Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project)

Owner: Mike Bobak
Created on Oct 07, 2020

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Physical data associated with samples from NCBI BioProject SRA######, PRJNA297691 (not yet public, 2015-11-18) References: Santoferrara L.F., Grattepanche J-D., Katz L.A., McManus G.B. (submitted) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? Grattepanche J-D., Santoferrara L.F., McManus G.B., Katz L.A. (submitted) Unexpected biodiversity of ciliates in marine samples. https://www.bco-dmo.org/dataset/626679

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Name	Value	Last Modified
@context	@context: @vocab: https://schema.org/ @id: https://www.bco-dmo.org/dataset/626679 @type: Dataset about: @id: http://lod.bco-dmo.org/id/award/54820 @type: MonetaryGrant funder: @id: https://www.bco-dmo.org/node/355 name: OCE-1130033 sameAs: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130033 sponsor: @id: http://lod.bco-dmo.org/id/person/50534 @type: Person name: David L. Garrison url: https://www.bco-dmo.org/person/50534 url: https://www.bco-dmo.org/award/54820 alternateName: SRA_CH0112 metadata creator: @id: https://www.bco-dmo.org/person/51375 @type: Person name: George B. McManus url: https://www.bco-dmo.org/person/51375 @id: https://www.bco-dmo.org/person/51376 @type: Person name: Laura A. Katz url: https://www.bco-dmo.org/person/51376 datePublished: 2015-11-23 description: <p>Physical data associated with samples from NCBI BioProject SRA######, PRJNA297691 (not yet public, 2015-11-18)</p> <p><strong>References:</strong></p> <p>Santoferrara L.F., Grattepanche J-D., Katz L.A., McManus G.B. (submitted) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?</p> <p>Grattepanche J-D., Santoferrara L.F., McManus G.B., Katz L.A. (submitted) Unexpected biodiversity of ciliates in marine samples.</p> distribution: @type: DataDownload contentUrl: https://www.bco-dmo.org/dataset/626679/data/download creativeWorkStatus: In Review datePublished: 2015-11-23 encodingFormat: text/tab-separated-values funder: @id: https://www.bco-dmo.org/node/355 @type: FundingAgency alternateName: NSF OCE identifier: @id: https://doi.org/10.13039/100000141 @type: PropertyValue propertyID: https://registry.identifiers.org/registry/doi url: https://doi.org/10.13039/100000141 value: doi:10.13039/100000141 name: NSF Division of Ocean Sciences identifier: http://lod.bco-dmo.org/id/dataset/626679 isAccessibleForFree: true keywords: biota, oceans license: https://creativecommons.org/licenses/by/4.0/ https://spdx.org/licenses/CC-BY-4.0 measurementTechnique: CTD Sea-Bird 9 name: Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project) producer: @id: https://www.bco-dmo.org/project/2164 @type: ResearchProject alternateName: CiliateSequencing description: The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish. Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a "rare biosphere". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates. This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives: Objective 1. Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales. Objective 2. Assess the contributions of different size classes of ciliates to overall assemblage diversity. Objective 3. Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa. Note: See the related collaborative project, "Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean", funded by awards OCE-1435515 and OCE-1436003. name: Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us? url: https://www.bco-dmo.org/project/2164 provider: @id: https://www.bco-dmo.org publisher: @id: https://www.bco-dmo.org @type: Organization alternateName: BCO-DMO identifier: http://lod.bco-dmo.org/id/affiliation/191 name: Biological and Chemical Data Management Office sameAs: http://www.re3data.org/repository/r3d100000012 url: https://www.bco-dmo.org subjectOf: @type: DataDownload about: https://www.bco-dmo.org/dataset/626679 contentUrl: https://www.bco-dmo.org/dataset/626679/iso creativeWorkStatus: In Review encodesCreativeWork: https://www.bco-dmo.org/dataset/626679 encodingFormat: http://www.isotc211.org/2005/gmd-noaa application/xml name: ISO 19115-2 (NOAA Profile) url: https://www.bco-dmo.org/dataset/626679 variableMeasured: @id: https://www.bco-dmo.org/dataset-parameter/626725 @type: PropertyValue name: cruise identification unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626726 @type: PropertyValue name: The geolocation of the collection: Atlantic Ocean unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626727 @type: PropertyValue name: Source of the sample: seawater unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626728 @type: PropertyValue name: In this case the organism is a sample of marine seawater unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626729 @type: PropertyValue name: sample collection device unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626730 @type: PropertyValue name: depth of water at sampling site unitText: meters @id: https://www.bco-dmo.org/dataset-parameter/626731 @type: PropertyValue name: date sample was collected unitText: dd-Mon-yyyy @id: https://www.bco-dmo.org/dataset-parameter/626732 @type: PropertyValue name: latitude; north is positive unitText: decimal degrees @id: https://www.bco-dmo.org/dataset-parameter/626733 @type: PropertyValue name: longitude; east is positive unitText: decimal degrees @id: https://www.bco-dmo.org/dataset-parameter/626734 @type: PropertyValue name: sample identification unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626735 @type: PropertyValue name: layer of water sampled unitText: unitless @id: https://www.bco-dmo.org/dataset-parameter/626736 @type: PropertyValue name: depth of sample unitText: meters @id: https://www.bco-dmo.org/dataset-parameter/626737 @type: PropertyValue name: temperature unitText: degrees Celsius @id: https://www.bco-dmo.org/dataset-parameter/626738 @type: PropertyValue name: salinity unitText: PSU @id: https://www.bco-dmo.org/dataset-parameter/626739 @type: PropertyValue name: dissolved oxygen unitText: mg L-1 @id: https://www.bco-dmo.org/dataset-parameter/626740 @type: PropertyValue name: chlorophyll fluorescence unitText: arbitrary units version: 2015-11-23	Extracted by http://clowder.ncsa.illinois.edu/extractors/deprecatedapi on Oct 7, 2020

Extracted by http://clowder.ncsa.illinois.edu/extractors/deprecatedapi on Oct 7, 2020

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datePublished: 2015-11-23
description: Physical data associated with samples from NCBI BioProject SRA######, PRJNA297691 (not yet public, 2015-11-18) References: Santoferrara L.F., Grattepanche J-D., Katz L.A., McManus G.B. (submitted) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? Grattepanche J-D., Santoferrara L.F., McManus G.B., Katz L.A. (submitted) Unexpected biodiversity of ciliates in marine samples.
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measurementTechnique:
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version: 2015-11-23

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Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project)

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