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An analysis of the Sargasso Sea resource and the consequences for database composition
2006
BMC Bioinformatics
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The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. ...
The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins. ...
Acknowledgements The authors wish to thank David Juan, Florencio Pazos, Luis Sanchez-Pulido and the referees for their useful critical input. ...
doi:10.1186/1471-2105-7-213
pmid:16623953
pmcid:PMC1513258
fatcat:pbaimezxkfalrmegtidegm3hba
The Marine Viromes of Four Oceanic Regions
2006
PLoS Biology
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Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. ...
A single sample was collected from the Sargasso Sea (labeled SAR) on 30 June 2005. ...
Acknowledgments The GOM, BBC, and Arctic samples were collected with the generous help of the crew and scientists aboard the research vessels Longhorn, Mirai, Raddisson, Walton Smith, and Vector. ...
doi:10.1371/journal.pbio.0040368
pmid:17090214
pmcid:PMC1634881
fatcat:yokkhah6afhvblh23jhzxakcdq
Estimating the extent of horizontal gene transfer in metagenomic sequences
2008
BMC Genomics
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The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time. ...
Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso ...
Financial support was provided by projects BFU2006-06003 from the Spanish Ministry of Education and Science (MEC) and GV/2007/050 from the Generalitat Valenciana, Spain. ...
doi:10.1186/1471-2164-9-136
pmid:18366724
pmcid:PMC2324111
fatcat:viq7b3malngllkvidzjhdikag4
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences
2011
BMC Genomics
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Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. ...
Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. ...
Acknowledgements We thank Stephan Schuster and Daniel Huson for allowing us to use MEGAN and MetaSim software for this work. We thank Sudha Chadaram for her help in preparing a web-server for INDUS. ...
doi:10.1186/1471-2164-12-s3-s4
pmid:22369237
pmcid:PMC3333187
fatcat:gg6tb3rxy5fppol6x3jlqcpqvm
Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre
2009
Applied and Environmental Microbiology
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These adaptations appear to include higher metabolic versatility and genomic plasticity to cope with the sparse and sporadic energy resources available, a preference for hydrophobic and smaller-volume ...
The deep sea (water depth of >2,000 m) represents the largest biome on Earth. ...
E.F.D., and sequencing support from the Department of Energy Genomics GTL Program. ...
doi:10.1128/aem.00473-09
pmid:19542347
pmcid:PMC2725473
fatcat:ifa77mqw3zgd5gh3nwvmzh43om
Sargassum Watch Warns of Incoming Seaweed
2016
EOS
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The Sargassum Watch System processes satellite data and feeds results to a Web portal, giving decision makers timely information on seaweed location and warnings for potential beaching events. ...
The Sargasso Sea Alliance thanks the National Oceanography Centre, UK for providing library facilities and overall support for this work. ...
However, the provision of the data does not, in and of itself, indicate U.S. government (or any department or agency thereof) support for any specific proposal contained in this report or that the Sargasso ...
doi:10.1029/2016eo058355
fatcat:agwsy3u6argpdekwgr2uoad6ei
A bibliometric analysis of scientific trends in phytoplankton research
2015
Annales de Limnologie
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We summarize the scientific trends in phytoplankton studies between 1991 and 2013 based on bibliometric analysis. ...
Under the context of fast scientific research development, the yearly numbers of dependent publications (in terms of multi-aquatic ecosystems and international collaborations) indicate a linear increasing ...
We acknowledge the editors and the anonymous reviewers for insightful suggestions on this work! This work was supported by National Natural Science Foundation of China (grant No. 41403071). ...
doi:10.1051/limn/2015019
fatcat:drlqk6a4yrgq5mg7ptzzqki5hu
Going Deeper: Metagenome of a Hadopelagic Microbial Community
2011
PLoS ONE
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A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. ...
In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). ...
Acknowledgments We would like to thank the BIOS scientific crew and R/V Atlantic Explorer crew for allowing us to join their BV42 cruise and Christine Shulse for help in sample collection. ...
doi:10.1371/journal.pone.0020388
pmid:21629664
pmcid:PMC3101246
fatcat:xitlttmxibhj3op7dr5ipxfn3a
A century of research on the larval distributions of the Atlantic eels: a re-examination of the data
2014
Biological Reviews
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adult eels spawn and how they find their spawning areas.
2) Analysis of the new database shows there is an east-west divergence of the two overlapping spawning areas and that there are differences in ...
ANALYSIS OF THE DATABASE
The new database provides the first chance to analyse comprehensively the catches of anguillid larvae from the last 100 years. ...
doi:10.1111/brv.12144
pmid:25291986
fatcat:nuaeogvl45cl5ghufz4b2xgquy
Challenges for genetic research in European eel management
2007
ICES Journal of Marine Science
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from pre-decline historical collections for critical long-term monitoring and modelling of its genetic composition; (ii) the analysis of adaptive genetic polymorphism (genes under selection) to detect ...
The catadromous European eel (Anguilla anguilla) is no exception. Its spawning habitat in the Sargasso Sea and long migration across the North Atlantic qualify it as marine. ...
Acknowledgements We thank the following for the lively and inspiring discus- ...
doi:10.1093/icesjms/fsm108
fatcat:vim2q3zozbcgdh5xpbsi6bibxy
Pteropods are excellent recorders of surface temperature and carbonate ion concentration
2017
Scientific Reports
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Pteropods are excellent recorders of surface temperature and carbonate ion concentration Keul, N.; Peijnenburg, K.T.C.A.; Andersen, N.; Kitidis, V.; Goetze, E.; Schneider, R.R. ...
Thomas and scientists from the AMT programme, as well as the crew of the RRS James Cook, for supporting zooplankton and oceanographic data collections on AMT22. ...
behalf of the German federal and state governments. ...
doi:10.1038/s41598-017-11708-w
pmid:28974691
pmcid:PMC5626693
fatcat:rne7pi7cknc7hprd4jyvcaybti
Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre
2020
Scientific Reports
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consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light. ...
In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the ...
The study presented herein is part of the internship of Luca Russo, under the supervision of Domenico D' Alelio, at Stazione Zoologica Anton Dohrn (Naples, Italy), and of the Master Thesis of Luigi Maria ...
doi:10.1038/s41598-020-59989-y
pmid:32098970
fatcat:tz7dfrnoprch3od4bl6pv5qgmi
Contribution of zooplankton fecal pellets to deep ocean particle flux in the Sargasso Sea assessed using quantitative image analysis
2012
Journal of Plankton Research
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pellet mass and the carbon flux of 0.5-1.7 mg m 22 day 21 and 0.07-0.25 mg C m 22 day 21 , respectively. ...
During the study, three mesoscale eddies passed through: a cyclonic eddy in bloom stage (February through mid-April), a decaying post-bloom mode-water eddy (late April through May), and an anticyclonic ...
We thank Tommy Dickey for access to unpublished data and the many BATS technicians and principal investigators for their contribution to the BATS data resources. ...
doi:10.1093/plankt/fbs053
fatcat:4a5ozj7jy5dydoeyhymfi3siyu
DMS dynamics in the most oligotrophic subtropical zones of the global ocean
2011
Biogeochemistry
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As metrics for the dynamics of DMS and the so-called 'summer DMS paradox' of elevated summer concentrations when surface chlorophyll a (Chl) and particulate organic carbon (POC) levels are lowest, we used ...
Our 'model based' experiments suggest that it is the limitation of phytoplankton/bacterial production and bacterial consumption of DMS by pervasive phosphorus limitation that is responsible for the 'summer ...
Johnson (JISAO, University of Washington) and T.S. Bates (PMEL, NOAA) for the maintenance and personal involvement in the Global Surface Seawater DMS Database. ...
doi:10.1007/s10533-011-9648-1
fatcat:j3nhnpolpzcdfgznnpiwx3arey
Is the Atlantic surface temperature a good proxy for forecasting the recruitment of European eel in the Guadalquivir estuary?
2015
Progress in Oceanography
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from an unofficial database on commercial catches provided by one of the main local marketer-buyers) were standardised to obtain a single time series on a monthly scale. ...
This study analysed the possibility of using the sea surface temperature (SST) of the Atlantic Ocean to predict the recruitment of European eels in one of the most important estuaries of the south of Europe ...
José Hernando Casal for providing data on the daily purchases of glass eel in the Guadalquivir estuary from November 14 of 1983 to May 27 of 1998 data base. We also thank Dr. Dudley B. ...
doi:10.1016/j.pocean.2014.10.007
fatcat:fi6mcheixvhhbmc5nveqkjuvwe
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