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Víctor M. Eguíluz - One of the best experts on this subject based on the ideXlab platform.
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scaling of species distribution explains the vast potential marine prokaryote diversity
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernandezgracia, Carlos M. DuarteAbstract:: 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 the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.
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Scaling of species distribution explains the vast potential marine prokaryote diversity.
Scientific reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernández-gracia, Carlos M. DuarteAbstract: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
Carlos M. Duarte - One of the best experts on this subject based on the ideXlab platform.
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scaling of species distribution explains the vast potential marine prokaryote diversity
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernandezgracia, Carlos M. DuarteAbstract:: 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 the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.
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Scaling of species distribution explains the vast potential marine prokaryote diversity.
Scientific reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernández-gracia, Carlos M. DuarteAbstract: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
Josep M. Gasol - One of the best experts on this subject based on the ideXlab platform.
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scaling of species distribution explains the vast potential marine prokaryote diversity
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernandezgracia, Carlos M. DuarteAbstract:: 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 the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.
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Scaling of species distribution explains the vast potential marine prokaryote diversity.
Scientific reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernández-gracia, Carlos M. DuarteAbstract: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
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use of phytoplankton derived dissolved organic carbon by different types of bacterioplankton
Environmental Microbiology, 2012Co-Authors: Hugo Sarmento, Josep M. GasolAbstract:Summary Phytoplankton and heterotrophic Prokaryotes are major components of the microbial food web and interact continuously: heterotrophic Prokaryotes utilize the dissolved organic carbon derived from phytoplankton exudation or cell lysis (DOCp), and mineralization by heterotrophic Prokaryotes provides inorganic nutrients for phytoplankton. For this reason, these communities are expected to be closely linked, although the study of the interactions between them is still a major challenge. Recent studies have presented interactions between phytoplankton and heterotrophic Prokaryotes based on coexistence or covariation throughout a time-series. However, a real quantification of the carbon flow within these networks (defined as the interaction strength, IS) has not been achieved yet. This is critical to understand the selectivity degree of bacteria responding to specific algal DOCp. Here we used microautoradiography to quantify the preferences of the major heterotrophic prokaryote phylogenetic groups on DOC derived from several representative phytoplankton species, and expressed these preferences as an IS value. The distribution of the ISs was not random but rather skewed towards weak interactions, in a similar way as the distributions described for stable complex nonmicrobial ecosystems, indicating that there are some cases of high specificity on the use of specific algal DOCp by some bacterial groups, but weak interactions are more common and may be relevant as well. The variety of IS patterns observed supports the view that the vast range of different resources (different types of organic molecules) available in the sea selects and maintains the high levels of diversity described for marine bacterioplankton.
Guillem Salazar - One of the best experts on this subject based on the ideXlab platform.
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scaling of species distribution explains the vast potential marine prokaryote diversity
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernandezgracia, Carlos M. DuarteAbstract:: 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 the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.
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Scaling of species distribution explains the vast potential marine prokaryote diversity.
Scientific reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernández-gracia, Carlos M. DuarteAbstract: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
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structure and function of the global ocean microbiome
Science, 2015Co-Authors: Shinichi Sunagawa, Guillem Salazar, Luis Pedro Coelho, Samuel Chaffron, Jens Roat Kultima, Karine Labadie, Bardya Djahanschiri, Georg Zeller, Daniel R Mende, Adriana AlbertiAbstract:Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, Prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
Aharon Oren - One of the best experts on this subject based on the ideXlab platform.
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then and now a systematic review of the systematics of Prokaryotes in the last 80 years
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2014Co-Authors: Aharon Oren, George M GarrityAbstract:In the 80 years that have passed since the first issue of Antonie van Leeuwenhoek was published, the field of prokaryote systematics has changed dramatically. The 4th edition of Bergey’s Manual of Determinative Bacteriology (1934) described 132 genera and 2,703 species. The numbers of genera and species with names with standing in the nomenclature in August 2013 were 2,390 and 11,482, respectively, including no more than 75 genera and 250 species that were recognized in 1934. In the years 2006–2012, on average 624 new species were added annually, most of which were described by scientists in Asian countries. We review the past and current species concept for the Prokaryotes and the current requirements for the description of new species, based on a ‘polyphasic’ approach. We discuss the impact of genomics and metagenomics and other new trends toward revitalization of prokaryote systematics, and provide some ideas and speculations on possible future developments in the field.
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taxonomy of the family halobacteriaceae a paradigm for changing concepts in prokaryote systematics
International Journal of Systematic and Evolutionary Microbiology, 2012Co-Authors: Aharon OrenAbstract:The halophilic Archaea of the family Halobacteriaceae (36 genera with 129 species with standing in nomenclature as of November 2011) provide an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods have influenced the way in which the taxonomy of a single group of Prokaryotes is treated. This review gives an overview of the taxonomy of the family Halobacteriaceae, showing the impact that methods of phenotypic characterization, numerical taxonomy, chemotaxonomy and especially polar lipid analysis, 16S rRNA gene sequence comparisons, multilocus type analysis and comparative genomics have had on their classification.
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How to Name New Genera and Species of Prokaryotes
Methods in Microbiology, 2011Co-Authors: Aharon OrenAbstract:Abstract Naming prokaryote taxa is an essential part in any description of new species, genera, families etc. There is no ‘official’, generally agreed, species concept for the Prokaryotes, and there exists no official classification of Bacteria and Archaea. However, the nomenclature of the Prokaryotes is governed by the general considerations, principles, rules and recommendations of the International Code of Nomenclature of Bacteria (‘The Bacteriological Code’), a document approved by the International Committee on Systematic Bacteriology in 1990. A new version of the Code will soon be published, to be named the International Code of Nomenclature of Prokaryotes. After a short introduction explaining the provisions of the Code, this chapter provides a practical guide for the formation of names of new genera and species to comply with the rules of the Code and with the recommended orthography so that the newly formed names may be validly published. Examples are provided of correctly formed names added in recent years, and these examples should enable also those not versed in Latin and Greek to propose correct names to be attached to newly described species. Although stability of names is a major aim of prokaryote nomenclature, renaming existing species is sometimes necessary based on advanced insights into prokaryote systematics. Therefore, information is also given about the rules and current practice relating to renaming species. Special provisions exist for the nomenclature of the cyanobacteria, a group of Prokaryotes traditionally covered by the rules of the International Code of Botanical Nomenclature.
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prokaryote diversity and taxonomy current status and future challenges
Philosophical Transactions of the Royal Society B, 2004Co-Authors: Aharon OrenAbstract:The Prokaryotes are by far the most abundant organisms inhabiting planet Earth. They are also by far the most diverse, both metabolically and phylogenetically; they encompass the Bacteria and the Archaea, two out of the three major divisions of living organisms. The current prokaryote species classification is based on a combination of genomic and phenotypic properties. The recommended cut-off value of 70% DNA-DNA similarity to delineate species signifies an extremely broad species definition for the Prokaryotes compared with the higher eukaryotes. The number of validly named species of Prokaryotes is currently slightly more than 6200. However, on the basis of small-subunit rDNA characterization of whole communities and other approaches, the more exact number of species present can be inferred to be at least two orders of magnitude larger. Classic culturing methods based on colony formation on agar are generally unsatisfactory for the recovery of bacteria from the environment. Many of the most abundant Prokaryotes in nature have not yet been brought into culture. Some of these may thrive by means of as yet unknown modes of energy generation. Several novel methods have recently enabled the isolation of some interesting organisms of environmental significance. A better coverage of the prokaryote diversity on Earth depends on such innovative approaches, combined with appropriate funding.
