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15 pages, 7 figures, supplementary information https://doi.org/10.1038/s42003-021-02112-2.-- All data generated or analyzed during this study are included in this published article (and its supplementary information files). All raw sequences are publicly available at both DOE’s JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed in Supplementary Data 1. The co-assembly for the MAG dataset construction can be found through ENA at https://www.ebi.ac.uk/ena with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457 and also in the companion website to this manuscript at https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/.-- All software used in this work is publicly available distributed by their respective developers, and it is described in “Methods”, including the versions and options used. Additional custom scripts to assign taxonomy to the M-geneDB genes and to filter and format FRA results are available through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457, The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem, This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 to SGA (CSP 612 “Microbial metagenomics and transcriptomics from a global deep-ocean expedition”). Additional funding was provided by the project MAGGY (CTM2017-87736-R) to S.G.A. from the Spanish Ministry of Economy and Competitiveness, Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya, and King Abdullah University of Science and Technology (KAUST) under contract OSR #3362 and by funding of the EMFF Program of the European Union (MERCLUB project, Grant Agreement 863584). The ICM researchers have had the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S). High-Performance computing analyses were run at the Marine Bioinformatics Service (MARBITS, https://marbits.icm.csic.es) of the Institut de Ciències del Mar (ICM-CSIC), Barcelona, Supercomputing Center (Grant BCV-2013-2-0001) and KAUST’s Ibex HPC

Settling marine aggregates, such as zooplankton fecal pellets and marine snow, transport organic matter from the surface ocean to the deep sea and are largely responsible for the ocean's sequestration of carbon. However, our understanding of the functioning of the biological pump and the distribution of particulate organic matter in the water column often hinge on limited bulk data from sediment traps, large volume filtration or instantaneous snap-shots from in situ optical systems that only see a small part of the particle and aggregate spectra. We evaluated the added value of combining different optical systems to detect a range of organic and inorganic particle types during a case-study in the Cape Blanc upwelling region. Laboratory calibrations showed that one camera system detected large organic aggregates well and in situ data showed that it correlated positively with fluorescence. The other camera was better at detecting small, mainly inorganic particles which were not seen by the first camera and correlated positively with turbidity. The combined deployments of the two optical systems together with fluorescence and turbidity sensors showed potentials for added insights into spatial (depth) and temporal (diurnal) particle dynamics. The case study exemplified the different efficiencies of two camera systems to detect particles of different types in marine waters. From this, the results highlighted the importance of discriminating between qualitative and quantitative ranges of imaging systems, in order to understand the quantitative range of sizes as well as types of particles detected by a given system. This is especially important when optical systems are used to estimate carbon fluxes and particulate organic matter distribution in the water column from vertical profiles of particle size-distribution and abundance.

WOS:000502962100001; International audience; In marine ecosystems, carbon export is driven by particle flux which is modulated by aggregation, remineralization, and grazing processes. Zooplankton contribute to the sinking flux through the egestion of fast sinking fecal pellets but may also attenuate the flux by tearing apart phytoplankton aggregates into small pieces through swimming activity or direct ingestion. Freely suspended cells, artificial monospecific aggregates from two different diatom species (Chaetoceros neogracile and Skeletonema merinol) and natural aggregates of Melosira sp. were independently incubated with five different copepod species (Acadia clausi, Temora longicomis, Calanus helgolandicus, Euterpina acutifrons, and Calanus hyperboreus). During the grazing experiments initiated with free diatoms, E. acutifrons feeding activity evidenced by ingestion rates of 157 +/- 155 ng Chl a ind(-1) d(-1), induced a significant increase of S. marinoi aggregation. Transparent exopolymeric particles (TEP) production was only slightly boosted by the presence of grazers and turbulences created by swimming may be the main trigger of the aggregation processes. All copepods studied were able to graze on aggregates and quantitative estimates led to chlorophyll a ingestion rates (expressed in Chla a equivalent, i.e., the sum of chlorophyll a and pheopigments in their guts) ranging from 4 to 23 ng Chl a(eq) ind(-1) d(-1). The relation between equivalent spherical diameters (ESDs) and sinking velocities of the aggregates did not significantly change after grazing, suggesting that copepod grazing did not affect aggregate density as also shown by Si:C and C:N ratios. Three main trends in particle dynamics could be identified and further linked to the copepod feeding behavior and the size ratio between prey and predators: (1) Fragmentation of S. marinoi aggregates by the cruise feeder T. longicomis and of Melosira sp. aggregates by C. hyperboreus at prey to predator size ratios larger than 15; (2) no change of particle dynamics in the presence of the detritic cruise feeder E acutifrons; and finally (3) re-aggregation of C. neogracile and S. marinoi aggregates when the two filter feeders A. clausi and C. helgolandicus were grazing on aggregate at prey to predator size ratios lower than 10. Aggregation of freely suspended cells or small aggregates was facilitated by turbulence resulting from active swimming of small copepods. However, stronger turbulence created by larger cruise feeders copepods prevent aggregate formation and even made them vulnerable to breakage.

The efficiency of deep-ocean CO2 sequestration is regulated by the relative balance between inorganic and organic carbon export respectively acting through the biological carbon pump (BCP) and the carbonate counter pump (CCP). The composition and abundance of calcifying species in the prevailing oceanic plankton community plays a major role in driving the CCP. Here we assess the role of these calcifying organisms in regulating the strength of the CCP in a Southern Ocean region (northern Scotia Sea) known to be a major hotspot for the drawdown of atmospheric CO2. We show that, when shelled pteropods dominate the calcifying community, the total annual reduction of CO2 transferred to the deep ocean doubles (17%) compared to when other plankton calcifiers dominate (3–9%). Furthermore, predation enhances their contribution through the removal of organic soft tissue. Pteropods are threatened in polar regions by ocean warming and acidification. We determine that their potential decline would have major implications to the comparative strengths of the BCP and CCP., The Scotia Sea, located in the Southern Ocean, is a major hotspot for the drawdown of atmospheric CO2. Here, the authors show that the strength of the carbonate counter pump doubles when shelled pteropods dominate the plankton calcifier community, counteracting the amount of CO2 transferred to the deep ocean.

This is the peer reviewed version of the following article: Thor, P., Bailey, A., Dupont, S., Calosi, P., Søreide, J.E., De Wit, P., ... Bellerby, R. (2017). Contrasting physiological responses to future ocean acidification among Arctic copepod populations. Global Change Biology, 24(1), e365-e377. https://doi.org/10.1111/gcb.13870, which has been published in final form at https://doi.org/10.1111/gcb.13870. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Widespread ocean acidification (OA) is modifying the chemistry of the global ocean, and the Arctic is recognized as the region where the changes will progress at the fastest rate. Moreover, Arctic species show lower capacity for cellular homeostasis and acid‐base regulation rendering them particularly vulnerable to OA. In the present study, we found physiological differences in OA response across geographically separated populations of the keystone Arctic copepod Calanus glacialis. In copepodites stage CIV, measured reaction norms of ingestion rate and metabolic rate showed severe reductions in ingestion and increased metabolic expenses in two populations from Svalbard (Kongsfjord and Billefjord) whereas no effects were observed in a population from the Disko Bay, West Greenland. At pHT 7.87, which has been predicted for the Svalbard west coast by year 2100, these changes resulted in reductions in scope for growth of 19% in the Kongsfjord and a staggering 50% in the Billefjord. Interestingly, these effects were not observed in stage CV copepodites from any of the three locations. It seems that CVs may be more tolerant to OA perhaps due to a general physiological reorganization to meet low intracellular pH during hibernation. Needless to say, the observed changes in the CIV stage will have serious implications for the C. glacialis population health status and growth around Svalbard. However, OA tolerant populations such as the one in the Disko Bay could help to alleviate severe effects in C. glacialis as a species.

Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1-86 mmin diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 mu L L-1), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested similar to 0.37 mu g-oil mg-C-dino (-1) d(-1), which could represent similar to 17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills.

Correlation between particulate organic carbon (POC) and calcium carbonate sinking through the deep ocean has led to the idea that ballast provided by calcium carbonate is important for the export of POC from the surface ocean. While this idea is certainly to some extent true, it is worth considering in more nuance, for example, examining the different effects on the aggregation and sinking of POC of small, non-sinking calcite particles like coccoliths and large, rapidly sinking calcite like planktonic foraminiferan tests. We have done that here in a simple experiment carried out in roller tanks that allow particles to sink continuously without being impeded by container walls. Coccoliths were efficiently incorporated into aggregates that formed during the experiment, increasing their sinking speed compared to similarly sized aggregates lacking added calcite ballast. The foraminiferan tests, which sank as fast as 700 m d−1, became associated with only very minor amounts of POC. In addition, when they collided with other, larger, foraminferan-less aggregates, they fragmented them into two smaller, more slowly sinking aggregates. While these effects were certainly exaggerated within the confines of the roller tanks, they clearly demonstrate that calcium carbonate ballast is not just calcium carbonate ballast- different forms of calcium carbonate ballast have notably different effects on POC aggregation, sinking, and export.