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How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long-term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV-III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long-term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non-recurrent changes characterize the dynamics of microbial assemblages.

Agricultural practices have raised the level of nutrients reaching aquifers. In Europe, nitrate 24 pollution is considered as one of the main threats for the quality of groundwater in agricultural 25 areas. Treatment wetlands (TWs), also known as Constructed Wetlands, are used for 26 groundwater treatment in areas with an important concentrations of nitrogen compounds; total 27 nitrogen removal depends on the type and operation scheme. Cork by-product from the 28 industry has shown clear adsorbent properties to remove organic pollutants. The work is 29 focused on the characterization of microbial communities involved in the nitrate-nitrogen 30 removal process in groundwater polluted from agricultural activities. The experimental design 31 allowed the comparison of nitrate removal efficiency depending on the filter media material, 32 cork by-product or gravel, used in two hybrid TWs (a vertical flow cell followed by a horizontal 33 subsurface flow cell), installed in areas close to two irrigated agricultural plots at the Lleida plain 34 area (Spain). Both physicochemical and microbial results were consistent and confirm the nitrate 35 removal efficiency using cork as a filter media. A significant (p=0.0025) higher removal in Bellvís 36 TW using cork compared with the Vilanova de la Barca gravel system was observed, achieving a 37 removal rate from 80 to 99% compared to the 5-46%, respectively. Regarding the community 38 composition of the two different TWs, microorganisms were mainly related to the phylum 39 Proteobacteria, and included members found to be key players in the nitrogen cycle, such as 40 ammonia and nitrite oxidizers, as well as denitrifiers. Also, the group Bacteroidetes turn to be 41 another abundant phylum from our bacterial dataset, whose members are suggested to be 42 strongly involved in denitrification processes. Some groups showed to prevail depending on the 43 type of media (cork or gravel); Firmicutes and Delta and Epsilonproteobacteria had a

[CAT] La campanya POSEIDÓN, organitzada per l’Instituto Español de Oceanografía (IEO), travessarà bona part de l’Atlàntic, viatjant des de Punta Arenas (Xile) a Les Palmes de Gran Canària, tot creuant l’Equador, i estudia el consum del carboni orgànic dissolt i la seva relació amb les comunitats microbianes que habiten l’oceà profund. - Equip i reptes - Diari de Campanya. Ciència i vida a bord: · 28 de febrer 2019. Marxem de campanya! · Les campanyes oceanogràfiques: ciència, burocràcia o aventura? Sortida des de Punta Arenas. Arrenca la Campanya Poseidón · Preparant-nos pel primer mostreig · 8 de marzo, Día Internacional de la Mujer · A la deriva · Carbono milenario almacenado en las profundidades oceánicas… · Under pressure · ¿A quién no le gusta una tarta? · Tothom pendent del CTD · El poder del mar i de l’observació · Investigating microbial communities of deep waters · Un mar de dades · L’exploració de l’oceà · Illes de Sargassum · El que amaga l’oceà superficial · Les “òmiques” del mar. Òmica? I què és això de l‘òmica? · Terra a la vista! - Exploradors del mar: · Converses des de l’Atlàntic · Parents llunyans · L’essencial és invisible als ulls · L'àtom de la vida. El carboni al mar. Anem a veure què passa amb el C al mar des del punt de vista químic… El paper fonamental dels microorganismes en el cicle del C al mar… · Les constants vitals del mar. La navegació. Paràmetres meteorològics. Paràmetres físics i químics de l’aigua de mar. Temperatura. La densitat. Les masses d’aigua i la circulació termohalina. La pressió · Lynn Margulis i l’origen de la cèl·lula eucariota · Ernst Haeckel · Les dones i l'oceanografia · Charles Darwin, [ES] ¿Quienes habitan las capas iluminadas del océano? Estudiamos los microorganismos marinos y su papel fundamental el océano

Los océanos tienen una importancia vital para el planeta y sus habitantes, sin embargoo, su estudio no está bien representado en los contenidos curriculares de la enseñanza obligatoria. Para fomentar esta aproximación a la ciencia y al mar, desde el Institut de Ciències del Mar (CSIC) en Barcelona, se propone a centros educativos el seguimiento en tiempo real de las campañas oceanográficas en las que participamos. Los científicos elaboran un diario de campaña y material didáctico que incluye propuestas de experimentos y la posibilidad de realizar preguntas a los científicos. En esta contribución se presentan específicamente 6 de las 15 campañas realizadas desde 2015, en cuyo seguimiento participaron más de 2000 alumnos de 36 centros escolares, involucrando a más de 80 científicos y personal técnico. A través de este seguimiento se han tratado diferentes temas científicos, humanos y sociales desde una perspectiva vivencial, transversal e interdisciplinar. Todo este material puede consultarse en http://icmdivulga.icm.csic.es/expedicions/. La valoración de este procedimiento indica que el seguimiento de una campaña oceanográfica es un recurso pedagógico eficiente que permite el acercamiento del mar y la ciencia a las aulas y promueve la sensibilidad ambiental desde las primeras etapas de la educación

The study of marine microbes has bloomed thanks to the use of molecular tools opening new windows into ecological studies. Oneof the major advances achieved last decade was the discovery of marine photoheterotrophic bacteria, which challenged our view onmicrobial food webs in the ocean. These organisms are heterotrophs that rely mainly on organic matter but are capable of harvestinglight to supplement their energy requirements. In the last years, we have used various approaches to uncover the ecology of a groupof marine photoheterotrophs, the aerobic anoxygenic phototrophic bacteria (AAPs). In particular, we have combined infrared mi-croscopy, quantitative PCR and Illumina sequencing with large sampling initiatives (i.e., the Blanes Bay Microbial Observatory andthe Malaspina circumnavigation expedition) as well as with manipulation experiments to explore their diversity, seasonality, biogeog-raphy and, more importantly, their functional role in marine ecosystems. Our results confirm that the AAPs are widely distributed inthe global surface oceans and that the different phylogenetic groups present a certain degree of biogeography. Moreover, we havedemonstrated that these bacteria show a clear seasonality both in abundance and community structure. But foremost, we have foundthat the AAPs are fast-growing bacteria contributing significantly to the recycling of organic matter and that they can be stimulatedby light in the marine environment. The results of our ongoing work will be presented and discussed in detail at the conference

We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group

Agricultural practices have raised the level of nutrients reaching aquifers. In Europe, nitrate pollution is considered as one of the main threats for the quality of groundwater in agricultural areas. Treatment wetlands (TWs), also known as Constructed Wetlands, are used for groundwater treatment in areas with an important concentration of nitrogen compounds; total nitrogen removal depends on the type and operation scheme. Cork by-product from the industry has shown clear adsorbent properties to remove organic pollutants. The work is focused on the characterization of microbial communities involved in the nitrate‑nitrogen removal process in groundwater polluted from agricultural activities. The experimental design allowed the comparison of nitrate removal efficiency depending on the filter media material, cork by-product or gravel, used in two hybrid TWs (a vertical flow cell followed by a horizontal subsurface flow cell), installed in areas close to two irrigated agricultural plots at the Lleida plain area (Spain). Both physicochemical and microbial results were consistent and confirm the nitrate removal efficiency using cork as a filter media. A significant (p = 0.0025) higher removal in Bellvís TW using cork compared with the Vilanova de la Barca gravel system was observed, achieving a removal rate from 80 to 99% compared to the 5–46%, respectively. Regarding the community composition of the two different TWs, microorganisms were mainly related to the phylum Proteobacteria, and included members found to be key players in the nitrogen cycle, such as ammonia and nitrite oxidizers, as well as denitrifiers. Also, the group Bacteroidetes turns to be another abundant phylum from our bacterial dataset, whose members are suggested to be strongly involved in denitrification processes. Some groups showed to prevail depending on the type of media (cork or gravel); Firmicutes and Delta and Epsilonproteobacteria had a significant higher abundance in the TW with cork, while Ac

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as ecologically significant taxonomic units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans

High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems

The impact of grazing, resource competition and light on prokaryotic growth and taxonomic composition in subtropical and tropical surface waters were studied through 10 microcosm experiments conducted between 30°N and 30°S in the Atlantic, Pacific and Indian oceans. Under natural sunlight conditions, significant changes in taxonomic composition were only observed after the reduction of grazing by sample filtration in combination with a decrease in resource competition by sample dilution. Sunlight exposure significantly reduced prokaryote growth (11 ± 6%) and community richness (14 ± 4%) compared to continuous darkness but did not significantly change community composition. The largest growth inhibition after sunlight exposure occurred at locations showing deep mixed layers. The reduction of grazing had an expected and significant positive effect on growth, but caused a significant decrease in community richness (16 ± 6%), suggesting that the coexistence of many different OTUs is partly promoted by the presence of predators. Dilution of the grazer‐free prokaryotic community significantly enhanced growth at the level of community, but consistently and sharply reduced the abundance of Prochlorococcus and SAR11 populations. The decline of these oligotrophic bacterial taxa following an increase in resource availability is consistent with their high specialization for exploiting the limited resources available in the oligotrophic warm ocean

Els microorganismes marins duen a terme importants processos biogeoquímics que tenen un paper fonamental en el funcionament i la sostenibilitat del planeta. El seu estudi ha prosperat significativament en els últims anys gràcies a l'ús d'eines moleculars. Un dels grans avenços de la passada dècada va ser el descobriment dels bacteris fotoheterotròfics marins, que va canviar la nostra visió de les xarxes tròfiques microbianes a l'oceà. Aquests organismes són heteròtrofs que fan servir principalment matèria orgànica però que són capaços d'obtenir energia addicional mitjançant la llum. A part dels cianobacteris i els bacteris que contenen proteorodopsina, els bacteris aeròbics anoxigènics fototròfics (AAPs) són el tercer grup més nombrós de procariotes fototròfiques a l'oceà. En aquesta xerrada, resumiré els avenços que s’han produït en l'última dècada en el coneixement d'aquests microorganismes, destacant les seves contribucions a entendre quina és la seva abundància i diversitat en gradients temporals i espacials i com aquesta varia amb els canvis ambientals, així com quin és el seu paper ecològic i la seva contribució al cicle del carboni

“Qui fa recerca a l’Antàrtida? Són joves o grans? Són dones o homes? Tots són científics/ques? Hi ha més coses a l’Antàrtida a part de pingüins i gel? On es du a terme la recerca: a dins de l’aigua, sota l’aigua o a terra ferma? Quan va començar el Consell Superior d’Investigacions Científiques (CSIC) a fer recerca antàrtica? Què es menja quan treballes a les aigües fredes de l’Oceà Austral? Es pot parlar amb els amics i la família, o fer ús de les xarxes socials com Instagram i Twitter, a un dels indrets més remots de la Terra? En aquesta taula rodona parlarem de la recerca que es fa al continent glaçat evitant caure en els tòpics més comuns de la recerca antàrtica i parlant amb els protagonistes reals de la recerca antàrtica que es fa des del CSIC. Abordarem aquest tema des de diversos punts de vista: generacional, professional i disciplinari, i de gènere.”

Marine viruses are the most abundant biological entities in marine ecosystems, and due to their life cycle’ they have an impact on biogeochemical cycles, contributing in making life possible in the oceans. These days, there is a large and well-established knowledge on what regards to viruses’ role in the marine ecosystems. They influence the particle size distribution, particle sinking rates, bacterial and algal biodiversity, and the release of organic compounds derived from biological metabolism. However, little is known about the influence that the interaction between environmental and biological factors may have on marine viruses’ communities. In Antarctic and the sub-Antarctic waters, phytoplankton blooms occur during the Austral summer, and is then when viruses and bacteria can reach their greatest abundance and activity rates. These algal blooms are usually dominated by different taxonomic groups: diatoms, dinoflagellates, haptophytes, cryptomones, etc. Besides, phytoplankton communities are accompanied by bacterial communities, and they are influenced by environmental conditions. Then, all these interactions may have a role in the function and structure of marine viruses. To test which are the main drivers contributing to shape viral community distribution and structure, four environmentally contrasting locations were sampled during the Austral summer-2015. Three locations were near Orkney and Anvers Islands close to the Antarctic Peninsula, and one in the South Georgia Islands in the sub-Antarctic Ocean. These locations presented different physicochemical and biological conditions (e.g. temperature, salinity, viral and bacterial abundance, phytoplankton taxa...). We characterized the physicochemical conditions and the phytoplankton community of these locations, and we studied the marine viral community structure by using the fingerprint technique: Randomly amplified polymorphic DNA-PCR (RAPD) that allowed to group similar viral communities. Indeed, the four

During summer, when oligotrophic conditions prevail offshore in the Mediterranean Sea, enhanced phytoplankton stripes are often observed in nearshore waters. In this study, we examine the cross-shore hydrographic variability and the associated microbial plankton communities in this zone. Detailed cross-shore underway sampling at 47 coastal sites spread along the Balearic and Catalan coasts revealed the widespread existence of narrow bands of warm and decreased salinity water beholding high phytoplankton biomass (up to 50-fold vs. offshore chlorophyll). Most intense physical and biological anomalies along these transects were generally constrained to the first hundred meters from the shoreline (i.e., a transition zone starting at ~400 m). We use Principal Component Analysis (PCA) and k-means cluster analysis to categorize temperature, salinity and chlorophyll (T, S and Chl) in three main types of cross-shore trends. Prevalence of exponential-shaped Chl trends was observed particularly in areas with shoreward directed winds (B1-type). The other two trends (B2 and B3) presented variations offthe coast produced by alongshore structures like river plumes, city outfalls and other features. Exponential-shaped cross-shore chlorophyll distribution (B1-type) accumulated 90% of the total transect Chl variation in the first 367 ± 190 m from the shoreline, whereas this distance was variable in the other profile types. Repeated daily sampling at one site with this transect typology revealed that wind forcing variations produced fast response on cross-shore T and S properties. Chl was less sensitive to changes at this time-scale. Phytoplankton communities exhibited site-dependent responses to the nearshore environment. Pico- and nanoplankton assemblages, typically dominating coastal assemblages during summer in the Mediterranean Sea, showed lower cross-shore variation. Conversely, larger response to nearshore conditions was observed in microplankton populations. These larger cells

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.