http://lod.bco-dmo.org/id/dataset/564378
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
2015-08-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project)
2015-08-05
publication
2015-08-05
revision
BCO-DMO Linked Data URI
2015-08-05
creation
http://lod.bco-dmo.org/id/dataset/564378
Sunny Jiang
University of California-Irvine
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: Jiang, S. (2015) Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-08-05) Version Date 2015-08-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/564378 [access date]
Identification of microbiome from different Pseudo-nitzschia species Dataset Description: Methods and Sampling: <p>Bacterial total genome DNA was extracted from the single species Pseudo-nitzschia culture. 16S rDNA pyrosequencing were carried out using the bTEFAP method based on the Titanium reagents and protocol for Genome Sequencer FLX System.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1131770 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1131770
completed
Sunny Jiang
University of California-Irvine
9498244768
5171 California Avenue, Ste 150
IRVINE
CA
926977600
sjiang@uci.edu
pointOfContact
asNeeded
Dataset Version: 2015-08-05
Unknown
project_type
attributes
NCBI_bioproject_id
Seqman II
Genome Sequencer FLX System
Light Microscope
Plankton Net
GeneAmp 2700 PCR system
theme
None, User defined
project
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Microscope - Optical
Plankton Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
SantaCruz_Plankton_Jiang
service
Deployment Activity
36.96023 N -122.01996W
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.
Interactions of bacteria, viruses and bloom-forming diatom genus Pseudo-nitzschia
https://osprey.bco-dmo.org/project/546769
Interactions of bacteria, viruses and bloom-forming diatom genus Pseudo-nitzschia
<p>This project seeks to elucidate the interactions between viruses, bacteria and toxic bloom-forming marine diatom genus Pseudo-nitzschia in the coastal marine environment. The cosmopolitan Pseudo-nitzschia sp. (Bacillariophyceae) causes harmful algal blooms in various parts of the world. Recent genome sequences of two marine diatoms revealed that bacterial genes contribute up to 5% of their genome make-up, highlighting the close association of marine diatoms with bacteria in evolutionary history. So far, few have looked at the interactions of diatoms with their epibiotic bacteria and none have studied the interactions of virus, bacteria and phytoplankton using direct experimental approach.</p>
<p>This project investigates the physiological, biochemical, genetic and ecological interactions of algae-microbe associations in order to decipher the influences of microbes on algal bloom dynamics and toxigenesis. By incorporating methods in phylogeny, physiology, biochemistry, comparative genomics and metagenomics, the research seeks answers to the following questions: 1) What are the epiphytic bacteria associating with different species of Pseudo-nitzschia and how do they change at different stages of the bloom? 2) How do these bacteria affect the physiology of the Pseudo- nitzschia hosts and how does the algal host regulate these microbial interactions? 3) Can viruses promote a bloom by selectively lysing algicidal bacteria, while creating opportunities for growth- promoting bacteria or vice versa? This project is guided by the preliminary research on microbe- algae interaction, where significantly different epibiotic bacterial communities were found to associate with two Pseudo-nitzschia species. Bacterial associates of one Pseudo-nitzschia sp. stimulated the growth of the algal-host but acted as a pathogen on another Pseudo-nitzschia sp. This project will expand the work on epibiotic bacterial community diversity and dynamics by sampling additional species of Pseudo-nitzschia and investigating the changes in epibiotic and planktonic bacterial community structure following the initiation, peak and decline phases of Pseudo-nitzschia blooms in coastal oceans. Algal host responses to epibionts association will be investigated using physiological experiments of binary and multi-culture experimental approaches. The chemical communication between algal host and epibiont bacteria will be addressed by looking at the algal exudate excretions and bacterial enzyme secretions using established LC-MS and enzyme assays. To illustrate the influences of viruses on bacterial-algal interaction, bacteriophages specific to epibiotic bacteria will be isolated and included in the physiological experiments.</p>
<p>Related Publications:</p>
<p>Sison-Mangus, M., Jiang, S., Tran, K. N., Kudela, R. M. Host-specific adaptation governs the interaction of the marine diatom, Pseudo-nitzschia and their microbiota. <em>ISME Journal</em> 8, 63-76 <a href="http://www.nature.com/ismej/journal/v8/n1/full/ismej2013138a.html">doi:10.1038/ismej.2013.138</a></p>
<p>Rowe, J.; Jiang, S. Interactions of bacterial microbiome with bloom forming marine diatom <em>pseudo-nitzchia</em>. Ocean Science Meeting. Honolulu, Hawaii. 2014. (<a href="http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17958">http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17958</a>)</p>
<p>Sison-Mangus, M.; Jiang, S.; Tran, K.; Kudela, R. Factors that influence the association between marine diatom <em>pseudo-nitzschia </em>and their bacterial associates. Ocean Science Meeting. Honolulu, Hawaii. 2014. (<a href="http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17910">http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17910</a>)</p>
<p>Sison-Mangus, M., S. C. Jiang. The microbiota of marine diatoms: is it influenced by algal host phylogeny? American Society for Liminology and Oceanography, Ocean Science Meeting, Salt Lake City, Utah, Feb. 20-24, 2012 (<a href="http://www.sgmeet.com/osm2012/viewabstract2.asp?AbstractID=12577">http://www.sgmeet.com/osm2012/viewabstract2.asp?AbstractID=12577</a>)</p>
<p><u>Sison-Mangus</u>, <u>M</u>. <u>P</u>.,
Tran, K.,
Jiang, S. Growth stimulation and killing of <em>pseudo-nitzschia </em>by non-native epibiotic bacteria. American Society for Liminology and Oceanography, Aquatic Science Meeting, San Juan, Pureto Rico, Feb. 13-18, 2011 (<a href="https://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=8790">https://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=8790</a>)</p>
<p>Tran, K., M., Sison-Mangus, S. C. Jiang. Bacterial diversity associated with toxic and non-toxic <em>pseudo-nitzschia</em> species. American Society for Liminology and Oceanography, Aquatic Science Meeting, San Juan, Pureto Rico, Feb. 13-18, 2011 (<a href="http://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=9063">http://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=9063</a>)</p>
bacteria, virus, diatom interactions
largerWorkCitation
project
eng; USA
biota
oceans
36.96023 N -122.01996W
2015-08-05
Santa Cruz Warf 36.96023 N, -122.01996 W
0
BCO-DMO catalogue of parameters from Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions 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/564381.rdf
Name: project_type
Units: dimensionless
Description:
http://lod.bco-dmo.org/id/dataset-parameter/564383.rdf
Name: attributes
Units: dimensionless
Description:
http://lod.bco-dmo.org/id/dataset-parameter/564385.rdf
Name: NCBI_bioproject_id
Units: dimensionless
Description:
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
176
https://datadocs.bco-dmo.org/file/vmmwMNVh4JyZpG/diatom_microbiome.csv
diatom_microbiome.csv
Primary data file for dataset ID 564378
download
https://osprey.bco-dmo.org/dataset/564378/data/download
download
onLine
dataset
<p>Bacterial total genome DNA was extracted from the single species Pseudo-nitzschia culture. 16S rDNA pyrosequencing were carried out using the bTEFAP method based on the Titanium reagents and protocol for Genome Sequencer FLX System.</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
Seqman II
Seqman II
PI Supplied Instrument Name: Seqman II PI Supplied Instrument Description:A Seqman II (version 9.0 DNASTAR Inc, Madison, WI, USA) was used for sequencing of bacterial 16s rDNA. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Genome Sequencer FLX System
Genome Sequencer FLX System
PI Supplied Instrument Name: Genome Sequencer FLX System PI Supplied Instrument Description:Genome Sequencer FLX System was used for pyroseqencing of pseudo-nitzschia microbiome. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Light Microscope
Light Microscope
PI Supplied Instrument Name: Light Microscope Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Plankton Net
Plankton Net
PI Supplied Instrument Name: Plankton Net PI Supplied Instrument Description:20um mesh size plankton net was used for sampling. 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/
GeneAmp 2700 PCR system
GeneAmp 2700 PCR system
PI Supplied Instrument Name: GeneAmp 2700 PCR system PI Supplied Instrument Description:GeneAmp 2700 PCR system (Applied Biosystems, Foster City, CA) was used for PCR amplification. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: SantaCruz_Plankton_Jiang
SantaCruz_Plankton_Jiang
Santa Cruz Warf
Santa Cruz Warf
dock
SantaCruz_Plankton_Jiang
Sunny Jiang
University of California-Irvine
Santa Cruz Warf
Santa Cruz Warf
dock