Posts Tagged 'biogeochemistry'

Rapid bioerosion in a tropical upwelling coral reef

Coral reefs persist in an accretion-erosion balance, which is critical for understanding the natural variability of sediment production, reef accretion, and their effects on the carbonate budget. Bioerosion (i.e. biodegradation of substrate) and encrustation (i.e. calcified overgrowth on substrate) influence the carbonate budget and the ecological functions of coral reefs, by substrate formation/consolidation/erosion, food availability and nutrient cycling. This study investigates settlement succession and carbonate budget change by bioeroding and encrusting calcifying organisms on experimentally deployed coral substrates (skeletal fragments of Stylophora pistillata branches). The substrates were deployed in a marginal coral reef located in the Gulf of Papagayo (Costa Rica, Eastern Tropical Pacific) for four months during the northern winter upwelling period (December 2013 to March 2014), and consecutively sampled after each month. Due to the upwelling environmental conditions within the Eastern Tropical Pacific, this region serves as a natural laboratory to study ecological processes such as bioerosion, which may reflect climate change scenarios. Time-series analyses showed a rapid settlement of bioeroders, particularly of lithophagine bivalves of the genus Lithophaga/Leiosolenus (Dillwyn, 1817), within the first two months of exposure. The observed enhanced calcium carbonate loss of coral substrate (>30%) may influence seawater carbon chemistry. This is evident by measurements of an elevated seawater pH (>8.2) and aragonite saturation state (Ωarag >3) at Matapalo Reef during the upwelling period, when compared to a previous upwelling event observed at a nearby site in distance to a coral reef (Marina Papagayo). Due to the resulting local carbonate buffer effect of the seawater, an influx of atmospheric CO2 into reef waters was observed. Substrates showed no secondary cements in thin-section analyses, despite constant seawater carbonate oversaturation (Ωarag >2.8) during the field experiment. Micro Computerized Tomography (μCT) scans and microcast-embeddings of the substrates revealed that the carbonate loss was primarily due to internal macrobioerosion and an increase in microbioerosion. This study emphasizes the interconnected effects of upwelling and carbonate bioerosion on the reef carbonate budget and the ecological turnovers of carbonate producers in tropical coral reefs under environmental change.

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An alternative to static climatologies: robust estimation of open ocean CO2 variables and nutrient concentrations from T, S, and O2 data using Bayesian neural networks

This work presents two new methods to estimate oceanic alkalinity (AT), dissolved inorganic carbon (CT), pH, and pCO2 from temperature, salinity, oxygen, and geolocation data. “CANYON-B” is a Bayesian neural network mapping that accurately reproduces GLODAPv2 bottle data and the biogeochemical relations contained therein. “CONTENT” combines and refines the four carbonate system variables to be consistent with carbonate chemistry. Both methods come with a robust uncertainty estimate that incorporates information from the local conditions. They are validated against independent GO-SHIP bottle and sensor data, and compare favorably to other state-of-the-art mapping methods. As “dynamic climatologies” they show comparable performance to classical climatologies on large scales but a much better representation on smaller scales (40–120 d, 500–1,500 km) compared to in situ data. The limits of these mappings are explored with pCO2 estimation in surface waters, i.e., at the edge of the domain with high intrinsic variability. In highly productive areas, there is a tendency for pCO2 overestimation due to decoupling of the O2 and C cycles by air-sea gas exchange, but global surface pCO2 estimates are unbiased compared to a monthly climatology. CANYON-B and CONTENT are highly useful as transfer functions between components of the ocean observing system (GO-SHIP repeat hydrography, BGC-Argo, underway observations) and permit the synergistic use of these highly complementary systems, both in spatial/temporal coverage and number of observations. Through easily and robotically-accessible observations they allow densification of more difficult-to-observe variables (e.g., 15 times denser AT and CT compared to direct measurements). At the same time, they give access to the complete carbonate system. This potential is demonstrated by an observation-based global analysis of the Revelle buffer factor, which shows a significant, high latitude-intensified increase between +0.1 and +0.4 units per decade. This shows the utility that such transfer functions with realistic uncertainty estimates provide to ocean biogeochemistry and global climate change research. In addition, CANYON-B provides robust and accurate estimates of nitrate, phosphate, and silicate. Matlab and R code are available at

Continue reading ‘An alternative to static climatologies: robust estimation of open ocean CO2 variables and nutrient concentrations from T, S, and O2 data using Bayesian neural networks’

Potential influence of ocean acidification on deep-sea Fe–Mn nodules and pelagic clays: an improved assessment by using artificial seawater

In order to assess the potential risk of metal release from deep-sea sediments in response to pH decrease in seawater, the mobility of elements from ferromanganese (Fe–Mn) nodules and pelagic clays was examined. Two geochemical reference samples (JMn-1 and JMS-2) were reacted with the pH-controlled artificial seawater (ASW) using a CO2-induced pH regulation system. Our experiments demonstrated that deep-sea sediments have weak buffer capacities by acid–base dissociation of surface hydroxyl groups on metal oxides/oxyhydroxides and silicate minerals. Element concentrations in the ASW were mainly controlled by elemental speciation in the solid phase and sorption–desorption reaction between the charged solid surface and ion species in the ASW. These results indicated that the release of heavy metals such as Mn, Cu, Zn and Cd should be taken into consideration when assessing the influence of ocean acidification on deep-sea environment.

Continue reading ‘Potential influence of ocean acidification on deep-sea Fe–Mn nodules and pelagic clays: an improved assessment by using artificial seawater’

Unnatural hypoxic regimes

Coastal hypoxia is increasing worldwide in response to human‐caused changes in global climate and biogeochemical cycles. In this paper, we view anthropogenic trends in coastal hypoxia through the lens of disturbance ecology and complexity theory. Complexity theory provides a framework for describing how estuaries and other coastal aquatic ecosystems respond to hypoxia by understanding feedback loops. Can it also be valuable in understanding how these ecosystems behave under shifting (i.e., unnatural) disturbance regimes? When viewed as a disturbance regime, shifts in the spatial (areal extent and fragmentation) and temporal (frequency and duration of events) characteristics of coastal hypoxia can be used to track changes into a non‐stationary future. Here, we consider options for increasing the resilience of coastal aquatic ecosystems to future, unnatural hypoxic regimes. To start, we define desirable states as ecosystems with long trophic chains and slow nutrient and carbon dynamics that produce many ecosystem services. We then work backward to describe circumstances dominated by positive feedbacks that can lead ecosystems toward an undesirable state (i.e., depauperate communities and chemically reduced sediments). Processes of degradation and recovery can be understood in the context of island biogeography whereby species diversity in habitats fragmented by hypoxia is determined by the balance between rapid local extinction, slow recolonization from the edges of hypoxic patches, and opportunities for ecological succession during between disturbance events. We review potential future changes associated with changing global climate and highlight ways to enhance coastal resilience. In addition to efforts to slow climate change, potential interventions include reduced nutrient and carbon loadings from rivers, restoration of aquatic vegetation, and managing for key species, including those that promote sediment oxygenation, that enhance water clarity, or that promote grazing on epiphytic algae through top‐down control.

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Impact of peatlands on carbon dioxide (CO2) emissions from the Rajang river and estuary, Malaysia

Tropical peat-draining rivers are known as potentially large sources of carbon dioxide (CO2) to the atmosphere due to high loads of carbon they receive from surrounding soils. However, not many seasonally resolved data are available, limiting our understanding of these systems. We report the first measurements of carbon dioxide partial pressure (pCO2) in the Rajang River and Estuary, the longest river in Malaysia. The Rajang River catchment is characterized by extensive peat deposits found in the delta region, and by human impact such as logging, land use and river damming. pCO2 averaged 2919±573µatm during the wet season and 2732±443µatm during the dry season. This is at the low end of reported values for Southeast Asian peat-draining rivers, but higher than values reported for Southeast Asian rivers that do not flow through peat deposits. However, dissolved inorganic carbon (DIC) and δ13C-DIC data did not suggest that peatlands were an important source of inorganic carbon to the river, with an average DIC concentration of 203.9±59.6µmolL−1 and an average δ13C-DIC of −8.06±1.90‰. Also, compared to rivers with similar peat coverage, the pCO2 in the Rajang was rather low. Thus, we suggest that peat coverage is, by itself, insufficient as sole predictor of CO2 emissions from peat-draining rivers, and that other factors, like the spatial distribution of peat in the catchment and pH, need to be considered as well. In the Rajang River, peatlands probably do not contribute much to the CO2 flux due to the proximity of the peatlands to the coast. CO2 fluxes to the atmosphere were 2.28±0.52gCm−2d−1 (wet season) and 2.45±0.45gCm−2d−1 (dry season), making the Rajang River a moderate source of carbon to the atmosphere.

Continue reading ‘Impact of peatlands on carbon dioxide (CO2) emissions from the Rajang river and estuary, Malaysia’

Effect of pH on transport and transformation of Cu-sediment complexes in mangrove systems


• Distribution of Cu in different binding phases of sediments changes with changing pH of the surrounding environment.
• Association of Cu organic matter increases at higher pH with sedimentary increases at higher pH.
• Cu-SOM complexes may disaggregate and increase mobility at higher pH.
• Increasing pH decreases lability of Cu complexes and increase mobility of Cu-complexes in sediments.
• Concentration Cu in residual phases remains unchanged under varying pH.



Impact of pH variation of overlying water column on transport and transformation of Cu-sediment complexes in the bottom mangrove sediments was investigated by using different metal extraction studies. The total Cu concentration in the studied sediments varied from ~64 ± 1 to 78 ± 2 mg·kg−1. The sequential extraction study showed that a major part of the sedimentary Cu (85–90% of the total sedimentary Cu) was present within the structure of the sediments with minimum mobility and bioavailability. The redistribution of non-residual Cu among the different binding phases of the sediments was observed at different pH. It was found that Cu shifted from the different non-residual binding phases to the organic binding phase of the sediments at higher pH. Partial leaching of sedimentary Cu-SOM complexes (with increasing stability as determined by kinetic extraction study) was observed at higher pH. This study infers that increase in pH of overlying water column may release Cu-SOM complexes and increase the mobility of Cu-complexes in mangrove systems.


Continue reading ‘Effect of pH on transport and transformation of Cu-sediment complexes in mangrove systems’

Biological regulation of carbonate chemistry during diatom growth under different concentrations of Ca2+ and Mg2


• A high biomass diatom growth could induce both Mg(OH)2 and CaCO3 precipitations.
• [Ca2+] and [Mg2+] could regulate diatom growth by determining carbon availability.
• Algae could overcome C limitation at the expense of lowering total alkalinity and pH.
• A possible biological regulation mechanism of carbonate chemistry is proposed.


Algal photosynthesis increases pH to a level that can induce CaCO3 and Mg(OH)2 precipitation. However, the roles of Mg2+ and Ca2+ in regulating the pH-carbonate system during algal growth are not well understood. We examined effects of different [Mg2+] (50 to 50,000 μM) under different [Ca2+] (500 to 10,000 μM) on pH, dissolved inorganic carbon (DIC) and total alkalinity (TA) during batch culture of the diatom Phaeodactylum tricornutum. The results showed that growth rates and biomass were higher when [Mg2+] increased under a fixed [Ca2+]. DIC and TA were almost depleted, decreasing from 1968 to ~50 μmol kg−1, and from 2171 to ~500 μmol kg−1, respectively. Paradoxically, higher [Mg2+] produced lower maximum pH, which could not be accounted for by DIC consumption. Our analysis reveals that this unexpected lower pH but larger decrease in TA was largely driven by Mg(OH)2 formation. A reduction in TA decreases pH, which stimulates algal carbon uptake by shifting carbonate species from CO32− to bio-available forms (CO2 and HCO3). The subsequent photosynthetic drawdown of DIC forces pH to rise again, which leads to more precipitation and again a decrease in TA. We built a conceptual model to explain this biological regulation, describing the dynamic feedback loop of diatom growth, DIC uptake, pH increase, mineral precipitation, TA decrease, pH reduction, and DIC uptake, which drives depletion of DIC and TA. This mechanism demonstrates that high-biomass algal growth can overcome carbon limitation in natural waters at the expense of lowering TA, particularly in eutrophic environments.

Continue reading ‘Biological regulation of carbonate chemistry during diatom growth under different concentrations of Ca2+ and Mg2’

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Ocean acidification in the IPCC AR5 WG II

OUP book