Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project)

Website: https://www.bco-dmo.org/dataset/564378
Version: 2015-08-05

Project
» Interactions of bacteria, viruses and bloom-forming diatom genus Pseudo-nitzschia (bacteria, virus, diatom interactions)
ContributorsAffiliationRole
Jiang, SunnyUniversity of California-Irvine (UC Irvine)Principal Investigator
Kinkade, DanieWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Acquisition Description

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.


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Parameters

ParameterDescriptionUnits
project_typedimensionless
attributesdimensionless
NCBI_bioproject_iddimensionless


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Instruments

Dataset-specific Instrument Name
Plankton Net
Generic Instrument Name
Plankton Net
Dataset-specific Description
20um mesh size plankton net was used for sampling.
Generic 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.

Dataset-specific Instrument Name
Seqman II
Generic Instrument Name
Automated DNA Sequencer
Dataset-specific Description
A Seqman II (version 9.0 DNASTAR Inc, Madison, WI, USA) was used for sequencing of bacterial 16s rDNA.
Generic Instrument Description
General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Dataset-specific Instrument Name
Genome Sequencer FLX System
Generic Instrument Name
Automated DNA Sequencer
Dataset-specific Description
Genome Sequencer FLX System was used for pyroseqencing of pseudo-nitzschia microbiome.
Generic Instrument Description
General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Dataset-specific Instrument Name
Light Microscope
Generic Instrument Name
Microscope - Optical
Generic 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".

Dataset-specific Instrument Name
GeneAmp 2700 PCR system
Generic Instrument Name
PCR Thermal Cycler
Dataset-specific Description
GeneAmp 2700 PCR system (Applied Biosystems, Foster City, CA) was used for PCR amplification.
Generic Instrument Description
General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)


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Deployments

SantaCruz_Plankton_Jiang

Website
Platform
Santa Cruz Warf
Start Date
2011-06-15
End Date
2011-06-15
Description
Sampling location for the project 'Diatom Microbiome' (PI: Sunny Jiang). A 20um mesh plankton net was used to collect sample.


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Project Information

Interactions of bacteria, viruses and bloom-forming diatom genus Pseudo-nitzschia (bacteria, virus, diatom interactions)

Coverage: Santa Cruz Warf 36.96023 N, -122.01996 W


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.

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.

Related Publications:

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. ISME Journal 8, 63-76 doi:10.1038/ismej.2013.138

Rowe, J.; Jiang, S. Interactions of bacterial microbiome with bloom forming marine diatom pseudo-nitzchia. Ocean Science Meeting. Honolulu, Hawaii. 2014. (http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17958)

Sison-Mangus, M.; Jiang, S.; Tran, K.; Kudela, R. Factors that influence the association between marine diatom pseudo-nitzschia and their bacterial associates. Ocean Science Meeting. Honolulu, Hawaii. 2014. (http://www.sgmeet.com/osm2014/viewabstract.asp?AbstractID=17910)

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 (http://www.sgmeet.com/osm2012/viewabstract2.asp?AbstractID=12577)

Sison-Mangus, M. P., 
Tran, K., 
Jiang, S. Growth stimulation and killing of pseudo-nitzschia by non-native epibiotic bacteria. American Society for Liminology and Oceanography, Aquatic Science Meeting, San Juan, Pureto Rico, Feb. 13-18, 2011  (https://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=8790)

Tran, K., M., Sison-Mangus, S. C. Jiang. Bacterial diversity associated with toxic and non-toxic pseudo-nitzschia species. American Society for Liminology and Oceanography, Aquatic Science Meeting, San Juan, Pureto Rico, Feb. 13-18, 2011 (http://www.sgmeet.com/aslo/sanjuan2011/viewabstract2.asp?AbstractID=9063)



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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