Description: The vast majority of freshly produced oceanic dissolved organic carbon (DOC) is derived from marine phytoplankton, then rapidly recycled by heterotrophic microbes. A small fraction of this DOC survives long enough to be routed to the interior ocean, which houses the largest and oldest DOC reservoir. DOC reactivity depends upon its intrinsic chemical composition and extrinsic environmental conditions. Therefore, recalcitrance is an emergent property of DOC that is analytically difficult to constrain. New isotopic techniques that track the flow of carbon through individual organic molecules show promise in unveiling specific biosynthetic or degradation pathways that control the metabolic turnover of DOC and its accumulation in the deep ocean. However, a multivariate approach is required to constrain current carbon fluxes so that we may better predict how the cycling of oceanic DOC will be altered with continued climate change. Ocean warming, acidification, and oxygen depletion may upset the balance between the primary production and heterotrophic reworking of DOC, thus modifying the amount and/or composition of recalcitrant DOC. Climate change and anthropogenic activities may enhance mobilization of terrestrial DOC and/or stimulate DOC production in coastal waters, but it is unclear how this would affect the flux of DOC to the open ocean. Here, we assess current knowledge on the oceanic DOC cycle and identify research gaps that must be addressed to successfully implement its use in global scale carbon models.

Description: Major uncertainties in air-sea gas flux parameterizations may arise from a yet unpredictable sea surface microlayer (SML). Its influence on gas exchange is twofold as organic matter, in particular surfactants, on one side and organisms enriched in the SML on the other can alter air-sea gas fluxes. However, spatial heterogeneity of the SML and its potential consequences for gas exchange are not well understood. This study examines the SML’s surfactant pool and the dynamics of microbial enrichment across the sharp hydrological front of a newly upwelled filament off Mauritania. The front was marked by a distinct decrease in temperature and salinity compared to the stratified water column outside the filament. Distinct chemical and microbial SML properties were observed and associated with the filament. Overall, organic matter in the SML was significantly higher concentrated inside the filament and in equivalence to the underlying water. Degradation indices derived from total amino acids (TAA) composition indicated production of fresh organic matter inside and increased degradation outside the filament. Moreover, a shift in the microbial community was observed, for instance Synechococcus spp. prevailed outside the filament. Autotrophic and heterotrophic microorganisms preferably colonized the SML outside the filament. Organic matter enrichment in the SML depended largely on the chemical nature of biomolecules. Total organic carbon (TOC), total nitrogen and total combined carbohydrates were only slightly enriched while glucose, TAA and surfactants were considerably enriched in the SML. Surfactant concentration was positively correlated to TAA, in particular to arginine and glutamic acid, indicating that fresh organic matter components enhanced surface activity. Further, TOC and surfactant concentration correlated significantly (r2 = 0.47, p-value 〈 0.001). The lower limit of this linear correlation hits approximately the lowest TOC concentration expected within the global surface ocean. This suggests that surfactants are primarily derived from autochthonous production and most refractory components are excluded. Using a previously established relationship between surfactants and CO2 gas exchange (Pereira et al., 2018), we estimated that surfactants suppressed gas exchange by 12% inside the filament. This could be of relevance for freshly upwelled filaments, which are often supersaturated in greenhouse gases.

Description: Anthropogenic activities are modifying the oceanic environment rapidly and are causing ocean warming and deoxygenation, affecting biodiversity, productivity, and biogeochemical cycling. In coastal sediments, anaerobic organic matter degradation essentially fuels the production of hydrogen sulfide and methane. The release of these compounds from sediments is detrimental for the (local) environment and entails socio-economic consequences. Therefore, it is vital to understand which microbes catalyze the re-oxidation of these compounds under environmental dynamics, thereby mitigating their release to the water column. Here we use the seasonally dynamic Boknis Eck study site (SW Baltic Sea), where bottom waters annually fall hypoxic or anoxic after the summer months, to extrapolate how the microbial community and its activity reflects rising temperatures and deoxygenation. During October 2018, hallmarked by warmer bottom water and following a hypoxic event, modeled sulfide and methane production and consumption rates are higher than in March at lower temperatures and under fully oxic bottom water conditions. The microbial populations catalyzing sulfide and methane metabolisms are found in shallower sediment zones in October 2018 than in March 2019. DNA-and RNA profiling of sediments indicate a shift from primarily organotrophic to (autotrophic) sulfide oxidizing Bacteria, respectively. Previous studies using data collected over decades demonstrate rising temperatures, decreasing eutrophication, lower primary production and thus less fresh organic matter transported to the Boknis Eck sediments. Elevated temperatures are known to stimulate methanogenesis, anaerobic oxidation of methane, sulfate reduction and essentially microbial sulfide consumption, likely explaining the shift to a phylogenetically more diverse sulfide oxidizing community based on RNA.

Description: From 2008 through 2019, a comprehensive research project, SFB 754, Climate - Biogeochemistry Interactions in the Tropical Ocean, was funded by the German Research Foundation to investigate the climate-biogeochemistry interactions in the tropical ocean with a particular emphasis on the processes determining the oxygen distribution. During three 4-year long funding phases, a consortium of more than 150 scientists conducted or participated in 34 major research cruises and collected a wealth of physical, biological, chemical, and meteorological data. A common data policy agreed upon at the initiation of the project provided the basis for the open publication of all data. Here we provide an inventory of this unique data set and briefly summarize the various data acquisition and processing methods used.

Description: Amino acids (AA) and carbohydrates (CHO) are important components of the marine organic carbon cycle. Produced mainly by phytoplankton as part of the particulate organic carbon (POC) fraction, these compounds can be released into the outer medium where they become part of the dissolved organic carbon (DOC) pool and are rapidly taken up by heterotrophs (e.g., bacteria). We investigated the quantity and quality of POC and DOC, AA and CHO composition in both pools in three different water masses in the Fram Strait (Arctic Ocean) in summer 2017. Polar Waters and Atlantic Waters showed similar concentrations of particulate and dissolved AA and CHO, despite Polar Waters showing the highest DOC concentrations. In Mixed Waters, where the two water masses mix with each other and with melting sea ice, the concentrations of particulate and dissolved AA and CHO were highest. AA and CHO composition differed substantially between the particulate and dissolved fractions. The particulate fraction (〉0.7 μm) was enriched in essential AA and the CHO galactose, xylose/mannose, and muramic acid. In the dissolved fraction non-essential AA, several neutral CHO, and acidic and amino CHO were enriched. We further investigated different size fractions of the particulate matter using a separate size fractionation approach (0.2–0.7 μm, 0.7–10 μm and 〉10 μm). The chemical composition of the 0.2–0.7 μm size-fraction had a higher contribution of non-essential AA and acidic and amino sugars, setting them apart from the 0.7–10 μm and 〉10 μm fractions, which showed the same composition. We suggest that the relative differences observed between different size fractions and DOC with regards to AA and CHO composition can be used to evaluate the state of organic matter processing and evaluate the contribution of autotrophic phytoplankton or more heterotrophic biomass. In the future, changing conditions in the Central Arctic Ocean (Atlantification, warming, decreasing ice concentrations) may increase primary production and consequently degradation. The AA and CHO signatures left behind after production and/or degradation processes occurred, could be used as tracers after the fact to infer changes in microbial loop processes and food web interactions.

Description: Pollution of the marine environment is an emerging threat. Nowadays, engineered nanoparticles (〈100 nm) such as zinc, copper and silver are widely used as antimicrobial agents, therefore often present in daily-life products. Consequently, the demand and production of nanoparticles are expected to increase. Here, we specifically focus on silver nanoparticles (AgNP). Once released into the environment, AgNPs pose an obvious ecotoxicological risk, potentially affecting ecosystem structure and functioning. For instance, phytoplankton-derived exudates, rich in acidic polysaccharides and amino acids, can abiotically aggregate into microgels such as transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP). Hence, microgels can bridge dissolved and particulate size fractions and facilitate aggregate formation with organic and mineral particles. Both physical and chemical properties make TEP and CSP attractive nutrient hotspots for heterotrophic bacterioplankton. Bacteria, in turn, utilize extracellular enzymes to access these carbon and nitrogen pools. However, knowledge about the mechanisms by which AgNPs might interact with and affect the biogeochemical cycling of TEP and CSP is still insufficient. Therefore, we conducted a mesocosm experiment in the Eastern Mediterranean Sea and investigated the effects of environmentally relevant concentrations of silver ions (Ag+) and AgNP on the properties of TEP and CSP (i.e., area and abundance) along with enzymatic activity measurements. Our results showed that cyanobacteria were likely the primary source of CSP in the ultra-oligotrophic Mediterranean Sea. Also, CSP contributed more to the microgel pool than TEP, as indicated by a strong relationship between CSP and heterotrophic microbial dynamics. While silver (i.e., Ag+ or AgNP) had overall only marginal effects, both species affected the relationships between cell-specific LAPase activity and CSP and cell-specific APase activity and phosphate levels. Thus, Ag+ and AgNP have the potential to regulate microgel dynamics. However, future studies are needed to derive a robust understanding of the effects of silver pollution on the coupling of microgel formation and degradation and the follow-on effect on biogeochemical cycles.

Description: Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2–3 μm, FL) and particle-associated (〉3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.

Description: Deoxygenation is tied to organic carbon (Corg) supply and utilization in marine systems. Under oxygen-depletion, bacteria maintain respiration using alternative electron acceptors such as nitrate. Since anaerobic respiration's energy yield is lower, Corg remineralization may be reduced and its residence time increased. We investigated the influence of oxygen and alternative electron acceptors' availability on Corg cycling by heterotrophic bacteria during a continuous culture experiment with Shewanella baltica, a facultative anaerobic γ-Proteobacteria in the Baltic Sea. We tested six different oxygen levels, from suboxic (〈5 µmol L-1 ) to fully oxic conditions, using media (salinity=14 g L-1 ) supplied with high (HighN) or low (LowN) inorganic nitrogen concentrations relative to glucose as labile Corg source. Our results show that suboxia limited DOC (glucose) uptake and cell growth only under LowN, while higher availability of alternative electron acceptors seemingly compensated oxygen limitation under HighN. N-loss was observed under suboxia in both nitrogen treatments. Under HighN, N-loss was highest and a C:N loss ratio of ~2.0 indicated that Corg was remineralized via denitrification. Under LowN, the C:N loss ratio under suboxia was higher (~5.5), suggesting dominance of other anaerobic respiration pathways, such as dissimilatory nitrate reduction to ammonium (DNRA). Bacterial growth efficiency was independent of oxygen concentration but higher under LowN (34±3.0%) than HighN (26±1.6%). Oxygen concentration also affected dissolved organic matter (DOM) cycling. Under oxic conditions, the release of dissolved combined carbohydrates was enhanced, and the amino acid-based degradation index (DI) pointed to more diagenetically altered DOM. Our results suggest bacterial Corg uptake in low-oxygen systems dominated by S. baltica can be limited by oxygen but compensated by high nitrate availability. Hence, suboxia diminishes Corg remineralisation only when alternative electron acceptors are lacking. Under high nitrate:Corg supply, denitrification leads to a higher N:C loss ratio, potentially counteracting eutrophication in the long run. Low nitrate:Corg supply may favour other anaerobic respiration pathways like DNRA, which sustains labile nitrogen in the system, potentially intensifying the cycle of eutrophication. Going forward, it will be crucial to establish the validity of our findings for S. baltica in natural systems with diverse organic substrates and microbial consortia.

Description: 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.

Description: Transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP), two prominent classes of gel−like particles in the ocean primarily produced by phytoplankton, play crucial roles in ecological and biogeochemical processes, influencing microbial nutrition, growth, and particle aggregation. The distribution of these particles is intricately linked to the spatiotemporal dynamics of phytoplankton. Mesoscale cyclonic eddies (CEs) are known to stimulate phytoplankton growth and influence particle transport, but their effects on TEP and CSP remain to be determined. In the Eastern Tropical North Atlantic (ETNA), we examined three CEs: one off the Mauritanian coast during summer (Mau), one offshore during winter (Sal), and another near Brava island during winter. Mau and Brava CEs were in their intensification/maturity phase, while the Sal CE was in its decay phase. Both TEP and CSP concentrations correlated with primary productivity, but TEP increased with chlorophyll−a concentration, whereas elevated CSP coincided also with the highest abundance of pico−nanophytoplankton (〈20 µm), mainly Synechococcus. Both gels exhibited a positive correlation with bacterial biomass production, indicating their consumption by heterotrophic bacteria. TEP total area in the epipelagic waters of all CEs (Mau, Brava, and Sal) was elevated compared to surrounding waters, with on average 4, 2.5, and 1.6−fold higher values, respectively. However, no significant difference in TEP size distribution was observed within any CEs and their surroundings. Similarly, CSP total area increased in the epipelagic waters of Mau and Brava CEs, with on average 5 and 2.4−fold higher values, respectively, compared to surrounding waters. CSP particles were notably larger in these two eddies, while the Sal CE showed no significant difference from surrounding waters in CSP abundance and size. Overall, TEP and CSP exhibited distinct responses to CEs, with increased concentrations during their intensification/maturation stage and remineralization dominating during their decaying stage.