Aquatic Eddy Covariance: The Method and Its Contributions to Defining Oxygen and Carbon Fluxes in Marine Environments

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 insights gained 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. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Using Chlorophyll Fluorescence to Determine the Fate of Photons Absorbed by Phytoplankton in the World's Oceans

Approximately 45% of the photosynthetically fixed carbon on Earth occurs in the oceans in phytoplankton, which account for less than 1% of the world's photosynthetic biomass. This amazing empirical observation implies a very high photosynthetic energy conversion efficiency, but how efficiently is the solar energy actually used? The photon energy budget of photosynthesis can be divided into three terms: the quantum yields of photochemistry, fluorescence, and heat. Measuring two of these three processes closes the energy budget. The development of ultrasensitive, seagoing chlorophyll variable fluorescence and picosecond fluorescence lifetime instruments has allowed independent closure on the first two terms. With this closure, we can understand how phytoplankton respond to nutrient supplies on timescales of hours to months and, over longer timescales, to changes in climate. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Organic Matter Supply and Utilization in Oxygen Minimum Zones

Organic matter (OM) plays a significant role in the formation of oxygen minimum zones (OMZs) and associated biogeochemical cycling. OM supply processes to the OMZ include physical transport, particle formation, and sinking as well as active transport by migrating zooplankton and nekton. In addition to the availability of oxygen and other electron acceptors, the remineralization rate of OM is controlled by its biochemical quality. Enhanced microbial respiration of OM can induce anoxic microzones in an otherwise oxygenated water column. Reduced OM degradation under low-oxygen conditions, on the other hand, may increase the CO2 storage time in the ocean. Understanding the interdependencies between OM and oxygen cycling is of high relevance for an ocean facing deoxygenation as a consequence of global warming. In this review, we describe OM fluxes into and cycling within two large OMZs associated with eastern boundary upwelling systems that differ greatly in the extent of oxygen loss: the highly oxygen-depleted OMZ in the tropical South Pacific and the moderately hypoxic OMZ in the tropical North Atlantic. We summarize new findings from a large German collaborative research project, Collaborative Research Center 754 (SFB 754), and identify knowledge gaps and future research priorities. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Machine Learning for the Study of Plankton and Marine Snow from Images

Quantitative imaging instruments produce a large number of images of plankton and marine snow, acquired in a controlled manner, from which the visual characteristics of individual objects and their in situ concentrations can be computed. To exploit this wealth of information, machine learning is necessary to automate tasks such as taxonomic classification. Through a review of the literature, we highlight the progress of those machine classifiers and what they can and still cannot be trusted for. Several examples showcase how the combination of quantitative imaging with machine learning has brought insights on pelagic ecology. They also highlight what is still missing and how images could be exploited further through trait-based approaches. In the future, we suggest deeper interactions with the computer sciences community, the adoption of data standards, and the more systematic sharing of databases to build a global community of pelagic image providers and users. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Ventilation of the Southern Ocean Pycnocline

Ocean ventilation is the transfer of tracers and young water from the surface down into the ocean interior. The tracers that can be transported to depth include anthropogenic heat and carbon, both of which are critical to understanding future climate trajectories. Ventilation occurs in both high- and midlatitude regions, but it is the southern midlatitudes that are responsible for the largest fraction of anthropogenic heat and carbon uptake; such Southern Ocean ventilation is the focus of this review. Southern Ocean ventilation occurs through a chain of interconnected mechanisms, including the zonally averaged meridional overturning circulation, localized subduction, eddy-driven mixing along isopycnals, and lateral transport by subtropical gyres. To unravel the complex pathways of ventilation and reconcile conflicting results, here we assess the relative contribution of each of these mechanisms, emphasizing the three-dimensional and temporally varying nature of the ventilation of the Southern Ocean pycnocline. We conclude that Southern Ocean ventilation depends on multiple processes and that simplified frameworks that explain ventilation changes through a single process are insufficient. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome

The annual patterns of plankton succession in the ocean determine ecological and biogeochemical cycles. The temporally fluctuating interplay between photosynthetic eukaryotes and the associated microbiota balances the composition of aquatic planktonic ecosystems. In addition to nutrients and abiotic factors, chemical signaling determines the outcome of interactions between phytoplankton and their associated microbiomes. Chemical mediators control essential processes, such as the development of key morphological, physiological, behavioral, and life-history traits during algal growth. These molecules thus impact species succession and community composition across time and space in processes that are highlighted in this review. We focus on spatial, seasonal, and physiological dynamics that occur during the early association of algae with bacteria, the exponential growth of a bloom, and also during its decline and recycling. We also discuss how patterns from field data and global surveys might be linked to the actions of metabolic markers in natural phytoplankton assemblages. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Biological Effects of Pharmaceuticals in the Marine Environment

Environmental pharmaceuticals represent a threat of emerging concern for marine ecosystems. Widely distributed and bioaccumulated, these contaminants could provoke adverse effects on aquatic organisms through modes of action like those reported for target species. In contrast to pharmacological uses, organisms in field conditions are exposed to complex mixtures of compounds with similar, different, or even opposing therapeutic effects. This review summarizes current knowledge of the main cellular pathways modulated by the most common classes of environmental pharmaceuticals occurring in marine ecosystems and accumulated by nontarget species—including nonsteroidal anti-inflammatory drugs, psychiatric drugs, cardiovascular and lipid regulator agents, steroidal hormones, and antibiotics—and describes an intricate network of possible interactions with both synergistic and antagonistic effects on the same cellular targets and metabolic pathways. This complexity reveals the intrinsic limits of the single-chemical approach to predict the long-term consequences and future impact of pharmaceuticals at organismal, population, and community levels. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Enzymology of Ocean Global Change

A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Ecological Leverage Points: Species Interactions Amplify the Physiological Effects of Global Environmental Change in the Ocean

Marine ecosystems are increasingly impacted by global environmental changes, including warming temperatures, deoxygenation, and ocean acidification. Marine scientists recognize intuitively that these environmental changes are translated into community changes via organismal physiology. However, physiology remains a black box in many ecological studies, and coexisting species in a community are often assumed to respond similarly to environmental stressors. Here, we emphasize how greater attention to physiology can improve our ability to predict the emergent effects of ocean change. In particular, understanding shifts in the intensity and outcome of species interactions such as competition and predation requires a sharpened focus on physiological variation among community members and the energetic demands and trophic mismatches generated by environmental changes. Our review also highlights how key species interactions that are sensitive to environmental change can operate as ecological leverage points through which small changes in abiotic conditions are amplified into large changes in marine ecosystems. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.