Rebuilding marine life.

Sustainable Development Goal 14 of the United Nations aims to "conserve and sustainably use the oceans, seas and marine resources for sustainable development". Achieving this goal will require rebuilding the marine life-support systems that deliver the many benefits that society receives from a healthy ocean. Here we document the recovery of marine populations, habitats and ecosystems following past conservation interventions. Recovery rates across studies suggest that substantial recovery of the abundance, structure and function of marine life could be achieved by 2050, if major pressures-including climate change-are mitigated. Rebuilding marine life represents a doable Grand Challenge for humanity, an ethical obligation and a smart economic objective to achieve a sustainable future.

Rebuild the Academy: Supporting academic mothers during COVID-19 and beyond.

The issues facing academic mothers have been discussed for decades. Coronavirus Disease 2019 (COVID-19) is further exposing these inequalities as womxn scientists who are parenting while also engaging in a combination of academic related duties are falling behind. These inequities can be solved by investing strategically in solutions. Here we describe strategies that would ensure a more equitable academy for working mothers now and in the future. While the data are clear that mothers are being disproportionately impacted by COVID-19, many groups could benefit from these strategies. Rather than rebuilding what we once knew, let us be the architects of a new world.

Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science.

Success and impact metrics in science are based on a system that perpetuates sexist and racist "rewards" by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals' meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change.

Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.

Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.

Negligible Greenhouse Gas Release from Sediments in Oyster Habitats.

After centuries of decline, oyster populations are now on the rise in coastal systems globally following aquaculture development and restoration efforts. Oysters regulate the biogeochemistry of coastal systems in part by promoting sediment nutrient recycling and removing excess nitrogen via denitrification. Less clear is how oysters alter sediment greenhouse gas (GHG) fluxes-an important consideration as oyster populations grow. Here, we show that sediments in oyster habitats produce carbon dioxide (CO2), with highest rates in spring (2396.91 ± 381.98 µmol CO2 m-2 h-1) following deposition of seasonal diatom blooms and in summer (2795.20 ± 307.55 µmol CO2 m-2 h-1) when temperatures are high. Sediments in oyster habitats also consistently released methane to the water column (725.94 ± 150.34 nmol CH4 m-2 h-1) with no seasonal pattern. Generally, oyster habitat sediments were a sink for nitrous oxide (N2O; -36.11 ± 7.24 nmol N2O m-2 h-1), only occasionally releasing N2O in spring. N2O release corresponded to high organic matter and dissolved nitrogen availability, suggesting denitrification as the production pathway. Despite potential CO2 production increases under aquaculture in some locations, we conclude that in temperate regions oysters have an overall negligible impact on sediment GHG cycling.

Beyond Bioextraction: The Role of Oyster-Mediated Denitrification in Nutrient Management.

Recently, interest has grown in using oyster-mediated denitrification resulting from aquaculture and restoration as mechanisms for reactive nitrogen (N) removal. To date, short-term N removal through bioextraction has received the most management interest, but there is a growing body of research that has shown oysters can also mediate the long-term removal of N through denitrification (the microbial conversion of reactive N to relatively inert dinitrogen (N2) gas). Oyster suspension feeding and ammonium release via waste and deposition of organic matter to the sediments can stimulate nitrification-denitrification near oyster reefs and aquaculture sites. Oysters also harbor a diverse microbial community in their tissue and shell promoting denitrification and thus enhanced N removal. Additionally, surface areas on oyster reefs provide a habitat for other filter-feeding macrofaunal communities that can further enhance denitrification. Denitrification is a complex biogeochemical process that can be difficult to convey to stakeholders. These complexities have limited consideration and inclusion of oyster-mediated denitrification within nutrient management. Although oyster-mediated denitrification will not be a standalone solution to excess N loading, it may provide an additional management tool that can leverage oyster aquaculture and habitat restoration as a N mitigation strategy. Here, we provide an overview of the biogeochemical processes involved in oyster-mediated denitrification and summarize how it could be incorporated into nutrient management efforts by various stakeholders.

A synthesis of methane emissions from shallow vegetated coastal ecosystems.

Vegetated coastal ecosystems (VCEs; i.e., mangroves, salt marshes, and seagrasses) play a critical role in global carbon (C) cycling, storing 10× more C than temperate forests. Methane (CH4 ), a potent greenhouse gas, can form in the sediments of these ecosystems. Currently, CH4 emissions are a missing component of VCE C budgets. This review summarizes 97 studies describing CH4 fluxes from mangrove, salt marsh, and seagrass ecosystems and discusses factors controlling CH4 flux in these systems. CH4 fluxes from these ecosystems were highly variable yet they all act as net methane sources (median, range; mangrove: 279.17, -67.33 to 72,867.83; salt marsh: 224.44, -92.60 to 94,129.68; seagrass: 64.80, 1.25-401.50 µmol CH4 m-2 day-1 ). Together CH4 emissions from mangrove, salt marsh, and seagrass ecosystems are about 0.33-0.39 Tmol CH4 -C/year-an addition that increases the current global marine CH4 budget by more than 60%. The majority (~45%) of this increase is driven by mangrove CH4 fluxes. While organic matter content and quality were commonly reported in individual studies as the most important environmental factors driving CH4 flux, they were not significant predictors of CH4 flux when data were combined across studies. Salinity was negatively correlated with CH4 emissions from salt marshes, but not seagrasses and mangroves. Thus the available data suggest that other environmental drivers are important for predicting CH4 emissions in vegetated coastal systems. Finally, we examine stressor effects on CH4 emissions from VCEs and we hypothesize that future changes in temperature and other anthropogenic activites (e.g., nitrogen loading) will likely increase CH4 emissions from these ecosystems. Overall, this review highlights the current and growing importance of VCEs in the global marine CH4 budget.

Low Greenhouse Gas Emissions from Oyster Aquaculture.

Production of animal protein is associated with high greenhouse gas (GHG) emissions. Globally, oyster aquaculture is increasing as a way to meet growing demands for protein, yet its associated GHG-emissions are largely unknown. We quantified oyster aquaculture GHG-emissions from the three main constituents of GHG-release associated with terrestrial livestock production: fermentation in the animal gut, manure management, and fodder production. We found that oysters release no methane (CH4) and only negligible amounts of nitrous oxide (0.00012 ± 0.00004 µmol N2O gDW-1 hr-1) and carbon dioxide (3.556 ± 0.471 µmol CO2 gDW-1 hr-1). Further, sediment fluxes of N2O and CH4 were unchanged in the presence of oyster aquaculture, regardless of the length of time it had been in place. Sediment CO2 release was slightly stimulated between 4 and 6 years of aquaculture presence and then returned to baseline levels but was not significantly different between aquaculture and a control site when all ages of culture were pooled. There is no GHG-release from oyster fodder production. Considering the main drivers of GHG-release in terrestrial livestock systems, oyster aquaculture has less than 0.5% of the GHG-cost of beef, small ruminants, pork, and poultry in terms of CO2-equivalents per kg protein, suggesting that shellfish aquaculture may provide a a low GHG alternative for future animal protein production compared to land based sources. We estimate that if 10% of the protein from beef consumption in the United States was replaced with protein from oysters, the GHG savings would be equivalent to 10.8 million fewer cars on the road.

Fate and Effect of Dissolved Silicon within Wastewater Treatment Effluent.

In large rivers, the ratios of silicon (Si)/nitrogen (N)/phosphorus (P) have changed dramatically as anthropogenic additions of N or P are not matched by Si. Wastewater effluent is a recognized source of N and P to coastal environments. Few previous studies, however, have examined the Si load of a large wastewater plant's effluent or the molar ratios of Si/N and Si/P in effluent. We examine the annual flux of dissolved silicon (DSi) carried by effluent from the second largest treatment plant by flow in the United States (Deer Island Treatment Plant, DITP, Boston, MA). We compare treatment plant nutrient fluxes to local urban river nutrient fluxes and trace the impact of the DITP DSi loading on receiving waters. Estimates (±95% confidence interval) of treated effluent (67 800 ± 1500 kmol DSi year-1) compared to untreated (69 500 kmol DSi year-1) indicate that the process of sewage treatment at DITP likely does not remove DSi. DITP effluent was Si-limited and this Si-limitation is reflected in the receiving waters (Massachusetts Bay). However, Si-limitation appears only in the area immediately surrounding the effluent discharge. We use these results to explain phytoplankton patterns in Massachusetts Bay and to provide the first estimate of DSi loading (3.6 Gmol SiO2 year-1) from wastewater effluent across the US.

Low ratios of silica to dissolved nitrogen supplied to rivers arise from agriculture not reservoirs.

Coastal marine systems are greatly altered by toxic marine algae, eutrophication and hypoxia. These problems have been linked to decreased ratios of dissolved silica to inorganic nitrogen (Si : DIN) delivered from land. Two mechanisms for this decline under consideration are enhanced nitrogen (N) fertiliser losses from agricultural lands or Si sequestration in reservoirs. Here we examine these mechanisms via nutrient concentrations in impoundments receiving water from 130 watersheds in a landscape representative of the agriculture that often dominates coastal nutrient inputs. Decreased Si : DIN was correlated with agriculture, not impoundment. Watersheds with > 60% agricultural land yielded highest DIN, whereas Si was uncorrelated with agricultural intensity. Furthermore, eutrophic lakes were dominated by Cyanobacteria that use little Si, so reservoirs did not diminish Si : DIN. Instead, Si : DIN increased slightly as reservoir residence time increased. These data suggest that impoundments in agricultural watersheds may enhance the water quality of coastal ecosystems, whereas fertiliser losses are detrimental.

Urban Dissolved Silica: Quantifying the Role of Groundwater and Runoff in Wastewater Influent.

Human impacts on silicon (Si) cycling are just being explored. In particular, we know little about the role of urban environments in altering the flux of Si from land to sea. Here we describe the annual load of dissolved Si (DSi) in the influent of the second largest wastewater treatment plant (by volume) in the United States (Deer Island Wastewater Facility, Boston, MA). We partition the ∼69 500 kmol DSi year(-1) influent load between three sources: runoff (12%), groundwater infiltration (39%), and sewage (49%). Based on these results, we hypothesized that instead of being delivered to local rivers, DSi in groundwater and runoff is redirected to the combined stormwater-sewage overflow system. To test this hypothesis we compared long-term (2007-2012) observations of DSi flux from the three urban rivers surrounding Boston to modeled DSi fluxes based on land use and land cover. As predicted, the modeled fluxes were higher than the measured fluxes indicating that the sewage infrastructure of Boston diverts watershed DSi to the treatment plant. This research increases our understanding of human changes to the Si cycle, demonstrates the potential usefulness of DSi as a groundwater infiltration tracer within sewage treatment systems, and highlights the underappreciated interannual variability of riverine DSi fluxes.

Salt marsh nitrogen cycling: where land meets sea.

Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.

Effects of nitrate and ammonium on assimilation of nitric oxide by Heterosigma akashiwo.

The harmful alga Heterosigma akashiwo possesses a hybrid nitrate reductase (NR) enzyme, NR2-2/2HbN, which has the potential to convert NO to nitrate for assimilation into biomass. In previous research, NR transcription in H. akashiwo was induced by nitrate while NR activity was inhibited by ammonium. Here, the capacity of H. akashiwo to use NO in the presence of nitrate and/or ammonium was investigated to understand the regulation of NO assimilation. Continuous cultures of H. akashiwo were acclimated to growth on nitrate, ammonium, or a mixture of both. Aliquots from these cultures were spiked with 15N-labeled NO. The expression of genes involved in nitrogen assimilation was evaluated, as well as nitrate reductase activity and assimilation of 15N-labeled nitrogen into algal biomass. Results showed that NO induced expression and activity of NR, and upregulated expression of GOGAT regardless of the presence of other inorganic nitrogen sources, while GS expression decreased over time. Furthermore, 15NO uptake and assimilation was significantly higher in cultures acclimated for growth on ammonium compared to cultures acclimated for growth on nitrate alone. Assimilation of NO may provide H. akashiwo with a competitive advantage in N-poor environments or areas with elevated NO.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study.

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas. Importance: Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Nitrogen fixation: a poorly understood process along the freshwater-marine continuum.

Although N2 fixation is a major component of the global N cycle and has been extensively studied in open-ocean and terrestrial ecosystems, rates and ecological dynamics remain virtually unknown for the inland and coastal aquatic ecosystems (lakes, wetlands, rivers, streams, estuaries) that connect terrestrial and marine biomes. This is due to the diversity of these habitats, as well as the traditional paradigm that N2 fixation rates were low to nonexistent, and therefore not important, in these ecosystems. We identify three major research themes to advance understanding of aquatic N2 fixation: 1) the biological diversity of diazotrophs and variability of N2 fixation rates, 2) the ecological stoichiometry of N2 fixation, and 3) the upscaling of N2 fixation rates from genes to ecosystems. Coordinating research across these areas will advance limnology and oceanography by fully integrating N2 fixation into ecological dynamics of aquatic ecosystems from local to global scales.

Evidence, causes, and consequences of declining nitrogen availability in terrestrial ecosystems.

The productivity of ecosystems and their capacity to support life depends on access to reactive nitrogen (N). Over the past century, humans have more than doubled the global supply of reactive N through industrial and agricultural activities. However, long-term records demonstrate that N availability is declining in many regions of the world. Reactive N inputs are not evenly distributed, and global changes-including elevated atmospheric carbon dioxide (CO2) levels and rising temperatures-are affecting ecosystem N supply relative to demand. Declining N availability is constraining primary productivity, contributing to lower leaf N concentrations, and reducing the quality of herbivore diets in many ecosystems. We outline the current state of knowledge about declining N availability and propose actions aimed at characterizing and responding to this emerging challenge.

Opportunities and Challenges for Including Oyster-Mediated Denitrification in Nitrogen Management Plans.

Nitrogen pollution is one of the primary threats to coastal water quality globally, and governmental regulations and marine policy are increasingly requiring nitrogen remediation in management programs. Traditional mitigation strategies (e.g., advanced wastewater treatment) are not always enough to meet reduction goals. Novel opportunities for additional nitrogen reduction are needed to develop a portfolio of long-term solutions. Increasingly, in situ nitrogen reduction practices are providing a complementary management approach to the traditional source control and treatment, including recognition of potential contributions of coastal bivalve shellfish. While policy interest in bivalves has focused primarily on nitrogen removal via biomass harvest, bivalves can also contribute to nitrogen removal by enhancing denitrification (the microbial driven process of bioavailable nitrogen transformation to di-nitrogen gas). Recent evidence suggests that nitrogen removed via enhanced denitrification may eclipse nitrogen removal through biomass harvest alone. With a few exceptions, bivalve-enhanced denitrification has yet to be incorporated into water quality policy. Here, we focus on oysters in considering how this issue may be addressed. We discuss policy options to support expansion of oyster-mediated denitrification, describe the practical considerations for incorporation into nitrogen management, and summarize the current state of the field in accounting for denitrification in oyster habitats. When considered against alternative nitrogen control strategies, we argue that enhanced denitrification associated with oysters should be included in a full suite of nitrogen removal strategies, but with the recognition that denitrification associated with oyster habitats will not alone solve our excess nitrogen loading problem.