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• Impacts from summertime MJO are quantified with observation data and an ecosystem model. • MJO modulates the SCS with enhanced mixing and upwelling, leading to more nanophytoplankton. • MJO-induced physical processes elongate the time lag between PP and export production, increasing their decoupling. In summer, the Madden-Julian Oscillation (MJO) greatly influences the intraseasonal variability of the South China Sea (SCS). Previous studies have revealed MJO effects on surface chlorophyll (Chl) concentration, but the impact of the MJO on the ecosystem's structure and functionality remains unexplored. Here, we investigated the marine ecosystem response to the MJO by analyzing phytoplankton pigment data collected in cruises from 2010 to 2014. The results indicated the strong influence of the MJO on the structure of phytoplankton size classes (PSCs) in the upper 50 m of the SCS basin. To further explore the ecosystem's response to MJO, we utilized a well-calibrated physical-biogeochemical model (ROMS-CoSiNE) of the SCS to conduct numerical experiments with and without MJO forcings. Our model demonstrated that MJO-induced deep mixing and upwelling increased nutrients in the upper layer, increasing the Chl concentration with a higher proportion of nanophytoplankton (15 %) and a lower proportion of picophytoplankton (−20 %). Moreover, The MJO-forced model experiment exhibited a substantial enhancement in primary production (56 %) and export production (23 %), resulting in a notable decrease in the e-ratio. This reduction in the e-ratio cannot be attributed to changes in PSCs but can be explained by the time lag between primary and export production. This lag was prolonged by the physical processes of upwelling and mixing, which slows down the particle sinking. Our results emphasize the important role of MJO in regulating the ecosystem at intraseasonal scale, thus improving our comprehension of the nonsteady dynamics of ecosystems in the SCS. [ABSTRACT FROM AUTHOR]

• We measured TEP from surface to deep waters across the Mediterranean Sea. • The proportion of TEP in the POC pool varies between ocean basins and depth layers. • Heterotrophic prokaryotes are a significant net source of TEP in the deep ocean. Transparent exopolymer particles (TEP) play a key role in ocean carbon export and structuring microbial habitats, but information on their distribution across different ocean basins and depths is scarce, particularly in the dark ocean. We measured TEP vertical distribution from the surface to bathypelagic waters in an east-to-west transect across the Mediterranean Sea (MedSea) and the adjacent North East Atlantic Ocean (NEA), and explored their physical and biological drivers. TEP ranged from 0.6 to 81.7 µg XG eq L−1, with the highest values in epipelagic waters above the deep chlorophyll maximum, and in areas near the Gibraltar and Sicily Straits. TEP were significantly related to particulate organic carbon (POC) in all basins and depth layers (epipelagic vs. deep), but the contribution of TEP to POC was higher in the NEA (85%, 79% and 67% in epi-, meso- and bathypelagic waters, respectively) than in the MedSea (from 53% to 62% in epipelagic waters, and from 45% to 48% in meso- and bathypelagic waters), coinciding with higher carbon to nitrogen particulate organic matter ratios in the NEA. The TEP connectivity between epipelagic waters and mesopelagic waters was less straightforward than between mesopelagic waters and bathypelagic waters, with a 23% and 55% of the variance in the relationship between layers explained respectively. Prokaryotes were found to be a likely net source of TEP as inferred by the significant direct relationship observed between prokaryotic heterotrophic abundance and TEP. This assumption was confirmed using experimental incubations, where prokaryotes produced TEP in concentrations ranging from 0.7 (Western Mediterranean, bathypelagic) to 232 (Western Mediterranean, mesopelagic) µg XG eq. L−1 day−1. [ABSTRACT FROM AUTHOR]

In the deep ocean, fluxes of particulate organic carbon (POC) and calcium carbonate are positively correlated, suggesting that CaCO 3 could increase sinking particle densities and/or protect the organic matter from degradation by prokaryotes, the so called “ballast effect”. Here, we used the PArticle Sinking Simulator (PASS) system to investigate the effect of increasing pressure on the biodegradation of calcifying Emiliania huxleyi aggregates. Incubations were carried out over a period of 10 days, simulating the changes in temperature and pressure in the water column of the NW Mediterranean Sea. Aggregates sinking from a depth of 200 m to 1700 m (assuming an average sinking velocity of 150 m d −1 ) were exposed to a natural mesopelagic prokaryotic community collected from 200 m. In contrast to previous studies, where silicifying diatom aggregates were used, the calcifying E. huxleyi aggregates were found to be more sensitive to degradation with increasing hydrostatic pressure (relative to constant atmospheric pressure). This was confirmed by changes in lipid composition which suggested increased cell lysis. Changes in particulate inorganic carbon and total alkalinity indicated that CaCO 3 dissolution might have been faster under pressure. Increased hydrostatic pressure also had a positive effect on particle aggregation, which may compensate for the effect of increased cell lysis. Our results imply that in coccolithophorid-dominated sinking aggregates, the ballasting and protection effects of coccoliths may collapse throughout the water column. The increased aggregation potential with pressure observed in these controlled conditions, may balance the loss of mineral ballast to a certain extent, although this needs to be confirmed in situ . [ABSTRACT FROM AUTHOR]

Transparent Exopolymer Particles (TEP) have received considerable attention since they were first described in the ocean more than 20 years ago. This is because of their carbon-rich composition, their high concentrations in ocean’s surface waters, and especially because of their ability to promote aggregation due to their high stickiness (i.e. biological glue). As large aggregates contribute significantly to vertical carbon flux, TEP are commonly seen as a key factor that drives the downward flux of particulate organic carbon (POC). However, the density of TEP is lower than that of seawater, which causes them to remain in surface waters and even move upwards if not ballasted by other particles, which often leads to their accumulation in the sea surface microlayer. Hence we question here the generally accepted view that TEP always increase the downward flux of POC via gravitational settling. In the present reassessment of the role of TEP, we examine how the presence of a pool of non-sinking carbon-rich particulate organic matter in surface waters influences the cycling of organic carbon in the upper ocean at daily to decadal time scales. In particular, we focus on the role of TEP in the retention of organic carbon in surface waters versus downward export, and discuss the potential consequences of climate change on this process and on the efficiency of the biological carbon pump. We show that TEP sink only when ballasted with enough high-density particles to compensate their low density, and hence that their role in vertical POC export is not solely linked to their ability to promote aggregation, but also to their contribution to the buoyancy of POC. It follows that the TEP fraction of POC determines the degree of retention and remineralization of POC in surface waters versus its downward export. A high TEP concentration may temporally decouple primary production and downward export. We identify two main parameters that affect the contribution of TEP to POC cycling; TEP stickiness, and the balance between TEP production and degradation rates. Because stickiness, production and degradation of TEP vary with environmental conditions, the role of TEP in controlling the balance between retention versus export, and hence the drawdown of atmospheric CO 2 by the biological carbon pump, can be highly variable, and is likely to be affected by climate change. [ABSTRACT FROM AUTHOR]

• Migrant biomass and respiratory flux were estimated in mesopelagic organisms. • The largest migrant biomass were mesopelagic fishes followed by decapods. • Fishes showed high values of respiratory flux at the centre-eastern coast of the gulf. • Midriff Islands region had one of the highest values of crustacean respiratory flux. • Micronekton respiratory flux was higher during June than during October. The biological carbon pump is the process that transports carbon vertically out of the mixed layer in the ocean. Besides the sinking flux of organic particles, active flux due to the daily vertical migration of zooplankton and micronekton promotes a significant carbon transport not fully accounted for or understood in the world's oceans. The diversity and abundance of epipelagic and mesopelagic species in the Gulf of California has been extensively studied, but the role of micronekton in carbon export has not yet been investigated. We studied the carbon flux promoted by juvenile and adult mesopelagic fishes and crustaceans (Decapoda and Euphausiidae) during the transition from the cold to warm period (June) and the onset of the warm season (October) in 2018. We provide the first estimation of migrant biomass and respiratory flux of the most abundant migratory species of mesopelagic fishes, decapods and euphausiids in the Gulf of California. The micronekton species collected accounted for a large biomass of mesopelagic fishes and pelagic crustaceans. The average migrant biomass estimates were 151.5 ± 101.2 mg C·m−2 during June and 90.9 ± 75.3 mg C·m−2 during October. The enzymatic activity of the electron transfer system (ETS) was measured as an estimate of their respiratory rates. Average specific ETS activity was significantly different between fishes and decapods, and between fishes and euphausiids (p < 0.05). The respiratory flux of fishes was predominant in the Gulf of California, followed by pelagic decapods and euphausiids. Seasonal changes in respiratory flux were observed for fishes (June: 6.1 ± 1.5 mg C·m−2·d−1; October: 3.2 ± 1.8 mg C·m−2·d−1) and decapods (June: 0.4 mg C·m−2·d−1; October: 0.7 ± 0.05 mg C·m−2·d−1). Respiratory flux estimation by crustaceans (decapods and euphausiids) and fishes together was 6.86 mg C·m−2·d−1 during June, and 4.21 mg C·m−2·d−1 during October 2018, suggesting a functional role of this large micronektonic fauna in the biological carbon export in this region. [ABSTRACT FROM AUTHOR]

• Primary production was time variable, with a 30-yr mean of 536.8 mg C m−2 d−1. • Primary production increased at a rate of 4 (mg C m−2 d−1) yr−1 from 1989–2018. • Export at 150 m averaged 27.9 mg C m−2 d−1 and 4.2 mg N m−2 d−1, with a PC:PN ratio of 7.99. • The export ratio was low (<0.06), and decreased over the 30-year period. • Several hypotheses are presented and discussed. Station ALOHA (A Long-term Oligotrophic Habitat Assessment) was established in the North Pacific Subtropical Gyre (22°45′N, 158°W) as an oligotrophic ocean benchmark to improve our understanding of processes that govern the fluxes of carbon (C) into and from the surface ocean. At approximately monthly intervals, measurements of the primary production of particulate C (PC) using the 14C method, and the export of PC and particulate nitrogen (PN) using surface-tethered sediment traps deployed at 150 m have been made along with a host of complementary physical, biological, and biogeochemical measurements. Euphotic zone depth-integrated (0–200 m) primary production ranged from 220.2 (standard deviation, SD, 10.8) mg C m−2 d−1 in Feb 2018 to 1136.5 (SD = 17.1) mg C m−2 d−1 in Jun 2000, with a 30-yr (1989–2018) mean of 536.8 (SD = 135.0) mg C m−2 d−1 (n = 271). Although the monthly primary production climatology was fairly well constrained, we observed substantial sub-decadal variability and a significant 0–125 m depth-integrated increasing trend of 4.0 (p < 0.01; 95% confidence interval, CI, 2.1–5.9) (mg C m−2 d−1) yr−1 since 1989, displaying a large relative increase of 37% (CI = 18–55%) in the lower portion (75–125 m) of the euphotic zone. Chlorophyll (Chl) a and suspended PC and PN concentrations also displayed significant (p < 0.01) increases in the 75–125 m region of the euphotic zone. PC export at 150 m exhibited both short-term (monthly) and longer-scale variability with a 30-yr mean of 27.9 (SD = 9.7, n = 265) mg C m−2 d−1. PC and PN export exhibited extended, multi-year periods of significantly lower or higher values compared to the 30-yr mean. These multi-year periods of anomalously low and high particle export, in the absence of contemporaneous variations in primary production, probably reflect periodic changes in remineralization efficiencies. The PC export ratio (e-ratio; PC export at 150 m ÷ 0–150 m depth-integrated 14C-based primary production) was low, with a 30-yr mean of 0.054 (SD = 0.021, n = 248), and exhibited a significant (p < 0.01) long-term decreasing trend over the 30-yr observation period. The 30-yr long-term increases in primary production (~37%), Chl a , and suspended PC and PN concentrations (~17%, 8%, and 8%, respectively) in the 75–125 m portion of the water column are hypothesized to result from an enhanced supply of nutrients to the lower portion of the water column over the past three decades. [ABSTRACT FROM AUTHOR]

• CO 2 fluxes vary from small outgassing to strong sink conditions. • Enhanced CO 2 uptake on the western domain was associated with salinity variations. • Increased haptophyte concentrations boosted the CO 2 uptake in the gyre. • Intense CO 2 uptake in the eastern domain (30°S) was associated with haptophytes. The influence of phytoplankton groups on carbon dynamics was investigated during six oceanographic spring cruises (three cruises were carried out in 2009, and another three were conducted in 2011) between the western (Brazil) and eastern (Africa) South Atlantic margins. A seventh cruise crossed the South Atlantic during the early winter of 2015. Sea surface temperature and salinity, oceanic and atmospheric partial pressure of CO 2 (p CO 2), chlorophyll a and other phytoplankton pigment data were gathered. Net CO 2 fluxes were calculated for each cruise, characterizing the ability of each region to take up atmospheric CO 2. We quantified phytoplankton chemotaxonomic groups using the HPLC/CHEMTAX approach. Thus, this study aimed to improve our understanding of the distribution of phytoplankton groups and their connection with the carbon biogeochemical cycle in the South Atlantic Ocean. Our results showed significant variations in both the zonal and meridional patterns of phytoplankton groups and the associated CO 2 uptake magnitudes. Diatoms and haptophytes dominated the coastal regions of Brazil and Africa, respectively, whereas the open ocean was dominated by haptophytes and the picoplanktonic cyanobacteria Prochlorococcus and Synechococcus. The CO 2 uptake capacity increased eastward from −7.1 mmol CO 2 m−2 d–1 on the Brazilian coast to −27.6 mmol CO 2 m−2 d–1 on the African coast. There was a significant negative relationship (p < 0.05) between the phytoplankton biomass and the difference in sea-air p CO 2 (Δ p CO 2), with increasing CO 2 uptake corresponding to increases in the biomasses of diatoms and haptophytes. Therefore, according to our analysis, haptophytes and diatoms were the main phytoplankton groups related to a high uptake of CO 2 along the South Atlantic Ocean regions covered in this study. Thus, we encourage further investigations on their traits and vulnerabilities to future environmental change scenarios. [ABSTRACT FROM AUTHOR]