Background: Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.

Results: Elevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.

Conclusions: We emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.

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.

The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models. 

Coastal upwelling zones are veritable hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, knowledge of the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM has yet to advance. We therefore carried out a comparative metatranscriptomics analysis with parallel sampling of bacterioplankton during experimental and natural phytoplankton blooms in the Northwest Iberian upwelling system. The experiment analysis uncovered a taxon-specific progression of transcriptional responses from bloom development, over early decay, to senescence phases. This included pronounced order-specific differences in regulation of glycoside hydrolases and peptidases along with transporters, supporting the notion that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of experiment and field blooms revealed a large degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the coastal DOM pool. Collectively, our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the short time scales typical of upwelling-driven phytoplankton blooms.

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.

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.

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.

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. IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B-12 and/or B-1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B-12 and B-1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B-12 and B-1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.

Roughly half of the global primary production originates from microscopic phytoplankton in marine ecosystems, converting carbon dioxide into organic matter. This organic matter pool consists of a myriad of compounds that fuel heterotrophic bacterioplankton. However, knowledge of the molecular mechanisms – particularly the metabolic pathways involved in the degradation and utilization of dissolved organic matter (DOM) – and transcriptional dynamics over spatiotemporal gradients are still scarce. Therefore, we studied the molecular mechanisms of bacterioplankton communities, including archaea, involved in the cycling of DOM, over different spatiotemporal scales in experiments and through field observations.

In seawater experiments, we found a divergence of bacterioplankton transcriptional responses to different organic matter compound classes (carbohydrates, nucleic acids, and proteins) and condensation states (monomers or polymers). These responses were associated with distinct bacterial taxa, suggesting pronounced functional partitioning of these compounds in the Sea. Baltic Proper mesocosms amended with two different river loadings (forest versus agriculture river water) revealed a divergence in gene expression patterns between treatments during bloom decay. This was particularly true for genes in phosphorus and nitrogen metabolism, highlighting the importance and sensitivity of interaction effects between river- and phytoplankton-derived DOM in regulating bacterial activity responses to changes in precipitation-induced riverine runoff.

In shipboard mesocosms in an Atlantic coastal upwelling system, we found significant changes in bacterioplankton transcription of hydrolyzing enzymes and membrane transporters from phytoplankton bloom development to senescence, primarily driven by phytoplankton-derived DOM and dissolved organic carbon dynamics. These responses differed substantially between bacterial orders, suggesting that functional resource partitioning is dynamically structured by temporal changes in DOM quantity and quality. Further analysis of these gene systems in a stratified fjord revealed pronounced divergence in transcription with depth and between bacterial taxa; moreover, transcription was more variable in the surface waters. This highlights the interplay between functional and physical partitioning of biogeochemical cycles. Collectively, the findings in this thesis contribute novel insights into the interdependency between prokaryotes and DOM by shedding light on the mechanisms involved in DOM cycling over ecologically relevant spatiotemporal scales.