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The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.

Three-dimensional hydrogels of organic polymers have been suggested to affect a variety of processes in the ocean, including element cycling, microbial ecology, food-web dynamics, and air-sea exchange. However, their abundance and distribution in the ocean are hardly known, strongly limiting an assessment of their global significance. As a consequence, marine gels are often disregarded in biogeochemical or ecosystem models. Here, we demonstrate the widespread abundance of microgels in the ocean, from the surface to the deep sea. We exhibit size spectra of two major classes of marine gels, transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) for three different ocean regimes: (a) Polar Seas, (b) Eastern Boundary Upwelling Systems, and (c) the oligotrophic open ocean. We show the variations of TEP and CSP over the water-column, and compare them to dissolved organic carbon (DOC). We also discuss how the observed distributional patterns inform about productivity and particle dynamics of these distinct oceanic regimes. Finally, we exploit current research topics, where consideration of microgels may give new insight into the role of organic matter for marine biogeochemical processes.

Abstract Transparent exopolymer particles (TEP) are a class of marine gel particles and important links between surface ocean biology and atmospheric processes. Derived from marine microorganisms, these particles can facilitate the biological pumping of carbon dioxide to the deep sea, or act as cloud condensation and ice nucleation particles in the atmosphere. Yet, environmental controls on TEP abundance in the ocean are poorly known. Here, we investigated some of these controls during the first multiyear time-series on TEP abundance for the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data collected at the Long-Term Ecological Research observatory HAUSGARTEN during 2009 to 2014 indicate a strong biological control with highest abundance co-occurring with the prymnesiophyte Phaeocystis pouchetii. Higher occurrence of P. pouchetii in the Arctic Ocean has previously been related to northward advection of warmer Atlantic waters, which is expected to increase in the future. Our study highlights the role of plankton key species in driving climate relevant processes; thus, changes in plankton distribution need to be accounted for when estimating the ocean’s biogeochemical response to global change.

The Baltic Sea is prone to oxygen deficiency due to the restricted water exchange with the North Sea in coincidence with a high biological oxygen demand. The partitioning of organic carbon between respiration, accumulation and export is co-determined by phytoplankton primary production and its subsequent bacterial remineralization. Here, we investigated net phytoplankton primary production, heterotrophic bacterial biomass production and dark CO2 fixation by on-board incubations with radiolabeled tracers in the Baltic Proper and in the Gulf of Riga after the main spring bloom. Results show that low phytoplankton standing stocks of ≤1.6 μg chlorophyll a L–1 sustained net primary production of 161–724 mg C m–2 d–1 under nitrogen limitation. Estimates of bacterial carbon remineralization suggest that freshly produced organic carbon was supplied to the aphotic zone at all stations. In the southern Baltic Proper, net primary production exceeded the bacterial carbon demand in the surface mixed layer, suggesting that organic matter derived from nutrient-limited primary production was available for export to bacterial communities below the oxycline. On average, 46% of heterotrophic bacterial production was mediated in oxygen minimum zones, revealing the high importance of organic matter recycling under hypoxic and anoxic conditions for the carbon budget. Dark CO2 fixation of up to 4.33 μg C L–1 d–1 in sulfide-free waters equaled 9–54% of the co-inciding heterotrophic bacterial carbon demand and may have provided another organic carbon source for heterotrophic activity. Substantially higher dark CO2 fixation up to 25.46 μg C L–1 d–1 was determined in sulfidic waters. Since our study was conducted 5 months after the major Baltic inflow event in winter 2014/2015, potential effects of deep water ventilation could be investigated. In the Gotland Basin, heterotrophic bacterial production in renewed oxygen-rich bottom water was similar to that in the uplifted oxygen-deficient former bottom water, while it was significantly reduced in sulfidic waters. Hence, our results suggest that the removal of hydrogen sulfide by inflow events has a high potential to increase bacterial carbon remineralization.

The Arctic Ocean plays a key role in regulating the global climate, while being highly sensitive to climate change. Temperature in the Arctic increases faster than the global average, causing a loss of multiyear sea-ice and affecting marine ecosystem structure and functioning. As a result, Arctic primary production and biogeochemical cycling are changing. Here, we investigated inter-annual changes in the concentrations of particulate and dissolved organic carbon (POC, DOC) together with biological drivers, such as phyto- and bacterioplankton abundance in the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data have been collected in summer at the Long-Term Ecological Research observatory HAUSGARTEN during eight cruises from 2009 to 2017. Our results suggest that the dynamic physical system of the Fram Strait induces strong heterogeneity of the ecosystem that displays considerable intra-seasonal as well as inter-annual variability. Over the observational period, DOC concentrations were significantly negatively related to temperature and salinity, suggesting that outflow of Central Arctic waters carrying a high DOC load is the main control of DOC concentration in this region. POC concentration was not linked to temperature or salinity but tightly related to phytoplankton biomass as estimated from chlorophyll-a concentrations (Chl-a). For the years 2009–2017, no temporal trends in the depth-integrated (0–100 m) amounts of DOC and Chl-a were observed. In contrast, depth-integrated (0–100 m) amounts of POC, as well as the ratio [POC]:[TOC], decreased significantly over time. This suggests a higher partitioning of organic carbon into the dissolved phase. Potential causes and consequences of the observed changes in organic carbon stocks for food-web structure and CO2 sequestration are discussed.

Shipping emissions are likely to increase significantly in the coming decades, alongside increasing emphasis on the sustainability and environmental impacts of the maritime transport sector. Exhaust gas cleaning systems (“scrubbers”), using seawater or fresh water as cleaning media for sulfur dioxide, are progressively used by shipping companies to comply with emissions regulations. Little is known about the chemical composition of the scrubber effluent and its ecological consequences for marine life and biogeochemical processes. If scrubbers become a central tool for atmospheric pollution reduction from shipping, modeling, and experimental studies will be necessary to determine the ecological and biogeochemical effects of scrubber wash water discharge on the marine environment. Furthermore, attention must be paid to the regulation and enforcement of environmental protection standards concerning scrubber use. Close collaboration between natural scientists and social scientists is crucial for progress toward sustainable shipping and protection of the marine environment.

Gel particles—a class of abundant transparent organic particles—have increasingly gathered attention in marine research. Field studies on the bacterial colonization of marine gels however are still scarce. So far, most studies on respective particles have focused on the upper ocean, while little is known on their occurrence in the deep sea. Here, we report on the vertical distribution of the two most common gel particle types, which are polysaccharide-containing transparent exopolymer particles (TEP) and proteinaceous Coomassie stainable particles (CSP), as well as numbers of bacteria attached to gel particles throughout the water column, from the surface ocean down to the bathypelagial (< 3,000 m). Our study was conducted in the Arctic Fram Strait during northern hemispheres' summer in 2015. Besides data on the bacterial colonization of the two gel particle types (TEP and CSP), we present bacterial densities on different gel particle size classes according to 12 different sampling depths at four sampling locations. Gel particles were frequently abundant at all sampled depths, and their concentrations decreased from the euphotic zone to the dark ocean. They were colonized by bacteria at all sampled water depths with risen importance at the deepest water layers, where fractions of bacteria attached to gel particles (%) increased within the total bacterial community. Due to the omnipresent bacterial colonization of gel particles at all sampled depths in our study, we presume that euphotic production of this type of organic matter may affect microbial species distribution within the whole water column in the Fram Strait, down to the deep sea. Our results raise the question if changes in the bacterial community composition and functioning on gel particles occur over depth, which may affect microbial respiration and remineralization rates of respective particles in different water layers.

Marine bacteria are the main consumers of freshly produced organic matter. Many enzymatic processes involved in the bacterial digestion of organic compounds were shown to be pH sensitive in previous studies. Due to the continuous rise in atmospheric CO2 concentration, seawater pH is presently decreasing at a rate unprecedented during the last 300 million years but the consequences for microbial physiology, organic matter cycling and marine biogeochemistry are still unresolved. We studied the effects of elevated seawater pCO2 on a natural plankton community during a large-scale mesocosm study in a Norwegian fjord. Nine Kiel Off-Shore Mesocosms for Future Ocean Simulations (KOSMOS) were adjusted to different pCO2 levels ranging initially from ca. 280 to 3000 µatm and sampled every second day for 34 days. The first phytoplankton bloom developed around day 5. On day 14, inorganic nutrients were added to the enclosed, nutrient-poor waters to stimulate a second phytoplankton bloom, which occurred around day 20. Our results indicate that marine bacteria benefit directly and indirectly from decreasing seawater pH. During the first phytoplankton bloom, 5-10% more transparent exopolymer particles were formed in the high pCO2 mesocosms. Simultaneously, the efficiency of the protein-degrading enzyme leucine aminopeptidase increased with decreasing pH resulting in up to three times higher values in the highest pCO2/lowest pH mesocosm compared to the controls. In general, total and cell-specific aminopeptidase activities were elevated under low pH conditions. The combination of enhanced enzymatic hydrolysis of organic matter and increased availability of gel particles as substrate supported up to 28% higher bacterial abundance in the high pCO2 treatments. We conclude that ocean acidification has the potential to stimulate the bacterial community and facilitate the microbial recycling of freshly produced organic matter, thus strengthening the role of the microbial loop in the surface ocean.