Josep M. Gasol

Staff Researcher

Phone: (34) 93 230 95 00

Josep M. Gasol

I am a Research Professor here, interested in planktonic microbe abundance and activity, and their ecosystem effects. This implies the study of the factors that regulate the abundance of planktonic microorganisms and those that regulate microorganism community structure (size, functional and taxonomical structure), and how the physical changes in the marine environment affect these parameters. As an example, how predation and resource availability regulate bacterial abundances, bacterial use of DOC, and how they regulate the composition of the microbial “black box” in terms of size structure, metabolic characteristics of the community, phylogenetic composition, and genomic content. This is approached by empirical analysis of data bases of organism abundance, growth and loss rates, generated mainly in cruises; by mesocosm and microcosm experiments; and by the combined use of image analysis and flow cytometry and metabolic fluorescent probes. Lately, I have also been interested in the functional aspects of diversity: how diversity and ecosystem functioning are linked, what is the functional relevance of functional gene diversity, etc.

I did my PhD at the UAB working on the microbes of one of the most interesting lakes in the world, Lake Cisó. I was then a postdoc at McGill University in Montreal where instead of focussing on one lake I tried to broaden to generalities about microbial community structure in as many lakes as possible. Of course, the next step had to be to work in the Ocean, the “great vast lake”…While my main workplace is the ocean, with special interest in the Microbial Observatory of Blanes Bay, where I coordinate the long term research, I always enjoy working in lakes and any other water bodies, as long as they are nice (and not yet spoiled by humans!).

Other than these mundane things, I like mountains, wildlife, photography, guitar playing and singing, particularly folk music, and I enjoy doing all these things with my kids!

FEATURED PAPERS

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Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation (2018)

M. Sebastián, J.C. Auguet, C. Restrepo-Ortiz, M.M. Sala, C. Marrasé, J.M. Gasol

Environmental Microbiology, 20, 713-723. DOI: 10.1111/1462-2920.14002

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Large-scale ocean connectivity and planktonic body size (2018)

E. Villarino, J.R. Watson, B. Jönsson, J.M. Gasol, G. Salazar, S.G. Acinas, M. Estrada, R. Massana, R. Logares, C.R. Giner, M.C. Pernice, M.P. Olivar, L. Citores, J. Corell, N. Rodríguez-Ezpeleta, J.L. Acuña, A. Molina-Ramírez, I. González-Gordillo, A. Cózar, E. Martí, J.A. Cuesta, S. Agustí, E. Fraile-Nuez, C.M. Duarte, X. Irigoien, G. Chust

Nature Communications, 9, 1-13. DOI: 10.1038/s41467-017-02535-8

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Seasonal dynamics of transparent exopolymer particles (TEP) and their drivers in the coastal NW Mediterranean Sea (2018)

E. Ortega-Retuerta, C. Marrasé, A. Muñoz-Fernández, M.M. Sala, R. Simó, J.M. Gasol

Science of The Total Environment, 631-632, 180-190. DOI: 10.1016/j.scitotenv.2018.02.341

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Sinking particles promote vertical connectivity in the ocean microbiome (2018)

M. Mestre, C. Ruiz-González, R. Logares, C.M. Duarte, J.M. Gasol, M.M. Sala

Proceedings of the National Academy of Sciences of the United States of America, 115, 6799-6807. DOI: 10.1073/pnas.1802470115

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Factors controlling the community structure of picoplankton in contrasting marine environments (2018)

J.L. Otero-Ferrer, P. Cermeño, A. Bode, B. Fernández-Castro, J.M. Gasol, X.A. G. Morán, E. Marañon, V. Moreira-Coello, M.M. Varela, M. Villamaña, B. Mouriño-Carballido

Biogeosciences, 15, 6199-6220. DOI: 10.5194/bg-15-6199-2018

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Introduction: The evolution of microbial ecology of the ocean (2018)

J.M. Gasol, D.L. Kirchman

1-46.

Microbial Ecology of the Ocean (2018)

J.M. Gasol, D.L. Kirchman

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PROJECTS

REMEI - REgulación del (meta) genóma procariótico de un ambiente costero marino: factores biológicos y oceanográficos que determinan la presencia y función bioquímica de procariotas planctónicas
Funding entity: MINECOStart: 01/01/2016End: 31/12/2018

GR DIFUMIC - Diversidad y función microbiana en sistemas acuáticos
Funding entity: GENCATStart: 01/01/2017End: 31/12/2020

See past projects

PAST PROJECTS

THESIS SUPERVISED

Spatial and temporal patterns of marine prokaryotic diversity along the particulate matter continuum
Author: M. Mestre MartínSupervisor: J.M. Gasol, M.M. Sala
Institution: Universidad de las Palmas de Gran CanariaYear: 2017

Uncovering Diversity and Structure of Bacteroidetes Populations in Marine Environments
Author: C. Díez VivesSupervisor: S.G. Acinas, J.M. Gasol
Institution: Universidad de las Palmas de Gran Canarias, Institut de Ciències del MarYear: 2013

Patterns in marine microbial community structure
Author: T. LefortSupervisor: J.M. Gasol Pique
Institution: Universidad de Las Palmas de Gran CanariaYear: 2012

Effects of solar radiation on marine bacterial and phytoplankton heterotrophic activities
Author: C. Ruiz GonzálezSupervisor: J.M. Gasol Pique, R. Simó
Institution: Universidad de Las Palmas de Gran CanariaYear: 2011

Effects of different allochthonous carbon sources on marine bacterioplankton diversity and function
Author: I. Lekunberri GarcíaSupervisor: J.M. Gasol Pique
Institution: Universitat Politècnica de CatalunyaYear: 2008

Links between bacterial divesity and carbon cycling in the sea
Author: L. Alonso SaezSupervisor: J.M. Gasol Pique
Institution: Universitat Politècnica de CatalunyaYear: 2006

Microorganisms in the ocean conform an extensive microbiome where individuals interact constantly with the particulate matter. However, most of the studies have focused on the free-living microorganisms, and to a lesser extent on the attached microorganisms but have not taken into account the organisms associated to particles of different sizes. The main objective of this thesis is to characterize the diversity of prokaryotes along the particulate matter continuum present in the ocean, as well as to describe its temporal and spatial variability at distinct scales. First of all, we propose a multiple size-fractionation as a sampling method that provides a better comprehension of the prokaryotic diversity than the commonly used sampling methods. Our work shows that each size-fraction contains distinct prokaryotic communities that vary at different spatial and temporal scales. In general, there is an increase of bacterial richness from the smaller to the larger particles, suggesting that larger particles may contribute with new niches. The main exception is the bathypelagic, where richness decreases form the small to the largest size-fractions. In contrast, Archaea presented higher richness in the smaller size-fractions and, although had lower diversity and relative abundance than bacteria, these increased with depth. We moreover classified taxonomic groups depending on whether they have preference for small size-fractions, for larger size-fractions, or do not have a clear preference for any size fraction. This classification is presented as an alternative to the traditional simple separation between free-living bacteria and attached bacteria. Most of the taxonomic groups maintain their preference for certain size fractions in space and time, although some taxonomic groups change their preferences in vertical profiles from the surface to the bathypelagic and along time. We also observed that the bathypelagic is dominated by prokaryotes which are also present in surface waters and that there is a vertical connectivity between prokaryotic communities along the water column through sinking particles. This connectivity causes bathypelagic biogeography to be closely linked to particle colonization in the ocean surface. Overall, this thesis reports on the complexity of prokaryotic communities present in the continuum of sizes and shows the need for disseminating this perspective to define more comprehensively the diversity of ocean prokaryotes Close

One of the main questions in microbial ecology is to understand what are the processes that structure and govern the species composition of communities. Answering to this question implies the need to detect bacterial species in environmental samples or at least to define ecologically meaningful “units of differentiation”. The dynamics and distribution of different broad taxonomic groups that constitute the bacterioplankton (at the phylum or class level) has been widely studied. The different large groups are known to follow different spatial distributions and seasonal cycles, but important variations also occur at lower levels (i.e. species or ecologically distinct populations). In this thesis we aimed to study some of these aspects for an important group of marine bacteria: the phylum Bacteroidetes. First at all, we evaluated the existing molecular tools in an updated phylogenetical and methodological context. Strengths and weaknesses of different probes used in different techniques were thoroughly studied and discussed, and alternatives were designed for some specific purposes related with the study of this group in marine environmental samples. Standing on these tools, we studied the phylum at different levels of resolution resulting from assorted molecular approaches. We related entire phylum abundances with environmental parameters as they vary spatially and temporally in the oceanic realm. We identified the most abundant phylotypes forming the Bacteroidetes assemblages and their ecological variability. Both the relative abundance and the changes in the phylotypes constituting the community followed clear spatial and seasonal patterns, which were thoroughly described. To increase the resolution of our study, we built extensive clone libraries including the 16S-ITS-23S ribosomal operon. The phylogenetic study of these sequences from different environmental samples showed that closely related phylotypes were organized in monophyletic clades of habitat-specific sequences. This confirmed that similar bacteria (in terms of the 16S rRNA) seem to present different physiologies, which would drive their distribution and adaption to specific ecological niches. The study of the distributions of these clades would help to understand the ecology of this group. Finally, we integrated the above information to design several clade-specific qPCR primer sets targeting putative Bacteroidetes ecotypes. These primers were thoroughly tested as the best possible compromise between specificity and performance for the intended purpose, and they were extensively evaluated in silico. An optimization of the qPCR technique workflow and a demonstration of its usefulness was carried out using the NS2b group. These primers offer a toolbox for hierarchical quantitative studies characterizing Bacteroidetes populations in different environments. Such studies should help to explore and Close

Understanding the distribution of the different picoplankton groups represents a central tenet of marine microbial ecology. Centering our study on the three major groups constituting the bulk picoplankton community (size 0.2-3 mm), we sought to analyze the distribution of autotrophic bacteria (Synechococcus and Prochlorococcus), photosynthetic Picoeukaryotes pPeuk, and heterotrophic bacteria. For that objective, two different strategies were used, the first one was based on flow cytometry for determining ataxonomic patterns in picoplankton distribution, and the second a comparative analysis approach for identifying broad patterns in bacterial phylogenetic community structure. Given that conversion factors (CFs) were necessary to translate group cell abundance into carbon biomass, but that large discrepancies for CF values of pPeuk had been reported in the literature, we first (re-) evaluated the CF for small phototrophic picoeukaryotes (<5 mm). On one hand, as the set of cultures of Peuk used for that purpose were maintained in non-axenic conditions, we compared two different methods for correcting errors in biomass estimation due to presence of bacteria. Secondly, a relatively higher CF value for pPeuk than those previously reported to date was found, with implications on the role generally attributed to pPeuk in the carbon cycling and other ecosystem processes. Applying this CF, we could identify patterns of variability in picoplankton group distribution at different spatio-temporal scales during winter in a NW Mediterranean coastal station and during a cruise performed in summer from coast to offshore off the Catalan coast. By focusing on the variability at the short time scale, our work showed not only evidences of coupling between picophytoplankton variability and the single-cell bacterial activities but also highlighted how a relatively small variation in meteorology changed considerably the structure of the microbial community. Different trends of variability were observed between the different picoplankton groups, pPeuk cell numbers exhibiting the highest spatio-temporal variability, and bacterial abundance the lowest. Opposite patterns between picoplankton community structure and chlorophyll a levels were observed not only spatially, but also at both the short-term and large temporal scale, suggesting that picoplankton group distribution are useful indicators of the ecosystem state. Finally, we assessed the biogeography of the bacterial phylogenetic groups along a continuum of environmental parameters such as chlorophyll a, temperature and salinity, and identified different patterns in bacterial community structure as related to phytoplankton biomass among coastal and open ocean ecosystems, suggesting unequal metabolic aptitudes of the different bacterial groups for utilizing algal-derived DOC. Close

Since the discovery, 20 years ago, that solar ultraviolet radiation (UVR, 280-400 nm) penetrates much deeper into the ocean’s water column than previously thought, knowledge on its effects on diverse surface processes and organisms has significantly increased, yet further research is needed for a good understanding of sun-organism interactions. Marine bacteria are considered some of the most susceptible to sunlight damage due to their small size and lack of pigments. Since they are primary consumers of dissolved organic matter (DOM) in seawater, one might expect that any effect on them will ultimately have implications for carbon and nutrient cycling. In this work, we contributed to increase the knowledge on the effects of sunlight on the heterotrophic uptake of DOM by bacteria, although we also devoted some effort to assess its impact on the osmoheterotrophic activity of phytoplankton. For that purpose, we combined bulk activity measurements with a single-cell approach involving microautoradiography for identification of both the responses at the community levels and particular responses and sensitivities to sunlight of different microorganisms. Our work highlights the role of solar radiation as a significant modulator of DOM fluxes through differentially affecting the diverse components of the planktonic food webs. The observed responses were shown to vary not only at different scales depending on changes in the light conditions, but also owing to the previous light-exposure history, the identity of the organisms involved, the substrates considered and the accuracy of our light incubation conditions. Whereas exposure to sunlight often led to a reduction in the amount of leucine incorporated, incubation under photosynthetically active radiation (PAR, 400-700 nm) conditions sometimes stimulated its uptake, and potential photoheterotrophy is discussed among other possibilities. In contrast, bulk assimilation of the organic compound dimethylsulfoniopropionate (DMSP) was often increased upon light exposure, particularly within the non-bacterial fraction. We also found that algal osmoheterotrophy seems to be widespread and more common than previously thought, particularly within the phytoplankton assemblages inhabiting the DMSP-rich summer polar waters, and that this behaviour was highly dependant on the light levels. The present thesis sheds light on the complexity of sun-microbe interactions and provides evidence of the need to afford the study of solar radiation effects on the different compartments of the microbial food webs. Close

Bacteria are the most abundant organisms on Earth and mediate many critical ecosystem processes. This indicates the great importance of the knowledge of the identity and population dynamics of the indigenous microorganisms. Initial studies in aquatic microbiology were carried out by traditional cultivation techniques. Later on, cell counts by epifluorescence techniques demonstrated how abundant bacteria were, and molecular techniques were developed and used to detect the most representatives bacteria in the environment. This is mainly because the culture media have nutrient contents (both organic and inorganic) which are several times more concentrated than those in the natural environment. This makes retrieving dominant organisms from an oligotrophic environment not an easy task, and generates selectivity for particular bacterial types, which are not very representative. A similar selection of bacteria also occurs in the natural environment, at another scale, when different allochthonous inputs take place. These can be due to natural processes, such as river run-offs, aerosol deposition, etc., or may have an anthropogenic origin, such as oil spills. In this thesis we evaluate the effect of several of these additions on bacterial community structure and function. There is an increasing interest in the isolation of naturally dominating organisms since it provides a better information about the metabolic capabilities of the organisms that are growing in the environment. Thus, we decided to evaluate how representative were the isolates obtained in the Mediterrranean Sea as compared to the sequences retrieved by molecular techniques such as cloning and DGGE fingerprinting. Our analysis highlighted the selectivity created by the growth media, but simultaneously allowed to increase our knowledge about the diversity in our study area, and provided a means for looking into the “rare microbial biosphere”, which cannot be analyzed with other techniques. To address the question of how nutrient addition modifies bacterial community structure and affects microbial function, we performed different mesocosm experiments, where we added different types of nutrients to water collected from Blanes Bay (NW Mediterranean Sea). Another mesocosm experiment was carried out to evaluate the effect of the oil spill that took place after the Prestige tanker accident in front of the Galician coast. Mesocosms experiments have been widely used to evaluate addition effects as a means to reproduce of the natural conditions. During these experiments different environmental parameters were measured and also bacterial production and abundance were monitored. Bacterial community structure was determined by the DGGE fingerprinting technique, which allows the comparison of different samples and further analysis of the dominant richness by the Shannon-Weaver index, based on the presence and absence of bands. These analyses showed the influence of grazers on the bacterial selection after the different additions and, for example, explained the effects of Saharan Dust deposition on microbial function and community metabolism, as an effect of the inorganic phosphorus and organic carbon contributed by the dust. In the oil spill mesocosm experiments, effects on bacterial structure, production and abundance were detected only with additions four times higher than the concentration found after the Prestige tanker accident. We also include an experimental study carried out in the North Atlantic during two different cruises, in which using dyalisis bags and transplant experiments we tested whether bottom-up conditions were stronger than top-down factors in determining microbial function and community structure. The results showed differences between experiments, but a general higher effect of bottom-up conditions than the effect of predators. The different experimental work included in this thesis allows for some generalizations, but also show some discrepancies, which we discuss in the last chapter. Close

Although our knowledge about bacterial diversity in marine waters and that about the role of bacteria in the oceanic carbon cycling have greatly advanced in the last decades, very little is known about the linkage between those important characteristics, particularly under in situ conditions. The study of such relationship is hampered by the difficulties in obtaining pure cultures from representative marine bacteria, which would provide information about their metabolic capacities. The recent development of single-cell techniques has allowed studying the activity of marine populations in situ, allowing advances on this topic. We are starting now to know what is the specific role of specific groups of bacteria in carbon cycling, and the relationship between bacterial community assemblage and the global magnitude and patterns of carbon cycling in the ocean. In this study, we assessed the linkage between bacterial diversity and function along two gradients in marine waters: a temporal gradient (a seasonal study in a coastal Mediterranean station), and a spatial gradient covering different trophic states in oceanic waters (from the Cape Blanc upwelling to the N Atlantic subtropical gyre). We first described exhaustively bacterial assemblage structure at both sites, with the simultaneous use of clone libraries, fluorescence in situ hybridization with specific probes and fingerprinting of genes encoding the 16S rRNA. Since both studies were focused on surface bacterial assemblages, Archaea were minor components and we focused on Bacteria. We also exhaustively described the use of carbon by bacteria at both sites, taking special care in identifying and constraining the limitations in the methodologies used for that purpose. Afterwards, we performed comparative studies in which changes in bacterial assemblage structure were systematically compared to changes in a range of in situ measurements of bacterial carbon processing, including bacterial respiration and production, since this type of comparisons in marine field studies are absent from the literature. Several similarities were found between both systems studied, in terms of bacterial community composition, such as the increasing abundances of the Roseobacter group in high-nutrients waters, and the predominance of SAR11 bacteria in less productive waters. However, and with the use of multivariate statistics and Mantel tests, a tight linkage between bacterial diversity and function could not be proved in neither of the gradients. This lack of pattern could be due to several reasons, including the fact that the bulk measurements that describe carbon function (bacterial biomass production or respiration) are so general and important for ecosystem maintenance that they are redundantly performed by different bacterial groups. However, a more specific study using a single-cell level approach (microautoradiography combined to fluorescent in situ hybridization) showed that different bacterial populations had significantly distinct patterns of carbon use along the seasonal study in Blanes Bay, which suggests that different bacterial groups are not equal in terms of carbon utilization. Finally, we studied the effect of a variable environmental factor, such as UV and PAR radiation, as it inhibited or stimulated the different bacterial groups. Environmental conditions were shown to affect differently the activity of specific bacterial groups and, thus, their role in the processing of carbon in the marine planktonic environment. Close

REMEI es un proyecto diseñado para comprender el potencial funcional de las comunidades microbianas y los factores que lo regulan. Combinaremos (a) la secuenciación del contenido genómico de una comunidad procariota costera (metagenoma, metaG) en coordinación con una descripción detallada de los ciclos biogeoquímicos en el ambiente de estudio, y (b) una serie de experimentos diseñados para entender los factores biológicos que regulan la presencia de cada función procariota. En (a) se espera entender cuáles son los factores oceanográficos y de estacionalidad que regulan la presencia de los diferentes genes y en (b), con la eliminación experimental controlada de la presión de depredación, los efectos de los virus, o la limitación por nutrientes y por carbono, esperamos entender cómo estos diferentes factores biológicos contribuyen a la regulación. Nuestros datos proporcionarán a) un catálogo completo de los genes del océano costero en el Mediterráneo noroccidental (a añadir a los análisis de una sola vez obtenidos mediante iniciativas como el Ocean Sampling Day o TaraOceans, b) la información obtenida experimentalmente ayudará en la interpretación de los numerosos otros estudios publicados recientemente de metagenomas marinos, o que están en curso, y que son trabajos primordialmente descriptivos. Nuestro objetivo es la generación de una base de datos de los genes asociados a una lista de atributos (por ejemplo, un gen pufM particular aparece en este momento particular del año y con estas condiciones oceánicas, y su aparición es reprimida, por ejemplo, por depredadores), Análisis filogenéticos de las muestras (de los fragmentos de 16S extraídos de los metaG) podría permitir la asociación de genes filogenéticamente no informativos a los probables organismos a los que pertenecen y con los análisis de metaG, en teoría sin sesgo, tendremos la oportunidad de estimar el crecimiento verdadero y las tasas de crecimiento brutas de procariotas a nivel de OTU, y también de genes funcionales. Sin embargo, también vamos a aislar procariotas con medios de cultivo innovadores que podrían servir como base para la comprensión de los vínculos entre la filogenia y la función y también vamos a analizar algunos SCG (genomas de células individuales) de organismos separados por citometría de flujo. Las fortalezas y originalidad del proyecto REMEI provienen del uso combinado de los metagenomas de referencia con la descripción estacional de los principales ciclos biogeoquímicos; y, sobre todo, ii) del uso de manipulaciones experimentales para determinar el papel de los virus, los depredadores y la limitación de nutrientes sobre cada una de las unidades taxonómicas de procariotas presentes en la comunidad (a través de los marcadores de 16S rDNA), y para cada uno de los genes identificados en la conjunto de la comunidad. Close