Silvia G Acinas

Silvia G Acinas
Spanish National Research Council | CSIC · Department of Marine Biology and Oceanography

PhD Biology

About

205
Publications
71,323
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
13,421
Citations
Additional affiliations
February 2007 - present
Institute of Marine Science, ICM-CSIC
Position
  • Researcher

Publications

Publications (205)
Preprint
Full-text available
Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phy...
Article
Full-text available
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis rev...
Article
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...
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
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing an...
Article
Full-text available
Mercury (Hg) 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 s...
Article
Full-text available
Measuring plankton and associated variables as part of ocean time-series stations has the potential to revolutionize our understanding of ocean biology and ecology and their ties to ocean biogeochemistry. It will open temporal scales (e.g., resolving diel cycles) not typically sampled as a function of depth. In this review we motivate the addition...
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
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their eco...
Article
Viruses are suspected to be lynchpins in ecosystem function, but so far we can only guess at their significance. DNA viruses are increasingly being recognized as significant components of biogeochemical cycling in the oceans. Dominguez-Huerta et al. explored global patterns of marine RNA virus occurrence by extracting virus sequences from Tara Ocea...
Article
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their eco...
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
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical s...
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...
Poster
Full-text available
Microbes carrying the hgcAB gene pair are primarily responsible for methylmercury (MeHg) production, transforming inorganic mercury (HgII) into MeHg. Recent work based on the detection of hgcAB genes in publicly available genomic data and metagenome-assembled genomes expanded our understanding of the phylogenetic diversity of potential Hg-methylato...
Article
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacte...
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...
Article
Full-text available
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale sp...
Article
Full-text available
Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencin...
Preprint
Full-text available
Although microbial interactions underpin ocean ecosystem functions, they remain barely known. Different studies have analyzed microbial interactions using static association networks based on omics-data. However, microbial associations are dynamic and can change across physicochemical gradients and spatial scales, which needs to be considered to un...
Article
Full-text available
Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll max...
Preprint
Full-text available
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Phytoplankton communities are generally studied by PCR amplification of bacterial (16S), nuc...
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...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.
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
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale sp...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
[ Now published in Nature Communications: https://doi.org/10.1038/s41467-021-24299-y ] Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of mo...
Preprint
Full-text available
Estimates of marine plastic stocks, a major threat to marine life (1), are far lower than expected from exponentially-increasing litter inputs, suggesting important loss factors (2, 3). These may involve microbial degradation, as the plastic-degrading polyethylene terephthalate enzyme (PETase) has been reported in marine microbial communities (4)....
Article
Full-text available
Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of ocean and host‐associated microbes. Global expeditions conducted over the past 15 years have sampled to ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red S...
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....
Article
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 is...
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...
Article
Full-text available
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recog...
Article
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 gl...
Preprint
Full-text available
Oceans connect all life and affect climate worldwide, and interestingly, the ocean’s smallest residents have a huge role in this process. The ocean microbiota modulates global biogeochemical cycles, which influences energy balance in the atmosphere. Unfortunately, the underlying factors structuring the ocean microbiota are unclear, and better under...
Article
Full-text available
Background: The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tro...
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 stand...
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...
Preprint
Full-text available
Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms ( selection , dispersal and ecological drift ) shape the smallest members of the tro...
Article
Full-text available
Global ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that...
Article
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 f...
Article
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity...
Preprint
Full-text available
Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlaying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropi...
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
Nowadays, there is a significant gap in the knowledge of the diversity and patterns for marine heterotrophic culturable microorganisms. In addition, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have isolated 1561 bacterial strains covering both photic (817) and aphotic layers (744...
Article
Full-text available
The role of macroalgae in Blue Carbon assessments has been controversial, partially due to uncertainties about the fate of exported macroalgae. Available evidence suggests that macroalgae are exported to reach the open ocean and the deep sea. Nevertheless, this evidence lacks systematic assessment. Here, we provide robust evidence of macroalgal exp...
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
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset of 195,728 vi...
Article
Full-text available
Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron av...
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...