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The research cruise M182 (MOSES Eddy-III) concludes a trilogy of research cruises conducted in the frame of the Helmholtz Association's Modular Observation Solutions for Earth Systems (MOSES) infrastructure, aiming at a comprehensive multi- and interdisciplinary study of ocean eddies in the northern tropical Atlantic. As an integral part of the BMBF-funded project "Role of eddies in the carbon pump of eastern upwelling systems - Demonstration Case Canary Current System" (REEBUS), launched in 2019, this study focuses on investigating the multi- layered influence of eddies on the lateral transport of biogeochemical properties and the carbon pump within deep-sea ecosystems. Ocean eddies have a significant impact on the physical, biogeochemical and biological aspects of coastal upwelling regions. Given the profound socio- economic impact of coastal upwelling areas, REEBUS takes a multidisciplinary approach to investigate the influence of ocean eddies on these systems. This expedition is motivated by the objective of acquiring novel insights into the functional dynamics of eddies, specifically elucidating their role in the CO2 source and sink functions inherent to eastern boundary upwelling systems. Furthermore, our investigative efforts encompassed a thorough examination of the biological carbon pump within both the designated upwelling areas and their associated oligotrophic regions. The synthesis of data from all REEBUS cruises, coupled with the inclusion of data from prior expeditions (MOSES Eddy-I and II) within this geographical region, promises to yield a high scientific potential.

Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world ' s oceans.

Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.

Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 mu m) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05-0.27) of FL bacteria (defined as the size-fraction <3.0 mu m) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.

The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 x 10(4) cells ml(-1). This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.

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

A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean's interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composi, Is included in the dissertation as a manuscript titled: Taxon-specific shifts in bacterial and archaeal transcription of dissolved organic matter cycling genes in a stratified fjord

Cobalamin (B12) is an essential cofactor that is exclusively synthesized by some prokaryotes while many prokaryotes and eukaryotes require an external supply of B12. The spatial and temporal availability of B12 is poorly understood in marine ecosystems. Field measurements of B12 along with a large set of ancillary biotic and abiotic factors were obtained during three oceanographic cruises in the NW Iberian Peninsula, covering different spatial and temporal scales. B12 concentrations were remarkably low (<1.5 pM) in all samples, being significantly higher at the subsurface Eastern North Atlantic Central Water than at shallower depths, suggesting that B12 supply in this water mass is greater than demand. Multiple regression models excluded B12 concentration as predictive variable for phytoplankton biomass or production, regardless of the presence of B12-requiring algae. Prokaryote production was the best predictor for primary production, and eukaryote community composition was better correlated with prokaryote community composition than with nutritional resources, suggesting that biotic interactions play a significant role in regulating microbial communities. Interestingly, co-occurrence network analyses based on 16S and 18S rRNA sequences allowed the identification of significant associations between potential B12 producers and consumers (e.g. Thaumarchaeota and Dynophyceae, or Amylibacter and Ostreococcus respectively), which can now be investigated using model systems in the laboratory.

Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.

Cobalamin (B12) is an essential cofactor that is exclusively synthesized by some prokaryotes while many prokaryotes and eukaryotes require an external supply of B12. The spatial and temporal availability of B12 is poorly understood in marine ecosystems. Field measurements of B12 along with a large set of ancillary biotic and abiotic factors were obtained during three oceanographic cruises in the NW Iberian Peninsula, covering different spatial and temporal scales. B12 concentrations were remarkably low (<1.5 pM) in all samples, being significantly higher at the subsurface Eastern North Atlantic Central Water than at shallower depths, suggesting that B12 supply in this water mass is greater than demand. Multiple regression models excluded B12 concentration as predictive variable for phytoplankton biomass or production, regardless of the presence of B12‐requiring algae. Prokaryote production was the best predictor for primary production, and eukaryote community composition was better correlated with prokaryote community composition than with nutritional resources, suggesting that biotic interactions play a significant role in regulating microbial communities. Interestingly, co‐occurrence network analyses based on 16S and 18S rRNA sequences allowed the identification of significant associations between potential B12 producers and consumers (e.g. Thaumarchaeota and Dynophyceae, or Amylibacter and Ostreococcus respectively), which can now be investigated using model systems in the laboratory

B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B-12 and/or B-1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B-12 and B-1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B-1 and B-12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B-12 and B-1 uptake, and Pelagibacterales expressed genes involved in vitamin B-1 uptake. Interestingly, the relative expression of vitamin B-12 and B-1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass.

Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced changes in bacterial growth, activity, and transcription related to DOM characteristics. Transcriptional responses differed between compound classes, with distinct gene sets ("core genes") distinguishing carbohydrates, proteins, and nucleic acids. Moreover, we found a strong divergence in functional transcription at the level of particular monomers and polymers (i.e., the condensation state), primarily in the carbohydrates and protein compound classes. These specific responses included a variety of cellular and metabolic processes that were mediated by distinct bacterial taxa, suggesting pronounced functional partitioning of organic matter. Collectively, our findings show that two important facets of DOM, compound class and condensation state, shape bacterial gene expression, and ultimately select for distinct bacterial (functional) groups. This emphasizes the interdependency of marine bacteria and labile carbon compounds for regulating the transformation of DOM in surface waters.

Domain-specific metabolic inhibitors are currently used to differentiate archaeal from bacterial activity. However, studies testing the specificity of these inhibitors are sparse or are based on cultured strains. We determined the inhibition specificity of erythromycin (EMY) and N1-guanyl-1,7-diaminoheptane (GC7) on bacterial and archaeal communities in the North Atlantic. EMY and GC7 are assumed to inhibit bacterial and archaeal activity, respectively. Heterotrophic prokaryotic activity was estimated via H-3-leucine incorporation on the cell-specific level using catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography (MICRO-CARD-FISH). In the water masses studied, the contribution of Thaumarchaeota to total picoplankton abundance ranged from 5 to 24% while Euryarchaeota contributed 2 to 6%; the relative abundance of Bacteria ranged from 29 to 48%. The addition of EMY and GC7 reduced the bulk leucine incorporation by similar to 77% and similar to 41%, respectively. Evaluation of the inhibition efficiency of EMY on a cell-specific level showed no difference between Archaea (76.0 +/- 14.2% [SD]) and Bacteria (78.2 +/- 9.5%). Similarly, the reduction of substrate uptake in GC7-treated samples was similar in Archaea (59.9 +/- 24%) and Bacteria (47.2 +/- 9.6%). Taken together, our results suggest that in complex open-ocean prokaryotic communities neither EMY nor GC7 is efficient as a domain-specific inhibitor.

Climate change is predicted to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture- influenced catchment areas were added to Baltic Sea Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment (before the phytoplankton bloom), but expression patterns diverged significantly upon bloom senescence.Notably, transcripts associated with phosphate metabolism were significantly enriched , whereas transcripts related to nitrogen metabolism were significantly lower in the agriculture river treatment compared to the boreal forest river treatment. The opposite pattern was observed in the boreal forest river water treatment. Overall, our results showed that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. This suggests that bacterial transformations of organic matter and nutrient cycling in coastal waters and estuarine environments are sensitive to changes in precipitation patterns in a catc

Climate change is projected to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture-influenced catchment areas (enriched in nitrogen) were added to Baltic Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment during phytoplankton development, but expression patterns diverged upon bloom senescence. This indicated that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. Notably, transcripts associated with phosphate metabolism were significantly enriched in the agriculture river treatment compared to the boreal forest river treatment, whereas transcripts related to nitrogen metabolism were significantly lower. The opposite pattern was observed in the boreal forest river water treatment. This suggests that bacterial transformations of organic matter and nutrient processing in coastal environments are sensitive to alterations in the precipitation-induced riverine runoff in a catchmen

Aphanizomenon, together with Dolichospermum and Nodularia, constitute the major genera of bloom forming filamentous nitrogen fixing cyanobacteria in the Baltic Sea. Like the other genera, Aphanizomenon displays summer blooms that are highly variable in magnitude and duration but unlike the others it is considered a holoplanktonic species. Still, the molecular mechanisms enabling Aphanizomenon year-round presence in surface waters are currently unknown. Here we combine analysis of Aphanizomenon population dynamics at the Linnaeus Microbial Observatory (LMO) station in the Baltic Proper over nine years (2011-2019) with associated gene expression patterns during 2016-2017 to identify annual abundance, and metabolic and life cycle strategies. Aphanizomenon biomass showed large annual variability and a consistent biovolume peak in summer, with bloom intensity ranging from 78-1334 mm3 m-3. 16S rRNA gene amplicon sequence data showed that one Aphanizomenon amplicon sequence variant (ASV) dominated, and its relative abundance correlated with biovolume measurements. Metatranscriptomic reads that mapped to an Aphanizomenon metagenome- assembled genome (MAG) revealed annually repeating gene expression patterns, resulting in distinct gene expression profiles during different meteorological seasons. Genes encoding proteins involved in several important functional classes, e.g. carbon fixation, photosynthesis, and associated photopigments showed seasonal variation, but were detected year round. Other genes, particularly those involved in nitrogen fixation, were highly expressed in summer, while absent in winter. Vitamin metabolism and phosphorus scavenging genes were preferentially expressed during the colder periods of the annual cycle. Together, these data show that Aphanizomenon regulates the molecular machinery on the seasonal scale, providing context to the observed dynamics of Aphanizomenon in the Baltic Proper and a foundation for understanding the ecology of these cyanoba

Microbial communities in surface waters of temperate seas are exposed to recurring annual seasonal variation in temperature and nutrient concentrations. To what extent bacterioplankton populations in natural communities alter their functional repertoire as a result of seasonal succession has not been thoroughly investigated. Here we use metatranscriptomics and leverage a comprehensive catalogue of metagenome-assembled genomes (MAGs) to follow gene expression in individual populations over a two-year time period at an offshore station in the Baltic Sea. We show that the collective expression of the MAGs changed in a consistent manner across seasons in the two years, forming clusters representing the four seasons, and that more than 80% of these displayed a recurring seasonal pattern. Furthermore, we found that the changes in expression could partly be explained by modulation of expression within the prokaryotic populations, since intra-population expression patterns also changed with season. Taken together, our results demonstrate how natural microbial populations alter their expression on the gene level, and how these changes drive large scale changes on both population and community level. This work aims to broaden the understanding of how microbes respond and adapt to their environment by preferentially altering their expressed genetic repertoire, and how microbial community dynamics can be explained through the gene expression of various populations constituting the community.