Phosphorus (P) and nitrogen (N) are essential nutrients for microbial growth, playing crucial roles in regulating the biological productivity of marine ecosystems. Over the last decades, the relatively higher increase in anthropogenic N compared to P inputs is causing a continuous increase in the N:P supply ratio to the global biosphere. The high N:P ratio of riverine discharge may seasonally cause P limitation in estuaries and river-dominated continental shelf waters. We conducted a mesocosm experiment simulating a P-deplete and a P-replete riverine discharge to coastal waters in NW Spain to assess the functional response of marine microplankton using a metatranscriptomic approach. By examining the expression of 40 well-documented genes related to P-metabolism in prokaryotic and eukaryotic gene expression, we uncovered pronounced changes in microbial P-metabolism induced by riverine N:P ratio in this productive system. Remarkably, heterotrophic bacteria and eukaryotic phytoplankton exhibited contrasting phosphate metabolism strategies in response to P deficiency, with the former mostly expressing genes coding for high-affinity transporters and the latter mostly transcribing genes related with low-affinity transporters. Our results also highlight distinct regulatory and adaptive mechanisms across different members of the prokaryotic and eukaryotic communities when exposed to varying P concentrations. Our findings shed light on the broader ecological and functional roles of these genes in nutrient cycling within aquatic ecosystems, with potential application for the design of diagnostic tools for P status in coastal productive systems.

The biotic component of the marine silica cycle strongly influences global biogeochemical cycling. Active uptake of dissolved silicic acid (dSi) occurs via silicon transporters (SITs), first characterized in diatoms but widely distributed in eukaryotes. Studying SITs and SIT-like (SIT-L) gene transcripts provides insights into the dynamics and evolutionary history of diverse biosilicifiers. Using a 2-yr metatranscriptomics dataset of Baltic Sea surface microbial communities, we identified SIT/SIT-L genes associated with 11 eukaryotic classes. Although diatoms were previously assumed to drive the Baltic Sea silica cycle, silicoflagellates dominated SIT/SIT-L expression over the sampling period. SIT/SIT-L expression and phylogenetic analyses revealed class-specific patterns, suggesting a complex evolutionary history in dinoflagellates and pronounced clade dynamics in diatoms. Overall, these unexpectedly complex and dynamic shifts in transcriptional investment in silicon transport revealed underappreciated microbial groups driving the Baltic Sea silica cycle.

The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.Availability and implementation The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

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.

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.

Background: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.

Results: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.

Conclusions: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans.

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.IMPORTANCEThe 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.

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.

In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (<2-3 μm in size) such as Synechococcus and picoeukaryotes. Their contribution and relevance to silica cycling are still under investigation. Field studies reporting the biogenic silica (bSi) standing stock in the pico-sized fraction are limited to silica-poor oligotrophic environments, and the mechanism of bSi accumulation in picoplankton remains unknown. We investigated the variability of bSi standing stocks in two size fractions (picoplankton, 0.22-3 mu m and microplankton, >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.

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 mu M) 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.IMPORTANCEThis 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.