Pablo Sánchez

Pablo Sánchez
Institut de Ciències del Mar · Marine Biology and Oceanography

PhD
Working with global marine metagenomics datasets at ICM-CSIC. Marbits bioinformatics core sysadmin.

About

59
Publications
14,468
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1,170
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Introduction
I am a bioinformatician at the Ecology of Marine Microorganisms group at ICM-CSIC. I am working with global marine metagenomics datasets, exploring the taxonomic and functional diversity of marine microbial communities through environmental genomics and transcriptomics, as well as the reconstruction and functional analysis of Metagenome Assembled Genomes and Single Amplified Genomes from marine ecosystems. I am the system administrator of Marbits, the marine bioinformatics core at ICM-CSIC
Additional affiliations
February 2012 - June 2013
Universitat de Girona
Position
  • Lecturer
Education
January 2002 - October 2012
Universitat Politècnica de Catalunya
Field of study
  • Biotechnology
September 1996 - September 2001
University of Barcelona
Field of study
  • Biology

Publications

Publications (59)
Article
Full-text available
Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of...
Article
Full-text available
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental gen...
Article
Full-text available
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental gen...
Article
Full-text available
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40%-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation int...
Preprint
Full-text available
Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standa...
Article
Full-text available
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 metageno...
Preprint
Full-text available
Microbial assemblages under sea ice of Dease Strait, Canadian Arctic, were sequenced for metagenomes and metatranscriptomes of the small size fraction (0.2 to 3 μm). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Towards summer, Bact...
Article
Full-text available
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potentia...
Preprint
Full-text available
Microbial reduction of inorganic divalent mercury (Hg ²⁺ ) 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 global ocean. Here, we explored the distribution of these gene...
Chapter
Full-text available
Oceans are no longer inaccessible places for data acquisition. High-throughput technological advances applied to marine sciences ( from genes to global current patterns ) are generating Big Data sets at unprecedented rates. How to manage, store, analyse, use and transform this data deluge into knowledge is now a fundamental challenge for ocean scie...
Article
Full-text available
The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles d...
Preprint
Full-text available
The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of s...
Preprint
Microbes are phylogenetically and metabolically diverse. Yet capturing this diversity, assigning functions to host organisms and exploring the biosynthetic potential in natural environments remains challenging. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally-distributed ocean microbial communitie...
Article
Full-text available
Background: 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 sta...
Preprint
Full-text available
Bridging the gap between the known and the unknown coding sequence space is one of the biggest challenges in molecular biology today. This challenge is especially extreme in microbiome analyses where between 40% to 60% of the coding sequences detected are of unknown function, and ignoring this fraction limits our understanding of microbial systems....
Preprint
Full-text available
The Arctic Ocean is a key player in the regulation of climate and at the same time is under increasing pressure as a result of climate change. Predicting the future of this ecosystem requires understanding of the responses of Arctic microorganisms to environmental change, as they are the main drivers of global biogeochemical cycles. However, little...
Preprint
Full-text available
Background: 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 stan...
Article
Surveying microbial diversity and function is accomplished by combining complementary molecular tools. Among them, metagenomics is a PCR free approach that contains all genetic information from microbial assemblages and is today performed at a relatively large scale and reasonable cost, mostly based on very short reads. Here we investigated the pot...
Article
Full-text available
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distribu...
Preprint
Full-text available
The deep sea, the largest compartment of the ocean, is an essential component of the Earth system, but the functional exploration of its microbial communities lags far behind that of other marine realms. Here we analyze 58 bathypelagic microbial metagenomes from the Atlantic, Indian, and Pacific Oceans in an unprecedented sampling effort from the M...
Article
Full-text available
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...
Article
Full-text available
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). Additi...
Article
Full-text available
The molecular diversity of the aquatic picocyanobacterial community cannot be accurately described using only the available universal 16S rRNA gene primers that target the whole bacterial and archaeal community. We show that the hypervariable regions V5, V6, and V7 of the 16S rRNA gene are better suited to study the diversity, community structure,...
Article
Aim Understanding how historical and contemporary processes shaped and maintain spatial patterns of genetic diversity is a major goal for conservation biologists. Here, we characterized the pattern of neutral genetic diversity and we inferred underlying processes in the habitat‐forming octocoral Paramuricea clavata in the Adriatic Sea, a peculiar p...
Preprint
Full-text available
Aerobic anoxygenic phototrophic (AAP) bacteria play a relevant role in the marine microbial food web, but little is known about their long-term seasonal dynamics. Using Illumina amplicon sequencing of the puf M gene coupled with multivariate, time series and co-occurrence analyses we examined their temporal dynamics over a decade at the Blanes Bay...
Article
Full-text available
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in m...
Article
Full-text available
Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promisin...
Article
Full-text available
Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples 1–4 , viral photosystem I (vPSI) gene...
Data
Appendix S2. Protein alignment used to construct the PsaD phylogenetic tree (Fig. 3A).
Data
Appendix S7. Protein alignment used to construct the RegA phylogenetic tree (Fig. S1D).
Data
Fig. S2. Multiple sequence alignment of the loop area in partial PsaA proteins. The arginine conserved in high %G + C viral sequences is marked in blue. Conserved negative amino acids are coloured in red. Names of the viral sequences represent reads/scaffolds or PCR products retrieved in this study (except for GQ268816).
Data
Table S2. Sequences used as query for the tblastn analysis.
Data
Appendix S3. Protein alignment used to construct the PsaB phylogenetic tree (Fig. 3B).
Data
Appendix S4. Protein alignment used to construct the DNApol phylogenetic tree (Fig. S1A).
Data
Appendix S5. Protein alignment used to construct the gp17 phylogenetic tree (Fig. S1B).
Data
Fig. S1. Maximum likelihood phylogenetic trees of (A) DNApol, (B) gp17, (C) gp23 and (D) RegA. Circles represent bootstrap values higher than 90%. Phage sequences retrieved in this study are coloured in red. The scale bar indicates the average number of amino acid substitutions per site.
Data
Appendix S6. Protein alignment used to construct the gp23 phylogenetic tree (Fig. S1C).
Article
Full-text available
Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrop...
Article
Full-text available
Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction center proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gen...
Article
Full-text available
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional...
Article
The presence of the green and Kemp’s ridley turtles is rare at Atlantic and Mediterranean Spanish waters, but the records have increased during the last decades.We reported a new set of records and reviewed all the historical observations of these species. The analysis of a mitochondrial DNA fragment of the newest records provided insights about th...
Article
To assess how initial size dispersion affects Sene- galese sole (Solea senegalensis, Kaup) growth, 128 fish were stocked either under homogeneous (HOM) or heterogeneous (HET) initial size disper- sion (standard length, CV 11.8% and 29.7% respectively), and also under low (LD) and high (HD) stocking density (60% and 180% of bottom occupation). After...
Article
Full-text available
Comparisons of the levels of genetic variation within and between a hatchery F-1 (FAR, n=116) of Senegalese sole, Solea senegalensis, and its wild donor population (ATL, n=26), both native to the SW Atlantic coast of the Iberian peninsula, as well as between the wild donor population and a wild western Mediterranean sample (MED, n=18), were carried...
Article
Growth is usually inversely correlated with stocking density of fish in culture. Senegalese sole aquaculture is affected by a high size variability and thus, this work tried to investigate the relationship of growth with density of two populations of 96 individually tagged Senegalese sole (318.7 ± 7.9 g; mean ± standard error of the mean). Fish wer...
Article
Full-text available
Morphological changes in Senegalese sole adults (Solea senegalensis Kaup, 1858) reared at two stocking density conditions (low stocking density, 60% of bottom occupation and high stocking density, 180% of bottom occupation) were investigated using geometric morphometrics. Canonical variate analysis on weight matrix scores, including the uniform com...

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