http://lod.bco-dmo.org/id/dataset/641102
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water from shoreside Lee-DaSilva Lee-DaSilva_Collection in the USA; Netherlands; Canada; Belgium; various locations each from 2012-2014 (CopepodMicrobiome project)
2016-03-18
publication
2016-03-18
revision
BCO-DMO Linked Data URI
2016-03-18
creation
http://lod.bco-dmo.org/id/dataset/641102
Dr Joana Carneiro da Silva
University of Maryland School of Medicine
principalInvestigator
Carol E. Lee
University of Wisconsin
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Carneiro da Silva, J., Lee, C. E. (2016) Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water from shoreside Lee-DaSilva Lee-DaSilva_Collection in the USA; Netherlands; Canada; Belgium; various locations each from 2012-2014 (CopepodMicrobiome project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version first) Version Date 2016-03-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/641102 [access date]
Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water Dataset Description: <p>Bacteria in the water and bacteria from the same location but directly associated (in the cuticle) with copepods were collected from several locations world-wide with pumps and nets from saline and fresh water.&nbsp; The acquired DNA was sequenced and sent to GenBank.&nbsp; The links are here.</p>
<p>These data will be available after January, 2017.</p> Methods and Sampling: <p>The water samples were collected this way:&nbsp;&nbsp;&nbsp; Approximately 10 liters of water were collected from a depth of 1 meter near the shore and filtered through a 3.0 micron filter to exclude sediment, algae, and other large particles. &nbsp; Then the water was passed through a 0.1 micron filter to collect bacteria. DNA was extracted from the filter with a&nbsp; MoBio PowerWater DNA isolation kit.</p>
<p>The copepods and their associated bacteria were collected this way:&nbsp; 100 pooled adult male and female <em>Eurytemora affinis</em> were collected via plankton tow from depth of ~1-2 meters from near the shore. These animals were isolated from the zooplankton community under a microscope, and homogenized in a glass pestle tissue grinder.&nbsp; DNA was extracted with a MoBio UltraClean Microbial DNA isolation kit.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046372 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046372
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046371 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046371
onGoing
Dr Joana Carneiro da Silva
University of Maryland School of Medicine
4107063559
Institute for Genome Sciences & Dept Microbiology and Immunology University of Maryland School of Medicine
Baltimore
MD
21201
jcsilva@som.umaryland.edu
pointOfContact
Carol E. Lee
University of Wisconsin
Department of Integrative BIology, Birge Hall 430 Lincoln Drive
Madison
WI
53706
USA
carollee@wisc.edu
pointOfContact
asNeeded
Dataset Version: first
Unknown
collection
sample_name
date_start
date_end
site
lat
lon
SRA_accession_number
Plankton net
Water pump
theme
None, User defined
brief description
sample identification
date_start
date end
site
latitude
longitude
accession number
featureType
BCO-DMO Standard Parameters
Plankton Net
Pump
instrument
BCO-DMO Standard Instruments
Lee-DaSilva_Collection
service
Deployment Activity
USA; Netherlands; Canada; Belgium; various locations each
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Dimensions: Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host
https://osprey.bco-dmo.org/project/2159
Dimensions: Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host
<p>Copepods form the largest biomass of metazoans on the planet, yet their microbiota remain largely unexplored. The microbial community associated with copepods might perform key metabolic processes that affect host fitness and ecosystem functioning. The copepod <em>Eurytemora affinis</em> is dominant in coastal habitats throughout the world, and recently has invaded inland freshwater habitats. Associated with <em>E. affinis</em>, preliminary sequencing revealed high diversity of microbial taxa, including many undescribed genera and families. There also were parallel shifts in microbial composition during independent invasions from saline to freshwater habitats. Yet, a core set of microbial taxa remained present in all copepod populations across all locations. The copepod microbiome is likely to play fundamental roles in biogeochemical processes in many aquatic ecosystems. Microbial-host interactions could influence invasive success, and exotic microbes in the invading consortia could have vital impacts on the invaded community. This study will address the following questions: (1) What is the taxonomic composition of the copepod microbiome, and how does it shift during habitat invasions? (Taxonomy, Genetics); (2) What metabolic functions are performed by the copepod microbiome? (Function, Genetics); and (3) What is the nature of copepod host-microbial interactions, and how do these interactions shift during invasions? (Functional Integration)</p>
<p>Research to address these questions includes: (1) high-throughput 16S sequencing, to identify the taxonomic composition of microbial assemblages associated with the copepod host in saline and freshwater environments, (2) shotgun sequencing of metagenomes and fosmids, and also comprehensive genome sequencing of key microbial taxa, to characterize the functional repertoire of genes in the copepod microbiome, and (3) reciprocal inoculation experiments, to explore functional interactions between the copepod host and its microbiome and whether the interactions evolve during invasions into novel habitats.</p>
<p>Characterizing the copepod microbiome will expose a largely undiscovered realm of microbial diversity. Moreover, this gene-centric analysis will provide invaluable insights into metabolic functions of the copepod microbiome, and how these functions might shift during copepod invasions. Results are expected to yield transformative insights into the taxonomic, functional, and genetic diversity of a largely unexplored component of the ecosystem, and how this diversity might become altered following invasions into novel habitats.</p>
<p>This study will provide integrated insights into the taxonomic, genetic, and functional diversity of the copepod microbiome. The assembled sequences will link specific metabolic functions with particular microbial taxa, illuminating functional diversity across deeply divergent lineages. Sequence data also will reveal genetic diversity of metabolic functions within microbial taxa, and the potential sharing of functions across taxa (e.g. via horizontal gene transfer). Moreover, these findings will reveal functional integration of the microbial-host consortia, including between the microbial community and its host.</p>
<p>Preliminary sequencing of the <em>E. affinis</em> microbiome uncovered a wide variety of potentially pathogenic taxa, including Salmonella, Shigella, Campylobacter, <em>Corynebacterium diphtheriae</em>, Yersinia, and <em>Vibrio cholerae</em>. Thus, <em>E. affinis</em> might play an important role as a reservoir and vector of waterborne disease.</p>
CopepodMicrobiome
largerWorkCitation
project
eng; USA
biota
oceans
USA; Netherlands; Canada; Belgium; various locations each
2016-03-18
Atlantic Coast, Gulf of Mexico, Great Lakes, North America, Netherlands
0
BCO-DMO catalogue of parameters from Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water from shoreside Lee-DaSilva Lee-DaSilva_Collection in the USA; Netherlands; Canada; Belgium; various locations each from 2012-2014 (CopepodMicrobiome project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/641125.rdf
Name: collection
Units: text
Description: <p>how the sample was collected; water by a pump; copepods and associated bacteria by a net</p>
http://lod.bco-dmo.org/id/dataset-parameter/641126.rdf
Name: sample_name
Units: coded text
Description: <p>how the sample is identified; the first initials correspond to the location and the W(water) and E(Eurytemora) indicates the method</p>
http://lod.bco-dmo.org/id/dataset-parameter/641127.rdf
Name: date_start
Units: day-three letter month-four digit year
Description: <p>date of start of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/641128.rdf
Name: date_end
Units: day-three letter month-four digit year
Description: <p>date of end of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/641129.rdf
Name: site
Units: text
Description: <p>sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/641130.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude of the collection; N is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/641131.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude of the collection; W is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/641132.rdf
Name: SRA_accession_number
Units: link
Description: <p>Sequence Read Archive. This makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries. The identification number of the sequence submitted to GenBank.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/641102/data/download
download
onLine
dataset
<p>The water samples were collected this way:&nbsp;&nbsp;&nbsp; Approximately 10 liters of water were collected from a depth of 1 meter near the shore and filtered through a 3.0 micron filter to exclude sediment, algae, and other large particles. &nbsp; Then the water was passed through a 0.1 micron filter to collect bacteria. DNA was extracted from the filter with a&nbsp; MoBio PowerWater DNA isolation kit.</p>
<p>The copepods and their associated bacteria were collected this way:&nbsp; 100 pooled adult male and female <em>Eurytemora affinis</em> were collected via plankton tow from depth of ~1-2 meters from near the shore. These animals were isolated from the zooplankton community under a microscope, and homogenized in a glass pestle tissue grinder.&nbsp; DNA was extracted with a MoBio UltraClean Microbial DNA isolation kit.</p>
Specified by the Principal Investigator(s)
<p>There was no way to isolate bacteria from their copepod hosts, so the entire sample was processed and the DNA from the whole thing was extracted.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Plankton net
Plankton net
PI Supplied Instrument Name: Plankton net PI Supplied Instrument Description:Some of the samples were collected by small boat (Blue Hammock Bayou and Lake Pontchartrain) very near the shore. The rest of the net collection was from throwing the plankton net off the dock. Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Water pump
Water pump
PI Supplied Instrument Name: Water pump PI Supplied Instrument Description:Battery powered water pump dropped into the water to depth of 1 m and pumped into 25L Nalgene carboys. Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
Deployment: Lee-DaSilva_Collection
Lee-DaSilva_Collection
shoreside Lee-DaSilva
shoreside
shoreside Lee-DaSilva
shoreside