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Due to the scarcity of organic matter (OM) sources in the bathypelagic (1000–4000 m depth), prokaryotic metabolism is believed to be concentrated on particles originating from the surface. However, the structure of active bathypelagic prokaryotic communities and how it changes across environmental gradients remains unexplored. Using a combination of 16S rRNA gene and transcripts sequencing, metagenomics, and substrate uptake potential measurements, here we aimed to explore how water masses aging and the quality of OM influence the structure of the active microbiome, and the potential implications for community function. We found that the relative contribution of taxa with a free-living lifestyle to the active microbiome increased in older water masses that were enriched in recalcitrant OM, suggesting that these prokaryotes may also play a substantial role in the bathypelagic metabolism of vast areas of the ocean. In comparison to particle-associated prokaryotes, free-living prokaryotes exhibited lower potential metabolic rates, and harbored a limited number of two-component sensory systems, suggesting they have less ability to sense and respond to environmental cues. In contrast, particle-associated prokaryotes carried genes for particle colonization and carbohydrate utilization that were absent in prokaryotes with a free-living lifestyle. Consistently, we observed that prokaryotic communities inhabiting older waters displayed reduced abilities to colonize particles, and higher capabilities to use complex carbon sources, compared to communities in waters with a higher proportion of labile OM. Our results provide evidence of regionalization of the bathypelagic active prokaryotic microbiome, unveiling a niche partitioning based on the quality of OM

A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean’s surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome

The Ocean microbiome has a crucial role in Earth’s biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2–3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome

Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, CARD-FISH subcommunity cell-counts or metagenomic-OTUs. Our calculations unveil a broad range of growth rates [0.3-10 d-1] with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa

This dataset contains the results of the fluorescent dissolved organic matter characterisation (FDOM) and water mass optimum multiparameter analysis from the MAFIA cruise (Migrants and Active Flux In the Atlantic ocean). Samples were collected in the tropical and subtropical Atlantic during the MAFIA cruise (April 2015) on board the BIO Hespérides. Seawater samples for biogeochemical analyses were collected at 13 stations (from the Brazilian coast to the Canary Islands), from the surface down to 3500 m, using a General Oceanics oceanographic rosette equipped with 24 l PVC Niskin bottles. Oxygen solubility was computed using the equation of Benson and Krause (1984). AOU (µmol/kg) was calculated by subtracting measured oxygen concentration from the oxygen solubility values at saturation, with respect to the atmosphere. Fluorescence measurements were performed with a Perkin-Elmer LS55 spectrofluorometer and FDOM was characterised by means of a Parallel Factor analysis. The flag denotes if FDOM values were from direct measurement or are interpolated values (some interpolated values were added to match the 16S amplicon data). Integrated values were estimated by multiplying the discrete measurements by the distance, in meters, between samples.The aim of this dataset was to jointly characterise the FDOM and water mass distributions to infer the processes that shape the dissolved organic matter pool in the deep ocean (water mass mixing and history vs. local processes)

This dataset contains the results of the fluorescent dissolved organic matter characterisation (FDOM) and water mass optimum multiparameter analysis from the MAFIA cruise (Migrants and Active Flux In the Atlantic ocean). Samples were collected in the tropical and subtropical Atlantic during the MAFIA cruise (April 2015) on board the BIO Hespérides. Seawater samples for biogeochemical analyses were collected at 13 stations (from the Brazilian coast to the Canary Islands), from the surface down to 3500 m, using a General Oceanics oceanographic rosette equipped with 24 l PVC Niskin bottles. Oxygen solubility was computed using the equation of Benson and Krause (1984). AOU (µmol/kg) was calculated by subtracting measured oxygen concentration from the oxygen solubility values at saturation, with respect to the atmosphere. Fluorescence measurements were performed with a Perkin-Elmer LS55 spectrofluorometer and FDOM was characterised by means of a Parallel Factor analysis. Integrated values were estimated by multiplying the discrete measurements by the distance, in meters, between samples. The contribution of each water mass to each sample was objectively quantified applying an optimum multiparameter analysis (excluding mixed layer samples, here < 100 m). The aim of this dataset was to jointly characterise the FDOM and water mass distributions to infer the processes that shape the dissolved organic matter pool in the deep ocean (water mass mixing and history vs. local processes)

Underwater hydrothermal systems release nutrient-rich fluids that are favorable for microbial activity. This allows the growth of a plethora of microorganisms that can be found inhabiting hydrothermal plumes, metalliferous sediments, or forming dense microbial biofilms or mats on the surrounding of the vents. Most of the current knowledge on the microbiology associated with underwater volcanic activity comes from the study of deep-sea hydrothermal vents. However, much less is known about shallow underwater hydrothermal systems. The submarine volcanic eruption that took place near El Hierro (Canary Islands) in October 2011 and gave rise to the Tagoro volcano, located only 1.8 km from land and approximately 89 m below the sea surface, provided a rare occasion to study almost in real time the microbiology associated with an underwater eruptive process, from its birth to the current degassing state, allowing investigations of its effects on the surrounding pelagic and benthic communities. In this chapter, we summarize what is known 10 years after the formation of the Tagoro submarine volcano, and we discuss what questions should be pursued in order to foster our knowledge of the microbiology associated with this volcano and its surrounding waters

[EN] Marine microorganisms are fundamental for life on Earth. For example, they have produced most of the oxygen existing in our planet and are errential in biogeochemical cycles and energy flow to different trophic levels. [...], [ES] Los microorganismos marinos son fundamentales para la vida en al Tierra. Por ejemplo, han producido la mayor parte del oxígeno de nuestro planeta y son esenciales en los ciclos biogeoquímicos y en el flujo de energía a los diferentes niveles tróficos. [...], [CAT] Els microorganismes marins són fonamentals per a la vida a la Terra. Per exemple, han produït la major part de l'oxigen del nostre planeta i són essencials en els cicles biogeoquímics i en el flux d'energia cap als diferents nivells tròfics. [...]

Microbes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystem

Prokaryotes represent a major fraction of marine biomass and play a key role in the global carbon cycle. We studied the vertical profiles (0–3500 m) of abundance, viability, and activity of prokaryotic communities along a productivity gradient in the subtropical and tropical Atlantic to assess whether there is a vertical linkage between surface productivity regimes and deep ocean prokaryotic communities. We found that latitudinal changes in the vertical patterns of cytometric variables were coupled with surface productivity: higher prokaryotic abundances and viabilities, and smaller cell sizes were observed below highly productive surface waters, an effect reaching down to the bathypelagic layer. Leucine uptake rates in deep waters showed no clear relationship with surface productivity. Changes in resource and energy allocation to growth vs. maintenance in hostile environments, cell-size-dependent metabolic requirements, and variability in leucine-to-carbon conversion may all be part of the array of factors involved in controlling the prokaryotic activity patterns that were measured. Our work adds to the recent findings that highlight the importance of vertical connectivity for prokaryotic communities in the dark ocean and unveils a remarkable impact of surface conditions in the viability of deep ocean prokaryotes. This is a key aspect when considering metabolic rates of prokaryotic communities in the bathypelagic realm

Anthropogenic perturbations have tripled the mercury (Hg) content of ocean waters compared to pre-anthropogenic conditions but the impact of this Hg increase is not uniform across the ocean. . In particular, the controls on contaminant levels of Hg and one of its dangerous species, methyl-mercury (MeHg), in the deep ocean at global scale remain largely unknown. We explored 52 globally-distributed deep ocean metagenomes and 26 metatranscriptomes of the Malapasina 2010 circumnavigation from two different plankton size fractions (0.2-0.8 ¿m and 0.8-20 ¿m), commonly referred to the life-style of free-living and particle-attached microorganisms, respectively. Our results unveil the biogeography and expression patterns of genes related to HgII reduction and MeHg degradation, merA and merB, respectively, in the bathypelagic (~ 4000 m) ocean realm. We report the main taxonomic players involved in the Hg volatilization and MeHg degradation in the poorly studied bathypelagic ocean including members of the Corynerbacteriales, Rhodobacterales, Alteromonadales, Oceanospirillales, Moraxellales and Flavobacteriales orders. Moreover, the composition of the organic matter and water masses age and were good predictors of the abundance and expression levels of merA and merB genes, and thus provided new insights into the global Hg biogeochemical cycle

There is a gap in knowledge on broad-scale diversity and functional patterns along the continuum between the photic and the dark ocean microbes, including trends in genome size (GS) and functional diversity. To address this gap, we present the Malaspina Microbial Vertical Profiles Metagenomes dataset, comprising 76 microbial metagenomes (0.2-3um) collected in 11 stations in the tropical and subtropical open oceans from 3 to 4,000 m deep, a 46.3 million gene catalog and 1,228 Metagenome-Assembled Genomes (MAGs). Our results show increased functional richness in the bathypelagic and a strong positive association between GS and depth for the most abundant phyla in samples up to 1,000 m, while this association is absent in the bathypelagic. Conversely, lower abundance taxa displayed a bimodal distribution of GS, with a smaller peak in the mesopelagic and a larger peak in the bathypelagic. Opposing trends were observed for protein-encoding gene density and functional diversity across epipelagic and deep ocean MAGs. Specifically, protein-encoding gene density was higher at the epipelagic and decreased towards the bathypelagic for most of the taxa, pointing out that genome streamlining generally holds true, but it is not universal for all microbes. Larger prokaryotic GS in the bathypelagic was associated with a higher prevalence of prophages and defense systems. We suggest that a combination of factors, including genome streamlining, metabolic diversification, viral infection, and molecular defense systems, drive the genomic diversity of marine prokaryotes across ocean layers

Dissolved organic matter (DOM) remineralization is limited to a greater or lesser degree at different layers in the ocean. In order to investigate the key abiotic and biotic factors that may enhance DOC remineralization in the deep ocean, we studied the changes in function and structure of deep prokaryotic communities after additions of the same amount of dissolved organic compounds with different quality. We performed experiments with deep sea prokaryotic assemblages subjected to four different treatments: CL (addition of labile DOC), CM (addition of a mix of organic compounds with different lability) and CR (addition of recalcitrant humic acids) and K (control). Prokaryotic biomass markedly increased when the labile compounds or the diverse chemical mixture were added (CL and CM treatments), whereas the prokaryotic response was lower under either the control K or CR treatments. Accordingly, we found lower activity and similar patterns of extracellular enzymatic activities in CR and K compared to CL and CM treatments. In all treatments a decrease in prokaryotic richness consistently occurred along the incubations, but interestingly, the decrease was lower in the control and in the CR treatments. Our results indicate that the chemical diversity of organic matter is a key factor determining microbial structure and activity in the deep ocean

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of microbial eukaryotes is still unclear. We explored the capacity of a natural eukaryotic community to incorporate a synthetic amino acid (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT) and compared it with that of prokaryotes throughout a 9-day survey in the NW Mediterranean. We found a large diversity of autotrophic and heterotrophic eukaryotic cells incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (50 ± 20%, mean ± SD). Among them, pennate diatoms exhibited a clear diel pattern of osmotrophic activity, with higher activity in the afternoon than in the morning. On the contrary, small eukaryotes (<5 µm) showed higher activity in the morning than in the afternoon, and the percentage of active cells was lower for phototrophs (0.6-7%) than for heterotrophs (13-17%). Centric diatoms dominated the eukaryotic HPG incorporation due to their high abundance and large sizes, accountig for up to 86% of the eukaryotic BONCAT signal. When comparing to the prokaryotic HPG incorporation, we estimated that the whole eukaryotic community accounted for 19-31% of total BONCAT signal. Together, these results suggest that osmotrophy may be relevant to eukaryote nutrition, especially for large phytoplankton, and highlight the significant role eukaryotes could play in the consumption of dissolved organic matter in marine systems

Marine prokaryotes play crucial roles in ocean’s biogeochemical cycles, being their contribution largely determined by their growth rates. To improve our understanding of microbial communities’ dynamics and structure, we estimated prokaryotic growth rates at high resolution, the amplicon sequence variant (ASV) level, using manipulation experiments in each of the four astronomical seasons with different treatments that reduced limiting growth factors such as predators, nutrient availability, viruses and light. Single-ASV-based growth rate calculations showed a continuous range of values, reaching almost 10 day-1. Mean growth rates per treatment increased as limiting factors were removed, and changed seasonally. Results revealed significant variability in growth rate distribution patterns even within closely related ASVs, and with no general taxonomic coherence observed after removal of each growth limiting factor. Reduction of these factors showed that most responsive ASVs were rare, and formed a pool of taxa with the potential to rapidly respond to environmental changes. In essence, our results highlight the significance of rare-responsive taxa often overlooked in whole-community studies and suggest high dynamism in marine microbial communities with a strong capacity to adapt to changing environments

Plastic is not usually composed of a polymer alone but it also presents a diverse pool of chemicals added to provide the final material with the properties required for its use. They can be released to the aquatic media during plastic degradation. In seawater, plastic releases dissolved organic carbon (DOC); a process which is enhanced by sunlight radiation. This DOC is making part of different molecules which are presumably plastic additives together with degradation products of the polymer. Here, we will show the results of several studies in which different types of plastic (including biodegradable and naturally aged plastics) were introduced in seawater and exposed to sunlight degradation. The amount of leached DOC and its optical properties were explored. Subsequently, the response of natural bacterial communities to the leachates were investigated using a combination of catalyzed reporter deposition fluorescence in situ hybridization and bioorthogonal non-canonical amino acid tagging. We found that the material released by the plastic in seawater present a characteristic fluorescence signal. Aged plastic released a higher amount of material than virgin plastic, and biodegradable plastic leached similar amounts of DOC with comparable microbial bioavailability than petrol-based plastics. Finally, we found that the community growing in the leachates was mainly composed of Alteromonas, followed by Roseobacter and unclassified Gammaproteobacteria. These results will contribute to better understand the impact of plastic in marine ecosystems and in the marine carbon cycle

The dark ocean contains the largest pool of microbes in aquatic systems and sustains half of the ocean's microbial activity. In contrast to the long-lasting paradigm of a homogenous and stable deep ocean, recent studies have unveiled that the deep realm displays great heterogeneity with an enormous and dynamic repository of microbial taxa, and that their physiological status is largely determined by the productivity of surface waters. Here we wanted to explore how the metabolic potential of deep ocean communities changes across a productivity gradient, likely as a consequence of the change in the intensity and frequency of surface-derived particles reaching the deep ocean. We used metagenomic data collected in a transect from the Eastern Mediterranean Sea to adjacent Atlantic waters and explored changes in gene content in the context of the environmental conditions and dissolved organic matter quality faced by the microbial assemblages. We unveiled that deep ocean communities from the phosphorus-limited Eastern Mediterranean Sea have less ability to colonize particles, less capacity to tune their metabolism in response to environmental changes, and more metabolic versatility than communities from the Atlantic ocean

Estuaries are among the most productive ecosystems in the world and are highly dynamic due to the interaction of freshwater and seawater, which results in strong spatial gradients in physico-chemical conditions. Bacterioplankton play a central role in these systems, driving the fluxes of carbon and energy, and being central for contaminant removal in human-impacted areas. Most studies on bacterioplankton dynamics have been carried out in temperate estuaries, and they show that salinity is a major factor driving bacterioplankton distribution. Tropical estuaries, although largely understudied, experience drastic variations in river discharge between the dry and the rainy seasons, influencing the spatial distribution of the salinity gradient and thus likely impacting bacterioplankton communities. Using Illumina sequencing of the 16S rRNA gene, here we studied bacterial communities from the Nicoya's Gulf (Costa Rica), a large tropical estuary characterized by high riverine discharge during the rainy season, to explore seasonal changes in the spatial distribution and connectivity of these communities along the Gulf. Our results show pronounced differences in bacterial diversity and community structure between seasons and zones within the estuary (the shallow upper Gulf, the middle zone and the lower zone, located in the marine end of the estuary). Bacterial communities from the different regions were more similar during the rainy season, suggesting a larger degree of microbial connectivity likely driven by the fast water circulation fueled by the riverine discharge. In the dry season, Enterobacteriales and Cyanobacteria dominated bacterial communities, whereas in the rainy season Alphaproteobacteria was the dominant group. These contrasting seasonal trends were consistent with the seasonal variations observed in bacterial assemblages during a year at a single station in the upper region of the Gulf. We conclude that the Gulf is highly dynamic in both the spatial and temp

Invisible to the naked eye, planktonic prokaryotes—comprising both bacteria and archaea—represent a large fraction of marine biomass, with abundances typically ranging from thousands to millions of cells per millilitre. From primary producers (photo- and chemoautotrophic) to heterotrophs, they display extremely diverse metabolisms and are of the utmost importance for the biogeochemical cycles in the ocean. During their involvement in elemental cycling, prokaryotes interact with the organic matter continuum (particulate and dissolved), utilising it as source of energy and carbon. In doing so, they transform the organic matter pool, diversifying it and remineralising compounds into their inorganic constituents. Moreover, by converting organic matter into biomass, prokaryotes return carbon into the marine trophic webs, a process known as the microbial loop. Hence, this pathway is crucial for organic matter cycling in the oceans. Upwelling regions represent some of the most productive marine systems, with large pools of organic matter subject to dynamic interactions with prokaryotic communities. Such environments thus have major importance for carbon cycling at the global scale, making very relevant the study of the prokaryotes that inhabit them. In this thesis we combine mesocosm experiments and synoptic field samplings to study prokaryotic communities in upwelling environments, with special attention to how they relate to organic matter cycling. The first half of the thesis is devoted to an upwelling simulation experiment carried out in the oligotrophic waters of the subtropical Eastern North Atlantic. By simulating different upwelling intensities and frequencies (singular pulse versus recurring upwelling), we studied how the dissolved organic matter pool and the prokaryotic communities respond to variable upwelling scenarios., First, we measured the dissolved organic matter concentrations and optical properties, observing that upwelling intensity was positively related to dissolved organic matter accumulations. Singular and recurring upwellings yielded mostly similar changes in concentrations and optical properties despite the markedly contrasting outcome of their phytoplankton blooms (a single large bloom in the singular mode versus sustained smaller blooms in the recurring one). Although optical properties suggested ongoing transformation of organic matter, the accumulated dissolved organic matter did not decrease, indicating that during the experiment production and consumption tended to be balanced. In parallel, prokaryotic successional patterns also displayed remarkable similarities in singular and recurring upwelling treatments. The dominant taxa within the successional assemblages differed mostly between the particleassociated and the free-living fractions, but upwelling modes also displayed some differences in composition. Thus, it is striking that prokaryotic communities shared common successional patterns even across size fractions under the different blooming scenarios. The second half of the thesis in turn explores how the influence of upwelling propagates down in the water column, addressing the vertical connectivity between highly productive surface waters and the prokaryotic communities inhabiting the water masses of the dark ocean. We studied natural communities along an oceanographic transect in the tropical and subtropical Atlantic (which included areas under the influence of the Northwest African upwelling system), showing how the standing stocks and physiological status of meso- and bathypelagic prokaryotes are coupled with surface productivity. We showed that the cell-viability of deep ocean prokaryotes increased under the productive waters of the upwelling, evidencing that its effect reaches the deep layers. The analysis of the water masses also showed that the distr