Jarone Pinhassi

Marine microbiomes exhibit seasonal dynamics in many ocean regions. While we can characterize the biodiversity and composition of ocean microbiomes, we lack a systematic understanding of how environmental drivers shape the seasonal succession of marine microbes. To leverage the pronounced temporal changes in growth conditions in the temperate waters of the Baltic Sea, we here report on dynamics in the prokaryoplankton community over 13 years at the Linnaeus Microbial Observatory (LMO), focusing on both free-living (FL; 0.2–3 μm fraction) and particle-associated (PA; >3 μm fraction) prokaryotes. As expected, our analysis showed a higher diversity in the PA compared to the FL fraction and that the grand majority of 16S rRNA gene amplicon sequence variants (ASVs) were consistently rare. Yet, to an unexpected degree also a majority of the abundant ASVs transitioned into the rare biosphere over extended periods of the year. Prokaryotes in both the PA and FL fractions showed pronounced seasonal dynamics, with notable differences between the fractions from phylum down to the ASV level. Abundant ASVs were strongly correlated to several environmental drivers, including nutrient concentrations, salinity and temperature. Intriguingly, at comparable temperatures in spring and autumn (e.g. at 12 °C), the community composition was strikingly different. This highlighted that specific temperature values per se are informative, but that the trajectories of change in temperature and other environmental drivers (low to high, high to low) merit attention in ecological research. Our data suggest that the community composition of prokaryoplankton in temperate regions strongly depend on factors beyond temperature and photoperiod values, including the history of the community, the direction of environmental change, and qualitative and quantitative levels of (in)organic nutrients, as well as biotic interactions.

Nutrient limitation in the Baltic Proper exhibits temporal variations, with nitrogen limiting diatom and dinoflagellate‐dominated spring blooms, while phosphorus constraints characterise the cyanobacterial summer blooms. Phosphorus is a key element for cellular functions and poses significant challenges for planktonic microbial communities under limited availability. Numerous studies have explored strategies phytoplankton and bacteria employ to cope with phosphorus scarcity. However, the temporal dynamics of phosphorus acquisition within natural communities remain poorly understood. Using metatranscriptomics, this study addresses this gap by examining how planktonic microbial communities acquire phosphorus over a year‐long monitoring at an offshore station. Targeting genes related to phosphorus degradation, transport and membrane remodelling, we unveil diverse strategies employed by planktonic microbial communities to acquire phosphorus. Our findings highlight transporter and membrane remodelling‐related genes are expressed at high levels across the year, suggesting their important role in coping with phosphorus acquisition. Our dataset reveals distinct strategies between phytoplankton and free‐living bacteria under nutrient‐limited conditions. While eukaryotic phytoplankton appear to rely more on recycling internal stores of phosphorus via membrane remodelling processes, free‐living bacteria appear more prone to optimize extracellular scavenging mechanisms. These insights reveal the complex physiological adjustments of marine microbial communities to fluctuating phosphorus availability in the Baltic Sea.

The Baltic Sea, with its pronounced gradient in temperature, salinity, and nutrient availability, provides a natural system to investigate microbial responses to eutrophication and climate change effects. While nutrient limitation in this system has been extensively studied, direct comparisons of phosphorus acquisition strategies across co-occurring prokaryotic and eukaryotic communities remain limited. This study provides a comprehensive analysis of how microbial plankton communities respond at the molecular level to shifts in phosphorus availability, by resolving both prokaryotic and eukaryotic strategies across spatial and seasonal gradients. By combining size-fractionation, community composition profiling, stoichiometry, and metatranscriptomics along a transect from the Bothnian Bay to the Bothnian Sea across spring and summer conditions, we identify both shared and domain-specific strategies of P acquisition. Results reveal that phosphorus acquisition is shaped by strong environmental gradients, with prokaryotes primarily relying on transporter-mediated uptake, while eukaryotes preferentially employ membrane remodelling and degradation pathways. These contrasting strategies varied across basins and seasons, reflecting differences in nutrient availability, temperature, and community structure. This integrative approach provides new insights into the functional ecology of microbial communities under shifting nutrient regimes and improves our ability to anticipate ecosystem response to eutrophication and climate change in the Baltic Sea.

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.

Bacteria in aquatic environments are a principal food source for predatory protists. Whereas interactions between bacteria and protists are recognized to determine the pathogenesis and epidemiology of several human pathogens, few studies have systematically characterized the interactions between specific aquatic bacteria and protists beyond the prey-predator relation. We, therefore, surveyed individual co-cultures between 18 different genome-sequenced marine bacteria with known virulence gene repertoires and three model protist species widely used for assessing bacteria-protist interactions. Strikingly, 10, 5, and 3 bacterial isolates were capable of lysing the protists Acanthamoeba polyphaga, Tetrahymena pyriformis, and Euglena gracilis , respectively. A majority of the bacteria were able to grow and/or maintain viable populations in the presence of viable protists. Some bacteria survived longer with viable protists but not heat-killed protists and were observed in protist vacuoles. In this respect, marine bacteria are similar to several protist-dependent human pathogens, including Legionella . Analyses of growth patterns in low-nutrient media showed that co-cultivation with A. polyphaga allowed one bacterial strain to overcome nutritional stress and obtain active growth. Five isolates depended on viable amoebae to grow, notwithstanding nutrient media status. The remarkable capability of these marine bacteria to survive encounters with, and even actively kill, model predatory protists under laboratory conditions suggests that diverse bacterial defense strategies and virulence mechanisms to access nutrients may be important in shaping microbial interactions. If verified with native marine and freshwater populations, the diversity of interactions uncovered here has implications for understanding ecological and evolutionary consequences of population dynamics in bacteria and protists. IMPORTANCE: The microbiome constitutes the base of food webs in aquatic environments. Its composition partly reflects biotic interactions, where bacteria primarily are considered prey of predatory protists. However, studies that focus on one or a few species have shown that some bacteria have abilities to escape grazing and may even be capable of lysing their protist predators. In this study, we substantially extend these findings by systematically investigating interactions among multiple taxa of both bacteria and protists. Our results show that marine bacteria display a wider and more complex range of interactions with their predators than generally recognized—from growth dependency to protist lysis. Given that such interactions play key roles in the pathogenesis and epidemiology of several human pathogens, our findings imply that bacterial virulence traits can contribute to defining the structure and ecology of aquatic microbiomes.

In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (3 µm) in the dissolved silica-replete Baltic Sea via biweekly time series samplings spanning 2 years. Time series data showed that the large changes in bSi standing stock in the Baltic Proper were primarily related to microplankton biomass and community composition. Meanwhile, picoplankton were, at times, surprisingly high contributors to total bSi year-round (up to 21.6%). Simultaneously, we performed microcosm incubation experiments with natural phytoplankton communities in each season to examine how nutrient additions affected bSi concentrations. In these experiments, increases in microplankton bSi were directly correlated to increases in diatom biomass, highlighting their influential role in the Baltic Sea silica cycle. Meanwhile, phosphorus additions triggered an increase in picoplankton bSi accumulation in all experiments. This uncovers a potential control of bSi accumulation in picoplankton, which can help identify the cellular mechanisms behind this process and uncover their role in silica cycling. The results link phytoplankton community composition and silica cycling, which is important for understanding the consequences of organism shifts due to climate change. IMPORTANCE: The marine carbon and silica cycles are tightly intertwined and largely controlled by diatoms. Nevertheless, recent studies, mostly in oligotrophic waters, have proposed new contributors to the marine silica cycle: picoplankton. Here, we report the first study of seasonal dynamics of biogenic silica (bSi) standing stock in microplankton and picoplankton in the silica-replete Baltic Sea. Microplankton bSi dynamics were correlated with changes in composition and biomass. Picoplankton were consistent contributors to bSi, and for the first time in diverse natural communities, we found a direct correlation between phosphorus and bSi accumulation. The results are important for understanding how climate change-predicted phytoplankton composition shifts will affect carbon and silica cycling and provide a direction for future research on nutrient controls of silica accumulation in picoplankton.

Through biosilicification, organisms incorporate dissolved silica (dSi) and deposit it as biogenic silica (bSi), driving the silicon (Si) cycle in aquatic systems. While Si accumulation in marine picocyanobacteria has been recently observed, its mechanisms and ecological implications remain unclear. This study investigates biosilicification in marine and brackish picocyanobacteria of the Synechococcus clade and two model freshwater coccoid cyanobacteria. Brackish strains showed significantly higher Si quotas when supplemented with external dSi (100 µM) compared to controls (up to 60.0 ± 7.3 amol Si.cell-1 versus 9.2 to 16.3 ± 2.9 amol Si.cell-1). Conversely, freshwater strains displayed no significant differences in Si quotas between dSi-enriched treatments and controls, emphasizing that not all phytoplanktons without an obligate Si requirement accumulate this element. The Si-accumulating marine and brackish picocyanobacteria clustered within the Synechococcus clade, whereas their freshwater counterparts formed a distinct sister group, suggesting a link between phylogeny and silicification. Rapid culture growth caused increased pH and led to dSi precipitation, influencing apparent dSi uptake; this was mitigated by pH control through bubbling. This phenomenon has significant implications for natural systems affected by phytoplankton blooms. In such environments, pH-induced silicon precipitation may reduce dSi availability impacting Si-dependent populations like diatoms. Our findings suggest brackish picocyanobacteria could significantly influence the Si cycle through at least two mechanisms: cellular Si accumulation and biologically induced changes in dSi concentrations. IMPORTANCE: This work provides the first evidence of biogenic silica accumulation in brackish picocyanobacteria and uncovers a link between phylogeny and biosilicification patterns. Our findings demonstrate that picocyanobacterial growth induces pH-dependent silica precipitation, which could lead to overestimations of cellular Si quotas by up to 85%. This process may drive substantial silica precipitation in highly productive freshwater and coastal marine systems, with potential effects on silica cycling and the population dynamics of Si-dependent phytoplankton. The extent of biosilicification in modern picocyanobacteria offers insights into the rock record, shedding light on the evolutionary and ecological dynamics that influence sedimentary processes and the preservation of biosilicification signatures in geological formations. Overall, this research adds to the significant impact that microorganisms lacking an obligate silica requirement may have on silica dynamics.

Temperature and dissolved organic matter (DOM) are important drivers of microbial activity, but their effects, alone or in combination, on the physiological responses of sub-arctic prokaryotic assemblages remain poorly understood. In a northern Baltic Sea one-month mesocosm experiment, we therefore exposed a coastal microbial community to temperature and nutrient regimes representative of winter and early summer (i.e., 1°C and 10°C, with and without DOM additions) in a 2×2 factorial design. Midway through the experiment, specific growth rates were highest for the 10°C plus DOM treatment (TN; ∼2.5 day ^-1 ), comparable for the 1°C plus DOM (N) and the 10°C (T) treatments at ∼1.0 day ^-1 ; and low for the control (1°C, no DOM enrichment [C]; 0.2 day ^-1 ). Taxonomic analysis of metatranscriptomes uncovered broad treatment specific responses, and a PERMANOVA on the 182,618 transcribed genes revealed statistically significant effects of both temperature and DOM, and significant interaction effects between the two (altogether involving 18% of genes). Significant differences in transcription identified by EdgeR analysis included Nitrosopumilus genes for ammonium uptake and ammonia oxidation in the 1°C mesocosms (C, N), membrane transporters for small organic acids in the N-treatment, genes for nitrogen and phosphorus assimilation along with molecular chaperones in the T-treatment, and dominance of Oceanospirillales genes for energy and growth metabolism in the TN-treatment. These metatranscriptomic responses were associated with changes in e.g. prokaryotic growth rates and growth efficiency, providing clues to how successional changes in community composition and metabolism are directed by temperature and DOM as central factors underlying environmental change. Importance: It is recognized that increases in temperature and dissolved organic matter loading are key to understanding how climate change will influence polar ecosystems. Still, little is known of the effects of these factors on the physiological responses of Arctic prokaryotes. Since prokaryotes are principal drivers of biogeochemical cycles, we investigated how temperature and dissolved organic matter influence prokaryotic transcriptional responses in taxonomy and metabolic pathways. The metatranscriptomics analyses uncovered broad treatment specific responses linked with changes in prokaryotic community composition, growth rates, and growth efficiency. Yet, and importantly, the expression of most metabolic functions remained stable, suggesting a pronounced functional resilience of the prokaryotic community enabled by shifts in the dominance of different taxa. This emphasizes the large potential and importance of identifying the metabolic functions that underlie the divergence of prokaryotic communities in response to environmental changes projected to alter some of the most vulnerable marine environments.

Unveiling the interactions among phytoplankton and bacteria at the level of species requires axenic isolates to experimentally demonstrate their mutual effects. In this study, we describe the interactions among the diatoms Pseudo‐nitzschia granii and Chaetoceros tenuissimus and their associated bacterial species, isolated from surface water of a coastal upwelling system using coculture experiments. Microalgae growth was assessed in axenic monocultures or in coculture with each of their co‐isolated bacteria in the presence or absence of B vitamins. Pseudo‐nitzschia granii growth was limited by B‐vitamin supply, except when cultured with the bacteria Jannaschia cystaugens, which seemed to provide adequate levels of B vitamins to the diatom. Chaetoceros tenuissimus growth was reduced in the absence of B vitamins. Moreover, the growth of C. tenuissimus was stimulated by Alteromonas sp. and Celeribacter baekdonensis during the exponential growth. These results show a diversity of specific interactions between the diatoms and co‐isolated bacteria, ranging from allelopathy to commensalism. Understanding how interactions between phytoplankton and bacteria modulate the structure and function of marine microbial plankton communities will contribute to a greater knowledge of plankton ecology and improve our ability to predict nutrient fluxes in marine ecosystems or the formation of blooms in a context of global change.

Prokaryotic maintenance respiration and associated metabolic activities constitute a considerable proportion of the total respiration of carbon to CO₂ in the ocean's mixed layer. However, seasonal influences on prokaryotic maintenance activities in terms of morphological and metabolic adaptations at low (winter) and high productivity (summer) are still unclear. To address this, we examined the natural prokaryotic communities at the mesocosm scale to analyse the differences in their morphological features and gene expression at low and high maintenance respiration, experimentally manipulated with the specific growth rate. Here, we showed that morphological features including membrane blebbing, membrane vesicles and cell‒cell connections occurred under high productivity. Metabolic adaptations associated with maintenance activities were observed under low productivity. Several Kyoto Encyclopedia of Genes and Genomes categories related to signal transduction, energy metabolism, and translational machinery supported maintenance activities under simulated winter conditions. Differential abundances of genes related to transporters, osmoregulation, nitrogen metabolism, ribosome biogenesis, and cold stress were observed. Our results demonstrate how specific growth rate in different seasons can influence resource allocation at the levels of morphological features and metabolic adaptations. This motivates further study of morphological features and their ecological role during high productivity, while investigations of metabolic adaptations during low productivity can advance our knowledge about maintenance activities.