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USGS2018

Patterns, pace and processes of water-quality variability: Examples from a long-studied estuary

Environmental time series have rich information content that is invaluable for measuring and understanding changes over time and guiding policies to manage change. I extracted information from measurements of 10 water‐quality constituents in upper San Francisco Bay from 1975 to 2016, one of the longest observational records in a U.S. estuary. Changes were detected at every time scale captured by monthly sampling. Long‐term trends included increased ammonium (+53%), nitrate + nitrate (+50%), silicate (+14%), Secchi depth (+42%), and decreased chlorophyll a (Chl a ) (−74%) and suspended particulate matter (−45%). Changes at the decadal scale included abrupt shifts (Chl a , nitrate + nitrite) and oscillations between shorter trends of increase and decrease (Secchi depth, phosphate). Long‐term trends were not expressed equally across all seasons, and seasonal patterns of change varied across constituents. These examples illustrate key features of environmental variability at the land–sea interface: (1) water‐quality components change continually at time scales from months to decades; (2) patterns of seasonal, multiyear, and multidecadal change are complex and vary across constituents; (3) primary drivers of change are freshwater inflow, the master regulator of estuarine dynamics, and human activities such as river damming, water diversions, wastewater discharge, environmental policies, and species introductions; (4) extracting the full information content of time series requires multiple analyses, each revealing a different layer of insight into how changes develop over time; (5) water‐quality variability is nonstationary, so future changes cannot be forecast reliably; (6) repeated observation is an essential method of Earth system science with applications in the design and performance measures of environmental policies.

California↗

USGS2022

Warming in the upper San Francisco Estuary: Patterns of water temperature change from five decades of data

Temperature is a key controlling variable from subcellular to ecosystem scales. Thus, climatic warming is expected to have broad impacts, especially in economically and ecologically valuable systems such as estuaries. The heavily managed upper San Francisco Estuary supplies water to millions of people and is home to fish species of high conservation, commercial, and recreational interest. Despite a long monitoring record (> 50 yr), we do not yet know how water temperatures have already changed or how trends vary spatially or seasonally. We fit generalized additive models on an integrated database of discrete water temperature observations to estimate long-term trends with spatio-seasonal variability. We found that water temperatures have increased 0.017°C yr −1 on average over the past 50 yr. Rates of temperature change have varied over time, but warming was predominant. Temperature increases were most widespread in the late-fall to winter (November to February) and mid-spring (April to June), coinciding with the winter development of juvenile Chinook salmon and spring spawning window of the endangered delta smelt. Warming was fastest in the northern regions, a key fish migration corridor with important tidal wetland habitat. However, no long-term temperature trends were detected in October and were only observed in some regions in May, July, and August. These results can help identify optimal areas for restoration or refugia to buffer the effects of a warming climate, and the methods can be leveraged to understand the spatiotemporal variability in climate warming patterns in other aquatic systems.

California↗

USGS2022

Corrigendum: Associations between cyanobacteria and indices of secondary production in the western basin of Lake Erie

In the last year, we became aware that data used in our above-referenced manuscript from 2018 published in Limnology and Oceanography contained significant errors. In the 2018 manuscript, we found that indices of secondary production were negatively correlated to indices of cyanobacterial abundance and toxicity. Unfortunately, one of our indices of cyanobacterial abundance (biovolume) and our measurement of toxicity (microcystin concentration) were inaccurate in the data we used in the 2018 manuscript. Upon discovering these errors, we immediately began correcting the repositories where these data were available. Having corrected those data repositories, we are now reporting on the re-analysis of the data using the methods previously described in the 2018 manuscript. Although the relationships are slightly different, our interpretation is that the conclusions of the 2018 manuscript are still valid using the corrected data. The data errors we experienced were traced to a spreadsheet that was used to share data among the research team, which had errors caused by mistakes in copy-pasting formulas instead of data and ‘inadvertent’ edits that were saved by the spreadsheet's auto-save function. We apologize to the scientific community for these errors.

Lake Erie↗

USGS1998

A mini drivepoint sampler for measuring pore water solute concentrations in the hyporheic zone of sand-bottom streams

A new method for collecting pore-water samples in sand and gravel streambeds is presented. We developed a mini drivepoint solution sampling (MINIPOINT) technique to collect pore-water samples at 2.5-cm vertical resolution. The sampler consisted of six small-diameter stainless steel drivepoints arranged in a 10-cm-diameter circular array. In a simple procedure, the sampler was installed in the streambed to preset drivepoint depths of 2.5, 5.0, 7.5, 10.0, 12.5, and 15.0 cm. Sampler performance was evaluated in the Shingobee River, Minnesota, and Pinal Creek, Arizona, by measuring the vertical gradient of chloride concentration in pore water beneath the streambed that was established by the uninterrupted injection to the stream for 3 d. Pore-water samples were withdrawn from all drivepoints simultaneously. In the first evaluation, the vertical chloride gradient was unchanged at withdrawal rates between 0.3 and 4.0 ml min-1 but was disturbed at higher rates. In the second evaluation, up to 70 ml of pore water was withdrawn from each drivepoint at a withdrawal rate of 2.5 ml min-1 without disturbing the vertical chloride gradient. Background concentrations of other solutes were also determined with MINIPOINT sampling. Steep vertical gradients were present for biologically reactive solutes such as DO, NH4/+, NO3/-, and dissolved organic C in the top 20 cm of the streambed. These detailed solute profiles in the hyporheic zone could not have been determined without a method for close interval vertical sampling that does not disturb natural hydrologic mixing between stream water and groundwater.

Limnology and Oceanography↗

USGS2001

Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (<=16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

Limnology and Oceanography↗

USGS1991

Estimating estuarine flushing and residence times in Charlotte Harbor, Florida, via salt balance and a box model

The new concept is that, over many tidal cycles, the tidally averaged "flow' (Qg) of water from the Gulf of Mexico, with a salinity of 35???, can be treated as a constant at any point in the estuary. This flow is used in a simple mixing equation to predict salinity in the estuary at different river inflows, and the predicted salinities are used to compute residence times for water in the estuary. The techniques developed to achieve optimal precision in the relation between river inflow and salinity include a newly derived equation to fit Qg by a least-squares method and a procedure to determine the optimal averaging period for river inflow. Results from Charlotte Harbor indicate that, under average (70 m3s-1) river inflow, 95% of the original water present in the harbor flushes into the gulf in 130 d. -from Authors

Limnology and Oceanography↗

USGS2004

Reach-scale isotope tracer experiment to quantify denitrification and related processes in a nitrate-rich stream, midcontinent United States

We conducted an in-stream tracer experiment with Br and 15 N-enriched NO 3 - to determine the rates of denitrification and related processes in a gaining NO 3 - -rich stream in an agricultural watershed in the upper Mississippi basin in September 2001. We determined reach-averaged rates of N fluxes and reactions from isotopic analyses of NO 3 - , NO 2 - , N 2 , and suspended particulate N in conjunction with other data in a 1.2-km reach by using a forward time-stepping numerical simulation that included groundwater discharge, denitrification, nitrification, assimilation, and air-water gas exchange with changing temperature. Denitrification was indicated by a systematic downstream increase in the d15N values of dissolved N 2 . The reach-averaged rate of denitrification of surface-water NO 3 - indicated by the isotope tracer was approximately 120 ± 20 µmol m -2 h -1 (corresponding to zero- and first-order rate constants of 0.63 µmol L -1 h -1 and 0.009 h -1 , respectively). The overall rate of NO 3 - loss by processes other than denitrification (between 0 and about 200 µmol m -2 h -1 ) probably was less than the denitrification rate but had a large relative uncertainty because the NO 3 - load was large and was increasing through the reach. The rates of denitrification and other losses would have been sufficient to reduce the stream NO 3 - load substantially in the absence of NO 3 - sources, but the losses were more than offset by nitrification and groundwater NO 3 - inputs at a combined rate of about 500-700 µmol m -2 h -1 . Despite the importance of denitrification, the overall mass fluxes of N 2 were dominated by discharge of denitrified groundwater and air-water gas exchange in response to changing temperature, whereas the flux of N 2 attributed to denitrification was relatively small. The in-stream isotope tracer experiment provided a sensitive direct reach-scale measurement of denitrification and related processes in a NO 3 - -rich stream where other mass-balance methods were not suitable because of insufficient sensitivity or offsetting sources and sinks. Despite the increasing NO 3 - load in the experimental reach, the isotope tracer data indicate that denitrification was a substantial permanent sink for N leaving this agricultural watershed during low-flow conditions.

Limnology and Oceanography↗

USGS2008

Dissolved oxygen transfer to sediments by sweep and eject motions in aquatic environments

Dissolved oxygen (DO) concentrations were quantified near the sediment-water interface to evaluate DO transfer to sediments in a laboratory recirculating flume and open channel under varying fluid-flow conditions. DO concentration fluctuations were observed within the diffusive sublayer, as defined by the time-averaged DO concentration gradient near the sediment-water interface. Evaluation of the DO concentration fluctuations along with detailed fluid-flow characterizations were used to quantify quasi-periodic sweep and eject motions (bursting events) near the sediments. Bursting events dominated the Reynolds shear stresses responsible for momentum and mass fluctuations near the sediment bed. Two independent methods for detecting bursting events using DO concentration and velocity data produced consistent results. The average time between bursting events was scaled with wall variables and was incorporated into a similarity model to describe the dimensionless mass transfer coefficient (Sherwood number, Sh) in terms of the Reynolds number, Re, and Schmidt number, Sc, which described transport in the flow. The scaling of bursting events was employed with the similarity model to quantify DO transfer to sediments and results showed a high degree of agreement with experimental data. ?? 2008, by the American Society of Limnology and Oceanography, Inc.

Limnology and Oceanography↗

USGS2026

Summertime methane and carbon dioxide emission rates and associated variables from a national-scale survey of 146 reservoirs in the United States

Reservoirs are globally important sources of greenhouse gases, but the magnitude of their emissions is highly uncertain. Here we present data for 146 reservoirs from two surveys of reservoir methane and carbon dioxide emissions, one at the regional scale in the midwestern United States and one at the national scale in the conterminous United States, plus data from one reservoir in Washington and another in Puerto Rico. At all reservoirs, ebullitive and diffusive emissions and basic physiochemistry were measured at 15-70 locations during one 22 to 64-hour period during the summers of 2016-2023, with four reservoirs revisited a second time. Concomitant water chemistry measurements were also made at an index site. The dataset is comprised of two geospatial files and seven .csv files containing greenhouse gas emissions, water chemistry, morphology, and other relevant data. These data comprise the largest multi-reservoir emissions dataset ever assembled using consistent measurement methods.

conterminous United States, Puerto Rico↗

USGS2003

Evaporation determined by the energy-budget method for Mirror Lake, New Hampshire

Evaporation was determined by the energy - budget method for Mirror Lake during the open water periods of 1982-1987. For all years, evaporation rates were low in spring and fall and highest during the summer. However, the times of highest evaporation rates varied during the 6 yr. Evaporation reached maximum rates in July for three of the years, in June for two of the years, and in August for one of the years. The highest evaporation rate during the 6-yr study was 0.46 cm d -1 during 27 May-4 June 1986 and 15-21 July 1987. Solar radiation and atmospheric radiation input to the lake and long-wave radiation emitted from the lake were by far the largest energy fluxes to and from the lake and had the greatest effect on evaporation rates. Energy advected to and from the lake by precipitation, surface water, and ground water had little effect on evaporation rates. In the energy - budget method , average evaporation rates are determined for energy - budget periods, which are bounded by the dates of thermal surveys of the lake . Our study compared evaporation rates calculated for short periods, usually ∼1 week, with evaporation rates calculated for longer periods, usually ∼2 weeks. The results indicated that the shorter periods showed more variability in evaporation rates, but seasonal patterns, with few exceptions, were similar.

New Hampshire↗

USGS2007

Long-term changes in abundance and diversity of macrophyte and waterfowl populations in an estuary with exotic macrophytes and improving water quality

We assessed species-specific coverage (km2) of a submerged aquatic vegetation (SAV) community in the fresh and upper oligohaline Potomac Estuary from 1985 to 2001 using a method combining field observations of species-proportional coverage data with congruent remotely sensed coverage and density (percent canopy cover) data. Biomass (estimated by density-weighted coverage) of individual species was calculated. Under improving water quality conditions, exotic SAV species did not displace native SAV; rather, the percent of natives increased over time. While coverage-based diversity did fluctuate and increased, richness-based community turnover rates were not significantly different from zero. SAV diversity was negatively related to nitrogen concentration. Differences in functional traits, such as reproductive potential, between the dominant native and exotic species may explain some interannual patterns in SAV. Biomass of native, as well as exotic, SAV species varied with factors affecting water column light attenuation. We also show a positive response by a higher trophic level, waterfowl, to SAV communities dominated by exotic SAV from 1959 to 2001. ?? 2007, by the American Society of Limnology and Oceanography, Inc.

Limnology and Oceanography↗

USGS2022

Taking steps to address inequities in open-access publishing through an early career publication honor

Access to resources—whether human, financial, or social—is a key indicator of research output and, in turn, academic career progression. However, resources are not equally distributed among scientists and disparities often stem from external factors. This reality is particularly impactful for early career researchers (ECRs) who have limited control over the resources available to them to advance their careers. The resources needed to fund open-access (OA) publishing are a well-known source of academic inequity (Ross-Hellauer 2022 ). Despite this, wide support for OA publishing exists across the scientific community, largely because OA articles increase access to the scientific literature by removing costly paywalls (Piwowar et al. 2018 ). Benefits of OA publishing also exist for individual researchers; OA studies are read and cited more, so much so that an “open access citation advantage” has been described (McCabe and Snyder 2014 ). Depending on the methods and journals studied, this advantage ranges from an 8 to 40% increase in citation rate (Piwowar et al. 2018 ). The OA publishing model is set to expand further, with influential groups seeking to mandate OA publishing (e.g., Plan S; Else 2021 ) including recent guidance from the United States Office of Science and Technology Policy (The White House 2022 ). However, OA publishing remains expensive, often prohibitively so, and OA fees deter ECRs broadly (Sarabipour et al. 2019 ), and particularly those from the Global South (Kwon 2022 ; Santidrián Tomillo et al. 2022 ).

Limnology and Oceanography Letters↗

USGS2009

Detection and characterization of benthic filamentous algal stands ( Cladophora sp.) on rocky substrata using a high-frequency echosounder

A high-frequency echosounder was used to detect and characterize percent cover and stand height of the benthic filamentous green alga Cladophora sp. on rocky substratum of the Laurentian Great Lakes. Comparisons between in situ observations and estimates of the algal stand characteristics (percent cover, stand height) derived from the acoustic data show good agreement for algal stands that exceeded the height threshold for detection by acoustics (~7.5 cm). Backscatter intensity and volume scattering strength were unable to provide any predictive power for estimating algal biomass. A comparative analysis between the only current commercial software (EcoSAV™) and an alternate method using a graphical user interface (GUI) written in MATLAB® confirmed previous findings that EcoSAV functions poorly in conditions where the substrate is uneven and bottom depth changes rapidly. The GUI method uses a signal processing algorithm similar to that of EcoSAV but bases bottom depth classification and algal stand height classification on adjustable thresholds that can be visualized by a trained analyst. This study documents the successful characterization of nuisance quantities of filamentous algae on hard substrate using an acoustic system and demonstrates the potential to significantly increase the efficiency of collecting information on the distribution of nuisance macroalgae. This study also highlights the need for further development of more flexible classification algorithms that can be used in a variety of aquatic ecosystems.

Great Lakes↗

USGS2003

Temperature correction in conductivity measurements

Electrical conductivity has been widely used in freshwater research but usual methods employed by limnologists for converting measurements to conductance at a given temperature have not given uniformly accurate results. The temperature coefficient used to adjust conductivity of natural waters to a given temperature varies depending on the kinds and concentrations of electrolytes, the temperature at the time of measurement, and the temperature to which measurements are being adjusted. The temperature coefficient was found to differ for various lake and stream waters, and showed seasonal changes. High precision can be obtained only by determining temperature coefficients for each water studied. Mean temperature coefficients are given for various temperature ranges that may be used where less precision is required.

Limnology and Oceanography↗

USGS2001

Quantifying groundwater discharge through fringing wetlands to estuaries: Seasonal variability, methods comparison, and implications for wetland-estuary exchange

Because groundwater discharge along coastal shorelines is often concentrated in zones inhabited by fringing wetlands, accurately estimating discharge is essential for understanding its effect on the function and maintenance of these ecosystems. Most previous estimates of groundwater discharge to coastal wetlands have been temporally limited and have used only a single approach to estimate discharge. Furthermore, groundwater input has not been considered as a major mechanism controlling pore-water flushing. We estimated seasonally varying groundwater discharge into a fringing estuarine wetland using three independent methods (Darcy's Law, salt balance, and Br- tracer). Seasonal patterns of discharge predicted by both Darcy's Law and the salt balance yielded similar seasonal patterns with discharge maxima and minima in spring and early fall, respectively. They differed, however, in the estimated magnitude of discharge by two- to fourfold in spring and by 10-fold in fall. Darcy estimates of mean discharge ranged between -8.0 and 80 L m-2 d-1, whereas the salt balance predicted groundwater discharge of 0.6 to 22 L m-2 d-1. Results from the Br- tracer experiment estimated discharge at 16 L m-2 d-t, or nearly equal to the salt balance estimate at that time. Based upon the tracer test, pore-water conductivity profiles, and error estimates for the Darcy and salt balance approaches, we concluded that the salt balance provided a more certain estimate of groundwater discharge at high flow (spring). In contrast, the Darcy method provided a more reliable estimate during low flow (fall). Groundwater flushing of pore water in the spring exported solutes to the estuary at rates similar to tidally driven surface exchange seen in previous studies. Based on pore-water turnover times, the groundwater-driven flux of dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and NH4+ to the estuary was 11.9, 1.6, and 1.3 g C or g N m-2 wetland for the 90 d encompassing peak spring discharge. Groundwater-induced flushing of the wetland subsurface therefore represents an important mechanism by which narrow fringing marshes may seasonally relieve salt stress and export material to adjacent water masses.

Limnology and Oceanography↗

USGS2000

Bioavailability of particle-associated silver, cadmium, and zinc to the estuarine amphipod Leptocheirus plumulosus through dietary ingestion

We conducted experiments to determine effects of particle type on assimilatory metal bioavailability to Leptocheirus plumulosus, an infaunal, estuarine amphipod that is commonly used in sediment toxicity tests. The following particles were used to represent natural food items encountered by this surface-deposit and suspension-feeding amphipod: bacterial exopolymeric sediment coatings, polymeric coatings made from Spartina alterniflora extract, amorphous iron oxide coatings, the diatom Phaeodactylum tricornutum, the chlorophyte Dunaliella tertiolecta, processed estuarine sediment, and fresh estuarine sediment. Bioavailability of the gamma-emitting radioisotopes 110mAg, 109Cd, and 65Zn was measured as the efficiency with which L. plumulosus assimilated metals from particles using pulse-chase methods. Ag and Cd assimilation efficiencies were highest from bacterial exopolymeric coatings. Zn assimilation efficiency exhibited considerable interexperimental variation; the highest Zn assimilation efficiencies were measured from phytoplankton and processed sediment. In general, Ag and Cd assimilation efficiencies from phytoplankton were low and not related to the proportion of metal associated with cell cytosol or cytoplasm, a phenomenon reported for other particle-ingesting invertebrates. Amphipod digestive processes explain differences in Ag and Cd assimilation efficiencies between exopolymeric coatings and phytoplankton. Results highlight the importance of labile polymeric organic carbon sediment coatings in dietary metals uptake by this benthic invertebrate, rather than recalcitrant organic carbon, mineralogical features such as iron oxides, or phytoplankton.

Limnology and Oceanography↗

USGS2003

The productivity of San Cristobal Reef, Puerto Rico

San Cristobal Reef, Puerto Rico, was the site of a community metabolism study based on a new upstream-downstream method with experimental channels 4 m deep. Net productivity rates varied from 0.03 to 1.85 g O 2 m –2 reef area·h –1 ( x = 0.39; n = 59). Respiration measurements of one reef section from which light was excluded ranged from 0.26 to 0.48 g O 2 ·m –2 reef area·h –1 . The linear regression equation y = 0.58 x – 0.18, where y = g O 2 ·m –2 reef area·h –1 and x = mEin·m –2 ·s –1 , describes the correlation between light and metabolism at this site. Net primary productivity was 2.45 g O 2 ·m –2 reef area and gross primary productivity 5.42. The ratio of gross primary productivity to 24-h respiration was 0.7. Productivity rates of this heterotrophic zone are lower than those reported for shallower reef zones with greater algal cover.

San Cristobal Reef↗

USGS2011

Methyl mercury dynamics in a tidal wetland quantified using in situ optical measurements

We assessed monomethylmercury (MeHg) dynamics in a tidal wetland over three seasons using a novel method that employs a combination of in situ optical measurements as concentration proxies. MeHg concentrations measured over a single spring tide were extended to a concentration time series using in situ optical measurements. Tidal fluxes were calculated using modeled concentrations and bi-directional velocities obtained acoustically. The magnitude of the flux was the result of complex interactions of tides, geomorphic features, particle sorption, and random episodic events such as wind storms and precipitation. Correlation of dissolved organic matter quality measurements with timing of MeHg release suggests that MeHg is produced in areas of fluctuating redox and not limited by buildup of sulfide. The wetland was a net source of MeHg to the estuary in all seasons, with particulate flux being much higher than dissolved flux, even though dissolved concentrations were commonly higher. Estimated total MeHg yields out of the wetland were approximately 2.5 μg m −2 yr −1 —4–40 times previously published yields—representing a potential loading to the estuary of 80 g yr −1 , equivalent to 3% of the river loading. Thus, export from tidal wetlands should be included in mass balance estimates for MeHg loading to estuaries. Also, adequate estimation of loads and the interactions between physical and biogeochemical processes in tidal wetlands might not be possible without long-term, high-frequency in situ measurements.

Limnology and Oceanography↗