Nutrient (nitrogen and phosphorus) pollution is an environmental problem of global concern because overenrichment of water bodies increases phytoplankton biomass and ecosystem metabolism, depletes oxygen in bottom waters, and increases the frequency and intensity of harmful algal blooms. These responses to nutrient pollution have motivated policies to reduce anthropogenic nutrient inputs. However, these policies have not been universally implemented and their success at reducing phytoplankton biomass is confounded by other components of global change that regulate the conversion of nutrients into biomass. These regulating processes themselves are changing in the Anthropocene. Our study is an assessment of changing phytoplankton biomass over the period 2000-2019, using chlorophyll a trends measured in 191 lakes and 159 estuarine-coastal sites. Our results show that phytoplankton biomass has decreased in most lakes, increased in most coastal sites, and the largest trends have been predominantly negative for lakes and positive for coastal sites. These results provide evidence of opposing directions of phytoplankton biomass change between lakes and coastal sites in this recent period of unprecedented global change. Nutrient pollution is a knotty environmental problem, and our study indicates that it might be a particularly challenging problem for ecosystems situated in densely populated landscapes where freshwater and sea water meet. Success at overcoming this challenge will require deeper scientific understanding of changes in processes that regulate the conversion of nutrients into phytoplankton biomass, substantial investments of time and resources to reduce nutrient inputs, and a flexible strategy designed to anticipate and adapt to a changing world.

Abstract Terrestrial plants are sensitive indicators of global warming because their annual cycles of growth and senescence are changing as warming proceeds. Single celled algae are distinct life forms capable of population bursts in any season, so there is uncertainty about phytoplankton phenology as a comparable indicator of global warming. We analyzed 4+ decades of monthly chlorophyll a measurements at two sites in San Francisco Bay and found abrupt shifts during summer months leading to a 48‐day advance in the annual pattern of chlorophyll‐a accumulation at one site and a 36‐day delay at the other. These large phenological changes were not associated with changing temperature, but they were associated with changes in top–down control by bivalve filter feeders as biological communities were restructured by (1) introduction of a non‐native clam, and (2) a shift in atmospheric forcing of the NE Pacific. This study illustrates that changes in phytoplankton phenology are not necessarily responses to or indicators of global warming. However, they can be indicators of human disturbances and natural climate oscillations having effects large enough to mask the effect of climate warming.

Limnology and Oceanography BulletinVolume 32, Issue 2 p. 71-72 ASLO News New Appointments as Raelyn Cole Editorial Fellows Jim Cloern, Jim Cloern [email protected] US Geological Survey, Middlefield Rd., Menlo Park, CA, 94025 USASearch for more papers by this author Jim Cloern, Jim Cloern [email protected] US Geological Survey, Middlefield Rd., Menlo Park, CA, 94025 USASearch for more papers by this author First published: 17 April 2023 https://doi.org/10.1002/lob.10570Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume32, Issue2May 2023Pages 71-72 RelatedInformation

Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and modern landscapes and a scenario of wetland restoration. Results show that a 77% loss of wetland habitats (primarily marshes) has reduced ecosystem NPP by 94%, C (energy) flow to herbivores by 89%, and detritus production by 94%. Our results also show that attainment of habitat restoration goals could recover 12% of lost NPP and measurably increase carbon flow to consumers, including at-risk species and their food resources. This case study illustrates how a simple approach for quantifying the loss of NPP from measured habitat losses can guide wetland conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success.

Peer-review and subject-matter editing is the backbone of scientific publishing. However, early-career researchers (ECRs) are given few opportunities to participate in the editorial process beyond reviewing articles. Thus, a disconnect exists: science needs high-quality editorial talent to conduct, oversee and improve the publishing process, yet we dedicate few resources to building editorial talent nor giving ECRs formal opportunities to influence publishing from within. ECRs can contribute to the publishing landscape in unique ways given their insight into new and rapidly developing publishing trends (e.g. open science). Here, we describe a two-way fellowship model that gives ECRs a "seat" at the editorial table of a field-leading journal. We describe both the necessary framework and benefits that can stem from editorial fellowships for ECRs, editors, journals, societies, and the ​broader scientific community.

Nutrient enrichment has degraded many of the world’s estuaries by amplifying algal production, leading to hypoxia/anoxia, loss of vascular plants and fish/shellfish habitat, and expansion of harmful blooms (HABs). Policies to protect coastal waters from the effects of nutrient enrichment require information to determine if a water body is impaired by nutrients and if regulatory actions are required. We compiled information to inform these decisions for San Francisco Bay (SFB), an urban estuary where the best path toward nutrient management is not yet clear. Our results show that SFB has high nutrient loadings, primarily from municipal wastewater; there is potential for high algal production, but that production is not fully realized; and SFB is not impaired by hypoxia or recurrent HABs. However, our assessment includes reasons for concern: nitrogen and phosphorus concentrations higher than those in other estuaries impaired by nutrient pollution, chronic presences of multiple algal toxins, a recent increase of primary production, and projected future hydroclimatic conditions that could increase the magnitude and frequency of algal blooms. Policymakers thus face the challenge of determining the appropriate protective policy for SFB. We identify three crucial next steps for meeting this challenge: (1) new research to determine if algal toxins can be reduced through nutrient management, (2) establish management goals as numeric targets, and (3) determine the magnitude of nutrient load reduction required to meet those targets. Our case study illustrates how scientific information can be acquired and communicated to inform policymakers about the status of nutrient pollution, its risks, and strategies for minimizing those risks.

Phytoplankton play key roles in the oceans by regulating global biogeochemical cycles and production in marine food webs. Global warming is thought to affect phytoplankton production both directly, by impacting their photosynthetic metabolism, and indirectly by modifying the physical environment in which they grow. In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the vast oligotrophic ocean regions because it is one of the few multidecadal records of measured net primary productivity (NPP). We analysed the time series of phytoplankton primary productivity at BATS site using machine learning techniques (ML) to show that increased water temperature over a 27-year period (1990–2016), and the consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light. The unbalanced availability of these resources with warming, coupled with ecological changes at the community level, is expected to intensify the oligotrophic state of open-ocean regions that are far from land-based nutrient sources.

Face-to-face interactions between journal editors and scientists can be valuable for both parties. For early career scientists, however, approaching an editor can be intimidating. The Association for the Sciences of Limnology and Oceanography (ASLO) provides space for editors and early career scientists to interact at conferences—typically in the form of workshops on various aspects of the editorial process. These structured events can then be followed by more informal interactions throughout the conference. For early career scientists, these events and interactions can help clarify journal scope and key aspects of the editorial process. For editors, talking with authors earlier in the process may ultimately make their jobs easier in the formal stages of a manuscript review. The COVID-19 pandemic has led to the cancellation of many scientific conferences, with current guidance from the U.S. Centers for Disease Control and Prevention categorizing large events where attendees travel from outside the local area in the highest risk category (CDC 2020). In lieu of the canceled ASLO meeting during the COVID-19 pandemic (which was to be in Madison, Wisconsin in June 2020), the Raelyn Cole Editorial Fellows designed a virtual event with the aim of connecting ASLO journal editors with students and early career scientists. The virtual event was designed to mimic both structured and informal opportunities for interactions between editors and early career authors. The goal was to provide a space for scientists to put faces with names and ask the editors questions. All ASLO editors in chief and deputy chiefs were enthusiastic to participate, but there was some collective hesitancy given the limited experience with large virtual events. Support was provided by our publishing partners at Wiley, who took the technical lead. This support included finding the best virtual platform to meet our goals, developing a meeting banner (Fig. 1), and arranging registration details so that participants could join the meeting seamlessly. The event was deemed an “experiment” as we had few examples to follow. The “Meet the Editors” event was designed in two parts to meet our goal for both structured and unstructured time. The first part was a 50-min prerecorded session of brief introductions by each editor followed by a panel moderated by the Raelyn Cole Editorial Fellows. The fellows selected and asked the editors a series of questions that participants submitted ahead of the event. The prerecording allowed for a seamless presentation (e.g., without delays or connectivity issues) and minimized the dependence of presenters on a stable internet connection (a key consideration for virtual conferences; Bonifati et al. 2020). We strived to maintain the “live” feeling during this portion of the event via our online presence in the chat box. Both editors and fellows were available to chat while the prerecording played as questions arose. In the second part, participants were routed to breakout rooms (Box 1) with different topics based on preferences indicated on their registration form. For this portion of the event participants' microphones and video feeds were unmuted for a more informal face-to-face discussion with the editors and Raelyn Cole Editorial Fellows. On the day of the event, participants were made more comfortable by an up-front description of the event layout and how the transition between panel and breakout rooms would work. Being a Productive Writer in Academia Meet L&O Deputy Editor Maggie Xenopoulos, L&O Bulletin Deputy Editor Chris Filstrup, and Raelyn Cole Fellow Scott Hotaling to discuss writing productivity. In this session, we will discuss practical strategies for getting writing projects done while maintaining balance between work and life. Common Writing Pitfalls and How to Avoid Them Meet L&O Editor Dave Hambright and Raelyn Cole Fellow Bridget Deemer to discuss writing pitfalls. We will discuss some of the most common flaws that lead to poorly reviewed manuscripts despite good underlying science. We will then discuss some techniques for avoiding these pitfalls. Peer Review—How it Works, Why We Need it, How Editors Use It Meet L&O Letters Editor Jim Cloern and Raelyn Cole Fellow Kelsey Poulson-Ellestad to discuss peer review—the process, its value to authors, editors and reviewers, and outcomes (including rejection). Effectively Writing and Submitting Methods Papers Meet L&O Methods Editor Paul Kemp and former Raelyn Cole Fellow Laura Falkenberg to discuss the methods paper. Specialized article types are an important component of the publishing landscape, but researchers are rarely trained in their production. Here, we will focus on one such article type—methods papers—and discuss why and how to write this kind of paper, as well as how to enhance the chances of a successful submission. While we will focus on methods papers, the advice will be broadly applicable to the preparation and submission of any paper, regardless of article type. In terms of the logistical preparations, our partners at Wiley created a running sheet for the meeting that laid out each stage of the event, how long it would last, and who was doing what. They also put together a step-by-step guide to support self-recorded introductions by each editor. Equipment checks before the event and assigning back up hosts also allowed for a very smooth event. We consider the event largely successful. We achieved a 63% attendance rate which is higher than average for virtual events (Alice Smith pers. comm.). With 63 attendees, the event rivaled in-person conference workshops, but with the ability to reach new constituents, with at least 30% of attendees coming from outside the ASLO society, and scientists from outside of North America representing ~14% of the total attendees (discussed further below). We attribute this broader audience to our promotion on Twitter, including the use of a banner visual (Fig. 1). Attendees were largely student (48%) and early career scientists (29%), meeting our goal to link early career scientists with editors. Of the 15 attendees who filled out our postevent survey, all were either student or early career scientists and 14 out of 15 were “very satisfied” or “extremely satisfied” with the event (Fig. 2). One benefit of a virtual meeting is that participation is open to everyone, and not limited to those in physical attendance at a meeting. In-person meetings can be challenging for those with less funding, those with disabilities, or those further from the meeting venue geographically (Fleming 2019; Vervoort et al. 2020). Given the international membership of ASLO, and our society goal to grow international membership, we made a point to advertise the event on Twitter with reference to international time zones in Asia, Africa, Australia, and Europe (Fig. 3). Overall, scientists attended the event from 11 different countries. Attendance outside North America spanned Australia, Europe, South America, and Africa, with these participants making up ~14% of the total attendees. Of the 37 scientists who registered but did not attend, 24 were outside North America (and represented 11 additional countries). Thus, international registrants were disproportionately likely to cancel their attendance. We expect that this was in part due to a time zone issue. The event was held at 4:30 pm in New York (EST, UTC-4), making it especially difficult to participate from many locations in Europe, Africa and Asia. This time zone issue is unavoidable. There was some discussion among the fellows and editors of hosting a second event at a different time to accommodate those left out of the first time slot, but instead we opted to post the prerecorded portion of the event on YouTube to allow greater access to the content (https://www.youtube.com/watch?v=yFq7KAvGA0U). A key lesson learned from our experience is the need to appropriately balance structured (prerecorded) and unstructured (small/interactive) portions of the event. Our survey responses show a stronger skew towards “extremely satisfied” for the breakout sessions than for the prerecorded panel (Fig. 2). We also had direct qualitative feedback that supports this outcome: “I wish the pre-recorded segment was shorter and the breakout sessions were longer…,” “The breakout sessions were too short,” and “I wish the breakout room had been more interactive (although our facilitator did a good job).” This speaks to the importance of interaction and networking, especially for early career scientists who may benefit from conversations about projects on tight timelines (Weissgerber et al. 2020). Synchronous events can promote the interaction and discussion that define conference settings, but the use of such approaches must be balanced with a need to minimize dependency on stable internet connections (Bonifati et al. 2020). Feedback from a data management conference that was moved online due to COVID-19 suggests very little differentiation in preference for live talks with live Q&A vs. streamed talks with live Q&A (Bonifati et al. 2020). This feedback suggests one tool for striking a balance could be to adopt a streamed talk (which has less reliance on stable internet connections) with a live Q&A. In implementing virtual events, our experience highlights the importance for networking facilitators to keep in mind the diversity of communication styles, comfort with the online platform, and potential accessibility issues. We employed several strategies to encourage broad participation including: (1) getting participants to answer a general question early to help them feel comfortable with the chat box; (2) encouraging participants to use whatever communication they felt comfortable with (either asking via video, chat box to the group, direct message to moderator in chat); and (3) having some prepared questions to start the discussion. Nonverbal cues are much more difficult to detect during online conversation (Fish et al. 1992) and different norms of interaction may make the forum intimidating to some groups (Niner et al. 2020). Discomfort may be particularly felt by minority groups such as those who do not speak English as a first language (Vervoort et al. 2020). Importantly, some participants may experience accessibility issues with a particular form of communication (e.g., audio, visual). Strategies that employ multiple modes for communicating can help overcome this discomfort and enhance accessibility (e.g., live chat alongside live discussion, and live polls; Vervoort et al. 2020). Importantly, we note that accessibility could be further improved in future events. That is, when asked about suggestions to improve future events, one participant stated “captioning to increase accessibility.” Such built in flexibility may empower attendees to be more involved participants (Vervoort et al. 2020). As many events move online in response to COVID-19, there are silver linings in the potential for more equitable access to virtual conference material (Vervoort et al. 2020; Weissgerber et al. 2020). By creating a free virtual networking event, rather than the traditional in-person workshop at an ASLO conference, we believe it was more accessible to a range of early career scientists from different geographic locations who may not have attended if it had been run as an in-person session. While scientific conferences come with substantial barriers to low- and middle-income socioeconomic classes (Vervoort 2020) and attendance by an international audience, the virtual exchange of information and ideas could be an important tool for creating more equitable opportunities. Time will tell if the move toward virtual networking and knowledge exchange will outlast the immediate needs of a global pandemic (Vervoort et al. 2020) and become integrated into the regular functioning of our scientific society. Thank you to ASLO editors, especially Adrienne Sponberg who helped coordinate and promote the event. We appreciate the help from our partners at Wiley, particularly Alice Smith and Michael Smeaton who led the technical implementation of the virtual event. We also thank the ASLO administration, especially Teresa Curto. This manuscript benefited from helpful note taking by Dani Glidewell, Erica Nejad, Jessica Beyer, Taylor Eddy, Eve Minkin, and Eilea Knotts. This article and the event described therein was made possible by the ASLO Raelyn Cole Editorial Fellowship.

Earth system science is boundless. There are no limits to the kinds of questions, problems, mysteries, or paradoxes that motivate our research and shape its direction. So how do we decide which directions to take, which questions to answer, what problems to solve? Sometimes our research is motivated by an unanticipated event requiring a degree of stochastic interpretive crystal ball gazing. Last year we ended our careers of more than four decades as life scientists at the USGS in Menlo Park, CA. We find ourselves in a state of reflection and want to share a story about a stochastic event that brought us together as collaborators, taught us essential lessons of life as research scientists, and seeded a friendship that endures.

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.

Impermanence is an ecological principle1 but there are times when changes occur nonlinearly as abrupt community shifts (ACSs) that transform the ecosystem state and the goods and services it provides2. Here, we present a model based on niche theory3 to explain and predict ACSs at the global scale. We test our model using 14 multi-decadal time series of marine metazoans from zooplankton to fish, spanning all latitudes and the shelf to the open ocean. Predicted and observed fluctuations correspond, with both identifying ACSs at the end of the 1980s4–7 and 1990s5,8. We show that these ACSs coincide with changes in climate that alter local thermal regimes, which in turn interact with the thermal niche of species to trigger long-term and sometimes abrupt shifts at the community level. A large-scale ACS is predicted after 2014—unprecedented in magnitude and extent—coinciding with a strong El Niño event and major shifts in Northern Hemisphere climate. Our results underline the sensitivity of the Arctic Ocean, where unprecedented melting may reorganize biological communities5,9, and suggest an increase in the size and consequences of ACS events in a warming world. Abrupt community shifts, for marine species from zooplankton to fish, are shown to occur with local climate changes in which warming pushes species beyond their thermal niche. This modelling approach suggests future events will be larger and have more broad-reaching impacts.

Science is moving quickly toward open access of peer-reviewed scientific articles and the data they report. This change began in the early 1990s with publication of digital editions of articles accessible freely to anyone with an internet connection. Today, different models of Open Access exist. Publication of the most common (Direct Open Access) has grown 30% annually since 2000, and exceeded 190,000 articles in 2009 (Laakso et al. 2011). ASLO has recognized this important trend and embraced Open Access publication by making open-access options available to authors in two of its journals (Limnology and Oceanography and Limnology and Oceanography Methods), while also launching a fully open-access journal, Limnology and Oceanography Letters, in 2016. In 2018, 36% of papers in L&O and 38% of papers in L&O-Methods were published OpenOnline, while all of L&O-Letters articles were open access. However, another equally important component of open science—online publication of the data reported in our papers—is a work in progress. The rationales for publishing data are compelling, and include: (1) making publicly funded research available to the public, (2) allowing others to ask new questions of our data, (3) advancing research and innovation through synthetic analyses across studies, and (4) fostering reproducibility of research (Borgman 2012). ASLO is strongly supportive of open data. For example, publication in L&O-Letters requires that authors place the data and metadata associated with all of its publications in a “public repository that issues a DOI so that future readers can access the exact version of the dataset used in the study.” To guide authors in this relatively new practice in science, one of us recently published a step-by-step guide for placing data and metadata in a public data repository that can be used for any research article or journal (Soranno 2019). Open data will become the norm, not only because of mandates from government funding agencies and push from scientific societies and publishers (Michener 2015), but also because it leads to a more robust and reproducible science. Although data publication leads to increased visibility and citations of our work (Piwowar et al. 2007), members of the scientific community have not universally embraced the open-data mandate. A survey of 500 papers published in high-impact journals found that only 9% deposited the full data sets required by journal policy (Alsheikh-Ali et al. 2011). Resistance comes partly because of uncertainty about how our data will be used. Borgman (2012) explains the conundrum: “The farther removed from the data collection activity, the harder it is to make use of someone else's data. Thus, it is not surprising that concerns for the misinterpretation and misuse of data are common reasons that researchers give for not sharing.” Publishers have addressed this concern through the creation of a relatively new article type—the data article, an article that thoroughly describes a noteworthy, valuable, or novel data set, as well as entire journals devoted to publishing data articles. For example, Nature Research launched Scientific Data in 2014 to publish data articles (“descriptors”). Authors also have other outlets for publishing detailed descriptions of their published data in journals devoted to data papers, such as Geosciences Data Journal (Wiley), Data in Brief (Elsevier), and Earth System Science Data (Copernicus Publications). More recently, journals that publish traditional research articles have also begun to publish data articles. Data articles provide an opportunity for us, as data producers, to share essential information to minimize the likelihood that our published data will be misinterpreted, misrepresented, or misunderstood by others who use them. They also provide data producers with an avenue for getting credit for the major effort involved in not only collecting data, but in describing them effectively for reuse. Data articles describe the essentials of who produced the data; when, where, and how they were produced; the purposes for which they were produced; detailed and thorough descriptions of the methods used; and steps of quality control and assurance. Data articles are peer-reviewed, have unique digital identifiers, are indexed (e.g., in Web of Science, Scopus, Google Scholar, and PubMed), and are cited. For example, the impact factor of Scientific Data was 5.9 in 2018 (https://www.nature.com/sdata/about/faq#q6). Therefore, data articles give us professional credit on par with that we receive for publishing traditional scientific articles. Our purpose here is to announce that the ASLO Board of Directors has accepted founding Editor-in-Chief Patricia Soranno's proposal that L&O-Letters publish Data Articles as a new article type. We have begun the process to open the journal for submissions of data articles by the end of 2019. As far as we are aware, this will provide the first dedicated outlet for publication of data articles in the aquatic sciences. We encourage you to begin thinking now about submissions to attract and facilitate use or reuse of your data sets. Stay tuned for an upcoming editorial in L&O-Letters that will provide more detail about the structure of Data Articles, criteria for publication, and how they will advance ASLO's commitment to open science. We welcome questions and comments to loletters-eic@aslo.org.

The San Francisco Bay (SFB) is the largest estuary on the west coast of the United States. It is an important transition zone between marine, freshwater, and inland terrestrial watersheds. The SFB is an important region for the cycling of nutrients and pollutants and it supports nurseries of ecologically and commercially important fisheries, including some threatened species. Phytoplankton community structure influences food web dynamics, and the taxonomy of the phytoplankton may be more important in determining primary food quality than environmental factors. As such, estimating food quality from phytoplankton community composition can be a robust tool to understand trophic transfer of energy. Recent work explores phytoplankton food quality in SFB through the use of microscopy and phytoplankton chemotaxonomy to evaluate how changes in phytoplankton composition may have influenced the recent trophic collapse of pelagic fishes in the northern part of the SFB. The objective of this study is to determine if the approach can also be applied to imaging spectroscopy data in order to quantify phytoplankton food quality from space. Imaging spectroscopy data of SFB from the Airborne VisibleInfrared Imaging Spectrometer (AVIRIS) was collected during the Hyperspectral Infrared (HyspIRI) Airborne Campaign in California (2013 2015) and used in this study. Estimates of ocean chlorophyll and phytoplankton community structure were determined using standard ocean chlorophyll algorithms and the PHYtoplankton Detection with Optics (PHYDOTax) algorithms. These were validated using in situ observations of phytoplankton composition using microscopic cell counts and phytoplankton chemotaxonomy from the US Geological Surveys ship surveys of the SFB. The findings from this study may inform the use of future high spectral resolution satellite sensors with the spatial resolution appropriate for coastal systems (e.g., HyspIRI) to assess food quality from space.

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

Coastal‐estuarine systems are among the most productive marine ecosystems and their special role in producing harvestable fish and shellfish has been attributed to high primary production fueled by nutrient runoff from land and efficient trophic transfer. Here we ask if phytoplankton species composition and their food quality based on the percentage of long‐chain essential fatty acids (LCEFA) is another factor contributing to high secondary production in these ecosystems. We used long‐term measurements of major phytoplankton taxonomic groups and estimated their content of LCEFA along the salinity gradient in coastal‐estuarine ecosystems, with emphasis on Chesapeake Bay and the Baltic Sea, and an oceanic transect. Our data show that cyanobacteria with low nutritional quality often dominate at low‐salinity regions, while intermediate to higher salinity regions produce diatoms and dinoflagellates that have a higher content of LCEFA and are thus a higher‐quality food resource for consumers. Higher salinity regions have less pronounced seasonal changes in the percentage of phytoplankton LCEFA compared to low salinity regions, providing a stable supply of nutritious phytoplankton to consumers. The phytoplankton LCEFA content is similarly high in coastal upwelling systems and it decreases further offshore in oligotrophic oceanic regions dominated by picophytoplankton. Our results from a broad range of coastal‐ecosystem types show that ecosystems at the land‐sea interface provide a valuable service by producing phytoplankton enriched in the biochemicals essential for consumers. High primary production, coupled with high quality of that production, explain why the production of fish and shellfish is high where land and sea meet.

Author(s): Cloern, James E.; Kay, Jane; Kimmerer, Wim; Mount, Jeffrey; Moyle, Peter B.; Mueller–Solger, Anke

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with over-production of phytoplankton. Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll-a (chl-a) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a. Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m-3 as a "protective" threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13 - 16 mg m-3 that would meet a SFB-wide 80 % saturation Water Quality Criterion (WQC) for DO. Higher "at risk" chl-a thresholds from 25 - 40 mg m-3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L-1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

Surveys across the world oceans have shown that phytoplankton biomass and production are dominated by small cells (picoplankton) where nutrient concentrations are low, but large cells (microplankton) dominate when nutrient‐rich deep water is mixed to the surface. I analyzed phytoplankton size structure in samples collected over 25 yr in San Francisco Bay, a nutrient‐rich estuary. Biomass was dominated by large cells because their biomass selectively grew during blooms. Large‐cell dominance appears to be a characteristic of ecosystems at the land–sea interface, and these places may therefore function as analogs to oceanic upwelling systems. Simulations with a size‐structured NPZ model showed that runs of positive net growth rate persisted long enough for biomass of large, but not small, cells to accumulate. Model experiments showed that small cells would dominate in the absence of grazing, at lower nutrient concentrations, and at elevated (+5°C) temperatures. Underlying these results are two fundamental scaling laws: (1) large cells are grazed more slowly than small cells, and (2) grazing rate increases with temperature faster than growth rate. The model experiments suggest testable hypotheses about phytoplankton size structure at the land–sea interface: (1) anthropogenic nutrient enrichment increases cell size; (2) this response varies with temperature and only occurs at mid‐high latitudes; (3) large‐cell blooms can only develop when temperature is below a critical value, around 15°C; (4) cell size diminishes along temperature gradients from high to low latitudes; and (5) large‐cell blooms will diminish or disappear where planetary warming increases temperature beyond their critical threshold.

Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate-driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll-a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind-driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll-a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll-a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1-3 years, by 3- to 19-fold increased abundances of five ocean-produced demersal fish and crustaceans and 2.5-fold increase of summer chlorophyll-a in the Bay. These changes reflect a slow biological process of estuary-ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate-mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to changing patterns of upwelling timing and intensity as the planet continues to warm.

The U.S. Geological Survey (USGS) maintains a place-based research program in San Francisco Bay (USA) that began in 1969 and continues, providing one of the longest records of water-quality measurements in a North American estuary. Constituents include salinity, temperature, light extinction coefficient, and concentrations of chlorophyll-a, dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. We describe the sampling program, analytical methods, structure of the data record, and how to access all measurements made from 1969 through 2015. We provide a summary of how these data have been used by USGS and other researchers to deepen understanding of how estuaries are structured and function differently from the river and ocean ecosystems they bridge.