http://lod.bco-dmo.org/id/dataset/885574
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
2022-12-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)
2022-12-19
publication
2022-12-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-10-04
publication
https://doi.org/10.26008/1912/bco-dmo.885574.1
Sheri Floge
Wake Forest University
principalInvestigator
Jeffrey Guasto
Tufts University
principalInvestigator
Richard J. Henshaw
ETH-Zurich
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: Henshaw, R. J. (2023) Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.885574.1 [access date]
Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates Dataset Description: <p><strong>The data in this data set is organized as follows:</strong></p>
<p>Accumulation Curves: The final processed data for each time point (T1-6), each replicate (A-D) with the average and SEM values tabled.&nbsp;</p>
<p>Filtrates_T#R: Where # is the time point number (1-6) and R the replicate (A-D). Each folder contains:</p>
<p>1) Three Excel sheets corresponding to the raw cell counts for each biological replicate (each with 3 repeats)</p>
<p>2) A supplemental folder containing a cell array with the full bacteria positions for each time point for each replicate (.mat format)</p>
<p>The chemotaxis data was collected by Dr. Richard J. Henshaw of Tufts University (Boston, MA, USA) from 3rd December 2020 to 8th October 2021. Queries about this dataset should be directed to rhenshaw@ethz.ch.</p> Methods and Sampling: <p><strong>Methods &amp; Sampling</strong></p>
<p>Vibrio alginolyticus (YM4; wild-type) from -80℃ stock were grown overnight in Marine 2216 media (Difco) by incubating at 30℃ and shaking at 600 revolutions per minute (RPM). The overnight culture was diluted 100-fold into fresh pre-warmed 2216 media and grown for three hours (30℃, shaking at 600 RPM) to O.D. ≈ 0.2. 2 ml of culture was then washed and resuspended (1,500 RCF for 5 min) in 0.5ml of artificial seawater (ASW).</p>
<p>Artificial seawater (ASW) was prepared following the NCMA ESAW Medium recipe, which was adapted from Harrison et al.and modified by Berges, and filtered through a 0.2um filter immediately prior to use.</p>
<p>A simple three-inlet gradient generation microfluidic device was used to produce the chemical gradients.&nbsp; Microfluidic devices were made using standard soft lithography techniques. Polydimethylsiloxane (Dow Corning SYLGARD 184) channels were cast on photoresist (Microchem) molds fabricated via photolithography and plasma bonded to standard glass slides. Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump(Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. A chemostimulus gradient develops in the channel via diffusion, and the chemotactic response of the cell population was observed over time. Imaging was performed with phasecontrast microscopy (4×, 0.13 NA objective; Nikon Ti-E) at 1 fps over the course of ~10 min using a CMOS camera (Blackfly S, Teledyne FLIR). An example of the gradient generator used can be found in&nbsp;http://dx.doi.org/10.1038/s41567-021-01247-7</p>
<p>This data set summarises the chemotactic response of a model marine bacteria (<em>Vibrio alginolyticus</em>&nbsp;YM4 wild-type) to filtered exudates of the cyanobacteria&nbsp;<em>Synechococcus&nbsp;</em>sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -&gt; T6), with the inital assays split into 4 biological replicates (named A, B, C, D). The two treatments were:</p>
<p>1). A control treatment (named "Control", or shortened to "C")</p>
<p>2). A phage-infected treatment (named "Phage", or shortened to "P"), where host Synechococcus were infected with the T-4 like Myovirus S-SSM5, with data collected over the pre-lysis cycle.</p>
<p>These treatments are fully described in:&nbsp;https://doi.org/10.1038/s43705-022-00169-6. The filtrates were kept frozen at -80C in 1ml aliquots, and only thawed to room temperature immediately prior to experimental use.</p>
<p>For each time point (T1-6), and replicate (A-D), three sets of chemotaxis assays were collected: Phage vs ASW, Control vs ASW, and Phage vs Control. (Each with three biological replicates with fresh cell suspensions, with three physical replicates per sample, totaling nine samples at each time point/sample replicate). The chemotactic preference of&nbsp;<em>Vibrio alginolyticus</em>&nbsp;was measured by analyzing the cell distribution over time, and comparing the cell populations on opposite sides of the channel.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829905 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829905
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829827 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829827
completed
Sheri Floge
Wake Forest University
207-841-0457
1834 Wake Forest Rd. Winston Hall, Rm 226
Winston-Salem
NC
27109
US
floges@wfu.edu
pointOfContact
Jeffrey Guasto
Tufts University
617-627-6838
Department of Mechanical Engineering Robinson Hall, Rm 173, 200 College Avenue
Medford
MA
02155
US
Jeffrey.Guasto@tufts.edu
pointOfContact
Richard J. Henshaw
ETH-Zurich
rhenshaw@ethz.ch
pointOfContact
asNeeded
Dataset Version: 1
Unknown
CMOS camera (Blackfly S, Teledyne FLIR)
Nikon Ti-E Inverted Microscope
Harvard Apparatus syringe pump
theme
None, User defined
Camera
Inverted Microscope
Pump
instrument
BCO-DMO Standard Instruments
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.
Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux
https://osprey.bco-dmo.org/project/783777
Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux
<p><em>NSF Award Abstract:</em><br />
Drifting photosynthetic microbes in surface ocean waters carry out nearly half of global carbon (C) fixation, both supporting the marine food web and reducing atmospheric carbon dioxide (CO2) levels. The fate of C in ocean ecosystems is controlled by myriad individual interactions within a highly interconnected planktonic food web, the sheer complexity of which has hindered predictive understanding of global C cycling. Chemical cues govern microbial interactions, and during infection, marine viruses manipulate the metabolism of phytoplankton and bacteria, facilitating the release of dissolved organic matter from infected cells. This research aims to determine how viral metabolic reprogramming of and organic matter release from intact, infected phytoplankton influences microbial interactions and C cycling. The interdisciplinary, collaborative nature of the project will enable direct training of two postdoctoral researchers, one graduate student, and undergraduate students in viral ecology, microfluidics, and metabolomics. An educational outreach program that engages middle school students in hands-on, high speed imaging of microbes will be expanded, and the project will culminate in a three-day workshop to advance the application of microfluidic devices and mass spectrometry analyses in microbial ecology.</p>
<p>The overarching hypothesis behind this research is that viral infection alters the chemical landscape of intact, infected picophytoplankton cells, attracting neighboring chemotactic bacteria and protistan zooplankton, and altering C flux pathways. To test this idea, a series of linked multi-scale laboratory-based experiments will be run to 1) Characterize the response of diverse model marine microbes to dissolved organic matter (DOM) released from intact, virus-infected picophytoplankton using microfluidics-based chemotaxis assays, 2) Identify key viral-derived DOM compounds eliciting chemotactic responses using stable isotope labeling, metabolomics analyses, and chemotaxis assays, and 3) Quantify micron-scale cross-trophic encounter dynamics and evaluate their impact on bulk-scale C cycling using liter-scale measurements of C dynamics linked to high spatiotemporal resolution live imaging of microbial food webs. The ultimate goal of the project is to develop a mechanistic understanding of the role of intact, virus-infected cells in oceanic C cycling.</p>
VIC
largerWorkCitation
project
eng; USA
oceans
2020-12-03
2021-10-08
Culture-based work
0
BCO-DMO catalogue of parameters from Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC 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
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
20708408089
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/7a1564e0-160d-47f9-974c-97dec1a3e547/content
download
https://doi.org/10.26008/1912/bco-dmo.885574.1
download
onLine
dataset
<p><strong>Methods &amp; Sampling</strong></p>
<p>Vibrio alginolyticus (YM4; wild-type) from -80℃ stock were grown overnight in Marine 2216 media (Difco) by incubating at 30℃ and shaking at 600 revolutions per minute (RPM). The overnight culture was diluted 100-fold into fresh pre-warmed 2216 media and grown for three hours (30℃, shaking at 600 RPM) to O.D. ≈ 0.2. 2 ml of culture was then washed and resuspended (1,500 RCF for 5 min) in 0.5ml of artificial seawater (ASW).</p>
<p>Artificial seawater (ASW) was prepared following the NCMA ESAW Medium recipe, which was adapted from Harrison et al.and modified by Berges, and filtered through a 0.2um filter immediately prior to use.</p>
<p>A simple three-inlet gradient generation microfluidic device was used to produce the chemical gradients.&nbsp; Microfluidic devices were made using standard soft lithography techniques. Polydimethylsiloxane (Dow Corning SYLGARD 184) channels were cast on photoresist (Microchem) molds fabricated via photolithography and plasma bonded to standard glass slides. Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump(Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. A chemostimulus gradient develops in the channel via diffusion, and the chemotactic response of the cell population was observed over time. Imaging was performed with phasecontrast microscopy (4×, 0.13 NA objective; Nikon Ti-E) at 1 fps over the course of ~10 min using a CMOS camera (Blackfly S, Teledyne FLIR). An example of the gradient generator used can be found in&nbsp;http://dx.doi.org/10.1038/s41567-021-01247-7</p>
<p>This data set summarises the chemotactic response of a model marine bacteria (<em>Vibrio alginolyticus</em>&nbsp;YM4 wild-type) to filtered exudates of the cyanobacteria&nbsp;<em>Synechococcus&nbsp;</em>sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -&gt; T6), with the inital assays split into 4 biological replicates (named A, B, C, D). The two treatments were:</p>
<p>1). A control treatment (named "Control", or shortened to "C")</p>
<p>2). A phage-infected treatment (named "Phage", or shortened to "P"), where host Synechococcus were infected with the T-4 like Myovirus S-SSM5, with data collected over the pre-lysis cycle.</p>
<p>These treatments are fully described in:&nbsp;https://doi.org/10.1038/s43705-022-00169-6. The filtrates were kept frozen at -80C in 1ml aliquots, and only thawed to room temperature immediately prior to experimental use.</p>
<p>For each time point (T1-6), and replicate (A-D), three sets of chemotaxis assays were collected: Phage vs ASW, Control vs ASW, and Phage vs Control. (Each with three biological replicates with fresh cell suspensions, with three physical replicates per sample, totaling nine samples at each time point/sample replicate). The chemotactic preference of&nbsp;<em>Vibrio alginolyticus</em>&nbsp;was measured by analyzing the cell distribution over time, and comparing the cell populations on opposite sides of the channel.</p>
Specified by the Principal Investigator(s)
<p>All data were processed using custom MATLAB scripts (version 2021a). The processing summary is:</p>
<p>1)&nbsp;Locate particles using a bandpass filter/peak finding algorithm (available:&nbsp;https://site.physics.georgetown.edu/matlab/)</p>
<p>2)&nbsp;Bin particles according to x-position to examine distribution across the field of view</p>
<p>An example of the analysis script is included in the dataset.</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
CMOS camera (Blackfly S, Teledyne FLIR)
CMOS camera (Blackfly S, Teledyne FLIR)
PI Supplied Instrument Name: CMOS camera (Blackfly S, Teledyne FLIR) PI Supplied Instrument Description:Imaging was performed with phasecontrast microscopy (4×, 0.13 NA objective; Nikon Ti-E) at 1 fps over the course of ~10 min using a CMOS camera (Blackfly S, Teledyne FLIR). An example of the gradient generator used can be found in http://dx.doi.org/10.1038/s41567-021-01247-7. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Nikon Ti-E Inverted Microscope
Nikon Ti-E Inverted Microscope
PI Supplied Instrument Name: Nikon Ti-E Inverted Microscope PI Supplied Instrument Description:Imaging was performed with phasecontrast microscopy (4×, 0.13 NA objective; Nikon Ti-E) at 1 fps over the course of ~10 min using a CMOS camera (Blackfly S, Teledyne FLIR). An example of the gradient generator used can be found in http://dx.doi.org/10.1038/s41567-021-01247-7. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Harvard Apparatus syringe pump
Harvard Apparatus syringe pump
PI Supplied Instrument Name: Harvard Apparatus syringe pump PI Supplied Instrument Description:Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump(Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. 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