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Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments

Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations

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

It is well known that only a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere, can be retrieved by isolation. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean and in the ocean particle microbiome. Here, we compared 16S rRNA gene sequences from a large collection (>2000) of cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding (16S Tags) datasets covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 22 samples used for isolation. These global datasets represent 60.322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2 -0.8 ¿m) and up to 45% in the largest particles (20-200 ¿m) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2–0.8 µm) and up to 45% in the largest particles (20–200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria

[EN] The details of this research, led by the Institut de Ciències del Mar (ICM-CSIC) and the Universitat Autònoma de Barcelona (UAB), are reported in an article published recently in the prestigious journal ISME Communications, [ES] Los detalles de la investigación, liderada por el Institut de Ciències del Mar (ICM-CSIC) y la Universitat Autònoma de Barcelona (UAB), se recogen en un artículo publicado recientemente en la prestigiosa revista ISME Communications, [CAT] Els detalls de la investigació, liderada per l'Institut de Ciències del Mar (ICM-CSIC) i la Universitat Autònoma de Barcelona (UAB), es recullen en un article publicat recentment a la prestigiosa revista ISME Communications

Microbial reduction of inorganic divalent mercury (Hg2+) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg2+ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle.

Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef's approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial diversity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef's Mandala with the aim of improving future studies on aquatic microbial ecology.

[ES] Biólogos marinos del Instituto de Ciencias del Mar (ICM-CSIC) y de la Universidad Autónoma de Barcelona (UAB) han descubierto la distribución y capacidad de las bacterias marinas de degradar el mercurio del océano, [CAT] Un equip liderat per l'Institut de Ciències del Mar (ICM-CSIC) de Barcelona i la Universitat Autònoma de Barcelona (UAB) ha desvetllat la distribució i capacitat dels bacteris heteròtrofs de degradar el mercuri oceànic

[ES] Investigadores del IDAEA, ICM, IQOG y la Universidade de Vigo tomarán muestras de agua y aire del océano Austral para analizar la contaminación antropogénica, [CAT] Investigadors de l’Institut de Diagnosi Ambiental i Estudis de l’Aigua (IDAEA-CSIC), l’Institut de Ciències del Mar (ICM-CSIC), l’Institut de Química Orgánica General (IQOG-CSIC) i la Universitat de Vigo comencen l’expedició ANTOM-II a l’oceà Austral per analitzar l’impacte dels contaminants emergents i compostos orgànics semi volàtils d’origen humà, [GA] As e os investigadores da UVigo, IDEAE-CSIC, ICM-CSIC e IQOG-CSIC partían nas últimas horas do porto arxentino de Ushuaia, a bordo do buque de investigación oceanográfica Hespérides, desde onde tomarán, no océano Austral, mostras de auga e aire para analizar a contaminación antropoxénica

[EN] Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef’s approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial diversity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef’s Mandala with the aim of improving future studies on aquatic microbial ecology., [ES] Ramon Margalef fue un científico pionero que introdujo un enfoque interdisciplinario a los estudios ecológicos. Sus estudios fueron de los primeros en incorporar diferentes conceptos en la literatura de la ecología acuática, desde los organismos y las interacciones de los ecosistemas hasta la evolución. Para llevar el enfoque de Margalef a los estudios científicos actuales, en este articulo exploramos su visión de la ecología acuática dentro de cuatro campos de estudio interrelacionados: teoría ecológica, diversidad microbiana, ciclos biogeoquímicos y cambios ambientales globales. Inspirándonos en sus estudios pasados, analizamos en este texto los desafíos científicos actuales y proponemos un enfoque integrado considerando el concepto unificador del Mandala de Margalef con el objetivo de mejorar los estudios futuros sobre la ecología microbiana acuática

Two strains isolated from a sample of activated sludge that was obtained from a seawater-based wastewater treatment plant on the southeastern Mediterranean coast of Spain have been characterized to achieve their taxonomic classification, since preliminary data suggested they could represent novel taxa. Given the uniqueness of this habitat, as this sort of plants are rare in the world and this one used seawater to process an influent containing intermediate products from amoxicillin synthesis, we also explored their ecology and the annotations of their genomic sequences. Analysis of their 16S rRNA gene sequences revealed that one of them, which was orange-pigmented, was distantly related to Vicingus serpentipes (family Vicingaceae) and to other representatives of neighbouring families in the order Flavobacteriales (class Flavobacteriia) by 88–89 % similarities; while the other strain, which was yellow-pigmented, was a putative new species of Lysobacter (family Xanthomonadaceae, order Xanthomonadales, class Gammaproteobacteria) with Lysobacter arseniciresistens as closest relative (97.3 % 16S rRNA sequence similarity to its type strain). Following a polyphasic taxonomic approach, including a genome-based phylogenetic analysis and a thorough phenotypic characterization, we propose the following novel taxa: Parvicella tangerina gen. nov., sp. nov. (whose type strain is AS29M-1T=CECT 30217T=LMG 32344T), Parvicellaceae fam. nov. (whose type genus is Parvicella), and Lysobacter luteus sp. nov. (whose type strain is AS29MT=CECT 30171T=LMG 32343T)

Microbial reduction of inorganic divalent mercury (Hg2+) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg2+ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle

[EN] Mercury (Hg) poses a recognized global environmental problem with worrisome environmental and public health impacts (UNEP 2019). While natural sources of Hg such as volcanic eruptions, geothermal activity and weathering of Hg-rich rocks in the earth’s crust have always existed, in the last century human activities such as artisanal and small-scale gold mining, coal combustion, production of non-ferrous metals, cement production and disposal of wastes containing Hg have outpaced natural sources. Around 80% of the Hg emitted to the atmosphere from natural and anthropogenic source is deposited in the ocean, resulting in a tripling of Hg concentrations in surface marine waters compared with pre-industrial levels. The World Health Organization has placed Hg among the top 10 chemicals of major public health concern. Spain is one of the 130 signatories of a global treaty, the Minamata Convention, that seeks to protect human health and the environment from the adverse effects of Hg and came into force in August 2017. Some of the convention’s proposed actions include a phase-out and phase-down of Hg use in a number of products and industrial processes, a ban on new Hg mines and the phase-out of existing ones, monitoring of Hg air emissions and releases to land and water, and regulation of the informal sector of artisanal and small-scale gold mining. The EU has also established environmental policies for monitoring and modelling global Hg distribution such as the Global Mercury Observation System. Understanding the global Hg biogeochemical cycle of the oceans is key for predicting Hg levels in aquatic food webs and evaluating the impact of reduction strategies on human exposure. […], [ES] El mercurio (Hg) plantea un problema ambiental reconocido a nivel mundial con preocupantes impactos ambientales y de salud pública (UNEP 2019). Si bien siempre han existido fuentes naturales de Hg como erupciones volcánicas, actividad geotérmica y meteorización de rocas ricas en Hg en la corteza terrestre, en el siglo pasado las actividades humanas como la minería de oro artesanal y en pequeña escala, la combustión de carbón, la producción de metales no-ferrosos, la producción de cemento y la eliminación de desechos que contienen Hg han superado a las fuentes naturales. Alrededor del 80% del Hg emitido a la atmósfera de fuentes naturales y antropogénicas se deposita en el océano, lo que ha resultado en una triplicación de las concentraciones de Hg en las aguas marinas superficiales en comparación con los niveles preindustriales. Por ello, la Organización Mundial de la Salud ha colocado al Hg entre las 10 principales sustancias químicas de mayor preocupación para la salud pública. España es uno de los 130 signatarios de un tratado global, el Convenio de Minamata, que busca proteger la salud humana y el medio ambiente de los efectos adversos del Hg y que entró en vigor en agosto del 2017. Algunas de las acciones propuestas del convenio incluyen una eliminación del uso de Hg en una serie de productos y procesos industriales, la prohibición de nuevas minas de Hg y la eliminación de las existentes, el monitoreo de las emisiones de Hg al aire y las liberaciones a la tierra y el agua, y la regulación del sector informal de minería de oro artesanal y en pequeña escala. En este contexto, la Unión Europea ha establecido políticas ambientales para monitorear y modelar la distribución global de Hg, un ejemplo es el Sistema Global de Observación de Mercurio. Comprender el ciclo biogeoquímico global del Hg en los océanos es clave para predecir los niveles de Hg en las redes alimentarias acuáticas y evaluar el impacto de las estrategias de reducción en la exposición humana. [, [CAT] El mercuri (Hg) planteja un problema ambiental reconegut a nivell mundial amb preocupants impactes ambientals i de salut pública (UNEP 2019). Si bé sempre han existit fonts naturals de Hg com les erupcions volcàniques, l’activitat geotèrmica i la meteorització de roques riques en Hg en l’escorça terrestre, en el segle passat les activitats humanes com la mineria d’or artesanal i en petita escala, la combustió de carbó, la producció de metalls no-ferrosos, la producció de ciment i l’eliminació de deixalles que contenen Hg han superat a les fonts naturals. Al voltant del 80% del Hg emès a l’atmosfera de fonts naturals i antropogèniques es diposita a l’oceà, la qual cosa ha resultat en una triplicació de les concentracions de Hg en les aigües marines superficials en comparació amb els nivells preindustrials. Per això, l’Organització Mundial de la Salut ha col·locat al Hg entre les 10 principals substàncies químiques de major preocupació per a la salut pública. Espanya és un dels 130 signataris d’un tractat global, el Conveni de Minamata, que busca protegir la salut humana i el medi ambient dels efectes adversos del Hg i que va entrar en vigor a l’agost del 2017. Algunes de les accions proposades del conveni inclouen l’eliminació de l’ús de Hg en una sèrie de productes i processos industrials, la prohibició de noves mines de Hg i l’eliminació de les existents, el monitoratge de les emissions de Hg a l’aire i els alliberaments a la terra i l’aigua, i la regulació del sector informal de mineria d’or artesanal i en petita escala. En aquest context, la Unió Europea ha establert polítiques ambientals per a monitorar i modelar la distribució global de Hg, un exemple és el Sistema Global d’Observació de Mercuri. Comprendre el cicle biogeoquímic global del Hg als oceans és clau per a predir els nivells de Hg en les xarxes alimentàries aquàtiques i avaluar l’impacte de les estratègies de reducció en l’exposició humana. […]

Cork matrices biofunctionalized with Moringa oleifera seed extracts (MoSe) have potential for use as a biofilter with antibacterial properties to reduce waterborne pathogens. The aim of this study was to evaluate the effect of cork biofunctionalized with active antimicrobial compounds of MoSe (f-cork) on the inhibition of Escherichia coli (InhEc). The LacZ gene from a strain of E. coli was used as the target sequence using viability quantification Polymerase Chain Reaction (qPCR) and differentiation of viable and dead bacteria through selective cell viability PMA staining. To perform this, a 27−4 fractional factorial design and a biofiltration system were used to evaluate the effect of the active protein in MoSe immobilized in granulated cork on InhEc. We found that the potential for antimicrobial activity increased with f-cork for an effective maximal bacterial reduction (99.99%; p < 0.05). The effect of f-cork functionalized with MoSe on E. coli viability was of 0.024% and 0.005% for the cells exposed to PMA, respectively, being the relevant conditions in treatment 2: (0 L/min) without aeration, (5%) MoSe and (5 mm) cork particle. In conclusion, the f-cork functionalized with MoSe presented biosorbent and antibacterial properties that effectively reduced the E. coli growth.

Cork matrices biofunctionalized with Moringa oleifera seed extracts (MoSe) have potential for use as a biofilter with antibacterial properties to reduce waterborne pathogens. The aim of this study was to evaluate the effect of cork biofunctionalized with active antimicrobial compounds of MoSe (f-cork) on the inhibition of Escherichia coli (InhEc). The LacZ gene from a strain of E. coli was used as the target sequence using viability quantification Polymerase Chain Reaction (qPCR) and differentiation of viable and dead bacteria through selective cell viability PMA staining. To perform this, a 27-4 fractional factorial design and a biofiltration system were used to evaluate the effect of the active protein in MoSe immobilized in granulated cork on InhEc. We found that the potential for antimicrobial activity increased with f-cork for an effective maximal bacterial reduction (99.99%; p < 0.05). The effect of f-cork functionalized with MoSe on E. coli viability was of 0.024% and 0.005% for the cells exposed to PMA, respectively, being the relevant conditions in treatment 2: (0 L/min) without aeration, (5%) MoSe and (5 mm) cork particle. In conclusion, the f-cork functionalized with MoSe presented biosorbent and antibacterial properties that effectively reduced the E. coli growth., This research was funded by Mexico-CONACYT, grant number 3006060 and grant by the UNESCO Chair on Sustainability of the Polytechnic University of Catalonia (Spain)., Peer Reviewed, Postprint (published version)

[EN] The world’s oceans sustain the life for an estimated total of 10 microbial cells. Marine bacteria are responsible for most part of the ocean respiration and are key in most biogeochemical cycles of the Earth. Accordingly, the study of the bacterial diversity present in different marine ecosystems is essential, and having access to their genomes through isolation or genomic centric studies is important to decipher their metabolic potential. Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. In this thesis, standard plating techniques allowed to create a marine culture collection of heterotrophic bacteria (MARINHET). More than 2000 isolates were retrieved from samples collected from a variety of oceanographic regions, from different depths including surface, mesopelagic and bathypelagic waters, and also covering different seasons and years. Chapter 1 describes the taxonomy, the phylogenetic diversity and the biogeography of culturable heterotrophic marine bacteria, and reveals that an important percentage of the strains (37 %) are 100 % identical in their partial 16S rRNA gene between photic and aphotic layers. In addition, we identified Alteromonas and Erythrobacter genera as the most frequently retrieved heterotrophic bacteria from the ocean in standard marine agar medium. [...], [ES] Los océanos contienen aproximadamente un total de 10 células microbianas. Las bacterias marinas son responsables de la mayor parte de la respiración que se produce en el océano y son esenciales en los ciclos biogeoquímicos de la Tierra. Estudiar la diversidad bacteriana de los ecosistemas marinos y tener acceso a los genomas mediante estudios dependientes e independientes de cultivo es importante para descifrar el potencial metabólico de las bacterias marinas. Los cultivos nos aportan información sobre la fisiología bacteriana, ecología y contenido genómico, pero la mayoría de los esfuerzos en aislar bacteria marinas provienen de la zona fótica del océano, dejando las profundidades marinas menos exploradas. En esta tesis, técnicas estándar de cultivo han permitido crear una colección marina de bacterias heterótrofas (MARINHET), compuesta por más de 2000 aislados, recuperados de varias regiones oceanográficas, de varias profundidades (superficie, mesopelágico y batipelágico), y cubriendo varias estaciones y años. El Capítulo 1 describe su taxonomía, diversidad filogenética y biogeografía y revela que un 37% de las cepas son 100% idénticas en la secuencia parcial del gen ribosomal 16S (16S rRNA) entre la zona fótica (superficie) y afótica (mesopelágico y batipelágico). Además, hemos identificado Alteromonas y Erythrobacter entre los géneros marinos heterótrofos más comunes que recuperamos en cultivo usando un medio marino estándar. [...], [CAT] Els oceans conten aproximadament un total de 10 cèl·lules microbianes. Els bacteris marins són responsables de la major part de la respiració que es produeix en l’oceà i són essencials en els cicles biogeoquímics de la Terra. Estudiar la diversitat bacteriana dels ecosistemes marins i tenir accés als genomes mitjançant estudis dependents o independents de cultiu és important per desxifrar el potencial metabòlic dels bacteris marins. El cultius ens aporten informació sobre la fisiologia bacteriana, ecologia i contingut genòmic, però la majoria dels esforços en aïllar bacteris marins provenen de la zona fòtica de l’oceà, deixant les profunditats marines menys explorades. En aquesta tesi, tècniques estàndard de cultiu han permès crear una col·lecció marina de cultius de bacteris heterotròfics (MARINHET), composada per més de 2000 aïllats, recuperats de diverses regions oceanogràfiques, de diverses profunditats (superfície, mesopelàgic i batipelàgic) i cobrint diverses estacions i anys. El Capítol 1 descriu la seva taxonomia, diversitat filogenètica i biogeografia i revela que un 37% de les soques aïllades són 100% idèntiques en el gen ribosomal 16S (16S rRNA) entre la zona fòtica (superfície) i afòtica (mesopelàgic i batipelàgic). A més, hem identificat Alteromonas i Erythrobacter entre els gèneres marins heterotròfics més comuns que recuperem en cultiu usant un medi marí estàndard. [...]

Cork matrices biofunctionalized with Moringa oleifera seed extracts (MoSe) have potential for use as a biofilter with antibacterial properties to reduce waterborne pathogens. The aim of this study was to evaluate the effect of cork biofunctionalized with active antimicrobial compounds of MoSe (f-cork) on the inhibition of Escherichia coli (InhEc). The LacZ gene from a strain of E. coli was used as the target sequence using viability quantification Polymerase Chain Reaction (qPCR) and differentiation of viable and dead bacteria through selective cell viability PMA staining. To perform this, a 27−4 fractional factorial design and a biofiltration system were used to evaluate the effect of the active protein in MoSe immobilized in granulated cork on InhEc. We found that the potential for antimicrobial activity increased with f-cork for an effective maximal bacterial reduction (99.99%; p < 0.05). The effect of f-cork functionalized with MoSe on E. coli viability was of 0.024% and 0.005% for the cells exposed to PMA, respectively, being the relevant conditions in treatment 2: (0 L/min) without aeration, (5%) MoSe and (5 mm) cork particle. In conclusion, the f-cork functionalized with MoSe presented biosorbent and antibacterial properties that effectively reduced the E. coli growth

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bac-terium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15% NaCl) and mesophilic (4-37 °C), oxidase-and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15:0, iso-C15:0 2-OH, and iso-C17:0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2%), Salegentibacter mishustinae (93.1%) and Mesonia mobilis (92.9%) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81% AAI; 78.9% ANI), M. phycicola (76% AAI; 76.3% ANI), Mesonia maritima (72% AAI, 74.9% ANI), Mesonia hippocampi (64% AAI, 70.8% ANI) and Mesonia algae (68% AAI; 72.2% ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia. We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups dis, Postprint (published version)

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups dis

Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia. We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans

Strain ISS155T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of Cellvibrionaceae, in the Gammaproteobacteria, with Agarilytica rhodophyticola 017T as closest relative (94.3¿% similarity). Its major cellular fatty acids are C18¿:¿1, C16¿:¿0 and C16¿:¿1; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2¿mol%. A phylogenomic analysis using UBCG merges strain ISS155T in a clade with A. rhodophyticola, Teredinibacter turnerae, Saccharophagus degradans and Agaribacterium haliotis type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available Cellvibrionaceae type strain genomes show that strain ISS155T is related to them by values lower than 60¿%, with a maximum of 58¿% to A. rhodophyticola 017T and 57¿% to T. turnerae T7902T and S. degradans 2-40T. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155T represents a new genus and species in Cellvibrionaceae, for which we propose the name Thalassocella blandensis gen. nov., sp. nov., and strain ISS155T (=CECT 9533T=LMG 31237T) as the type strain