Global census of the significance of giant mesopelagic protists to the marine carbon and silicon cycles.

Thriving in both epipelagic and mesopelagic layers, Rhizaria are biomineralizing protists, mixotrophs or flux-feeders, often reaching gigantic sizes. In situ imaging showed their contribution to oceanic carbon stock, but left their contribution to element cycling unquantified. Here, we compile a global dataset of 167,551 Underwater Vision Profiler 5 Rhizaria images, and apply machine learning models to predict their organic carbon and biogenic silica biomasses in the uppermost 1000 m. We estimate that Rhizaria represent up to 1.7% of mesozooplankton carbon biomass in the top 500 m. Rhizaria biomass, dominated by Phaeodaria, is more than twice as high in the mesopelagic than in the epipelagic layer. Globally, the carbon demand of mesopelagic, flux-feeding Phaeodaria reaches 0.46 Pg C y-1, representing 3.8 to 9.2% of gravitational carbon export. Furthermore, we show that Rhizaria are a unique source of biogenic silica production in the mesopelagic layer, where no other silicifiers are present. Our global census further highlights the importance of Rhizaria for ocean biogeochemistry.

Low-Density Plastic Debris Dispersion beneath the Mediterranean Sea Surface.

Plastic is a widespread marine pollutant, with most studies focusing on the distribution of floating plastic debris at the sea surface. Recent evidence, however, indicates a significant presence of such low density plastic in the water column and at the seafloor, but information on its origin and dispersion is lacking. Here, we studied the pathways and fate of sinking plastic debris in the Mediterranean Sea, one of the most polluted world seas. We used a recent Lagrangian plastic-tracking model, forced with realistic parameters, including a maximum estimated sinking speed of 7.8 m/d. Our simulations showed that the locations where particles left the surface differed significantly from those where they reached the seafloor, with lateral transport distances between 119 and 282 km. Furthermore, 60% of particles deposited on the bottom coastal strip (20 km wide) were released from vessels, 20% from the facing country, and 20% from other countries. Theoretical considerations furthermore suggested that biological activities potentially responsible for the sinking of low density plastic occur throughout the water column. Our findings indicate that the responsibility for seafloor plastic pollution is shared among Mediterranean countries, with potential impact on pelagic and benthic biota.

Making marine image data FAIR.

Underwater images are used to explore and monitor ocean habitats, generating huge datasets with unusual data characteristics that preclude traditional data management strategies. Due to the lack of universally adopted data standards, image data collected from the marine environment are increasing in heterogeneity, preventing objective comparison. The extraction of actionable information thus remains challenging, particularly for researchers not directly involved with the image data collection. Standardized formats and procedures are needed to enable sustainable image analysis and processing tools, as are solutions for image publication in long-term repositories to ascertain reuse of data. The FAIR principles (Findable, Accessible, Interoperable, Reusable) provide a framework for such data management goals. We propose the use of image FAIR Digital Objects (iFDOs) and present an infrastructure environment to create and exploit such FAIR digital objects. We show how these iFDOs can be created, validated, managed and stored, and which data associated with imagery should be curated. The goal is to reduce image management overheads while simultaneously creating visibility for image acquisition and publication efforts.

Assessing Representation Learning and Clustering Algorithms for Computer-Assisted Image Annotation-Simulating and Benchmarking MorphoCluster.

Image annotation is a time-consuming and costly task. Previously, we published MorphoCluster as a novel image annotation tool to address problems of conventional, classifier-based image annotation approaches: their limited efficiency, training set bias and lack of novelty detection. MorphoCluster uses clustering and similarity search to enable efficient, computer-assisted image annotation. In this work, we provide a deeper analysis of this approach. We simulate the actions of a MorphoCluster user to avoid extensive manual annotation runs. This simulation is used to test supervised, unsupervised and transfer representation learning approaches. Furthermore, shrunken k-means and partially labeled k-means, two new clustering algorithms that are tailored specifically for the MorphoCluster approach, are compared to the previously used HDBSCAN*. We find that labeled training data improve the image representations, that unsupervised learning beats transfer learning and that all three clustering algorithms are viable options, depending on whether completeness, efficiency or runtime is the priority. The simulation results support our earlier finding that MorphoCluster is very efficient and precise. Within the simulation, more than five objects per simulated click are being annotated with 95% precision.

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.

Fuzzy Overclustering: Semi-Supervised Classification of Fuzzy Labels with Overclustering and Inverse Cross-Entropy.

Deep learning has been successfully applied to many classification problems including underwater challenges. However, a long-standing issue with deep learning is the need for large and consistently labeled datasets. Although current approaches in semi-supervised learning can decrease the required amount of annotated data by a factor of 10 or even more, this line of research still uses distinct classes. For underwater classification, and uncurated real-world datasets in general, clean class boundaries can often not be given due to a limited information content in the images and transitional stages of the depicted objects. This leads to different experts having different opinions and thus producing fuzzy labels which could also be considered ambiguous or divergent. We propose a novel framework for handling semi-supervised classifications of such fuzzy labels. It is based on the idea of overclustering to detect substructures in these fuzzy labels. We propose a novel loss to improve the overclustering capability of our framework and show the benefit of overclustering for fuzzy labels. We show that our framework is superior to previous state-of-the-art semi-supervised methods when applied to real-world plankton data with fuzzy labels. Moreover, we acquire 5 to 10% more consistent predictions of substructures.

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone.

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April-June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128-512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.

MorphoCluster: Efficient Annotation of Plankton Images by Clustering.

In this work, we present MorphoCluster, a software tool for data-driven, fast, and accurate annotation of large image data sets. While already having surpassed the annotation rate of human experts, volume and complexity of marine data will continue to increase in the coming years. Still, this data requires interpretation. MorphoCluster augments the human ability to discover patterns and perform object classification in large amounts of data by embedding unsupervised clustering in an interactive process. By aggregating similar images into clusters, our novel approach to image annotation increases consistency, multiplies the throughput of an annotator, and allows experts to adapt the granularity of their sorting scheme to the structure in the data. By sorting a set of 1.2 M objects into 280 data-driven classes in 71 h (16 k objects per hour), with 90% of these classes having a precision of 0.889 or higher. This shows that MorphoCluster is at the same time fast, accurate, and consistent; provides a fine-grained and data-driven classification; and enables novelty detection.

In situ imaging reveals the biomass of giant protists in the global ocean.

Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 µm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones.

Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein.

Nitrogen Fuelling of the Pelagic Food Web of the Tropical Atlantic.

We estimated the relative contribution of atmosphere (ic Nitrogen (N) input (wet and dry deposition and N fixation) to the epipelagic food web by measuring N isotopes of different functional groups of epipelagic zooplankton along 23°W (17°N-4°S) and 18°N (20-24°W) in the Eastern Tropical Atlantic. Results were related to water column observations of nutrient distribution and vertical diffusive flux as well as colony abundance of Trichodesmium obtained with an Underwater Vision Profiler (UVP5). The thickness and depth of the nitracline and phosphocline proved to be significant predictors of zooplankton stable N isotope values. Atmospheric N input was highest (61% of total N) in the strongly stratified and oligotrophic region between 3 and 7°N, which featured very high depth-integrated Trichodesmium abundance (up to 9.4×10(4) colonies m(-2)), strong thermohaline stratification and low zooplankton δ15N (~2‰). Relative atmospheric N input was lowest south of the equatorial upwelling between 3 and 5°S (27%). Values in the Guinea Dome region and north of Cape Verde ranged between 45 and 50%, respectively. The microstructure-derived estimate of the vertical diffusive N flux in the equatorial region was about one order of magnitude higher than in any other area (approximately 8 mmol m(-2) d(1)). At the same time, this region received considerable atmospheric N input (35% of total). In general, zooplankton δ15N and Trichodesmium abundance were closely correlated, indicating that N fixation is the major source of atmospheric N input. Although Trichodesmium is not the only N fixing organism, its abundance can be used with high confidence to estimate the relative atmospheric N input in the tropical Atlantic (r2 = 0.95). Estimates of absolute N fixation rates are two- to tenfold higher than incubation-derived rates reported for the same regions. Our approach integrates over large spatial and temporal scales and also quantifies fixed N released as dissolved inorganic and organic N. In a global analysis, it may thus help to close the gap in oceanic N budgets.

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

BACKGROUND: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. RESULTS: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. CONCLUSIONS: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies.

Effects of elevated seawater pCO(2) on gene expression patterns in the gills of the green crab, Carcinus maenas.

BACKGROUND: The green crab Carcinus maenas is known for its high acclimation potential to varying environmental abiotic conditions. A high ability for ion and acid-base regulation is mainly based on an efficient regulation apparatus located in gill epithelia. However, at present it is neither known which ion transport proteins play a key role in the acid-base compensation response nor how gill epithelia respond to elevated seawater pCO(2) as predicted for the future. In order to promote our understanding of the responses of green crab acid-base regulatory epithelia to high pCO(2), Baltic Sea green crabs were exposed to a pCO(2) of 400 Pa. Gills were screened for differentially expressed gene transcripts using a 4,462-feature microarray and quantitative real-time PCR. RESULTS: Crabs responded mainly through fine scale adjustment of gene expression to elevated pCO(2). However, 2% of all investigated transcripts were significantly regulated 1.3 to 2.2-fold upon one-week exposure to CO(2) stress. Most of the genes known to code for proteins involved in osmo- and acid-base regulation, as well as cellular stress response, were were not impacted by elevated pCO(2). However, after one week of exposure, significant changes were detected in a calcium-activated chloride channel, a hyperpolarization activated nucleotide-gated potassium channel, a tetraspanin, and an integrin. Furthermore, a putative syntaxin-binding protein, a protein of the transmembrane 9 superfamily, and a Cl(-)/HCO(3)(-) exchanger of the SLC 4 family were differentially regulated. These genes were also affected in a previously published hypoosmotic acclimation response study. CONCLUSIONS: The moderate, but specific response of C. maenas gill gene expression indicates that (1) seawater acidification does not act as a strong stressor on the cellular level in gill epithelia; (2) the response to hypercapnia is to some degree comparable to a hypoosmotic acclimation response; (3) the specialization of each of the posterior gill arches might go beyond what has been demonstrated up to date; and (4) a re-configuration of gill epithelia might occur in response to hypercapnia.

Elevated seawater PCO2 differentially affects branchial acid-base transporters over the course of development in the cephalopod Sepia officinalis.

The specific transporters involved in maintenance of blood pH homeostasis in cephalopod molluscs have not been identified to date. Using in situ hybridization and immunohistochemical methods, we demonstrate that Na(+)/K(+)-ATPase (soNKA), a V-type H(+)-ATPase (soV-HA), and Na(+)/HCO(3)(-) cotransporter (soNBC) are colocalized in NKA-rich cells in the gills of Sepia officinalis. mRNA expression patterns of these transporters and selected metabolic genes were examined in response to moderately elevated seawater Pco(2) (0.16 and 0.35 kPa) over a time course of 6 wk in different ontogenetic stages. The applied CO(2) concentrations are relevant for ocean acidification scenarios projected for the coming decades. We determined strong expression changes in late-stage embryos and hatchlings, with one to three log2-fold reductions in soNKA, soNBCe, socCAII, and COX. In contrast, no hypercapnia-induced changes in mRNA expression were observed in juveniles during both short- and long-term exposure. However, a transiently increased ion regulatory demand was evident during the initial acclimation reaction to elevated seawater Pco(2). Gill Na(+)/K(+)-ATPase activity and protein concentration were increased by ~15% during short (2-11 days) but not long-term (42-days) exposure. Our findings support the hypothesis that the energy budget of adult cephalopods is not significantly compromised during long-term exposure to moderate environmental hypercapnia. However, the downregulation of ion regulatory and metabolic genes in late-stage embryos, taken together with a significant reduction in somatic growth, indicates that cephalopod early life stages are challenged by elevated seawater Pco(2).

Dickkopf related genes are components of the positional value gradient in Hydra.

Hydra is a classical model organism to understand fundamental developmental biological processes such as regeneration and axis formation. Here, we show that two genes which share some similarity with members of the Dickkopf family of proteins, HyDkk1/2/4-A and HyDkk1/2/4-C, are co-expressed in gland cells and regulated by the positional value gradient. While HyDkk1/2/4-A is expressed throughout the gastric region, HyDkk1/2/4-C has a graded expression pattern with a high level of transcripts just below the tentacle zone and absence of expression in the budding zone. Blocking the activity of GSK-3beta caused a drastic downregulation of HyDkk1/2/4-C expression in the gastric tissue. Experimental reduction of the number of HyDkk1/2/4-C-expressing cells resulted in expansion of the HyWnt expression domain in the hypostome. Thus, similar to Dickkopf proteins in vertebrates, one of the functions of HyDkk1/2/4-C in hydra may be to antagonize Wnt signalling.