Institution
Stazione Zoologica Anton Dohrn
Facility•Naples, Campania, Italy•
About: Stazione Zoologica Anton Dohrn is a facility organization based out in Naples, Campania, Italy. It is known for research contribution in the topics: Mediterranean sea & Population. The organization has 882 authors who have published 2427 publications receiving 78201 citations. The organization is also known as: Naples Zoological Station & Stazione Zoologica Anton Dohrn.
Topics: Mediterranean sea, Population, Gene, Ciona intestinalis, Benthic zone
Papers published on a yearly basis
Papers
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TL;DR: This work identifies ocean microbial core functionality and reveals that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
Abstract: 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.
1,934 citations
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United States Department of Energy1, Kyoto University2, Marine Biological Laboratory3, University of Queensland4, Stanford University5, University of California, Berkeley6, McGill University7, National Institute of Genetics8, Aix-Marseille University9, Dalhousie University10, University of Tokyo11, Tokyo Metropolitan University12, Tohoku University13, University of South Florida14, Hokkaido University15, Stazione Zoologica Anton Dohrn16, IBM17, University of Maryland, College Park18, University of California, San Francisco19, University of Edinburgh20, Oak Ridge National Laboratory21, Los Alamos National Laboratory22
TL;DR: A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development.
Abstract: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
1,582 citations
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École Normale Supérieure1, J. Craig Venter Institute2, Joint Genome Institute3, Alfred Wegener Institute for Polar and Marine Research4, University of Konstanz5, University of Wisconsin–Milwaukee6, University of Melbourne7, University of Washington8, University of Nantes9, University of Wisconsin-Madison10, Ghent University11, University of Rhode Island12, Sewanee: The University of the South13, University of Arizona14, Hebrew University of Jerusalem15, Georgia Institute of Technology16, Leibniz Institute for Neurobiology17, Stazione Zoologica Anton Dohrn18, University of British Columbia19, Stanford University20, Scottish Association for Marine Science21, University of North Carolina at Wilmington22
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
1,500 citations
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Pierre-and-Marie-Curie University1, Centre national de la recherche scientifique2, Kaiserslautern University of Technology3, Spanish National Research Council4, École Normale Supérieure5, Commissariat à l'énergie atomique et aux énergies alternatives6, Katholieke Universiteit Leuven7, Vrije Universiteit Brussel8, Academy of Sciences of the Czech Republic9, Sewanee: The University of the South10, University of Évry Val d'Essonne11, Canadian Institute for Advanced Research12, University of Bremen13, Stazione Zoologica Anton Dohrn14, IFREMER15, European Bioinformatics Institute16, Kyoto University17, Max Delbrück Center for Molecular Medicine18, University of Paris19, Aix-Marseille University20, Bigelow Laboratory For Ocean Sciences21, National Science Foundation22, University of Western Brittany23
TL;DR: Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.
1,378 citations
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TL;DR: The species populating the vent sites comprise a suite of organisms that are resilient to naturally high concentrations of pCO2 and indicate that ocean acidification may benefit highly invasive non-native algal species.
Abstract: A high-profile Royal Society report in 2005, followed by similar reports worldwide, high-lighted the fact that relatively little is known about the ecosystem effects of ocean acidification. Work to date has been largely limited to short-term experiments on isolated aspects of marine communities. Hall-Spencer et al. adopted an alternative approach, tracking the response to CO2 release from volcanic vent sites off the island of Ischia in the Bay of Naples, where ocean acidification has prevailed perhaps for centuries. Typical rocky shore communities rich in calcareous organisms thrive at normal pH, shifting to communities lacking scleractinian corals and low in sea urchin and algal numbers at low pH. The results show that such sites can act as natural experiments against which to test laboratory and modelled predictions of the effects of ocean acidification. The ecological impact of ocean acidification as a result of climate change is difficult to predict. A natural CO2 venting site is used here to demonstrate the shifts occurring in a rocky shore marine community as a result of a pH gradient. The atmospheric partial pressure of carbon dioxide (
) will almost certainly be double that of pre-industrial levels by 2100 and will be considerably higher than at any time during the past few million years1. The oceans are a principal sink for anthropogenic CO2 where it is estimated to have caused a 30% increase in the concentration of H+ in ocean surface waters since the early 1900s and may lead to a drop in seawater pH of up to 0.5 units by 2100 (refs 2, 3). Our understanding of how increased ocean acidity may affect marine ecosystems is at present very limited as almost all studies have been in vitro, short-term, rapid perturbation experiments on isolated elements of the ecosystem4,5. Here we show the effects of acidification on benthic ecosystems at shallow coastal sites where volcanic CO2 vents lower the pH of the water column. Along gradients of normal pH (8.1–8.2) to lowered pH (mean 7.8–7.9, minimum 7.4–7.5), typical rocky shore communities with abundant calcareous organisms shifted to communities lacking scleractinian corals with significant reductions in sea urchin and coralline algal abundance. To our knowledge, this is the first ecosystem-scale validation of predictions that these important groups of organisms are susceptible to elevated amounts of . Sea-grass production was highest in an area at mean pH 7.6 (1,827 μatm
) where coralline algal biomass was significantly reduced and gastropod shells were dissolving due to periods of carbonate sub-saturation. The species populating the vent sites comprise a suite of organisms that are resilient to naturally high concentrations of and indicate that ocean acidification may benefit highly invasive non-native algal species. Our results provide the first in situ insights into how shallow water marine communities might change when susceptible organisms are removed owing to ocean acidification.
1,291 citations
Authors
Showing all 895 results
Name | H-index | Papers | Citations |
---|---|---|---|
Giorgio Bernardi | 114 | 657 | 48049 |
Robb Krumlauf | 95 | 231 | 29920 |
Chris Bowler | 87 | 288 | 35399 |
Roberto Danovaro | 84 | 415 | 23735 |
Enrico Alleva | 62 | 311 | 11498 |
David J. Scanlan | 58 | 164 | 12388 |
Ferdinando Boero | 54 | 237 | 8474 |
Sergio Papa | 54 | 309 | 10571 |
Diana Boraschi | 54 | 263 | 10231 |
Angelo Fontana | 52 | 373 | 13216 |
Lisandro Benedetti-Cecchi | 51 | 165 | 8111 |
Adrianna Ianora | 49 | 169 | 7847 |
Marco Taviani | 49 | 234 | 7489 |
Gian Luigi Russo | 47 | 151 | 12947 |
Simonetta Fraschetti | 46 | 139 | 6965 |