The 2024 “Hacking Limnology” Workshop Series and Virtual Summit: Increasing inclusion, participation, and representation in the aquatic sciences
No abstract available.
Limnology & Oceanography Bulletin↗
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The 2025 “Hacking Limnology” Workshop Series and DSOS Virtual Summit: A half decade of data-intensive aquatic science
No abstract available.
Limnology & Oceanography Bulletin↗
Assessment of multiple ecosystem metabolism methods in an estuary
Ecosystem metabolism is a key ecological attribute and easy to describe, but quantifying metabolism in estuaries is challenging. Properly scaling measurements through time and space requires consideration of hydrodynamics and mixing water from heterogeneous sources, making any estimation uncertain. Here, we compared three methods for modeling ecosystem metabolism in a portion of the Sacramento-San Joaquin Delta. Metabolism estimates based on laboratory incubations, continuous in situ buoys, and an oxygen isotope approach all indicated the system was net heterotrophic, and calculated rates were comparable in magnitude when averaged over the 2-month study. Daily metabolic rates based on in situ buoys were the most variable, likely due to horizontal and vertical advection and poor portrayal of the dissolved oxygen budget. After temporally averaging in situ buoy estimates or smoothing the dissolved oxygen time series for tidal effects, rates were more comparable to the other methods, which may be necessary to account for tidal advection and unbalanced contributions from subhabitats within the metabolic footprint. Incubation-based rates represent the finest temporal and spatial scale and only account for pelagic processes, which may explain why incubation-based rates were lower than the other two methods. The oxygen isotope method provided temporally and spatially integrated rates that were bracketed by the other two methods and may be a valuable tool in systems matching the model requirements. Because uncertainty arises in each method from a number of assumptions and scaling calculations, the resolution of metabolic rates in estuaries is likely coarser and more variable than in other aquatic ecosystems.
California↗
Identifying conditions associated with outliers produced by three different chlorophyll fluorometers: A comparison of instrumentation and development of correction formulae
Measurements of chlorophyll concentration reported by fluorometers (fChl) are used in environmental research and monitoring, as inputs to models, and in the interpretation of remote sensing data. Researchers and managers benefit from understanding how to interpret and ensure the accuracy of fChl data collected by in situ fluorometers. Although fChl values produced by different manufacturers are often in agreement with discrete laboratory-derived Chlorophyll a (Chl a ) concentration measurements, there are instances in which results significantly differ. Further, when measuring fChl side by side, different fluorometers may report values that differ significantly from each other, despite passing calibration checks prior to deployment. We compared environmental conditions and phytoplankton species composition associated with instances in which fChl measurements from three different fluorometers (EXO2 Total Algae Smart Sensor, YSI Inc./Xylem Inc., Yellow Springs, Ohio; FluoroProbe III, bbe Moldaenke GmbH, Kiel, Germany; WETStar, Sea-Bird Scientific, Bellevue, Washington) were significantly different from laboratory-derived Chl a concentrations. Results indicated that elevated primary productivity, as indicated by high pH, dissolved oxygen, and the ratio of Chl a to phaeophytin, were correlated with underestimated fChl values recorded by each sensor. After removing outliers, we determined unique correction guidance for each of the three sensors and demonstrated that after applying correction formulae, fChl measurements produced by each sensor became directly comparable.
California↗
[Book review] Aquatic Ecology: Scale, Pattern and Process, edited by Paul S. Giller, Alan G. Hildrew, and David G. Raffaelli
Review of: Aquatic ecology : scale, pattern, and process. Paul S Giller; A G Hildrew; D G Raffaelli; British Ecological Society. Symposium; American Society of Limnology and Oceanography. Oxford ; Boston : Blackwell Scientific Publications, 1994. xiii, 649 p. : ill., maps ; 24 cm.
Fisheries Review↗
Turbidity, light, temperature, and hydropeaking control primary productivity in the Colorado River, Grand Canyon
Dams and river regulation greatly alter the downstream environment for gross primary production (GPP) because of changes in water clarity, flow, and temperature regimes. We estimated reach-scale GPP in five locations of the regulated Colorado River in Grand Canyon using an open channel model of dissolved oxygen. Benthic GPP dominates in Grand Canyon due to fast transport times and low pelagic algal biomass. In one location, we used a 738 days time series of GPP to identify the relative contribution of different physical controls of GPP. We developed both linear and semimechanistic time series models that account for unmeasured temporal covariance due to factors such as algal biomass dynamics. GPP varied from 0 g O 2 m −2 d −1 to 3.0 g O 2 m −2 d −1 with a relatively low annual average of 0.8 g O 2 m −2 d −1 . Semimechanistic models fit the data better than linear models and demonstrated that variation in turbidity primarily controlled GPP. Lower solar insolation during winter and from cloud cover lowered GPP much further. Hydropeaking lowered GPP but only during turbid conditions. Using the best model and parameter values, the model accurately predicted seasonal estimates of GPP at 3 of 4 upriver sites and outperformed the linear model at all sites; discrepancies were likely from higher algal biomass at upstream sites. This modeling approach can predict how changes in physical controls will affect relative rates of GPP throughout the 385 km segment of the Colorado River in Grand Canyon and can be easily applied to other streams and rivers.
Arizona↗
Model-based interpretation of sediment concentration and vertical flux measurements in a shallow estuarine environment
A one-dimensional numerical model describing tidally varying vertical mixing and settling was used to interpret sediment concentrations and vertical fluxes observed in the shoals of South San Francisco Bay by two acoustic Doppler velocimeters (ADVs) at elevations of 0.36 m and 0.72 m above bed. Measured sediment concentrations changed by up to 100 g m −3 over the semidiurnal tidal cycle. These dynamics were dominated by local resuspension and settling. Multiple particle class models suggested the existence of a class with fast settling velocities ( w s of 9.0 × 10 −4 m s −1 in spring and 5.8 × 10 −4 m s −1 in fall) and a slowly settling particle fraction ( w s of <1 × 10 −7 m s −1 in spring and 1.4 × 10 −5 m s −1 in fall). Modeled concentrations of slowly settling particles at 0.36 m were as high as 20 g m −3 during fall and varied with the spring-neap cycle while fine sediment concentrations in spring were constant around 5 g m −3 . Analysis of in situ water column floc size distributions suggested that floc properties in the lower part of the water column were most likely governed by particle-size distribution on the bed and not by coagulation, validating our multiple particle size approach. A comparison of different sediment bed models with respect to model performance, sensitivity, and identifiability suggested that the use of a sediment erosion model linear in bottom shear stress τ b ( E = M ( τ b − τ c )) was the most appropriate choice to describe the field observations when the critical shear stress τ c and the proportionality factor M were kept constant.
California↗
Evidence for the assimilation of ancient glacier organic carbon in a proglacial stream food web
We used natural abundance δ 13 C, δ 15 N, and Δ 14 C to compare trophic linkages between potential carbon sources (leaf litter, epilithic biofilm, and particulate organic matter) and consumers (aquatic macroinvertebrates and fish) in a nonglacial stream and two reaches of the heavily glaciated Herbert River. We tested the hypothesis that proglacial stream food webs are sustained by organic carbon released from glacial ecosystems. Carbon sources and consumers in the nonglacial stream had carbon isotope values that ranged from -30‰ to -25‰ for δ 13 C and from -14‰ to 53‰ for Δ 14 C reflecting a food web sustained mainly on contemporary primary production. In contrast, biofilm in the two glacial stream sites was highly Δ 14 C-depleted (-215‰ to 175‰) relative to the nonglacial stream consistent with the assimilation of ancient glacier organic carbon. IsoSource modeling showed that in upper Herbert River, macroinvertebrates (Δ 14 C = -171‰ to 22‰) and juvenile salmonids (Δ 14 C = −102‰ to 17‰) reflected a feeding history of both biofilm (~ 56%) and leaf litter (~ 40%). We estimate that in upper Herbert River on average 36% of the carbon incorporated into consumer biomass is derived from the glacier ecosystem. Thus, 14 C-depleted glacial organic carbon was likely transferred to higher trophic levels through a feeding history of bacterial uptake of dissolved organic carbon and subsequent consumption of 14 C-depleted biofilm by invertebrates and ultimately fish. Our findings show that the metazoan food web is sustained in part by glacial organic carbon such that future changes in glacial runoff could influence the stability and trophic structure of proglacial aquatic ecosystems.
Limnology and Oceanography↗
Rapid water quality change in the Elwha River estuary complex during dam removal
Dam removal in the United States is increasing as a result of structural concerns, sedimentation of reservoirs, and declining riverine ecosystem conditions. The removal of the 32 m Elwha and 64 m Glines Canyon dams from the Elwha River in Washington, U.S.A., was the largest dam removal project in North American history. During the 3 yr of dam removal—from September 2011 to August 2014—more than ten million cubic meters of sediment was eroded from the former reservoirs, transported downstream, and deposited throughout the lower river, river delta, and nearshore waters of the Strait of Juan de Fuca. Water quality data collected in the estuary complex at the mouth of the Elwha River document how conditions in the estuary changed as a result of sediment deposition over the 3 yr the dams were removed. Rapid and large-scale changes in estuary conditions—including salinity, depth, and turbidity—occurred 1 yr into the dam removal process. Tidal propagation into the estuary ceased following a large sediment deposition event that began in October 2013, resulting in decreased salinity, and increased depth and turbidity in the estuary complex. These changes have persisted in the system through dam removal, significantly altering the structure and functioning of the Elwha River estuary ecosystem.
Washington↗
Habitat, not resource availability, limits consumer production in lake ecosystems
Food web productivity in lakes can be limited by dissolved organic carbon (DOC), which reduces fish production by limiting the abundance of their zoobenthic prey. We demonstrate that in a set of 10 small, north temperate lakes spanning a wide DOC gradient, these negative effects of high DOC concentrations on zoobenthos production are driven primarily by availability of warm, well-oxygenated habitat, rather than by light limitation of benthic primary production as previously proposed. There was no significant effect of benthic primary production on zoobenthos production after controlling for oxygen, even though stable isotope analysis indicated that zoobenthos do use this resource. Mean whole-lake zoobenthos production was lower in high-DOC lakes with reduced availability of oxygenated habitat, as was fish biomass. These insights improve understanding of lake food webs and inform management in the face of spatial variability and ongoing temporal change in lake DOC concentrations.
Wisconsin and Michigan↗
Climate change impacts on lake thermal dynamics and ecosystem vulnerabilities
Using water column temperature records collected since 1968, we analyzed the impacts of climate change on thermal properties, stability intensity, length of stratification, and deep mixing dynamics of Lake Tahoe using a modified stability index (SI). This new SI is easier to produce and is a more informative measure of deep lake stability than commonly used stability indices. The annual average SI increased at 16.62 kg/m 2 /decade although the summer (May–October) average SI increased at a higher rate (25.42 kg/m 2 /decade) during the period 1968–2014. This resulted in the lengthening of the stratification season by approximately 24 d. We simulated the lake thermal structure over a future 100 yr period using a lake hydrodynamic model driven by statistically downscaled outputs of the Geophysical Fluid Dynamics Laboratory Model (GFDL) for two different green house gas emission scenarios (the A2 in which greenhouse-gas emissions increase rapidly throughout the 21 st Century, and the B1 in which emissions slow and then level off by the late 21 st Century). The results suggest a continuation and intensification of the already observed trends. The length of stratification duration and the annual average lake stability are projected to increase by 38 d and 12 d and 30.25 kg/m 2 /decade and 8.66 kg/m 2 /decade, respectively for GFDLA2 and GFDLB1, respectively during 2014–2098. The consequences of this change bear the hallmarks of climate change induced lake warming and possible exacerbation of existing water quality, quantity and ecosystem changes. The developed methodology could be extended and applied to other lakes as a tool to predict changes in stratification and mixing dynamics.
California, Nevada↗
Metabolic and physiochemical responses to a whole-lake experimental increase in dissolved organic carbon in a north-temperate lake
Over the last several decades, many lakes globally have increased in dissolved organic carbon (DOC), calling into question how lake functions may respond to increasing DOC. Unfortunately, our basis for making predictions is limited to spatial surveys, modeling, and laboratory experiments, which may not accurately capture important whole-ecosystem processes. In this article, we present data on metabolic and physiochemical responses of a multiyear experimental whole-lake increase in DOC concentration. Unexpectedly, we observed an increase in pelagic gross primary production, likely due to a small increase in phosphorus as well as a surprising lack of change in epilimnetic light climate. We also speculate on the importance of lake size modifying the relationship between light climate and elevated DOC. A larger increase in ecosystem respiration resulted in an increased heterotrophy for the treatment basin. The magnitude of the increase in heterotrophy was extremely close to the excess DOC load to the treatment basin, indicating that changes in heterotrophy may be predictable if allochthonous carbon loads are well-constrained. Elevated DOC concentration also reduced thermocline and mixed layer depth and reduced whole-lake temperature. Results from this experiment were quantitatively different, and sometimes even in the opposite direction, from expectations based on cross-system surveys and bottle experiments, emphasizing the importance of whole-ecosystem experiments in understanding ecosystem response to environmental change.
Limnology and Oceanography↗
Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation
Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. We measured changes in commonly used optical properties and indices in DOM leached from peat soil, plants, and algae following biological and photochemical degradation to determine whether they provide unique signatures that can be linked to original DOM source. Changes in individual optical parameters varied by source material and process, with biodegradation and photodegradation often causing values to shift in opposite directions. Although values for different source materials overlapped at the end of the 111-day lab experiment, multivariate statistical analyses showed that unique optical signatures could be linked to original DOM source material even after degradation, with 17 optical properties determined by discriminant analysis to be significant (p<0.05) in distinguishing between DOM source and environmental processing. These results demonstrate that inferring the source material from optical properties is possible when parameters are evaluated in combination even after extensive biological and photochemical alteration.
Limnology and Oceanography↗
Intertidal salt marshes as an important source of inorganic carbon to the coastal ocean
Dynamic tidal export of dissolved inorganic carbon (DIC) to the coastal ocean from highly productive intertidal marshes and its effects on seawater carbonate chemistry are thoroughly evaluated. The study uses a comprehensive approach by combining tidal water sampling of CO 2 parameters across seasons, continuous in situ measurements of biogeochemically-relevant parameters and water fluxes, with high-resolution modeling in an intertidal salt marsh of the U.S. northeast region. Salt marshes can acidify and alkalize tidal water by injecting CO 2 (DIC) and total alkalinity (TA). DIC and TA generation may also be decoupled due to differential effects of marsh aerobic and anaerobic respiration on DIC and TA. As marsh DIC is added to tidal water, the buffering capacity first decreases to a minimum and then increases quickly. Large additions of marsh DIC can result in higher buffering capacity in ebbing tide than incoming tide. Alkalization of tidal water, which mostly occurs in the summer due to anaerobic respiration, can further modify buffering capacity. Marsh exports of DIC and alkalinity may have complex implications for the future, more acidified ocean. Marsh DIC export exhibits high variability over tidal and seasonal cycles, which is modulated by both marsh DIC generation and by water fluxes. The marsh DIC export of 414 g C m −2 yr −1 , based on high-resolution measurements and modeling, is more than twice the previous estimates. It is a major term in the marsh carbon budget and translates to one of the largest carbon fluxes along the U.S. East Coast.
Massachusetts↗
Spatio-temporal development of vegetation die-off in a submerging coastal marsh
In several places around the world, coastal marsh vegetation is converting to open water through the formation of pools. This is concerning, as vegetation die-off is expected to reduce the marshes' capacity to adapt to sea level rise by vegetation-induced sediment accretion. Quantitative analyses of the spatial and temporal development of marsh vegetation die-off are scarce, although these are needed to understand the bio-geomorphic feedback effects of vegetation die-off on flow, erosion, and sedimentation. In this study, we quantified the spatial and temporal development of marsh vegetation die-off with aerial images from 1938 to 2010 in a submerging coastal marsh along the Blackwater River (Maryland, U.S.A). Our results indicate that die-off begins with conversion of marsh vegetation into bare open water pools that are relatively far (> 75 m) from tidal channels. As vegetation die-off continues, pools expand, and new pools emerge at shorter and shorter distances from channels. Consequently larger pools are found at larger distances from the channels. Our results suggest that the size of the pools and possibly the connection of pools with the tidal channel system have important bio-geomorphic implications and aggravate marsh deterioration. Moreover, we found that the temporal development of vegetation die-off in moderately degraded marshes is similar as the spatial die-off development along a present-day gradient, which indicates that the contemporary die-off gradient might be considered a chronosequence that offers a unique opportunity to study vegetation die-off processes.
Limnology and Oceanography↗
Spectral wave dissipation by submerged aquatic vegetation in a back-barrier estuary
Submerged aquatic vegetation is generally thought to attenuate waves, but this interaction remains poorly characterized in shallow-water field settings with locally generated wind waves. Better quantification of wave–vegetation interaction can provide insight to morphodynamic changes in a variety of environments and also is relevant to the planning of nature-based coastal protection measures. Toward that end, an instrumented transect was deployed across a Zostera marina (common eelgrass) meadow in Chincoteague Bay, Maryland/Virginia, U.S.A., to characterize wind-wave transformation within the vegetated region. Field observations revealed wave-height reduction, wave-period transformation, and wave-energy dissipation with distance into the meadow, and the data informed and calibrated a spectral wave model of the study area. The field observations and model results agreed well when local wind forcing and vegetation-induced drag were included in the model, either explicitly as rigid vegetation elements or implicitly as large bed-roughness values. Mean modeled parameters were similar for both the explicit and implicit approaches, but the spectral performance of the explicit approach was poor compared to the implicit approach. The explicit approach over-predicted low-frequency energy within the meadow because the vegetation scheme determines dissipation using mean wavenumber and frequency, in contrast to the bed-friction formulations, which dissipate energy in a variable fashion across frequency bands. Regardless of the vegetation scheme used, vegetation was the most important component of wave dissipation within much of the study area. These results help to quantify the influence of submerged aquatic vegetation on wave dynamics in future model parameterizations, field efforts, and coastal-protection measures.
Limnology and Oceanography↗
Dissolved methane in the Beaufort Sea and the Arctic Ocean, 1992-2009; sources and atmospheric flux
Methane concentration and isotopic composition was measured in ice-covered and ice-free waters of the Arctic Ocean during eleven surveys spanning the years of 1992-1995 and 2009. During ice-free periods, methane flux from the Beaufort shelf varies from 0.14 to 0.43 mg CH4 m-2 day-1. Maximum fluxes from localized areas of high methane concentration are up to 1.52 mg CH4 m-2 day-1. Seasonal buildup of methane under ice can produce short-term fluxes of methane from the Beaufort shelf that varies from 0.28 to 1.01 to mg CH4 m-2 day-1. Scaled-up estimates of minimum methane flux from the Beaufort Sea and pan-Arctic shelf for both ice-free and ice-covered periods range from 0.02 Tg CH4 yr-1 and 0.30 Tg CH4 yr-1 respectively to maximum fluxes of 0.18 Tg CH4 yr-1 and 2.2 Tg CH4 yr-1 respectively. A methane flux of 0.36 Tg CH4 yr-1from the deep Arctic Ocean was estimated using data from 1993-94. The flux can be as much as 2.35 Tg CH4 yr-1 estimated from maximum methane concentrations and wind speeds of 12 m/s, representing only 0.42% of the annual atmospheric methane budget of ~560 Tg CH4 yr-1. There were no significant changes in methane fluxes during the time period of this study. Microbial methane sources predominate with minor influxes from thermogenic methane offshore Prudhoe Bay and the Mackenzie River delta and may include methane from gas hydrate. Methane oxidation is locally important on the shelf and is a methane sink in the deep Arctic Ocean.
Limnology and Oceanography↗
A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium
Phytoplankton are critical component of the food web in most large rivers and estuaries, and thus identifying dominant controls on phytoplankton abundance and species composition is important to scientists, managers, and policymakers. Recent studies from a variety of systems indicate that ammonium ( NH + 4 ) in treated wastewater effluent decreases primary production and alters phytoplankton species composition. However, these findings are based mainly on laboratory and enclosure studies, which may not adequately represent natural systems. To test effects of effluent high in ammonium on phytoplankton at the ecosystem scale, we conducted whole-river–scale experiments by halting discharges to the Sacramento River from the regional wastewater treatment plant (WWTP), and used a Lagrangian approach to compare changes in phytoplankton abundance and species composition in the presence (+EFF) and absence (−EFF) of effluent. Over 5 d of downstream travel from 20 km above to 50 km below the WWTP, chlorophyll concentrations declined from 15–25 to ∼2.5 μg L −1 , irrespective of effluent addition. Benthic diatoms were dominant in most samples. We found no significant difference in phytoplankton abundance or species composition between +EFF and −EFF conditions. Moreover, greatest declines in chlorophyll occurred upstream of the WWTP where NH + 4 concentrations were low. Grazing by clams and zooplankton could not account for observed losses, suggesting other factors such as hydrodynamics and light limitation were responsible for phytoplankton declines. These results highlight the advantages of conducting ecosystem-scale, Lagrangian-based experiments to understand the dynamic and complex interplay between physical, chemical, and biological factors that control phytoplankton populations.
California↗