Purpose of Review The changes or updates in ocean biogeochemistry component have been mapped between CMIP5 and CMIP6 model versions, and an assessment made of how far these have led to improvements in the simulated mean state of marine biogeochemical models within the current generation of Earth system models (ESMs). Recent Findings The representation of marine biogeochemistry has progressed within the current generation of Earth system models. However, it remains difficult to identify which model updates are responsible for a given improvement. In addition, the full potential of marine biogeochemistry in terms of Earth system interactions and climate feedback remains poorly examined in the current generation of Earth system models. Summary Increasing availability of ocean biogeochemical data, as well as an improved understanding of the underlying processes, allows advances in the marine biogeochemical components of the current generation of ESMs. The present study scrutinizes the extent to which marine biogeochemistry components of ESMs have progressed between the 5th and the 6th phases of the Coupled Model Intercomparison Project (CMIP).

Among marine organisms, gelatinous zooplankton (GZ; cnidarians, ctenophores, and pelagic tunicates) are unique in their energetic efficiency, as the gelatinous body plan allows them to process and assimilate high proportions of oceanic carbon. Upon death, their body shape facilitates rapid sinking through the water column, resulting in carcass depositions on the seafloor ("jelly-falls"). GZ are thought to be important components of the biological pump, but their overall contribution to global carbon fluxes remains unknown. Using a data-driven, three-dimensional, carbon cycle model resolved to a 1°global grid, with a Monte Carlo uncertainty analysis, we estimate that GZ consumed 7.9-13 Pg C y −1 in phytoplankton and zooplankton, resulting in a net production of 3.9-5.8 Pg C y −1 in the upper ocean (top 200 m), with the largest fluxes from pelagic tunicates. Non-predation mortality (carcasses) comprised 25% of GZ production, and combined with the much greater fecal matter flux, total GZ particulate organic carbon (POC) export at 100 m was 1.6-5.2 Pg C y −1 , equivalent to 32-40% of the global POC export. The fast sinking GZ export resulted in a high transfer efficiency (T eff) of 38-62% to 1,000 m and 25-40% to the seafloor. Finally, jelly-falls at depths >50 m are likely unaccounted for in current POC flux estimates and could increase benthic POC flux by 8-35%. The significant magnitude of and distinct sinking properties of GZ fluxes support a critical yet underrecognized role of GZ carcasses and fecal matter to the biological pump and air-sea carbon balance. Plain Language Summary Marine ecosystems play a critical role in the global carbon cycle through food web regulation of air-sea carbon fluxes and the transfer of organic carbon from the upper oceans to the deep sea. The carcasses of gelatinous zooplankton (GZ), which include jellyfish and salps, have been found in mass seafloor depositions ("jelly-falls") in many locations. These jelly-falls are thought to be a fast mechanism for carbon sequestration, yet no global studies on their overall impact have been done. Using a database of GZ observations, we suggest that the inclusion of previously unaccounted for GZ carbon in seafloor carbon deposition could increase current estimates by 8-35%. This previously unconsidered flux represents a substantial amount of carbon sequestered in the deep sea.

The rise of in situ plankton imaging systems, particularly high-volume imagers such as the In Situ Ichthyoplankton Imaging System, has increased the need for fast processing and accurate classification tools that can identify a high diversity of organisms and nonliving particles of biological origin. Previous methods for automated classification have yielded moderate results that either can resolve few groups at high accuracy or many groups at relatively low accuracy. However, with the advent of new deep learning tools such as convolutional neural networks (CNNs), the automated identification of plankton images can be vastly improved. Here, we describe an image processing procedure that includes preprocessing, segmentation, classification, and postprocessing for the accurate identification of 108 classes of plankton using spatially sparse CNNs. Following a filtering process to remove images with low classification scores, a fully random evaluation of the classification showed that average precision was 84% and recall was 40% for all groups. Reliably classifying rare biological classes was difficult, so after excluding the 12 rarest taxa, classification accuracy for the remaining biological groups became > 90%. This method provides proof of concept for the effectiveness of an automated classification scheme using deep-learning methods, which can be applied to a range of plankton or biological imaging systems, with the eventual application in a variety of ecological monitoring and fisheries management contexts.

International audienceImaging systems were developed to explore the fine scale distributions of plankton (<10 m), but they generate huge datasets that are still a challenge to handle rapidly and accurately. So far, imaged organisms have been either classified manually or pre-classified by a computer program and later verified by human operators. In this paper, we post-process a computer-generated classification, obtained with the common ZooProcess and PlanktonIdentifier toolchain developed for the ZooScan, and test whether the same ecological conclusions can be reached with this fully automatic dataset and with a reference, manually sorted, dataset. The Random Forest classifier outputs the probabilities that each object belongs in each class and we discard the objects with uncertain predictions, i.e. under a probability threshold defined based on a 1% error rate in a self-prediction of the learning set. Keeping only well-predicted objects enabled considerable improvements in average precision, 84% for biological groups, at the cost of diminishing recall (by 39% on average). Overall, it increased accuracy by 16%. For most groups, the automatically-predicted distributions were comparable to the reference distributions and resulted in the same size-spectra. Automatically-predicted distributions also resolved ecologically-relevant patterns, such as differences in abundance across a mesoscale front or fine-scale vertical shifts between day and night. This post-processing method is tested on the classification of plankton images through Random Forest here, but is based on basic features shared by all machine learning methods and could thus be used in a broad range of applications

The Marine Biogeochemistry Library (MARBL) is a prognostic ocean biogeochemistry model that simulates marine ecosystem dynamics and the coupled cycles of carbon, nitrogen, phosphorus, iron, silicon, and oxygen. MARBL is a component of the Community Earth System Model (CESM); it supports flexible ecosystem configuration of multiple phytoplankton and zooplankton functional types; it is also portable, designed to interface with multiple ocean circulation models. Here, we present scientific documentation of MARBL, describe its configuration in CESM2 experiments included in the Coupled Model Intercomparison Project version 6 (CMIP6), and evaluate its performance against a number of observational data sets. The model simulates present‐day air‐sea CO2 flux and many aspects of the carbon cycle in good agreement with observations. However, the simulated integrated uptake of anthropogenic CO2 is weak, which we link to poor thermocline ventilation, a feature evident in simulated chlorofluorocarbon distributions. This also contributes to larger‐than‐observed oxygen minimum zones. Moreover, radiocarbon distributions show that the simulated circulation in the deep North Pacific is extremely sluggish, yielding extensive oxygen depletion and nutrient trapping at depth. Surface macronutrient biases are generally positive at low latitudes and negative at high latitudes. CESM2 simulates globally integrated net primary production (NPP) of 48 Pg C yr−1 and particulate export flux at 100 m of 7.1 Pg C yr−1. The impacts of climate change include an increase in globally integrated NPP, but substantial declines in the North Atlantic. Particulate export is projected to decline globally, attributable to decreasing export efficiency associated with changes in phytoplankton community composition.

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Mesoscale fronts occur frequently in many coastal areas and often are sites of elevated productivity; however, knowledge of the fine-scale distribution of zooplankton at these fronts is lacking, particularly within the mid-trophic levels. Furthermore, small (<13 cm) gelatinous zooplankton are ubiquitous, but are under-studied, and their abundances underestimated due to inadequate sampling technology. Using the In Situ Ichthyoplankton Imaging System (ISIIS), we describe the fine-scale distribution of small gelatinous zooplankton at a sharp salinitydriven front in the Southern California Bight. Between 15 and 17 October 2010, over 129 000 hydromedusae, ctenophores, and siphonophores within 44 taxa, and nearly 650 000 pelagic tunicates were imaged in 5450 m 3 of water. Organisms were separated into 4 major assemblages which were largely associated with depth-related factors. Species distribution modeling using boosted regression trees revealed that hydromedusae and tunicates were primarily associated with temperature and depth, siphonophores with dissolved oxygen (DO) and chlorophyll a fluorescence, and ctenophores with DO. The front was the least influential out of all environmental variables modeled. Additionally, except for 6 taxa, all other taxa were not aggregated at the front. Results provide new insights into the biophysical drivers of gelatinous zooplankton distributions and the varying influence of mesoscale fronts in structuring zooplankton communities.