Following the publication of the original article [1], the author reported that there is a discre... more Following the publication of the original article [1], the author reported that there is a discrepancy on the presentation of eq. 3 between the PDF and HTML. The PDF shows the correct presentation. The original article has been updated to correct this.
bioinformatic analyses and comparative genomics 5 Metagenomic 16S rDNA Illumina Tags are a powerf... more bioinformatic analyses and comparative genomics 5 Metagenomic 16S rDNA Illumina Tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities1
Association for the Sciences of Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Mount... more Association for the Sciences of Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Mountains of the Sea, 26 February - 3 March 2017, Honolulu, Hawai`i
Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entit... more Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed an...
15th International Congress of Protistology, International Society of Preotistologists (ISOP), 30... more 15th International Congress of Protistology, International Society of Preotistologists (ISOP), 30 July - 4 August 2017 , Prague, Czech Republic
Background: Ecolocial interctions among microorganisms are fundamental for ecosystem function, ye... more Background: Ecolocial interctions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions by associations across time and space, which can be represented as association networks. Links in these networks could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally-driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not.Results: We present EnDED (Environmentally-Driven Edge Detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally-driven. The four approaches are Sign Pattern, Overlap, Interaction Information, and Data Processing Inequality. We tested EnDED o...
Bacteriophage genomes can be regarded as an ensemble of modules which are accessible to the whole... more Bacteriophage genomes can be regarded as an ensemble of modules which are accessible to the whole phage population via recombination. The time spent by prophages in the bacterial host provides them with the opportunity to exchange modules with other prophages or infecting phages. Here we analyze the modular structure of a set of 457 phages and 760 prophages extracted from completely sequenced bacterial genomes using the ACLAME database and its associated tools. We identified 91 modules of proteins with similar phylogenetic profiles. Of these, 25 and 6 are associated with temperate and virulent phages, respectively; 57 are restricted to a host or small group of hosts; and 55 could be annotated with a phage function. We use the transposable phages as a study case and show how the inclusion of prophages allows us to unveil new types of genome organization (i.e. novel module combinations) and obtain insight into the host range for this particular group, highlighting the utility of prophage prediction to better characterize phage diversity.
The network analysis tools (NeAT) (http://rsat.ulb. ac.be/neat/) provide a user-friendly web acce... more The network analysis tools (NeAT) (http://rsat.ulb. ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobi... more The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac .be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.
Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for ... more Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in B1 h.
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in natu... more Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and...
The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet... more 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 drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically s...
Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombinati... more Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At leas...
Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombinati... more Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tn). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase (TnpR/I/S+T) and transposase (TnpA). We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial p...
The deep sea, the largest compartment of the ocean, is an essential component of the Earth system... more 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 Malaspina Global Expedition, to resolve the metabolic architecture of the deep ocean microbiome. The Malaspina Deep-Sea Gene Collection, 71% of which consists of novel genes, reveals a strong dichotomy between the functional traits of free-living and particle-attached microorganisms, and shows relatively patchy composition challenging the paradigm of a uniform dark ocean ecosystem. Metagenome Assembled Genomes uncovered 11 potential new phyla, establishing references for deep ocean microbial taxa, and revealed mixotrophy to be a widespread trophic strategy in the deep ocean. These results expand our understanding of the functional diversity...
Predicting responses of plankton to variations in essential nutrients is hampered by limited in s... more 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 availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. Plain Language Summary Marine phytoplankton require iron for their growth and proliferation. According to John Martin's iron hypothesis, fertilizing the ocean with iron could dramatically increase photosynthetic activity, thus representing a biological means to counteract global warming. However, while there is a constantly growing knowledge of how iron is distributed in the ocean and about its role in cellular processes in marine photosynthetic groups such as diatoms and cyanobacteria, less is known about how iron availability shapes plankton communities and how they respond to it. In the present work, we exploited recently published Tara Oceans data sets to address these questions. We first defined specific subcommunities of co-occurring organisms that co-vary with iron availability in the oceans. We then identified specific patterns of adaptation and acclimation to iron in different groups of phytoplankton. Finally, we validated our global results at local scale, specifically in the Marquesas archipelago, where recurrent phytoplankton blooms are believed to be a result of iron fertilization. By 10.1029/2018GB006022 Global Biogeochemical Cycles PISCES (Aumont et al., 2015) is a more complex global ocean biogeochemical model than ECCO2-DARWIN, representing two phytoplankton groups, two zooplankton grazers, two particulate size classes, dissolved inorganic carbon, dissolved organic carbon, oxygen, and alkalinity, as well as nitrate, phosphate, silicic acid, ammonium, and iron as limiting nutrients. In brief, PISCES accounts for iron inputs from
Following the publication of the original article [1], the author reported that there is a discre... more Following the publication of the original article [1], the author reported that there is a discrepancy on the presentation of eq. 3 between the PDF and HTML. The PDF shows the correct presentation. The original article has been updated to correct this.
bioinformatic analyses and comparative genomics 5 Metagenomic 16S rDNA Illumina Tags are a powerf... more bioinformatic analyses and comparative genomics 5 Metagenomic 16S rDNA Illumina Tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities1
Association for the Sciences of Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Mount... more Association for the Sciences of Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Mountains of the Sea, 26 February - 3 March 2017, Honolulu, Hawai`i
Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entit... more Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed an...
15th International Congress of Protistology, International Society of Preotistologists (ISOP), 30... more 15th International Congress of Protistology, International Society of Preotistologists (ISOP), 30 July - 4 August 2017 , Prague, Czech Republic
Background: Ecolocial interctions among microorganisms are fundamental for ecosystem function, ye... more Background: Ecolocial interctions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions by associations across time and space, which can be represented as association networks. Links in these networks could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally-driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not.Results: We present EnDED (Environmentally-Driven Edge Detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally-driven. The four approaches are Sign Pattern, Overlap, Interaction Information, and Data Processing Inequality. We tested EnDED o...
Bacteriophage genomes can be regarded as an ensemble of modules which are accessible to the whole... more Bacteriophage genomes can be regarded as an ensemble of modules which are accessible to the whole phage population via recombination. The time spent by prophages in the bacterial host provides them with the opportunity to exchange modules with other prophages or infecting phages. Here we analyze the modular structure of a set of 457 phages and 760 prophages extracted from completely sequenced bacterial genomes using the ACLAME database and its associated tools. We identified 91 modules of proteins with similar phylogenetic profiles. Of these, 25 and 6 are associated with temperate and virulent phages, respectively; 57 are restricted to a host or small group of hosts; and 55 could be annotated with a phage function. We use the transposable phages as a study case and show how the inclusion of prophages allows us to unveil new types of genome organization (i.e. novel module combinations) and obtain insight into the host range for this particular group, highlighting the utility of prophage prediction to better characterize phage diversity.
The network analysis tools (NeAT) (http://rsat.ulb. ac.be/neat/) provide a user-friendly web acce... more The network analysis tools (NeAT) (http://rsat.ulb. ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobi... more The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac .be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.
Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for ... more Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in B1 h.
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in natu... more Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and...
The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet... more 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 drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically s...
Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombinati... more Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At leas...
Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombinati... more Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tn). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase (TnpR/I/S+T) and transposase (TnpA). We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial p...
The deep sea, the largest compartment of the ocean, is an essential component of the Earth system... more 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 Malaspina Global Expedition, to resolve the metabolic architecture of the deep ocean microbiome. The Malaspina Deep-Sea Gene Collection, 71% of which consists of novel genes, reveals a strong dichotomy between the functional traits of free-living and particle-attached microorganisms, and shows relatively patchy composition challenging the paradigm of a uniform dark ocean ecosystem. Metagenome Assembled Genomes uncovered 11 potential new phyla, establishing references for deep ocean microbial taxa, and revealed mixotrophy to be a widespread trophic strategy in the deep ocean. These results expand our understanding of the functional diversity...
Predicting responses of plankton to variations in essential nutrients is hampered by limited in s... more 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 availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. Plain Language Summary Marine phytoplankton require iron for their growth and proliferation. According to John Martin's iron hypothesis, fertilizing the ocean with iron could dramatically increase photosynthetic activity, thus representing a biological means to counteract global warming. However, while there is a constantly growing knowledge of how iron is distributed in the ocean and about its role in cellular processes in marine photosynthetic groups such as diatoms and cyanobacteria, less is known about how iron availability shapes plankton communities and how they respond to it. In the present work, we exploited recently published Tara Oceans data sets to address these questions. We first defined specific subcommunities of co-occurring organisms that co-vary with iron availability in the oceans. We then identified specific patterns of adaptation and acclimation to iron in different groups of phytoplankton. Finally, we validated our global results at local scale, specifically in the Marquesas archipelago, where recurrent phytoplankton blooms are believed to be a result of iron fertilization. By 10.1029/2018GB006022 Global Biogeochemical Cycles PISCES (Aumont et al., 2015) is a more complex global ocean biogeochemical model than ECCO2-DARWIN, representing two phytoplankton groups, two zooplankton grazers, two particulate size classes, dissolved inorganic carbon, dissolved organic carbon, oxygen, and alkalinity, as well as nitrate, phosphate, silicic acid, ammonium, and iron as limiting nutrients. In brief, PISCES accounts for iron inputs from
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