Evidence of infaunal effects on porewater advection and biogeochemistry in permeable sediments: A proposed infaunal functional group framework

Bioturbating infauna significantly modify reaction and transport processes in permeable sediments, though most studies to date are limited in the scope of species examined. We conducted a comparative field study measuring density-dependent effects of six common bioturbating species on porewater advection and biogeochemistry, across three intertidal permeable sediment habitats. The species in this study are; head-down like deposit feeders (Abarenicola pacifica and Balanoglossus aurantiacus), surface deposit feeders (Diopatra cuprea and Onuphis jenneri) and gallery diffusers (Upogebia pugettensis and Neotrypaea californiensis). Tracer loss from gel diffusers was used to assess relative differences in porewater advection among sites, and porewater peepers were used to measure solute concentrations of carbon, nitrogen, phosphate, and silicate in experimental plots. Characteristic surface features of different infauna were counted and used as a proxy for infaunal density. Density of surface features was then used in regression analyses as an explanatory variable affecting porewater transport and chemistry. Significant infaunal density effects on porewater transport or biogeochemistry were found in all but one species, D. cuprea. The species-specific attributes and mechanisms by which these infauna affect permeable sediment processes are explored. A process based functional group framework is presented for permeable sediments. Bulk granulometric properties also were assessed. There were little to no within-site effects of porosity, hydraulic conductivity, or organic matter on porewater transport and biogeochemistry. However, significant across-site differences in granulometry and site properties were found and these are addressed in relation to infaunal effects on porewater transport and chemistry

Infaunal Effects on Permeable Sediment Processes

The role of infauna on permeable sediment processes is poorly understood due to methodological limitations and a lack of empirical data. The interactions among porewater flows, sediments, and biogenic structures present a physically and biogeochemically complex sedimentary environment in which traditional measurement techniques and heuristic models are of minimal applicability. Chapter one provides an executive summary of this research. The second chapter describes a field investigation of the impact of the common lugworm and two species of thalassinid shrimp on porewater transport and chemistry in permeable sediments. In this work, novel experimental methods are employed to measure infaunal effects on porewater transport and chemistry. This experiment found differential effects of each taxon on porewater transport and solute chemistry that were highly related to infaunal functional characteristics, and independent of sediment properties. Results from the field study prompted a laboratory microcosm study of lugworm effects on permeable sediment solute fluxes, presented in chapter three. Flow-through sediment microcosms mimicked tidal draining of intertidal flats and measured the effects of lugworms on sediment biogeochemistry. Lugworms were found to significantly alter solute fluxes as well as stoichiometric ratios from the microcosms. The potential ecosystem consequences of stoichiometric changes to regenerated solutes are explored with a new metric. Finally, chapter four presents a synthesis examination of the infaunal functional attributes important to permeable sediment processes with a multi-site, multi-species field investigation. Head-down deposit feeders were found to have similar effects on advection and chemistry, whereas other infauna had differential effects linked to the composition and morphology of the burrow/tube. The mechanisms by which different infauna may affect permeable sediment properties are discussed, and include consideration of covariates such as organism activity and density. The results from this research highlight the importance of infauna to permeable sediment processes, while recognizing the limitations of their effects under different physical regimes. Benthic infauna play a significant role in the biogeochemistry of common permeable sediment habitats in coastal and near-shore environments. The results presented herein suggest the loss of large bioturbating infauna from permeable sediments due to human activities may result in significant changes to coastal biogeochemical cycles

Omega Oracle: forecasting estuarine carbonate weather

There are serious concerns about ecological, social, and economic impacts in the Pacific Northwest due to Ocean Acidification (OA). We built a system to predict aragonite saturation state (Ω) of seawater in Netarts Bay, Oregon based on large scale forcing parameters. An artificial neural network – trained against a continuous, multiyear monitoring record of carbonate chemistry – learns a regression estimate of Ω based on seasonality, tides, and wind conditions. This approach is agnostic to the details of the underlying chemical and biological processes offering a distinct modelling perspective. The result is a conceptually simpler and more strictly empirical parameterization and a model that is flexible in application due to dependence on only easily obtainable parameters. Forecast validation by a cross validation method indicates good prediction performance, particularly for the high frequency content of the Ω time series, over periods of stable wind forecasting. Our forecast model demonstrates that the complex temporal dynamics of carbonate chemistry within an estuary can emerge from forcing operating on longer timescales. This further elucidates the management and commercial value of this model; experimental work with calcifiers suggests the details of these high frequency chemical dynamics are critical to the magnitude of stress imposed. Lastly, these forecasts, deployed as a web application, can facilitate OA mitigation strategies by providing aquaculturists with real-time predictions for consideration in operational decisions. Numerous sites, including on the Salish Sea, are poised to soon have viable training data for application of this method. Broader deployment promises to enable comparison between sites and expansion of direct aquaculture and management applications. Expansion to other sites is expected to require altered explanatory variables but this exercise may itself yield insight. Relatedly, we note the potential of this approach to help constrain timescales and sources (natural and anthropogenic) of contributions to physiological OA stress

Ecosystem effects of shell aggregations and cycling in coastal waters: an example of Chesapeake Bay oyster reefs

Disease, overharvesting, and pollution have impaired the role of bivalves on coastal ecosystems, some to the point of functional extinction. An underappreciated function of many bivalves in these systems is shell formation. The ecological significance of bivalve shell has been recognized; geochemical effects are now more clearly being understood. A positive feedback exists between shell aggregations and healthy bivalve populations in temperate estuaries, thus linking population dynamics to shell budgets and alkalinity cycling. On oysterreefs a balanced shell budget requires healthy long-lived bivalves to maximize shell input permortality event thereby countering shell loss. Active and dense populations of filter-feeding bivalves couple production of organic-rich waste with precipitation of calcium carbonate minerals, creating conditions favorable for alkalinity regeneration. Although the dynamics of these processes are not well described, the balance between shell burial and metabolic acid production seems the key to the extent of alkalinity production vs. carbon burial as shell. We present an estimated alkalinity budget that highlights the significant role oyster reefs once played in the Chesapeake Bay inorganic-carbon cycle. Sustainable coastal and estuarine bivalve populations require a comprehensive understanding of shell budgets and feedbacks among population dynamics, agents of shell destruction, and anthropogenic impacts on coastal carbonate chemistry

Mechanistic understanding of ocean acidification impacts on larval feeding physiology and energy budgets of the mussel M. californianus

Ocean acidification (OA) - a process describing the ocean’s increase in dissolved carbon dioxide (PCO2) and a reduction in pH and aragonite saturation state (Ωar) due to higher concentrations of atmospheric CO2 – is considered a threat to bivalve mollusks and other marine calcifiers. While many studies have focused on the effects of OA on shell formation and growth, we present findings on the separate effects of PCO2, Ωar, and pH on larval feeding physiology (initiation of feeding, gut fullness, and ingestion rates) of the California mussel Mytilus californianus. We found elevated PCO2 delays initiation of feeding, while gut fullness and ingestion rates were best predicted by Ωar; however, pH was not found to have a significant effect on these feeding processes under the range of OA conditions tested. We also modeled how OA impacts on initial shell development and feeding physiology might subsequently affect larval energy budget components (e.g. scope for growth) and developmental rate to 260 µm shell length, a size at which larvae typically become pediveligers. Our model predicted that Ωar impacts on larval shell size and ingestion rates over the initial 48 h period of development would result in a developmental delay to the pediveliger stage of \u3e 4 days, compared with larvae initially developing in supersaturated conditions (Ωar \u3e 1). Collectively, these results suggest that predicted increases in PCO2 and reduced Ωar values may negatively impact feeding activity and energy balances of bivalve larvae, reducing their overall fitness and recruitment success

Seasonal patterns of estuarine acidification in seagrass beds of the Snohomish Estuary, WA

Recent studies have begun to explore physical and biogeochemical mechanisms of carbonate chemistry variability in a variety of coastal habitats, including coral reefs, upwelling margins, and inland seas. To our knowledge, there have been limited mechanistic studies of annual carbonate chemistry variability in nearshore estuarine environments. Here, we present autonomous sensor and grab sample data of carbonate chemistry covering a 10 month period from two subtidal seagrass bed sites in Possession Sound, WA. Simple mass balance stoichiometric models are used to evaluate seasonal drivers of carbonate system parameters in the seagrass beds. Simulations of increasing anthropogenic carbon (Canth) burdens in the habitats reveal seasonal differences in the magnitude of carbonate system responses. The addition of Canth alters the thermodynamic buffer factors (e.g. the Revelle factor) of the carbonate system, decreasing the system’s ability to buffer natural variability in the seagrass habitat on high-frequency (e.g. tidal, diel) and seasonal timescales. As a result, the most harmful carbonate system indices for many estuarine organisms (minimum pHT, minimum Ωarag, and maximum pCO2(s.w.)) change most rapidly with increasing Canth. We highlight how the observed seasonal climatology and non-linear response of the carbonate system to increasing Canth drive the timing of the crossing of established physiological stress thresholds for endemic organisms, as well as thresholds relevant for water quality management. In this system, the relative benefits of the seagrass beds in locally mitigating ocean acidification during the growing season increase with the higher atmospheric CO2 levels predicted toward 2100. Presently however, these mitigating effects are mixed due to intense diel cycling of CO2 driven by community metabolism

Evidence of infaunal effects on porewater advection and biogeochemistry in permeable sediments: A proposed infaunal functional group framework

Bioturbating infauna significantly modify reaction and transport processes in permeable sediments, though most studies to date are limited in the scope of species examined. We conducted a comparative field study measuring density-dependent effects of six common bioturbating species on porewater advection and biogeochemistry, across three intertidal permeable sediment habitats. The species in this study are; head-down like deposit feeders (Abarenicola pacifica and Balanoglossus aurantiacus), surface deposit feeders (Diopatra cuprea and Onuphis jenneri) and gallery diffusers (Upogebia pugettensis and Neotrypaea californiensis). Tracer loss from gel diffusers was used to assess relative differences in porewater advection among sites, and porewater peepers were used to measure solute concentrations of carbon, nitrogen, phosphate, and silicate in experimental plots. Characteristic surface features of different infauna were counted and used as a proxy for infaunal density. Density of surface features was then used in regression analyses as an explanatory variable affecting porewater transport and chemistry. Significant infaunal density effects on porewater transport or biogeochemistry were found in all but one species, D. cuprea. The species-specific attributes and mechanisms by which these infauna affect permeable sediment processes are explored. A process based functional group framework is presented for permeable sediments. Bulk granulometric properties also were assessed. There were little to no within-site effects of porosity, hydraulic conductivity, or organic matter on porewater transport and biogeochemistry. However, significant across-site differences in granulometry and site properties were found and these are addressed in relation to infaunal effects on porewater transport and chemistry

Comparison of larval development in domesticated and naturalized stocks of the Pacific oyster Crassostrea gigas exposed to high pCO₂ conditions

Ocean acidification (OA) has had significant negative effects on oyster populations on the west coast of North America over the past decade. Many studies have focused on the physiological challenges experienced by young oyster larvae in high pCO₂/low pH seawater with reduced aragonite saturation state (Ωarag), which is characteristic of OA. Relatively few, by contrast, have evaluated these impacts upon fitness traits across multiple larval stages and between discrete oyster populations. In this study, we conducted 2 replicated experiments, in 2015 and 2016, using larvae from naturalized ‘wild’ and selectively bred stocks of the Pacific oyster Crassostrea gigas from the US Pacific Northwest and reared them in ambient (~400 µatm) or high (~1600 µatm) pCO₂ seawater from fertilization through final metamorphosis to juvenile ‘spat.’ In each year, high pCO₂ seawater inhibited early larval development and affected the timing, but not the magnitude, of mortality during this stage. The effects of acidified seawater on metamorphosis of pediveligers to spat were variable between years, with no effect of seawater pCO₂ in the first experiment but a ~42% reduction in spat in the second. Despite this variability, larvae from selectively bred oysters produced, on average, more (+ 55 and 37%) and larger (+ 5 and 23%) spat in ambient and high pCO₂ seawater, respectively. These findings highlight the variable and stage-specific sensitivity of larval oysters to acidified seawater and the influence that genetic factors have in determining the larval performance of C. gigas exposed to high pCO₂ seawater

Ocean acidification stress index for shellfish (OASIS): Linking Pacific oyster larval survival and exposure to variable carbonate chemistry regimes

Understanding larval bivalve responses to variable regimes of seawater carbonate chemistry requires realistic quantification of physiological stress. Based on a degree-day modeling approach, we developed a new metric, the ocean acidification stress index for shellfish (OASIS), for this purpose. OASIS integrates over the entire larval period the instantaneous stress associated with deviations from published sensitivity thresholds to aragonite saturation state (ΩAr) while experiencing variable carbonate chemistry. We measured survival to D-hinge and pre-settlement stage of four Pacific oyster (Crassostrea gigas) cohorts with different histories of carbonate chemistry exposure at the Whiskey Creek Hatchery, Netarts Bay, OR, to test the utility of OASIS as a stress metric and document the effects of buffering seawater in mitigating acute and chronic exposure to ocean acidification. Each cohort was divided into four groups and reared under the following conditions: 1) stable, buffered seawater for the entire larval period; 2) stable, buffered seawater for the first 48 hours, then naturally variable, unbuffered seawater; 3) stable, unbuffered seawater for the first 48 hours, then buffered seawater; and 4) stable, unbuffered seawater for the first 48 hours, then naturally variable, unbuffered seawater. Patterns in Netarts Bay carbonate chemistry were dominated by seasonal upwelling at the time of the experimental work, resulting in naturally highly variable ΩAr for the larvae raised in the unbuffered treatments. Two of the four cohorts showed strongly positive responses to buffering in survival to 48 hours; three of the four, in survival to pre-settlement. OASIS accurately predicted survival for two of the three cohorts tested (the fourth excluded due to other environmental factors), suggesting that this new metric could be used to better understand larval bivalve survival in naturally variable environments. OASIS may also be useful to an array of diverse stakeholders with increasing access to highly resolved temporal measurements of carbonate chemistry