Carbonate coral sands are an integral part of the carbon and nutrient cycles in subtropical and tropical coastal environments. Recent studies indicate that nearshore carbonate sands may be hotspots for organic matter production and respiration, but the processes and their controls are poorly understood due to a lack of noninvasive in situ measurements. We deployed a new triple-sensor aquatic eddy covariance instrument to quantify seasonal O-2-fluxes over a coral sand platform at similar to 10 m water depth in the Florida Keys. The noninvasive measurements revealed the strong influences of light and bottom currents on magnitude and dynamics of the benthic metabolism. Light penetration through the clear water column facilitated substantial microphytobenthos production, making the seafloor a source of oxygen during daylight hours. Daytime benthic O-2 release to the water column ranged between 0.6 mmol O-2 m(-2) h(-1) (winter) and 4.8 mmol O-2 m(-2) h(-1) (summer), while nighttime sediment O-2 respiration varied between -1.2 mmol O-2 m(-2) h(-1) (winter) and -3.3 mmol O-2 m(-2) h(-1) (summer). Bottom currents modulated the fluxes, emphasizing the role of advective pore water exchange for biogeochemical reactions in the highly permeable sediment. Similar magnitudes and dynamics of daytime sediment O-2 release and nighttime O-2 uptake revealed a tight coupling between production and degradation of highly labile photosynthetic products. We use the results to explain why O-2 respiration rates in permeable carbonate sands of oligotrophic subtropical/tropical environments can reach similar magnitudes as those reported from permeable silicate sand beds of nutrient-rich temperate inner shelves.

The aquatic eddy covariance technique is increasingly used to determine oxygen (O-2) fluxes over benthic ecosystems. The technique uses O-2 measuring systems that have a high temporal and numerical resolution. In this study, we performed a series of lab and field tests to assess a new optical submersible O-2 meter designed for aquatic eddy covariance measurements and equipped with an existing ultra-high speed optical fiber sensor. The meter has a 16-bit digital-to-analog-signal conversion that produces a 0-5 V output at a rate up to 40 Hz. The device was paired with an acoustic Doppler velocimeter. The combined meter and fiber-optic O-2 sensor's response time was significantly faster in O-2-undersaturated water compared to in O-2-supersaturated water (0.087 vs. 0.12 s), but still sufficiently fast for aquatic eddy covariance measurements. The O-2 optode signal was not sensitive to variations in water flow or light exposure. However, the response time was affected by the direction of the flow. When the sensor tip was exposed to a flow from the back rather than the front, the response time increased by 37%. The meter's internal signal processing time was determined to be similar to 0.05 s, a delay that can be corrected for during postprocessing. In order for the built-in temperature correction to be accurate, the meter should always be submerged with the fiber-optic sensor. In multiple 21-47 h field tests, the system recorded consistently high-quality, low-noise O-2 flux data. Overall, the new meter is a powerful option for collecting robust aquatic eddy covariance data.

AbstractMegaripples are current‐generated seafloor bedforms of well‐sorted sand or gravel and wavelengths over 1 m. In this aquatic eddy covariance study, we measured large rates of benthic primary production and respiration for a shallow‐water sandy megaripple field exposed to strong tidally driven currents and intense sunlight. Current and light were the main short‐term drivers of a highly dynamic oxygen exchange. Daytime oxygen release as high as 300 mmol m−2 d−1 and nighttime oxygen uptake up to −100 mmol m−2 d−1 were likely sustained by current‐driven transport of oxygen, nutrients, and organic matter (fuel) into and out of the sand and superimposed by rapid internal cycling. Seasonal differences in temperature (45%) and light (69%) between April and September were the main long‐term drivers of substantially greater rates of gross primary production and respiration in September. The megaripples functioned as an intense metabolic hotspot with carbon cycling rates larger than those of most near‐shore sediments.

The marine nitrogen cycle is a main driver of ocean productivity and affects global climate. Despite decades of study, we still have an incomplete understanding of the role of the marine nitrogen cycle in the Earth system. While marine sediments play a major role in nitrogen cycling in the ocean, magnitudes and mechanisms are largely unconstrained. Recent research suggests that permeable sandy sediments on the highly energetic and dynamic continental shelf are key components of the marine nitrogen cycle, but data to quantify their contribution are lacking. Here, we use insights from measurements and modeling studies to substantiate the hypothesis that shelf sediments are an overlooked driver of the marine nitrogen cycle. Specifically, we propose that permeable shelf sediments are sites for intense nitrogen conversions and suggest a three‐pronged approach to address unresolved controversies.

Many coastal ecosystems, such as coral reefs and seagrass meadows, currently experience overgrowth by fleshy algae due to the interplay of local and global stressors. This is usually accompanied by strong decreases in habitat complexity and biodiversity. Recently, persistent, mat-forming fleshy red algae, previously described for the Black Sea and several Atlantic locations, have also been observed in the Mediterranean. These several centimetre high mats may displace seagrass meadows and invertebrate communities, potentially causing a substantial loss of associated biodiversity. We show that the sessile invertebrate biodiversity in these red algae mats is high and exceeds that of neighbouring seagrass meadows. Comparative biodiversity indices were similar to or higher than those recently described for calcifying green algae habitats and biodiversity hotspots like coral reefs or mangrove forests. Our findings suggest that fleshy red algae mats can act as alternative habitats and temporary sessile invertebrate biodiversity reservoirs in times of environmental change.

In shallow estuarine environments, the time scales of hydrodynamic processes that control particle distribution may outpace the time scales of phytoplankton patch formation through reproduction.Consequently, physical processes can dominate the distribution of the phytoplankton, but these processes and their dynamics are not well understood.Here we used flow measurements with a bottom mounted Acoustic Doppler Current Profiler (ADCP), shipboard hydrographic transects, drifter releases, and Rhodamine dye to characterize the smallscale flow environment and its effect on dispersion processes in a shallow estuarine environment, Apalachicola Bay, Florida.Spatial spectra of salinity and chlorophyll followed a power law behavior of -3 at length scales of 250 m -5 km.The ADCP data revealed the presence of a vertically sheared flow that was strongly modulated by tides and bottom topography.Tidal flows had a characteristic magnitude of 20 -40 cm s -1 , with durations of flow reversals between the near-surface and bottom flows.Drifter triplets indicated shear and strain rates on the order of 10 -3 -10 -4 s -1 , and single particle dispersion rates (diffusivity) of 0.1 m 2 s -1 .The area evolution of the dye patch observed by a drone corresponded to eddy diffusivity comparable to those estimated from drifters, or about 0.1 m 2 s -1 .The dye patch experiments demonstrate how physical processes at scales of 1-100 m can affect the shape and development of phytoplankton patches in the bay.Vertical shear, produced by wind directions deviating from flow direction, can broaden and divide a plankton patch by transporting different depths of a patch in different directions.When winds and currents are aligned, shear leads to elongation and narrowing of the patch.The results indicate that the small-scale flow environment in estuaries can be pivotal in controlling the distribution and dispersal of planktonic organisms and thereby becomes a decisive factor for the development and breakdown of phytoplankton communities.

Aquatic eddy covariance (AEC) is increasingly being used to study benthic oxygen (O2) flux dynamics, organic carbon cycling, and ecosystem health in marine and freshwater environments. Because it is a noninvasive technique, has a high temporal resolution (∼15 min), and integrates over a large area of the seafloor (typically 10-100 m2), it has provided new insights on the functioning of aquatic ecosystems under naturally varying in situ conditions and has given us more accurate assessments of their metabolism. In this review, we summarize biogeochemical, ecological, and biological insightsgained from AEC studies of marine ecosystems. A general finding for all substrates is that benthic O2 exchange is far more dynamic than earlier recognized, and thus accurate mean values can only be obtained from measurements that integrate over all timescales that affect the local O2 exchange. Finally, we highlight new developments of the technique, including measurements of air-water gas exchange and long-term deployments.

Oil contamination of beaches causes significant damage as these ecosystems are unique habitats that provide foraging and nesting grounds for a variety of animals including endangered species, and play pivotal roles in shore line protection and coastal economies. Even small oil spills in the ocean result in sizable slicks that currents transport to sandy beaches that line a third of the global shoreline. Weathering during transit reduces the degradability, viscosity and density of the oil, influencing its fate at the shore. While photolysis, biodegradation, tidal pumping, and seasonal sediment movement facilitate relatively rapid removal of stranded oil from sandy beaches of temperate and warm climes, thick buried oil layers persist for decades in armored gravel beaches of cold shores, emphasizing the controls of beach morphodynamics, biodegradation, and climate in the recovery from beach oil pollution.

Gulf of Mexico (GOM) ecosystems are interconnected by numerous physical and biological processes. After the Deepwater Horizon (DWH) disaster, these ecological processes facilitated dispersal of oil-spill toxicants or were damaged and broken. A considerable portion of post-DWH research focused on higher levels of biological organization (i.e., populations, communities, and ecosystems) spanning at least four environments (onshore, coastal, open ocean, and deep benthos). Damage wrought by the oil spill and mitigation efforts varied considerably across ecosystems. Whereas all systems show prolonged impacts because of cascading effects that impacted functional connections within and between communities, deep-sea and mesopelagic environments were particularly hard hit and have shown less resilience than shallow environments. In some environments, such as marshes or the deep-sea benthos, products from the spill are still biologically accessible. Some shallow ecosystems show signs of recovery, and populations of some species show resilience; however, a return to a “pre-spill” state is questionable. Importantly, habitats in which large amounts of energy flow through the ecosystem (marshes, coastal regions) recovered more quickly than low energy habitats (deep-sea benthos). Functional interactions between Gulf of Mexico systems are more complex and widespread than generally recognized. Moreover, ecosystems in the Gulf are subject to multiple stressors that can combine to impart greater, and less predictable, impacts. To help mitigate the effects of future insults, we identified four salient areas of research that should be addressed for each of the major environments within the GOM: establishing monitoring systems; quantifying coupling between GOM ecosystems; developing criteria for assessing the “vulnerability” and “resilience” of species, communities, and ecosystems; and developing holistic predictive modeling.

The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations ( e.g ., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.

Since the 2010 Deepwater Horizon (DWH) oil spill, the Gulf of Mexico Research Initiative (GOMRI) has studied the oil spill from the perspectives of ocean environment, ecosystems, socioeconomics and human health. As GOMRI sunsets in its tenth year after the DWH oil spill, synthesis efforts recently took place to assess the accomplishments of the program. In this paper, we report on DWH modeling as part of GOMRI's Synthesis and Legacy effort. We compile a list of 330 published applications by GOMRI, the Natural Resource Damage Assessment (NRDA), and others studying the DWH oil spill and look at a wide range of subjects, tools, achievements, and integration with field research. We offer highlights and synthesis based on discussions and public webinars held in 2019 and 2020. We synthesize the significant achievements and advancements that have been made in integrating the various disciplines and domains from a modeling perspective. There was a large diversity of tools used, including at least 74 unique modeling systems. Most studies employed circulation models. These hydrodynamic models were often coupled to wave, river, and atmosphere models, as well as representations of high pressure physics and oil chemistry. Several research groups used Lagrangian transport models and statistical inference to track subsurface oil. Some coupled biophysical models were also employed to study oil fate and weathering, larval transport, biological effects, and population dynamics. In a few cases, such biophysical models were linked to marine populations and to humans through socioeconomics effects and ecosystem services. We consider models made for response planning and remediation, damage assessment, and restoration planning. There are relatively few socioeconomic or human health models, although those few examples make good use of biophysical modeling products. Our conclusions offer some insights on how the development of new tools has better prepared us for studying environmental management challenges in the Gulf of Mexico.

The aquatic eddy covariance technique stands out as a powerful method for benthic O2 flux measurements in shelf environments because it integrates effects of naturally varying drivers of the flux such as current flow and light. In conventional eddy covariance instruments, the time shift caused by spatial separation of the measuring locations of flow and O2 concentration can produce substantial flux errors that are difficult to correct. We here introduce a triple O2 sensor eddy covariance instrument (3OEC) that by instrument design eliminates these errors. This is achieved by positioning three O2 sensors around the flow measuring volume, which allows the O2 concentration to be calculated at the point of the current flow measurements. The new instrument was tested in an energetic coastal environment with highly permeable coral reef sands colonised by microphytobenthos. Parallel deployments of the 3OEC and a conventional eddy covariance system (2OEC) demonstrate that the new instrument produces more consistent fluxes with lower error margin. 3OEC fluxes in general were lower than 2OEC fluxes, and the nighttime fluxes recorded by the two instruments were statistically different. We attribute this to the elimination of uncertainties associated with the time shift correction. The deployments at ∼ 10 m water depth revealed high day- and nighttime O2 fluxes despite the relatively low organic content of the coarse sediment and overlying water. High light utilisation efficiency of the microphytobenthos and bottom currents increasing pore water exchange facilitated the high benthic production and coupled respiration. 3OEC measurements after sunset documented a gradual transfer of negative flux signals from the small turbulence generated at the sediment–water interface to the larger wave-dominated eddies of the overlying water column that still carried a positive flux signal, suggesting concurrent fluxes in opposite directions depending on eddy size and a memory effect of large eddies. The results demonstrate that the 3OEC can improve the precision of benthic flux measurements, including measurements in environments considered challenging for the eddy covariance technique, and thereby produce novel insights into the mechanisms that control flux. We consider the fluxes produced by this instrument for the permeable reef sands the most realistic achievable with present-day technology.

Microorganisms are central and cross-cutting to oil spill response strategies. Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of petroleum (oil and gas) that enters the marine environment. Key ecosystem services provided by microbes, such as organic matter and nutrient cycling, may be adversely affected by oil contamination. The Deepwater Horizon (DWH) oil spill was the first large scale environmental disaster to which the methods of genomics were applied to determine microbial response to a major perturbation. Here we present a case study on coastal ecosystems to highlight the knowledge gained by application of genomics tools to interrogate mechanisms of petroleum hydrocarbon degradation and to elucidate impacts of oil exposure on ecosystem health and functioning. At Pensacola Beach, results showed that oiling led to a large increase in the growth of indigenous microbes in the form of a series of bacterial blooms. Oil contamination strongly selected for microbial groups capable of hydrocarbon degradation. Oil was degraded and benthic microbial communities returned to near baseline levels approximately one year after oil came ashore. These results indicate that when small particles (< 1 cm) of weathered light oil are buried in the coastal zone, biodegradation by indigenous microbial communities is sufficient for the rapid mitigation of oil contamination after a major spill, whereas larger sand-oil-aggregates take longer to completely degrade because of their unfavorable surface to volume ratio. “Operation Deep Clean” removed these aggregates and enhanced biodegradation insofar as many larger oil aggregates were broken down into smaller ones thereby increasing the surface area available for microbial attack. For environmental managers, these results suggest that biodegradation in beach sands is relatively rapid because oxygen can easily penetrate to the buried oil, and resources may be better placed elsewhere in environments where degradation is limited by oxygen availability or microbial access to hydrocarbons. While specialist microbial groups such as nitrifiers show promise as bioindicators of oil contamination in coastal ecosystems, more work is needed to further validate these biomarkers. Despite substantial progress, a predictive understanding of the fate and impacts of oil spills remains hampered by challenges in interpreting the in situ activity and ecosystem response of benthic microbial populations. To advance this understanding, a dedicated funding mechanism is needed to support fundamental research. A polyphasic approach is encouraged that employs metagenomics in the field along with cultivation and microcosm or mesocosm experiments in the laboratory. Further, research during future disasters would be greatly facilitated by improved coordination between the emergency responders directing mitigation efforts and scientists investigating the success of those efforts.

Microorganisms are central and cross-cutting to oil spill response strategies. Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of petroleum (oil and gas) that enters the marine environment. Key ecosystem services provided by microbes, such as organic matter and nutrient cycling, may be adversely affected by oil contamination. The Deepwater Horizon (DWH) oil spill was the first large scale environmental disaster to which the methods of genomics were applied to determine microbial response to a major perturbation. Here we present a case study on coastal ecosystems to highlight the knowledge gained by application of genomics tools to interrogate mechanisms of petroleum hydrocarbon degradation and to elucidate impacts of oil exposure on ecosystem health and functioning. At Pensacola Beach, results showed that oiling led to a large increase in the growth of indigenous microbes in the form of a series of bacterial blooms. Oil contamination strongly selected for microbial groups capable of hydrocarbon degradation. Oil was degraded and benthic microbial communities returned to near baseline levels approximately one year after oil came ashore. These results indicate that when small particles (< 1 cm) of weathered light oil are buried in the coastal zone, biodegradation by indigenous microbial communities is sufficient for the rapid mitigation of oil contamination after a major spill, whereas larger sand-oil-aggregates take longer to completely degrade because of their unfavorable surface to volume ratio. “Operation Deep Clean” removed these aggregates and enhanced biodegradation insofar as many larger oil aggregates were broken down into smaller ones thereby increasing the surface area available for microbial attack. For environmental managers, these results suggest that biodegradation in beach sands is relatively rapid because oxygen can easily penetrate to the buried oil, and resources may be better placed elsewhere in environments where degradation is limited by oxygen availability or microbial access to hydrocarbons. While specialist microbial groups such as nitrifiers show promise as bioindicators of oil contamination in coastal ecosystems, more work is needed to further validate these biomarkers. Despite substantial progress, a predictive understanding of the fate and impacts of oil spills remains hampered by challenges in interpreting the in situ activity and ecosystem response of benthic microbial populations. To advance this understanding, a dedicated funding mechanism is needed to support fundamental research. A polyphasic approach is encouraged that employs metagenomics in the field along with cultivation and microcosm or mesocosm experiments in the laboratory. Further, research during future disasters would be greatly facilitated by improved coordination between the emergency responders directing mitigation efforts and scientists investigating the success of those efforts.

Alkanes are ubiquitous in marine ecosystems and originate from diverse sources ranging from natural oil seeps to anthropogenic inputs and biogenic production by cyanobacteria. Enzymes that degrade cyanobacterial alkanes (typically C15-C17 compounds) such as the alkane monooxygenase (AlkB) are widespread, but it remains unclear whether or not AlkB variants exist that specialize in degradation of crude oil from natural or accidental spills, a much more complex mixture of long-chain hydrocarbons. In the present study, large-scale analysis of available metagenomic and genomic data from the Gulf of Mexico (GoM) oil spill revealed a novel, divergent AlkB clade recovered from genomes with no cultured representatives that was dramatically increased in abundance in crude-oil impacted ecosystems. In contrast, the AlkB clades associated with biotransformation of cyanobacterial alkanes belonged to 'canonical' or hydrocarbonoclastic clades, and based on metatranscriptomics data and compared to the novel clade, were much more weakly expressed during crude oil biodegradation in laboratory mesocosms. The absence of this divergent AlkB clade in metagenomes of uncontaminated samples from the global ocean survey but not from the GoM as well as its frequent horizontal gene transfer indicated a priming effect of the Gulf for crude oil biodegradation likely driven by natural oil seeps.

Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.

Sediment–water oxygen fluxes are widely used as a proxy for organic carbon production and mineralization at the seafloor. In situ fluxes can be measured non-invasively with the aquatic eddy covariance technique, but a critical requirement is that the sensors of the instrument are able to correctly capture the high-frequency variations in dissolved oxygen concentration and vertical velocity. Even small changes in sensor characteristics during deployment as caused, e.g. by biofouling can result in erroneous flux data. Here we present a dual-optode eddy covariance instrument (2OEC) with two fast oxygen fibre sensors and document how erroneous flux interpretations and data loss can effectively be reduced by this hardware and a new data analysis approach. With deployments over a carbonate sandy sediment in the Florida Keys and comparison with parallel benthic advection chamber incubations, we demonstrate the improved data quality and data reliability facilitated by the instrument and associated data processing. Short-term changes in flux that are dubious in measurements with single oxygen sensor instruments can be confirmed or rejected with the 2OEC and in our deployments provided new insights into the temporal dynamics of benthic oxygen flux in permeable carbonate sands. Under steady conditions, representative benthic flux data can be generated with the 2OEC within a couple of hours, making this technique suitable for mapping sediment–water, intrawater column, or atmosphere–water fluxes.

Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name "Candidatus Macondimonas diazotrophica" gen. nov., sp. nov. "Ca. M. diazotrophica" appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.