increased nitrate entrainment, reduced water column stratification, and lower near-surface chlorophyll a concentrations all result from this enhanced mixing. The model also captured a dependence on regenerated nitrogen observed in nutrient uptake experiments performed during the Northeast Monsoon. Our numerical experiments also indicate that variability in mean pycnocline depth causes up to a 25% reduction in areal chlorophyll a concentration. We hypothesize that such shifts in pycnocline depth may contribute to the interannual variations in primary production and surface chlorophyll a concentration that have been previously observed in this region.

Wiggert, J. D.↗