Posts Tagged 'biogeochemistry'

Assessing the effects of ocean warming and acidification on the seagrass Thalassia hemprichii

Seagrass beds serve as important carbon sinks, and it is thought that increasing the quantity and quality of such sinks could help to slow the rate of global climate change. Therefore, it will be important to (1) gain a better understanding of seagrass bed metabolism and (2) document how these high-productivity ecosystems are impacted by climate change-associated factors, such as ocean acidification (OA) and ocean warming (OW). A mesocosm-based approach was taken herein in which a tropical, Western Pacific seagrass species Thalassia hemprichii was cultured under either control or OA-simulating conditions; the temperature was gradually increased from 25 to 31 °C for both CO2 enrichment treatments, and it was hypothesized that this species would respond positively to OA and elevated temperature. After 12 weeks of exposure, OA (~1200 ppm) led to (1) increases in underground biomass and root C:N ratios and (2) decreases in root nitrogen content. Rising temperatures (25 to 31 °C) increased the maximum quantum yield of photosystem II (Fv:Fm), productivity, leaf growth rate, decomposition rate, and carbon sequestration, but decreased the rate of shoot density increase and the carbon content of the leaves; this indicates that warming alone does not increase the short-term carbon sink capacity of this seagrass species. Under high CO2 and the highest temperature employed (31 °C), this seagrass demonstrated its highest productivity, Fv:Fm, leaf growth rate, and carbon sequestration. Collectively, then, it appears that high CO2 levels offset the negative effects of high temperature on this seagrass species. Whether this pattern is maintained at temperatures that actually induce marked seagrass stress (likely beginning at 33–34 °C in Southern Taiwan) should be the focus of future research.

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Enhanced silica export in a future ocean triggers global diatom decline

Diatoms account for up to 40% of marine primary production and require silicic acid to grow and build their opal shell3. On the physiological and ecological level, diatoms are thought to be resistant to, or even benefit from, ocean acidification. Yet, global-scale responses and implications for biogeochemical cycles in the future ocean remain largely unknown. Here we conducted five in situ mesocosm experiments with natural plankton communities in different biomes and find that ocean acidification increases the elemental ratio of silicon (Si) to nitrogen (N) of sinking biogenic matter by 17 ± 6 per cent under pCO2 conditions projected for the year 2100. This shift in Si:N seems to be caused by slower chemical dissolution of silica at decreasing seawater pH. We test this finding with global sediment trap data, which confirm a widespread influence of pH on Si:N in the oceanic water column. Earth system model simulations show that a future pH-driven decrease in silica dissolution of sinking material reduces the availability of silicic acid in the surface ocean, triggering a global decline of diatoms by 13–26 per cent due to ocean acidification by the year 2200. This outcome contrasts sharply with the conclusions of previous experimental studies, thereby illustrating how our current understanding of biological impacts of ocean change can be considerably altered at the global scale through unexpected feedback mechanisms in the Earth system.

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Sinking diatoms trap silicon in deep seawater of acidified oceans

The seas are acidifying as a result of carbon dioxide emissions. It now emerges that this will alter the solubility of the shells of marine organisms called diatoms — and thereby change the distribution of nutrients and plankton in the ocean.

The ecologically dominant phytoplankton in much of the ocean are a group of unicellular organisms known as diatoms. Writing in Nature, Taucher et al. present a study that uses a combination of experimental, observational and modelling approaches to examine how the diatom-driven effects of ocean acidification — a consequence of rising carbon dioxide concentrations in seawater — will affect biogeochemical cycles. The separate lines of evidence suggest that ocean acidification will have far-reaching effects on the export of elements to the deep ocean.

Diatoms are highly efficient at converting dissolved CO2 into organic carbon through photosynthesis, whereupon this organic carbon becomes incorporated into particles that sink rapidly to the deep ocean. Diatoms therefore serve as primary engines of a ‘biological pump’ that exports carbon to the deep ocean for sequestration. Each diatom cell is enclosed in a shell of silica (SiO2, where Si is silicon), and the solubility of the silicon in this biomineral is pH-sensitive — it becomes less soluble as seawater acidity rises. Although these features of diatoms are familiar to marine scientists, their combined implications for future biogeochemical cycles in the context of ocean acidification had not been explored.

Enter Taucher and colleagues. They carried out a series of five experiments in various parts of the ocean in which natural phytoplankton communities were grown in large enclosures (with volumes of 35–75 cubic metres) known as mesocosms, which simulated future ocean acidification. When the authors measured the elemental composition of the diatom-derived debris at the bottom of the mesocosms, they observed much higher ratios of silicon to nitrogen than the ratios of particles suspended near the surface. This suggested that, at low seawater pH, diatom silica shells were dissolving much more slowly than nitrogen-containing compounds in the same sinking material. In other words, silicon was being exported from the surface to deeper waters preferentially to nitrogen. The authors validated this finding using records of silicon-to-nitrogen ratios in sinking biological detritus in the open ocean, measured as a function of seawater pH, and obtained from particle-collecting sediment traps deployed by research vessels.

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Dimethylsulfoniopropionate (DMSP) and dimethyl sulfide (DMS) dynamics in the surface ocean

Dimethyl sulfide (DMS) is a trace gas produced in the ocean that plays an important role in climate and contributes to the Earths energy balance. DMS is a product of the enzymatic cleavage of dimethyl sulfoniopropionate (DMSP), which is produced by certain phytoplankton species and bacteria. Processes within the DMS/P cycles in the surface ocean are complex and vary with time and space. In the sea surface microlayer (SML), which is the interface between the ocean and the atmosphere, DMS concentration may be altered relative to subsurface water (SSW), by elevated biological activity, light intensity, and gas exchange. The aim of this thesis is to determine the importance of the SML in DMS/P dynamics and air-sea exchange by developing a more robust technique for SML sampling to better understand the dynamics of DMSP and DMS, and comparing their dynamics in the SML and SSW in coastal waters and the open ocean. In addition, the impact of warming and ocean acidification on DMS/P dynamics is investigated to determine how they will be impacted by future climate change.

To characterize DMS dynamics in the SML, a more effective method for sampling trace gases in the SML was developed (Chapter 2). The method is reliant on diffusion through a gas-permeable tube due to the concentration gradient. The floating tube was tested and calibrated under semi-controlled conditions using coastal water, where its reproducibility, accuracy and effectiveness were established. The potential benefits of this new technique for sampling trace gases in the SML include reduced loss of DMS to air. The higher reproducibility and accuracy compared to other techniques confirmed the potential of the floating tube technique for trace gas measurement in the SML.

The method developed in Chapter 2 was applied in sampling of DMS in the SML along a coastal-open ocean gradient (Chapter 3), and in various water masses of the open ocean (Chapter 4). In both chapters, DMSP and DMS dynamics were related to biological, biogeochemical, and physical properties of the SML and SSW. Sampling was conducted over 3 months at three different stations with different degrees of coastal and open water influence around Wellington, New Zealand in Chapter 3. DMSP was significantly enriched in the SML in most sampling events and DMSP and DMS enrichments were influenced by biological production and bacterial consumption. Overall, there was no temporal trends or coastal-offshore gradient in DMS or related biogeochemical variables in the SML. However, DMS concentration, and also DMS to DMSP ratio, were significantly correlated with solar radiation indicating a role for light as a determinant of DMSP and DMS in the SML. In open ocean waters around the Chatham Rise, east of New Zealand, the SML and SSW in water masses of different phytoplankton composition and biomass were sampled (Chapter 4). There was no chlorophyll a enrichment in the SML, and bacterial and DMSP enrichment were only apparent at one station, despite sampling within a phytoplankton bloom. Furthermore, there were no relationships between DMSP and phytoplankton biomass or community composition in the SML, although DMSP was negatively correlated with PAR. DMS was only significantly enriched in the SML at one station. DMS and DMSP concentrations were correlated in both SML and SSW, with the differing slopes attributed to DMS loss in the SML. Daily deck incubations were carried out to quantify DMSP and DMS processes in the SML, including the net effect of light on DMS/P, bacterial consumption of DMS/P and DMS production, and DMS air-sea flux. Air-sea flux was the main pathway with a DMS flux of 1.0-11.0 µmol m-2 d-1 that concurs with climatological predictions for the region. Excluding air-sea emission, biological DMS production was the dominant process in the SML relative to biological consumption and the net effect of light. SML DMS yield was not significantly different to that in the SSW, and consequently processes within the SML do not significantly affect regional DMS emissions.

The impact of ocean acidification and warming on DMSP and DMS concentrations was established for New Zealand coastal waters. Four mesocosm experiments, in which temperature and pH were manipulated to values projected for the years 2100 and 2150, were carried out over three years with the initial phytoplankton community differing in composition and bloom status (Chapter 6:). Temporal changes in DMSP and DMS were established and linked to changes in community composition and biogeochemistry. Results indicate that future warming may have greater influence on DMS production than ocean acidification. The observed reduction in DMSP at warmer temperatures was associated with changes in phytoplankton community, and in particular with a decrease in small flagellates. As nutrient availability also influenced the response this should also be considered in models of future DMS. Although DMS concentration decreased under future conditions of ocean acidification and higher temperature, this decrease was not as significant as reported by other studies.

The results in this thesis contribute to a better understanding of DMSP and DMS dynamics in the surface ocean. The floating tube method developed to sample DMS in the SML, will permit the study of DMS in the SML in various oceanic regions with improved accuracy. This technique may also have potential for measuring other trace gases in the SML. Application of this technique in coastal and open ocean waters demonstrated differences in DMS dynamics in the SML between these regions. DMS enrichment in the SML was rarely found, and DMS enrichment does not affect DMS air-sea flux significantly. Biological and biogeochemical variables and DMS/P process rates need to be established to further understanding of DMS/P dynamics in the SML and near surface water. Finally, results suggest that impacts of future climate change on DMS emissions may not be as significant as reported elsewhere, but that phytoplankton community composition plays a role and must be considered in future scenario models to better predict future DMS emissions. 

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Influence of climate on seawater quality and green mussel production

This study aimed to investigate the relationships between atmospheric parameters, seawater quality and green mussel production which were cultured in pond, estuary and coastal areas. Seawater and mussel samples were collected from mussel farms in the inner Gulf of Thailand from January to December 2019. Climate data were obtained from the Thai Meteorological Department. The correlations between selected atmospheric and seawater parameters were developed using linear and non-linear models. The influence of seawater quality on mussel production was evaluated using principal component analysis and stepwise multiple linear regression. The effects of atmospheric variation on green mussel productivity were simulated. The results showed that high air temperature and rainfall caused an increase in seawater temperature and a decrease in salinity, respectively. It was observed that the most influential factors affecting mussel production were nutrients and dissolved oxygen in ponds, temperature and salinity in estuaries, and nutrients and pH in coastal areas. The simulation indicated that mussel production can deteriorate when air temperature reaches 34°C and rainfall is higher than 200 mm per month. Our results suggest that under climate change events, locations with less riverine influence can provide higher mussel productivity. These results can be used as a guideline for farmers during a climate change event.

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Monsoon-driven biogeochemical dynamics in an equatorial shelf sea: time-series observations in the Singapore Strait


  • Multi-year time-series data show strong monsoonal seasonality.
  • River input from regional peatlands is a major driver of seasonal variation.
  • Light limitation likely modulates phytoplankton response to nutrient input.
  • Lower buffer capacity from peatland carbon remineralisation raises diel pH variation.


Coastal tropical waters are experiencing rapid increases in anthropogenic pressures, yet coastal biogeochemical dynamics in the tropics are poorly studied. We present a multi-year biogeochemical time series from the Singapore Strait in Southeast Asia’s Sunda Shelf Sea. Despite being highly urbanised and a major shipping port, the strait harbours numerous biologically diverse habitats and is a valuable system for understanding how tropical marine ecosystems respond to anthropogenic pressures. We observed strong seasonality driven by the semi-annual reversal of ocean currents: dissolved inorganic nitrogen (DIN) and phosphorus varied from ≤0.05 μmol l−1 during the intermonsoons to ≥4 μmol l−1 and ≥0.25 μmol l−1, respectively, during the southwest monsoon. Si(OH)4 exceeded DIN year-round. Based on nutrient concentrations, their relationships to salinity and coloured dissolved organic matter, and the isotopic composition of NOx, we infer that terrestrial input from peatlands is the main nutrient source. This input delivered dissolved organic carbon (DOC) and nitrogen, but was notably depleted in dissolved organic phosphorus. In contrast, particulate organic matter showed little seasonality, and the δ13C of particulate organic carbon (−21.0 ± 1.5‰) is consistent with a primarily autochthonous origin. The seasonal pattern of the diel changes in dissolved O2 suggests that light availability controls primary productivity more than nutrient concentrations. However, diel changes in pH were greater during the southwest monsoon, when remineralisation of terrestrial DOC lowers the seawater buffer capacity. We conclude that terrestrial input results in mesotrophic conditions, and that the strait might undergo further eutrophication if nutrient inputs increase during seasons when light availability is high. Moreover, the remineralisation of terrestrial DOC within the Sunda Shelf may enhance future ocean acidification.

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Mangrove trace metal biogeochemistry response to global climate change

This review discusses observed impacts from different climate change-driven pressures on mangrove’s role in modulating trace metal transfer at the land-ocean interface. It contributes to the literature in a global context and shows mangroves as mitigators or providing positive feedback to metal mobilization. Most chalcophile metals2+ accumulate in mangrove soils associated with sulfides while high sedimentation rates avoid their oxidation. Exudation of oxygen by roots fixates Fe, which co-precipitates metals as oxyhydroxides in the rhizosphere. These two biogeochemical processes reduce trace metal availability to plants and their mobility within estuaries. However, climate change-driven pressures alter this geochemical equilibrium. Increasing atmospheric CO2 and temperature, and the intensity and frequency of extreme climatic events, have proved to affect mangrove functioning and cover, but no direct observation on the impact on metal biogeochemistry is presently available, whereas sea level rise and saline intrusion impacts on the fate of metals have already been observed. Sea level rise increases erosion, that dissociates deposited sulfides releasing metals to the water column. Released metals adsorb onto suspended particles and can re-deposit in the estuary or are exported to continental shelf sediments. Saline intrusion may oxidize deeper sediment layers releasing metals to porewaters. Part of the mobilized metals may remain in solution complexed with DOM and have their bioavailability increased, as shown by high bioaccumulation factors and biomagnification and high metal concentrations in the estuarine biota, which results in higher human exposure through fisheries consumption. Since erosion occurs preferentially at the sea border and higher sedimentation at the higher reaches of the estuary, triggering mangroves migration landward, spatial gradients are formed, and shall be taken into consideration when planning mitigation or adaptation strategies. These observations suggest disruption of traditional humans dwelling in mangrove dominated coastlines by increasing contamination of coastal fisheries, often the principal protein source for those groups and an important source of income. Further research into the environmental and socioeconomic impacts of climate change driven alterations to metal biogeochemical processes in mangroves as contaminant levels are expected to increase.

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The tidal freshwater river zone: physical properties and biogeochemical contribution to estuarine hypoxia and acidification – the “hydrologic switch”


  • Global trends in tidal freshwater zone (TFZ) biogeochemistry are reviewed.
  • TFZs provide significant substrate to facilitate estuarine hypoxia and acidification.
  • Extent of impairment varies as a function of hydrologic connectivity.
  • Changes in biogeochemical processes in TFZs due to sea level rise are also discussed.
  • Conceptual models to design future research directions are described at length.


The river’s role as the aquatic continuum, transporting and transforming terrestrial material in transit to sea, has long been appreciated. Along this aquatic continuum lies an enigmatic river stretch known as the tidal freshwater zone (TFZ). Because it oscillates along the daily tidal cycle, yet records no salinity, TFZs are often overlooked or sporadically studied. Additionally, research efforts into TFZs have been disproportionately focused on the intertidal zone rather than the subtidal zone. The limited studies to date do, however, highlight the subtidal TFZ’s importance in both the removal and transformation of terrestrial material before exchange at sea, and, as both a primary production and respiration hotspot. The shifts between biogeochemical activity within the TFZ vary in a semi-predictable manner based on hydrologic state. Presented here is a conceptual model, defining the TFZ as inseparable from the traditionally studied estuary by reviewing the relevant literature. The TFZ acts as a “fluidized bed reactor” which depends on marine and aquatic material delivery and tidally prolonged retention times. Subsequently, TFZ biogeochemical byproducts affect the saline estuarine reach’s chemistry, water quality, and ecology. Specifically, TFZ biogeochemistry contributes significantly to episodic acidification and deoxygenation in the saline reaches, due to a hydrologic switch. Therefore, conceptualizing the TFZ and estuary as a single entity oscillating jointly between river and ocean dominated forces, within the framework of the pulse-shunt concept, developed in low order stream networks, is most apt. TFZ ecological and hydrological restoration efforts, like those occurring in the traditional estuary, will be needed to mitigate hydrologic switch events in the future.

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Global predictions of coral reef dissolution in the Anthropocene

Arising from K. Davis et al. Communications Earth & Environment (2021)

Coral reef frameworks are constructed by calcifying organisms and are highly sensitive to ocean acidification. Shifting baselines in seawater chemistry have already had measurable impacts on net ecosystem calcification (Gnet) on coral reefs1, and projections of ocean acidification portray a poor future for reefs in the Anthropocene2. While experimental approaches have revealed much about this trajectory, we lack a clear understanding of: i) the drivers and predictors of net calcification at ecosystem scales, and ii) accurate predictions of when ecosystem calcification will reach net dissolution in the 21st century.

Through a meta-analysis approach, the recent study in Communications Earth & Environment by Davis et al.3 provides important insights into ecosystem-scale calcification on coral reefs. Based upon 53 publications spanning 36 coral reef sites around the world, the study provides a more nuanced understanding of the global drivers of Gnet. Cover of reef calcifiers (predominantly corals) and depth are key predictors of global ecosystem calcification, with evidence of seasonality and wave action as additional factors influencing Gnet3. The meta-analysis outlines important knowledge gaps and research needs and highlights the limited data available for assessing changes in ecosystem calcification at the same reefs through time.

Under future projections, ocean acidification is expected to shift coral reefs from a state of net calcification to net dissolution through reductions in pH and aragonite saturation states (Ωa)4,5. The exact timing of this is unclear, in part due to methodological differences, but estimates of when coral reefs will cross a tipping point to net dissolution vary substantially from 2031 to 20826, 20707, and 2060 to 20804. Through the compilation of Gnet from a subset of sites with repeated measurements (6 of the 36 available coral reefs; n = 29 of the available 116 surveys), Davis et al.3 extrapolate linear predictions of Gnet decline (1975–2017) to conclude that average global net-zero calcification will occur around the year 2054, based on a decline in Gnet of 4.3 ± 1.9% yr−1.

Extrapolating estimates of Gnet into the 21st century based upon the available historical data is complex. We identify four issues with this approach:

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Responses of a natural phytoplankton community from the Drake Passage to two predicted climate change scenarios

Contrasting models predict two different climate change scenarios for the Southern Ocean (SO), forecasting either less or stronger vertical mixing of the water column. To investigate the responses of SO phytoplankton to these future conditions, we sampled a natural diatom dominated (63%) community from today’s relatively moderately mixed Drake Passage waters with both low availabilities of iron (Fe) and light. The phytoplankton community was then incubated at these ambient open ocean conditions (low Fe and low light, moderate mixing treatment), representing a control treatment. In addition, the phytoplankton was grown under two future mixing scenarios based on current climate model predictions. Mixing was simulated by changes in light and Fe availabilities. The two future scenarios consisted of a low mixing scenario (low Fe and higher light) and a strong mixing scenario (high Fe and low light). In addition, communities of each mixing scenario were exposed to ambient and low pH, the latter simulating ocean acidification (OA). The effects of the scenarios on particulate organic carbon (POC) production, trace metal to carbon ratios, photophysiology and the relative numerical contribution of diatoms and nanoflagellates were assessed. During the first growth phase, at ambient pH both future mixing scenarios promoted the numerical abundance of diatoms (∼75%) relative to nanoflagellates. This positive effect, however, vanished in response to OA in the communities of both future mixing scenarios (∼65%), with different effects for their productivity. At the end of the experiment, diatoms remained numerically the most abundant phytoplankton group across all treatments (∼80%). In addition, POC production was increased in the two future mixing scenarios under OA. Overall, this study suggests a continued numerical dominance of diatoms as well as higher carbon fixation in response to both future mixing scenarios under OA, irrespective of different changes in light and Fe availability.

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Seasonal carbonate system vis-a-vis pH and salinity in selected tropical estuaries: implications on polychaete diversity and composition towards predicting ecological health


  • The role of salinity-pH gradient coupled with carbonate species on the polychaete community distribution was studied.
  • Salinity-pH was positively correlated with carbonate and DOC.
  • pCO2 was positively correlated with POC, DIC and CO2.
  • High levels of carbonate species and low pH have a greater impact on polychaete diversity and richness.


Salinity and pH play a fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes in the estuarine ecosystem. In this study, the influence of salinity-pH gradient and carbonate system on polychaete diversity in Ennore, Uppanar, Vellar, and Kaduvaiyar estuaries was investigated. Water and sediment samples were collected from September 2017 to August 2018. Univariate and multivariate statistical analyses were employed to define ecological status. Temperature, Salinity, pH, and partial pressure of carbon-di-oxide varied between 21 and 30°C; 29 and 39 ppt; 7.4 and 8.3; and 89.216 and 1702.558 µatm, respectively. PCA and CCA results revealed that DO, chlorophyll, carbonate species, and sediment TOC have a higher influence on polychaete community structure. Forty-two species such as Ancistrosyllis parva, Cossura coasta, Eunice pennata, Euclymene annandalei, Lumbrineris albidentata, Capitella capitata, Prionospio cirrifera, P. pinnata, P. cirrobranchiata, and Notomastus sp. were found dominantly in all estuaries. Shannon index values ranged between 1.619 (UE-1) and 3.376 (VE-2). Based on these findings, high levels of carbonate species and low pH have a greater impact on polychaete diversity and richness values. The results of the AMBI Index revealed that stations UE-1, UE-2, UE-3 in Uppanar, EC-1, EC-2 in Ennore indicate “moderately disturbed”, while other stations are under the “slightly disturbed” category. This trend was quite evident in M-AMBI as well.

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Modeling carbon budgets and acidification in the Mediterranean Sea ecosystem under contemporary and future climate

We simulate and analyze the effects of a high CO2 emission scenario on the Mediterranean Sea biogeochemical state at the end of the XXI century, with a focus on carbon cycling, budgets and fluxes, within and between the Mediterranean sub-basins, and on ocean acidification. As a result of the overall warming of surface water and exchanges at the boundaries, the model results project an increment in both the plankton primary production and the system total respiration. However, productivity increases less than respiration, so these changes yield to a decreament in the concentrations of total living carbon, chlorophyll, particulate organic carbon and oxygen in the epipelagic layer, and to an increment in the DIC pool all over the basin. In terms of mass budgets, the large increment in the dissolution of atmospheric CO2 results in an increment of most carbon fluxes, including the horizontal exchanges between eastern and western sub-basins, in a reduction of the organic carbon component, and in an increament of the inorganic one. The eastern sub-basin accumulates more than 85% of the absorbed atmospheric CO2. A clear ocean acidification signal is observed all over the basin, quantitatively similar to those projected in most oceans, and well detectable also down to the mesopelagic and bathypelagic layers.

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Microbial alkalinity production and silicate alteration in methane charged marine sediments: implications for porewater chemistry and diagenetic carbonate formation

A numerical reaction-transport model was developed to simulate the effects of microbial activity and mineral reactions on the composition of porewater in a 230-m-thick Pleistocene interval drilled in the Peru-Chile Trench (Ocean Drilling Program, Site 1230). This site has porewater profiles similar to those along many continental margins, where intense methanogenesis occurs and alkalinity surpasses 100 mmol/L. Simulations show that microbial sulphate reduction, anaerobic oxidation of methane, and ammonium release from organic matter degradation only account for parts of total alkalinity, and excess CO2 produced during methanogenesis leads to acidification of porewater. Additional alkalinity is produced by slow alteration of primary aluminosilicate minerals to kaolinite and SiO2. Overall, alkalinity production in the methanogenic zone is sufficient to prevent dissolution of carbonate minerals; indeed, it contributes to the formation of cemented carbonate layers at a supersaturation front near the sulphate-methane transition zone. Within the methanogenic zone, carbonate formation is largely inhibited by cation diffusion but occurs rapidly if cations are transported into the zone via fluid conduits, such as faults. The simulation presented here provides fundamental insight into the diagenetic effects of the deep biosphere and may also be applicable for the long-term prediction of the stability and safety of deep CO2 storage reservoirs.

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Spatiotemporal variability in kelp forest and seagrass ecosystems: can local biogeochemical modification combat acidification stress?

Anthropogenic carbon dioxide (CO2) emissions have driven widespread ocean acidification (OA). OA has reduced surface ocean pH by at least 0.1 pH units since the beginning of the industrial era and global models forecast a further decrease of 0.3 to 0.4 pH units by the end of the century. Submerged aquatic vegetation, such as kelp forests and seagrass beds, has the potential to locally ameliorate OA by removing CO2 during photosynthesis and storing it as fixed carbon. Thus, understanding the contribution of these habitats to local biogeochemistry is essential to inform coastal management and policy, especially as the impacts of anthropogenic climate change become more prevalent. The following work describes high resolution spatiotemporal variability in seagrass and kelp forest biogeochemistry (Chapters 1 and 2) and in the surface canopy extent of a giant kelp forest (Chapter 3).

In order to understand the contributions of kelp forest and seagrass metabolism to their respective local biogeochemistry, we must determine the natural variability in these systems and disentangle the physical and biological drivers of local biogeochemical variability. In Chapter 1, I deployed an extensive instrument array in Monterey Bay, CA, inside and outside of a kelp forest to assess the degree to which kelp locally ameliorates present-day acidic conditions, which we expect to be further exacerbated by OA. Interactions between upwelling exposure, internal bores, and biological production shaped the local biogeochemistry inside and outside of the kelp forest. Significantly elevated pH, attributed to kelp canopy productivity, was observed at the surface inside the kelp forest. This modification was largely limited to a narrow band of surface water, implying that while kelp forests have the potential to locally ameliorate ocean acidification stress, this benefit may largely be limited to organisms living in the upper part of the canopy. In Chapter 2, I quantified net community production (NCP) over a mixed seagrass-coral community on Ngeseksau Reef, Ngermid Bay, Republic of Palau. We observed a net heterotrophic diel signal over the deployment, but dissolved oxygen (O2) fluxes during the day were largely positive, illustrating daytime autotrophy. pH, O2, and temperature followed a clear diel pattern with maxima typically occurring in the afternoon. The relationship between tidal regime and time of day drove the magnitude of the signals observed. The case studies described in Chapters 1 and 2 emphasize the importance of high-resolution measurements (high temporal frequency as well as high horizontal and vertical spatial resolution) and consideration of the multiple drivers responsible for shaping the observed biogeochemical variability. In addition to the photosynthetic biomass (kelp and seagrass) at the center of these studies, the physical environment played an important role in dictating the signals observed, in particular water circulation and residence time.

Biogeochemical studies rarely look beyond a few deployment sites, but the ecosystem contributing to the local biogeochemical variability includes influences from beyond those discrete points. Describing the area around these discrete points is important for accurate assessment of factors driving the signals observed at those points. Remote sensing can help us capture and describe the spatial patterns of biomass contributing to changes observed in our chemical records. In Chapter 3, I established a low altitude unmanned aerial vehicle (UAV) record of giant kelp surface areal extent over 18 months on the wave-protected side of Cabrillo Point (Hopkins Marine Station) in Monterey Bay, CA. This was the same canopy responsible for elevating pH in Chapter 1; however, in this case, the kelp canopy mapping did not overlap in time with biogeochemical measurements in the kelp forest. I compared the UAV kelp classification to canopy cover determined from Landsat satellite images obtained over the same period. There was a linear relationship between the drone kelp ratio and Landsat kelp canopy fraction for spatially-matched pixels; a Landsat kelp fraction of 0.64 was equivalent to 100% kelp cover in the drone data. The level of resolution provided by UAV, compared with Landsat images, could allow more detailed mapping of kelp responses to environmental change. Future studies should pair mapping flights with biogeochemical measurements to quantify the relationship between changes in canopy area and the relative surface canopy modification of pH.

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Equilibrium calculations of iron speciation and apparent iron solubility in the Celtic Sea at ambient seawater pH using the NICA-Donnan model

We used a combined ion pairing – organic matter speciation model (NICA-Donnan) to predict the organic complexation of iron (Fe) at ambient pH and temperature in the Celtic Sea. We optimized our model by direct comparison with Fe speciation determined by Adsorptive Cathodic Stripping Voltammetry using the added Fe-binding ligand 1-nitroso-2-naphthol (HNN) in the presence and absence of natural organic matter. We compared determined Fe speciation with simulated titrations obtained via application of the NICA-Donnan model with four different NICA parameter sets representing a range of binding site strengths and heterogeneities. We tested the assumption that binding sites scale to dissolved organic carbon (DOC) concentrations in marine waters. We found that a constant low DOC concentration resulted in an improved fit of our titration data to the simulated titrations, suggesting that inputs of autochthonous marine DOM may not increase the heterogeneity or concentrations of Fe binding sites. Using the optimal parameter set, we calculated pFe(III)´ (−log(∑Fe(OH)i3−i)) and apparent Fe(III) solubility (SFe(III)app) at ambient pH and temperature in the water column of the Celtic Sea. SFe(III)app was defined as the sum of aqueous inorganic Fe(III) species and Fe(III) bound to DOM formed at a free Fe (Fe3+) concentration equal to the limiting solubility of Fe hydroxide (Fe(OH)3(s)). SFe(III)app was within range of the determined dissolved Fe concentrations observed after winter mixing on the shelf and in waters >1500 m depth at our most offshore stations. Our study supports the hypothesis that the ocean dissolved Fe inventory is controlled by the interplay between Fe solubility and Fe binding by organic matter, although the overall number of metal binding sites in the marine environment may not be directly scalable to DOC concentrations.

Continue reading ‘Equilibrium calculations of iron speciation and apparent iron solubility in the Celtic Sea at ambient seawater pH using the NICA-Donnan model’

Differences in organic carbon release between conchocelis and thalli of Pyropia haitanensis and responses to changes in light intensity and pH


  • DOC production rate of thallus was much higher than that of conchocelis.
  • DOC production rate of thallus tends to increase with light intensity.
  • Ocean acidification did not significantly change the DOC production rate of thallus.


The large-scale cultivation of macroalgae has the potential to act as a carbon sink because macroalgae can release a large amount of organic carbon into the surrounding seawater. However, this needs to be evaluated on the basis of the entire life cycle under a background of changes in pH and light intensity. The present study investigated the difference in organic carbon release between conchocelis and thallus stages of the economically important red alga Pyropia haitanensis in response to three light intensities (10, 50, and 500 μmol m−2 s−1) and two pH conditions (current pH: 8.1, projected future pH: 7.5). The study found that regardless of the light intensity and pH values, the growth rates, production rates of tissue carbon, and dissolved organic carbon (DOC) of thalli tended to be higher than those of conchocelis, by more than 170%, 85%, and 106%, respectively. The DOC production rate was higher than the production rate of particulate organic carbon (POC) by at least two orders of magnitude. Positive correlations were found between growth rate and production rates of tissue carbon and growth rate and DOC production rate, but no clear relationship was found between growth and POC production. The DOC production rate of thallus tended to increase with light intensity but was not significantly influenced by ocean acidification. However, decay of tissue caused by exposure of the conchocelis to high light intensity resulted in increased POC and DOC production rates, indicating the complexity of organic carbon release by Phaitanensis. This study provides insights into the release of organic carbon during the complete life cycle of Phaitanensis, and the results can further our understanding of the carbon metabolism of this cultivated macroalgal species.

Continue reading ‘Differences in organic carbon release between conchocelis and thalli of Pyropia haitanensis and responses to changes in light intensity and pH’

Annual hypoxia causing long-term seawater acidification: evidence from low-molecular-weight organic acids in the Changjiang Estuary and its adjacent sea area


  • High concentrations of LMWOAs were detected in nearshore seawater.
  • The Changjiang runoff was the main source of the LMWOAs.
  • LMWOAs have evident impacts on the seawater acidification.
  • Annual hypoxia could cause long-term seawater acidification.


In this study, components, concentrations, distribution characteristics, sources of low-molecular-weight organic acids (LMWOAs) and relationships among the annual hypoxia, LMWOAs and seawater acidification were investigated in the Changjiang Estuary and its adjacent sea area in July 2015. Lactic, acetic and formic acids were detected in the seawater samples in the study area, and their total concentrations (ΣLMWOAs) varied from 0 to 262.6 μmol·L−1, with an average value of 39.2 μmol·L−1. In the surface seawater, high concentration areas of ΣLMWOAs occurred in the sea area near the Changjiang Estuary and the Hangzhou Bay, and north of study area. In the sampling stations along transect A6, high concentration areas of ΣLMWOAs appeared in the bottom seawater of nearshore stations and middle seawater of offshore stations. The terrigenous inputs, especially the Changjiang runoff, were the dominant sources for LMWOAs in the sampling period. The consistency of hypoxia areas, high concentration areas of ΣLMWOAs and low pH value areas in winter and summer suggested that annual hypoxia could cause the long-term seawater acidification by producing LMWOAs in the Changjiang Estuary and its adjacent sea area.

Continue reading ‘Annual hypoxia causing long-term seawater acidification: evidence from low-molecular-weight organic acids in the Changjiang Estuary and its adjacent sea area’

Assessing the state of the Barents Sea using indicators: how, when, and where?

Two end-to-end ecosystem models, NORWECOM.E2E and NoBa Atlantis, have been used to explore a selection of indicators from the Barents Sea Management plans (BSMP). The indicators included in the BSMP are a combination of simple (e.g. temperature, biomass, and abundance) and complex (e.g. trophic level and biomass of functional groups). The abiotic indicators are found to serve more as a tool to report on climate trends rather than being ecological indicators. It is shown that the selected indicators give a good overview of the ecosystem state, but that overarching management targets and lack of connection between indicators and management actions makes it questionable if the indicator system is suitable for direct use in management as such. The lack of socio-economic and economic indicators prevents a holistic view of the system, and an inclusion of these in future management plans is recommended. The evaluated indicators perform well as an assessment of the ecosystem, but consistency and representativeness are extremely dependent on the time and in what area they are sampled. This conclusion strongly supports the inclusion of an observing system simulation experiment in management plans, to make sure that the observations represent the properties that the indicators need.

Continue reading ‘Assessing the state of the Barents Sea using indicators: how, when, and where?’

Predictive model for gross community production rate of coral reefs using ensemble learning methodologies

Coral reefs play a vital role in maintaining the ecological balance of the marine ecosystem. Various marine organisms depend on coral reefs for their existence and their natural processes. Coral reefs provide the necessary habitat for reproduction and growth for various exotic species of the marine ecosystem. In this article, we discuss the most important parameters which influence the lifecycle of coral and coral reefs such as ocean acidification, deoxygenation and other physical parameters such as flow rate and surface area. Ocean acidification depends on the amount of dissolved Carbon dioxide (CO2). This is due to the release of H+ ions upon the reaction of the dissolved CO2 gases with the calcium carbonate compounds in the ocean. Deoxygenation is another problem that leads to hypoxia which is characterized by a lesser amount of dissolved oxygen in water than the required amount for the existence of marine organisms. In this article, we highlight the importance of physical parameters such as flow rate which influence gas exchange, heat dissipation, bleaching sensitivity, nutrient supply, feeding, waste and sediment removal, growth and reproduction. In this paper, we also bring out these important parameters and propose an ensemble machine learning-based model for analyzing these parameters and provide better rates that can help us to understand and suitably improve the ocean composition which in turn can eminently improve the sustainability of the marine ecosystem, mainly the coral reefs

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A unique diel pattern in carbonate chemistry in the seagrass meadows of Dongsha island: the enhancement of metabolic carbonate dissolution in a semienclosed lagoon

In contrast to other seagrass meadows where seawater carbonate chemistry generally shows strong diel variations with higher pH but lower partial pressure of CO2 (pCO2) during the daytime and lower pH but higher pCO2 during nighttime due to the alternation in photosynthesis and respiration, the seagrass meadows of the inner lagoon (IL) on Dongsha Island had a unique diel pattern with extremely high pH and low pCO2 across a diel cycle. We suggest that this distinct diel pattern in pH and pCO2 could be associated with the enhancement of total alkalinity (TA) production coupled to carbonate sediment dissolution in a semienclosed lagoon. The confinement of the IL may hamper water exchange and seagrass detritus export to the adjacent open ocean, which may result in higher organic matter loading to the sediments, and longer residence time of the water in the IL, accompanied by microbial respiration (both aerobic and anaerobic) that may reduce carbonate saturation level to drive carbonate dissolution and thus TA elevation, thereby forming such a unique diel pattern in carbonate chemistry. This finding further highlights the importance of considering TA production through metabolic carbonate dissolution when evaluating the potential of coastal blue carbon ecosystems to buffer ocean acidification and to absorb atmospheric CO2, in particular in a semienclosed setting.

Continue reading ‘A unique diel pattern in carbonate chemistry in the seagrass meadows of Dongsha island: the enhancement of metabolic carbonate dissolution in a semienclosed lagoon’

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