DOC :: Ocean Carbon & Biogeochemistry

Studying marine ecosystems and biogeochemical cycles in the face of environmental change

Archive for DOC

Coastal DOM database – CoastDOM v1

Posted by hbenway

· Wednesday, February 28th, 2024

We present the first edition of a global database (CoastDOM v1) and a resulting data manuscript, which compiles previously published and unpublished measurements of DOC, DON, and DOP in coastal waters, consisting of 62,338 (DOC), 20,356 (DON), and 13,533 (DOP) data points, respectively.

CoastDOM v1 includes observations of concentrations from all continents between 1978 and 2022. However, most data were collected in the Northern Hemisphere, with a clear gap in DOM measurements from the Southern Hemisphere.

This dataset will be useful for identifying global spatial and temporal patterns in DOM and will help facilitate the reuse of DOC, DON, and DOP data in studies aimed at better characterizing local biogeochemical processes; closing nutrient budgets; estimating carbon, nitrogen, and phosphorous pools; and establishing a baseline for modelling future changes in coastal waters.

The aim is to publish an updated version of the database periodically to determine global trends of DOM levels in coastal waters, and so if you have DOM data lying around, please submit it to Christian Lønborg (c.lonborg@ecos.au.dk).

CITATIONS

Lønborg et al. 2024. A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v1), Earth Syst. Sci. Data, 16, 1107–1119, https://doi.org/10.5194/essd-16-1107-2024

Lønborg et al. 2023.A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v.1). PANGAEA, https://doi.org/10.1594/PANGAEA.964012

Identifying the water mass composition of a sample has never been so easy!

Posted by mmaheigan

· Thursday, August 31st, 2023

When we collect seawater in any point of the ocean, we are collecting a mix of water masses from different origin that traveled until there keeping their salinity and temperature properties. The Atlantic Ocean is likely the most complex basin in term of water masses containing more than 15 in its depths. Some of them were “born” in the North Atlantic Ocean, others in the Southern Ocean, even in the Mediterranean Sea! And when we collect a seawater sample we can know which water masses are there, where they come from, what happened to each of them during their journey to us, what story can they tell us.

The variation of any non-conservative property (such as dissolved organic carbon or nutrients) in the deep open ocean depends on the mixing of those water masses and on the biogeochemical processes affecting it (such as heterotrophic respiration). But the effect of the water mass mixing is usually very high, so in order to study the biogeochemical processes, it is necessary to remove that effect.

On the other hand, estimating the contribution of the water masses composing a sample is useful to trace the distribution of each water mass identifying the depth of maximum water mass contribution or the depth-range where the water mass is dominant contributing > 50%. Ocean biogeochemists and microbiologists can get more out of their data estimating the impact of water mass mixing on the variability of any chemical (e.g. inorganic nutrients and dissolved organic carbon) or biological (e.g. prokaryotic heterotrophic abundance and production) property.

Knowing the contribution of each water mass to each sample was not an easy task and required expertise on the origin, circulation and mixing patterns of the water masses present in the study area. This could be even harder in very complex oceanic basin such as the deep Atlantic Ocean. The most commonly used methodology is the Optimum Multi-Parameter (OMP) analysis that was first applied by Tomczak in 1981. However, this methodology is time consuming and requires availability of a large set of quality-controlled chemical variables (e.g. nutrients, oxygen,..) together with a deep knowledge of the oceanography of the studied area. Those chemical variables are not always available or do not have the required quality by contrast to potential temperature and salinity that are high standard core variables in any cruise or database. In a recent research article, we applied multi-regression machine learning models to solve ocean water mass mixing. The models tested were trained using the solutions from OMP analyses previously applied to samples from cruises in the Atlantic Ocean. Extremely Randomized Trees algorithm yielded the highest score (R² = 0.9931; mse = 0.000227). The model allows solving the mixing of water masses in the Atlantic Ocean using potential temperature, salinity, latitude, longitude and depth. Potential temperature and salinity are the most commonly collected and curated variables in oceanography both from oceanographic cruises and autonomous vehicles (e.g. ARGO) avoiding the use of less commonly measured chemical variables which also require longer and time-consuming analyses of both the water samples and the data.

Figure 1. A16 section for the contribution of the water masses (A) AAIW5, (B) ENACW12, (C) AAIW3, (D) MW, (E) LSW, (F) ISOW, (G) CDW and (H) WSDW obtained with the Extremely Randomized Trees algorithm. Ocean Data View software (Schlitzer, 2015).

We also provide the code with instructions where any user can easily introduce the required variables (latitude, longitude, depth, temperature and salinity) of the chosen Atlantic samples and obtain the water mass proportion of each one in a fast and easy way. Actually, it would allow the user to obtain this information in real time during a cruise.

New research using other methods like OMP and its variants can be incorporated to the existing model increasing its accuracy and prediction capacity. Help us to improve the model and increase its spatial resolution!

Ocean biogeochemists and microbiologists can benefit from this tool even if they do not have a deep knowledge of the oceanography of the studied area. Identifying the water masses composition of a sample has never been so easy!

Author
Cristina Romera-Castillo (Instituto de Ciencias del Mar-CSIC, Barcelona, Spain)

Twitter: @crisrcas

Does dark carbon fixation supply labile DOC to the deep ocean?

Posted by mmaheigan

· Thursday, March 30th, 2023

Nitrifying microbes are the most abundant chemoautotrophs in the dark ocean. Though better known for their role in the nitrogen cycle, they also fix dissolved inorganic carbon (DIC) into biomass and thus play an important role in the global carbon cycle. The release of organic compounds by these microbes may represent an as-yet unaccounted for source of dissolved organic carbon (DOC) available to heterotrophic marine food webs. Quantifying how much DIC these microbes fix and release again into the ambient seawater is critical to a complete understanding of the carbon cycle in the deep ocean.

To address this knowledge gap, a recent study grew ten diverse nitrifier cultures and measured their cellular carbon (C) content, DIC fixation yields and DOC release rates. The results indicate that nitrifiers release between 5 and 15% of their recently fixed DIC as DOC (Figure 1). This would equate to global ocean fluxes of 0.006–0.02 Pg C yr⁻.

Figure 1. DOC release by ten different chemoautotrophic nitrifying (ammonia- and nitrite-oxidizing) microbes. The diversity of marine nitrifiers used in this study comprises all genera currently available as axenic cultures. Species and strain names are given for completeness.

Our results provide values for biogeochemical models of the global carbon cycle, and help to further constrain the relationship between C and N fluxes in the nitrification process. Elucidating the lability and fate of carbon released by nitrifiers will be the crucial next step to understand its implications for marine food-web functioning and the biological sequestration of carbon in the ocean.

Authors:
Barbara Bayer (University of California, Santa Barbara and University of Vienna)
Kelsey McBeain (University of California, Santa Barbara)
Craig A. Carlson (University of California, Santa Barbara)
Alyson E. Santoro (University of California, Santa Barbara)

How do coccolithophores survive the darkness?

Posted by mmaheigan

· Friday, April 1st, 2022

Coccolithophores have survived several major extinction events over geologic time. The most significant was the asteroid impact at the K/T boundary, followed by months of darkness. Additionally, coccolithophores regularly reside in the twilight zone, just beyond the reach of sunlight. A paper recently published in the New Phytologist addresses how these photosynthetic algae can persist and grow, albeit slowly, in darkness using osmotrophy.

The authors discovered that the osmotrophic uptake of certain types of dissolved organic carbon (DOC) can support survival in low light. They completed a 30-day darkness experiment to determine how the concentration of several DOC compounds affects growth. The coccolithophore species Cruciplacolithus neohelis growth rate increased with the increasing concentration of dissolved organic compounds. They also examined the kinetics of short-term uptake of radiolabeled DOC compounds and found that the uptake rate generally showed Michaelis-Menten-like saturation kinetics. All radiolabeled DOC compounds were incorporated into the POC fraction, but surprisingly also into the particulate inorganic carbon (PIC) fraction (i.e., calcite coccoliths).

These results suggest that osmotrophic uptake in coccolithophores may be significant enough to be included in carbon cycle models, especially if they can simultaneously take up a wide range of organic compounds. Surprisingly, we detected ¹⁴C-DOC in the PIC fraction after only 24 hours. This remarkably rapid incorporation is most likely due to the respiration of radiolabeled DOC into dissolved inorganic carbon (DIC), subsequently used by coccolithophores for calcification. These results have implications for the biological carbon pump and alkalinity pump paradigms, as we confirmed that both POC and PIC originate from DOC on short time scales.

Partitioning carbon export into particulate and dissolved pools from biogeochemical profiling float observations

Posted by mmaheigan

· Thursday, December 17th, 2020

Carbon export from the surface into the deep ocean via the biological pump is a significant sink for atmospheric carbon dioxide. The relative contributions of sinking particles—particulate organic carbon (POC) and dissolved organic carbon (DOC)—to the total export affect the efficiency of carbon export.

In a recent study published in Global Biogeochemical Cycles, the authors used measurements from biogeochemical profiling floats in the Northeast Pacific from 2009 to 2017 to estimate net community production (NCP), an analog for carbon export. In order to close three tracer budgets (nitrate, dissolved inorganic carbon, and total alkalinity), the authors combined these float measurements with data from the Ocean Station Papa mooring and recently developed algorithms for carbonate system parameters. By constraining end-member nutrient ratios of the POC and DOC produced, this multi-tracer approach was used to estimate regional NCP across multiple depth horizons throughout the annual cycle, partition NCP into the POC and DOC contributions, and calculate particulate inorganic carbon (PIC) production, a known ballast material for sinking particles (Figure 1). The authors also estimated POC attenuation with depth, POC export across deeper horizons, and in situ export efficiency via a particle backscatter-based approach.

With the advent of “fully-loaded” biogeochemical profiling floats equipped with nitrate, oxygen, pH and bio-optical sensors, this approach may be used to assess the magnitude and efficiency of carbon export in other ocean regions from a single platform, which will greatly reduce the risks and costs associated with traditional ship-based measurements, while broadening the spatiotemporal scales of observation.

Figure caption: Climatological mean NCP (blue line) over the entire study period (2009-2017); the POC portion of NCP (filled blue area), the DOC portion (white space) and PIC production rate (red line), in the mixed layer (left), and the euphotic zone (right). The numbers in parentheses are the integrated annual NCP rates for each curve and uncertainty reported was determined using a Monte Carlo approach.

Authors:
William Haskell (MBARI, now Mote Marine Laboratory)
Andrea Fassbender (MBARI, now PMEL)
Jacki Long (MBARI)
Joshua Plant (MBARI)

Will global change “stress out” ocean DOC cycling?

Posted by mmaheigan

· Tuesday, September 29th, 2020

The dissolved organic carbon (DOC) pool is vital for the functioning of marine ecosystems. DOC fuels marine food webs and is a cornerstone of the earth’s carbon cycle. As one of the largest pools of organic matter on the planet, disruptions to marine DOC cycling driven by climate and environmental global changes can impact air-sea CO2 exchange, with the added potential for feedbacks on Earth’s climate system.

Figure 1. Simplified view of major dissolved organic carbon (DOC) sources (black text) and sinks (yellow text) in the ocean.

Since DOC cycling involves multiple processes acting concurrently over a range of time and space scales, it is especially challenging to characterize and quantify the influence of global change. In a recent review paper published in Frontiers in Marine Science, the authors synthesize impacts of global change-related stressors on DOC cycling such as ocean warming, stratification, acidification, deoxygenation, glacial and sea ice melting, inflow from rivers, ocean circulation and upwelling, and atmospheric deposition. While ocean warming and acidification are projected to stimulate DOC production and degradation, in most regions, the outcomes for other key climate stressors are less clear, with much more regional variation. This synthesis helps advance our understanding of how global change will affect the DOC pool in the future ocean, but also highlights important research gaps that need to be explored. These gaps include for example a need for studies that allow to understand the adaptation of degradation/production pathways to global change stressors, and their cumulative impacts (e.g. temperature with acidification).

Authors:
C. Lønborg (Aarhus University)
C. Carreira (CESAM, Universidade de Aveiro)
Tim Jickells (University of East Anglia)
X.A. Álvarez-Salgado (CSIC, Instituto de Investigacións Mariñas)

An Important Biogeochemical Link between Organic and Inorganic Carbon Cycling: Contributions of Organic Alkalinity

Posted by mmaheigan

· Wednesday, April 8th, 2020

As a part of dissolved organic carbon (DOC), organic acid charge groups can contribute significantly to total alkalinity (TA) in natural waters. Such a contribution is termed as organic alkalinity (OrgAlk). Beyond being part of TA, OrgAlk represents an important biogeochemical linkage between organic and inorganic carbon cycling. In other words, the biogeochemical cycling of organic acid charge groups – i.e. their sources, sinks, and biogeochemical behaviors – directly impacts pH and carbonate speciation, which may ultimately influence air-water CO₂ exchange and inorganic carbon fluxes. However, the effects of OrgAlk is often ignored or treated as a calculation uncertainty in many aquatic CO₂ studies. How we treat and study OrgAlk may need a new paradigm under biogeochemical cycles.

Based on direct titration data of OrgAlk, the authors of a recent study conducted a comprehensive assessment of OrgAlk variability, sources, and characteristics in a sub-estuary of Waquoit Bay (Massachusetts). The sub-estuary is influenced by a salt marsh, groundwater input, and offshore water. Both the salt marsh and groundwater OrgAlk contributed up to 4.3% of the TA across all sampled seasons. Estuarine OrgAlk:DOC ratios varied across space and time, which suggests that their abundances are controlled by different biogeochemical processes. In addition, the study demonstrates the insufficiency of using a fixed proportion of DOC to account for OrgAlk, as well as the challenge of using measured pH, TA, and dissolved inorganic carbon (DIC) to estimate OrgAlk. The effects of OrgAlk in these waters are equivalent to a pH change of ~ 0.03 – 0.26, or a pCO₂ change of ~30–1600 matm. If extrapolating OrgAlk results to other coastal systems ranging from estuaries to continental shelves, OrgAlk would exert a strong control on both carbonate speciation and, ultimately, air-sea CO₂ fluxes. This study provides a new conceptual framework for cycling of OrgAlk species and associated links between DOC and DIC pools in coastal systems (Figure 1).

Figure caption: A conceptual model of organic alkalinity cycling in coastal systems. BioP and ChemP represent in-situ biological production and chemical production of organic acid charge groups, respectively. Alk denotes total alkalinity. Arrows with dashed lines indicate processes that were not studied in the present study. The values in the boxes of pH, pCO₂, and buffer capacity represent the magnitude of OrgAlk effects on pH, pCO₂, and buffer capacity in the range of OrgAlk% in TA observed in this study (0.9 – 4.3%).

Authors
Shuzhen Song (East China Normal University)
Zhaohui Aleck Wang (Woods Hole Oceanographic Institution)
Meagan Eagle Gonneea (U. S. Geological Survey)
Kevin D. Kroeger (U. S. Geological Survey)

Tiny, but effective: Gelatinous zooplankton and the ocean biological carbon pump

Posted by mmaheigan

· Wednesday, March 25th, 2020

Barely visible to the naked eye, gelatinous zooplankton play important roles in marine food webs. Cnidaria, Ctenophora, and Urochordata are omnipresent and provide important food sources for many more highly developed marine organisms. These small, nearly transparent organisms also transport large quantities of “jelly-carbon” from the upper ocean to depth. A recent study in Global Biogeochemical Cycles focused on quantifying the gelatinous zooplankton contribution to the ocean carbon cycle.

Figure 1. Processes and pathways or gelatinous carbon transfer to the deep ocean.

Using >90,000 data points (1934 to 2011) from the Jellyfish Database Initiative (JeDI), the authors compiled global estimates of jellyfish biomass, production, vertical migration, and jelly carbon transfer efficiency. Despite their small biomass relative to the total mass of organisms living in the upper ocean, their rapid, highly efficient sinking makes them a globally significant source of organic carbon for deep-ocean ecosystems, with 43-48% of their upper ocean production reaching 2000 m, which translates into 0.016 Pg C yr^-1.

Figure 2. Mass deposition event of jellyfish at 3500 m in the Arabian Sea (Billett et al. 2006).

Sediment trap data have suggested that carbon transport associated with large, episodic gelatinous blooms in localized open ocean and continental shelf regions could often exceed phytodetrital sources, in particular instances. These mass deposition events and their contributions to deep carbon export must be taken into account in models to better characterize marine ecosystems and reduce uncertainties in our understanding of the ocean’s role in the global carbon cycle.

Links:

Jellyfish Database Initiative http://jedi.nceas.ucsb.edu, http://jedi.nceas.ucsb.edu-dmo.org/dataset/526852 )

Authors:
Mario Lebrato (Christian‐Albrechts‐University Kiel and Bazaruto Center for Scientific Studies, Mozambique)
Markus Pahlow (GEOMAR)
Jessica R. Frost (South Florida Water Management District)
Marie Küter (Christian‐Albrechts‐University Kiel)
Pedro de Jesus Mendes (Marine and Environmental Scientific and Technological Solutions, Germany)
Juan‐Carlos Molinero (GEOMAR)
Andreas Oschlies (GEOMAR)

Unexpected DOC additions in the deep Atlantic

Posted by mmaheigan

· Tuesday, January 7th, 2020

Oceanic dissolved organic carbon (DOC) ultimately exchanges with atmospheric CO₂ and thus represents an important carbon source/sink with consequence for climate. Most of the DOC is recalcitrant to microbial degradation, with some fractions surviving for thousands of years. Therefore, DOC in the deep ocean was thought to be stable or to decrease slowly over decades to centuries due to biotic and abiotic sinks. However, a study published in Global Biogeochemical Cycles shows that there are some zones of the deep Atlantic Ocean where recalcitrant DOC experiences net production. Using data from oceanographic cruises across the Atlantic Ocean, the authors first identified the major water masses in the basin and the percentage of each in every sample taken for DOC analysis. The study revealed net additions of 27 million tons of dissolved organic carbon per year in the deep South Atlantic. On the other hand, the North Atlantic serves as a net sink, removing 298 million tons of carbon annually. DOC production observed in the deep Atlantic is probably due to the sinking particles that solubilize into DOC, since DOC enrichment was most evident at latitudes characterized as elevated productivity divergence zones.

Figure 1. Water masses along GO-SHIP line A16 (colored dots) and recalcitrant DOC variations due to biogeochemical processes (black dots within each water mass) in the deep Atlantic Ocean. Water mass domains are defined as the set of samples with the corresponding water mass proportion ≥50%. Recalcitrant DOC latitudinal variations per water stratum due to biogeochemical processes (ΔDOC) is in μmol kg^-1. Numbers on the plots are DOC values for the corresponding dots. Scales (not shown) are the same for all the plots, from -4 to 6 μmol kg^-1. Positive (negative) ΔDOC indicates values higher (lower) than the average DOC calculated for each water mass using an optimum multiparameter (OMP) analysis. DOC = dissolved organic carbon. AAIW = Antarctic Intermediate Water; UNADW = upper North Atlantic Deep Water; ISOW = Iceland Scotland Overflow Water; CDW = Circumpolar Deep Water; WSDW = Weddell Sea Deep Water. Figure created with Ocean Data View (Schlitzer, 2015).

Considering that the net DOC production over the entire Atlantic basin euphotic zone is 0.70–0.75 Pg C year^-1, the authors estimated that 30–39% of that DOC is consumed in the deep Atlantic subsequent to its export by overturning circulation. The upper North Atlantic Deep Water (UNADW) acts as the primary sink, accounting for 66% of the recalcitrant DOC removal in the North Atlantic. Conversely, the Antarctic Intermediate Water (AAIW) is the primary recipient, with 45% of recalcitrant DOC production in the South Atlantic, closely followed by the old UNADW that gains 44% of the recalcitrant DOC in the southern basin.

The Atlantic works as a mosaic of water masses, where both removal and addition of recalcitrant DOC occurs, with the dominant term dependent on the origin, temperature, age and depth of the water masses. The production of recalcitrant DOC in the deep ocean should be considered in biogeochemical models dealing with the carbon cycle and climate.

Authors:
C. Romera-Castillo and J. L. Pelegrí (Instituto de Ciencias del Mar, CSIC, Spain)
M. Álvarez (Instituto Español de Oceanografía, Spain)
D. A. Hansell (University of Miami, USA)
X. A. Álvarez-Salgado (Instituto de Investigaciones Marinas, CSIC, Spain)

Estimating the large-scale biological pump: Do eddies matter?

Posted by mmaheigan

· Wednesday, December 4th, 2019

One factor that limits our capacity to quantify the ocean biological carbon pump is uncertainty associated with the physical injection of particulate (POC) and dissolved (DOC) organic carbon to the ocean interior. It is challenging to integrate the effects of these pumps, which operate at small spatial (<100 km) and temporal (<1 month) scales. Previous observational and fine-scale modeling studies have thus far been unable to quantify these small-scale effects. In a recent study published in Global Biogeochemical Cycles, authors explored the influence of these physical carbon pumps relative to sinking (gravity-driven) particles on annual and regional scales using a high-resolution (2 km) biophysical model of the North Atlantic that simulates intense eddy-driven subduction hotspots that are consistent with observations.

Figure 1: North Atlantic idealized double gyre ocean biophysical model. Top: Sea surface temperature, surface chlorophyll and mixed-layer depth during the spring bloom (March 21). Bottom: total export of organic carbon (POC+DOC) at 100 and individual contributions from the gravitational (particle sinking) and subduction (mixing, eddy advection and Ekman pumping) pumps for one day during the spring bloom (March 21) and averaged annually. Physical subduction hotspots visible on the daily export contribute little to the annual export due to strong compensation of upward and downward motions.

The authors showed that eddy dynamics can transport carbon below the mixed-layer (500-1000 m depth), but this mechanism contributes little (<5%) to annual export at the basin scale due to strong compensation between upward and downward fluxes (Figure 1). Additionally, the authors evidenced that small-scale mixing events intermittently export large amounts of suspended DOC and POC.

These results underscore the need to expand the traditional view of the mixed-layer carbon pump (wintertime export of DOC) to include downward mixing of POC associated with short-lived springtime mixing events, as well as eddy-driven subduction, which can contribute to longer-term ocean carbon storage. High-resolution measurements are needed to validate these model results and constrain the magnitude of the compensation between upward and downward carbon transport by small-scale physical processes.

Authors:
Laure Resplandy (Princeton University)
Marina Lévy (Sorbonne Université)
Dennis J. McGillicuddy Jr. (WHOI)

Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.

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