http://lod.bco-dmo.org/id/dataset/880924
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
2022-09-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Population changes in Halobacteriovorax cultured with protist & prey
2022-09-22
publication
2022-09-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-08-14
publication
https://doi.org/10.26008/1912/bco-dmo.880924.1
Henry Neal Williams
Florida A&M University
principalInvestigator
Huan Chen
Florida State University - National High Magnetic Field Lab
principalInvestigator
Ahkinyala Cobb-Abdullah
Virginia Union University
principalInvestigator
Sven A. Kranz
Florida State University
principalInvestigator
Michael R. Stukel
Florida State University
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: Williams, H. N., Chen, H., Kranz, S., Stukel, M., Cobb-Abdullah, A., Xue, J. (2023) Population changes in Halobacteriovorax cultured with protist & prey. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-09-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.880924.1 [access date]
Population Changes Dataset Description: <p>These data were published in Williams et al. (2016): Figs 1 and 3.</p>
<p>Data have been published “as is”. Final review by the data submitter was not received after it was imported into the BCO-DMO data system. There were no outstanding questions</p> Methods and Sampling: <p>To establish microcosms for the experiment, water samples were collected from the Apalachicola Bay (N 30° 4' 26.436", W 84° 10' 48.874") in northwest Florida, USA. About 20 liters of seawater (SW) were collected in sterile plastic bottles. The samples were transported on ice (4 ℃) to the Microbial Ecology Laboratory at Florida A&amp;M University within two hours. To establish the microcosms, water samples were first filtered through 5 μm membrane filters (Whatman Laboratory, NJ) to remove debris and larger organisms. Then 600 ml was dispensed into each of three (A, B, and C) 1-liter flasks to create the various microcosms as shown in Figure 1. For treatment D, 600 ml of SW samples were filtered through 0.8 μm membrane filters to remove protist. One subsample labeled W was unfiltered. All microcosm flasks were shaken at 80 rpm at 25 ℃ for 120 h. Samples (5 ml) were collected every 3 hours, dispensed in a 96-well microtiter plate and the OD measured at 600 nm using an Absorbance Microplate Reader Q4 (BIO-TEK Instruments Inc., USA). Population changes in <em>HBx</em> and <em>V. parahaemolyticus</em> were monitored by culture- and qPCR-based methods as described below. The protocol described here is similar to that published by Williams et al. (2016). A key difference is those investigators also filtered the microcosm samples through a 0.1 µm filter to allow viruses to pass into the filtrate as their investigation included monitoring of virus numbers in the various microcosm treatments, and did not include protists.</p>
<p><strong>Enumeration of </strong><strong><em>HBx</em></strong><strong> and <em>V. parahaemolyticus </em>by culture-dependent method</strong></p>
<p>At 3-h intervals, 1 ml was collected from all microcosms (A, B, D, and W) and 10-fold dilutions of these prepared in sterile SW. &nbsp;One tenth (0.1) ml taken from three of these dilutions (10<sup>-6</sup>, 10<sup>-7</sup>, 10<sup>-8</sup>) was inoculated on seawater yeast extract (SWYE) agar in duplicate to obtain countable numbers of CFU of <em>V. parahaemolyticus</em>. All plates were incubated at 28°C ± 0.5°C for 24 hours, and colony-forming units (CFU) were counted. To culture <em>HBx</em> requires a prey bacterium suspension. The suspension was prepared by flooding a SWYE agar plate with an overnight-grown culture of <em>Vibrio parahaemolyticus </em>with 5 ml of autoclaved SW. The fluid remained undisturbed on the surface of the plate for 5 minutes. The culture was then suspended in the fluid using s circular motion with a sterile L-shaped spreader. The resulting suspension was transferred into a 15 ml tube and used as the stock prey suspension. One ml of the prey stock suspension was inoculated into tubes along with samples (5, 1, 0.1 ml) from each of the microcosms. In cases where the sample volume was less than 5 ml, autoclaved SW was added to bring the final sample volume to 5 ml). The suspension was added to top agar, and the mixture mixed mechanically and overlaid onto the surface of bottom agar in agar plates. The plates were cultured at room temperature for 3 to 5 days and examined daily for plaques typical of <em>HBx</em>, Plaque –forming units (PFU).were counted. The daily counts of <em>HBx</em> and <em>V. parahaemolyticus</em> were plotted and changes over the course of the experiment were observed and compared with counts of protist during the same time period. &nbsp;</p>
<p><strong>DNA extraction from water samples for qPCR</strong></p>
<p>For DNA extraction, a 1 ml sample was collected from each microcosm at each time interval, and 250 μl was used for DNA extraction. Genomic DNA was isolated using the PowerSoil® DNA Isolation Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instructions and the DNA was quantified with a NanoDrop ND-1000 UV spectrophotometer (Thermo Scientific, Wilmington, USA). The DNA samples were stored at -20 °C prior to use.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948758 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948758
completed
Henry Neal Williams
Florida A&M University
850-599-3550
School of the Environment, FS Humphries Research Center 1515 Martin Luther King, Jr., Blvd
allahassee
FL
32307
USA
henryneal.williams@famu.edu
pointOfContact
Huan Chen
Florida State University - National High Magnetic Field Lab
(850) 644-1745
ICR Program, US National High Magnetic Field Laboratory 1800 E. Paul Dirac Dr
Tallahassee
FL
32310-3706
USA
huan.chen@magnet.fsu.edu
pointOfContact
Ahkinyala Cobb-Abdullah
Virginia Union University
(804) 257-5610
Department of Natural Sciences 220-A Ellison Hall, 1500 N Lombardy Street
Richmond
VA
23220
USA
amabdullah@vuu.edu
pointOfContact
Sven A. Kranz
Florida State University
609-937-9144
6100 Main St.
Houston
TX
77005-1827
USA
skranz@rice.edu
pointOfContact
Michael R. Stukel
Florida State University
815-258-3875
Earth, Ocean, and Atmos. Science Building (EOA) Rm. 6089 1011 Academic Way
Tallahassee
FL
32306
USA
mstukel@fsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Treatment
Time
Optical_Density
Protists
Vibrio
Halobacteriovorax
CytoFLEX Flow Cytometer
Absorbance Microplate Reader Q4
CFX96 Touch Deep Well Real-Time PCR Detection System
NanoDrop ND-1000 UV spectrophotometer
theme
None, User defined
treatment
incubation time or duration
optical_density
abundance
featureType
BCO-DMO Standard Parameters
Flow Cytometer
plate reader
qPCR Thermal Cycler
Spectrophotometer
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.
Excellence in Research: Assessing the Control by Multiple Micropredators on Bacterial Communities in Estuarine Environments and Characterization of Prey Lysis Products Resulting from Each Predator
https://osprey.bco-dmo.org/project/851540
Excellence in Research: Assessing the Control by Multiple Micropredators on Bacterial Communities in Estuarine Environments and Characterization of Prey Lysis Products Resulting from Each Predator
<p>NSF Award Abstract:</p>
<p>Microbes are the most abundant organisms on Earth and play an important role as degraders, cycling nutrients in the environment. Too many or too few bacteria may disrupt a sensitive ecological balance and proper functioning of environmental processes such as carbon, nitrogen and phosphorus cycles. The abundance of bacteria populations in any given environment is controlled by various biological, chemical and physical mechanisms. Among the biological agents are microscopic predators, or micropredators, of bacteria. The most studied of these are protists, viruses that infect bacteria, and a group of bacteria collectively known as the Bdellovibrio and like organisms (BALOs). These micropredators prey upon certain bacteria to obtain required nutrients or other cellular material for their replication. In the process, cellular products from the prey bacteria are released into the environment and utilized as nutrients by other microbes. Although the micropredators co-occur, and likely interact, in nature, most experimental studies have investigated their activities individually, rather than collectively. As a result, little is known about their collective role in controlling bacteria populations and the cycling of nutrients. The goal of the proposed research is to address this gap in knowledge by investigating all three as a collective group under simulated natural conditions representing a range of temperature, salinity and abundance of prey. This project is conducted at two Historically Black Universities (HBCUs) with strong records of training and mentoring students and postdocs from underrepresented populations in science. The project benefits up to 100 students by providing unique and meaningful educational and research training experiences at the undergraduate and graduate student levels and for early-career scientist. Specific activities include courses on scientific writing and presenting results at annual project workshops as well as national and international scientific meetings. Graduate students are being trained in modern advanced methodologies in chemistry and microbiology. There is an ongoing assessment module to document education and training outcomes.</p>
<p>Up to now, the two mainly accepted mechanisms of mortality in bacterial populations are heterotrophic protist grazing and viral infection. Increasingly, it has become evident that an understudied group of predatory bacteria, BALOs, can also contribute to bacterial mortality. Yet, the mechanisms underlying the dynamics of BALO-prey interactions are poorly understood, as are the interactions among the micropredators, BALOs, protists and bacterial viruses. Ultimately, these processes may have contrasting influences on the structure and functioning of the microbial loop, including impacting higher trophic levels and biogeochemical cycles. The investigators hypothesize that environmental factors significantly influence how mortality in bacterial populations is partitioned among the micropredators. To test this hypothesis researchers are (1) investigating the interactions amongst the micropredators, (2) examining the molecular-level composition and dynamics of dissolved organic matter as the result of the different mortality processes by the NMR/ FT-ICR mass spectrometry (MS) hybrid approach, and (3) modeling these tri-trophic dynamics. Intellectual Merit: Results from this research will define a new mechanistic understanding of mortality dynamics that influence the microbial loop and oceanic biogeochemical cycles.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Predators of bacteria
largerWorkCitation
project
eng; USA
oceans
-84.180243
-84.180243
30.07401
30.07401
2022-09-22
0
BCO-DMO catalogue of parameters from Population changes in Halobacteriovorax cultured with protist & prey
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/880949.rdf
Name: Treatment
Units: unitless
Description: <p>Experimental Conditions: 'Sw Fil. 5 + V.p.': sea water (SW) passed through 0.5µm filter to remove larger particles but retaining microbes (protists, bacteria, viruses) with V. parahaemolyticus (V.p.) added as prey bacterium. 'Auto SW + V.p.': Autoclaved sterilized SW amended with V.p.'SW no V.p.': SW unfiltered with no V.p. added.SW Fil. 0.8 + V.p.'- SW passed through a 0.8µm filter to remove most protists and amended with V.p.'Fil. 0.2 + V.p.': SW passed through a 0.2 µm filter to select for viruses and amended with V.p.'Natural + V.p.': Natural SW unfiltered amended with V.p.</p>
http://lod.bco-dmo.org/id/dataset-parameter/880950.rdf
Name: Time
Units: hours
Description: <p>Time since expt start</p>
http://lod.bco-dmo.org/id/dataset-parameter/880951.rdf
Name: Optical_Density
Units: OD units
Description: <p>Optical Density</p>
http://lod.bco-dmo.org/id/dataset-parameter/880952.rdf
Name: Protists
Units: counts per ml
Description: <p>Protist Abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/880953.rdf
Name: Vibrio
Units: gene copies per reaction
Description: <p>Vibrio Abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/880954.rdf
Name: Halobacteriovorax
Units: gene copies per reaction
Description: <p>Halobacteriovorax (Hbx) Abundance</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
9629
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/951ac7fc-7ec3-45b8-822e-9dfee03999e5/content
download
https://doi.org/10.26008/1912/bco-dmo.880924.1
download
onLine
dataset
<p>To establish microcosms for the experiment, water samples were collected from the Apalachicola Bay (N 30° 4' 26.436", W 84° 10' 48.874") in northwest Florida, USA. About 20 liters of seawater (SW) were collected in sterile plastic bottles. The samples were transported on ice (4 ℃) to the Microbial Ecology Laboratory at Florida A&amp;M University within two hours. To establish the microcosms, water samples were first filtered through 5 μm membrane filters (Whatman Laboratory, NJ) to remove debris and larger organisms. Then 600 ml was dispensed into each of three (A, B, and C) 1-liter flasks to create the various microcosms as shown in Figure 1. For treatment D, 600 ml of SW samples were filtered through 0.8 μm membrane filters to remove protist. One subsample labeled W was unfiltered. All microcosm flasks were shaken at 80 rpm at 25 ℃ for 120 h. Samples (5 ml) were collected every 3 hours, dispensed in a 96-well microtiter plate and the OD measured at 600 nm using an Absorbance Microplate Reader Q4 (BIO-TEK Instruments Inc., USA). Population changes in <em>HBx</em> and <em>V. parahaemolyticus</em> were monitored by culture- and qPCR-based methods as described below. The protocol described here is similar to that published by Williams et al. (2016). A key difference is those investigators also filtered the microcosm samples through a 0.1 µm filter to allow viruses to pass into the filtrate as their investigation included monitoring of virus numbers in the various microcosm treatments, and did not include protists.</p>
<p><strong>Enumeration of </strong><strong><em>HBx</em></strong><strong> and <em>V. parahaemolyticus </em>by culture-dependent method</strong></p>
<p>At 3-h intervals, 1 ml was collected from all microcosms (A, B, D, and W) and 10-fold dilutions of these prepared in sterile SW. &nbsp;One tenth (0.1) ml taken from three of these dilutions (10<sup>-6</sup>, 10<sup>-7</sup>, 10<sup>-8</sup>) was inoculated on seawater yeast extract (SWYE) agar in duplicate to obtain countable numbers of CFU of <em>V. parahaemolyticus</em>. All plates were incubated at 28°C ± 0.5°C for 24 hours, and colony-forming units (CFU) were counted. To culture <em>HBx</em> requires a prey bacterium suspension. The suspension was prepared by flooding a SWYE agar plate with an overnight-grown culture of <em>Vibrio parahaemolyticus </em>with 5 ml of autoclaved SW. The fluid remained undisturbed on the surface of the plate for 5 minutes. The culture was then suspended in the fluid using s circular motion with a sterile L-shaped spreader. The resulting suspension was transferred into a 15 ml tube and used as the stock prey suspension. One ml of the prey stock suspension was inoculated into tubes along with samples (5, 1, 0.1 ml) from each of the microcosms. In cases where the sample volume was less than 5 ml, autoclaved SW was added to bring the final sample volume to 5 ml). The suspension was added to top agar, and the mixture mixed mechanically and overlaid onto the surface of bottom agar in agar plates. The plates were cultured at room temperature for 3 to 5 days and examined daily for plaques typical of <em>HBx</em>, Plaque –forming units (PFU).were counted. The daily counts of <em>HBx</em> and <em>V. parahaemolyticus</em> were plotted and changes over the course of the experiment were observed and compared with counts of protist during the same time period. &nbsp;</p>
<p><strong>DNA extraction from water samples for qPCR</strong></p>
<p>For DNA extraction, a 1 ml sample was collected from each microcosm at each time interval, and 250 μl was used for DNA extraction. Genomic DNA was isolated using the PowerSoil® DNA Isolation Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instructions and the DNA was quantified with a NanoDrop ND-1000 UV spectrophotometer (Thermo Scientific, Wilmington, USA). The DNA samples were stored at -20 °C prior to use.</p>
Specified by the Principal Investigator(s)
<p><strong>Quantitative PCR assays </strong></p>
<p>TaqMan based quantitative PCR assay for <em>V. parahaemolyticus</em> and SYBR green based qPCR assays for <em>HBx</em> and presumptive protist were conducted (Table 1)&nbsp;. All qPCR assays were performed using the BioRad Real-Time PCR system. For TaqMan based qPCR, the reaction mixture (20 µl) contained 1x PerfeCTa qCPR ToughMix (Quanta Biosciences, Beverly, MA), 0.5 µM of each primer, and 2.5 µl of the template DNA. QPCR reactions were performed in duplicate and amplification protocols consisted with a hold at 95 °C for 2 min, followed by 45 cycles of 94 °C 5s, 59 °C 45 s. SYBR green-based qPCR reaction mixture (15 µl) contained 1x SsoAdvanced Universal SYBR Green Supermix (Bio-Rad, Hercules, CA), 0.5 µM of each primer, and 2.5 µl of the template DNA. The amplification conditions for <em>HBx</em> consisted of a hold at 94°C for 2 min, followed by 45 cycles of 94°C 30s, 62°C 10 s, and 72°C 10 s. The amplification conditions for presumptive protist consisted of a hold at 94°C for 2 min, followed by 30 cycles of 94°C 30s, 55°C 30 s, and 72°C 45 s.</p>
<p>A calibration curve with concentrations spanning the range from 10 to 10<sup>6</sup> gene copies per reaction, with two replicates, was prepared. Duplicate no-template controls (NTC) were included in each run. The amplification efficiencies (AE) were calculated based on the equation: AE= 10(-1/slope)<sup> –1</sup>. A summary of qPCR target organisms, primer/ probe name, and sequences are detailed in Table 1.</p>
<p>About the lower limit of detection (LLOD): Theoretically the LLOD for qPCR is 3 gene copies per reaction. In our experiment, we use the lowest point of our standard curve as the lower limit of quantification (LLOQ) which is 10 gene copies per reaction. The LLOD can also be calculated based on the methods mentioned in these two papers: Staley et al. (2012) and Xue et al (2019): which is the inverse log of five times the difference between the Y-intercept and the upper 99% confidence interval of the intercept divided by the slope based on the standard curve.</p>
<p>The LLOD for flow cytometry is 2 cells per ml.</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
CytoFLEX Flow Cytometer
CytoFLEX Flow Cytometer
PI Supplied Instrument Name: CytoFLEX Flow Cytometer PI Supplied Instrument Description:CytoFLEX Flow Cytometer (Beckman Coulter Life Sciences Headquarters, Indianapolis, IN 46268, USA) Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Absorbance Microplate Reader Q4
Absorbance Microplate Reader Q4
PI Supplied Instrument Name: Absorbance Microplate Reader Q4 PI Supplied Instrument Description:Absorbance Microplate Reader Q4 (BIO-TEK Instruments Inc., USA) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
CFX96 Touch Deep Well Real-Time PCR Detection System
CFX96 Touch Deep Well Real-Time PCR Detection System
PI Supplied Instrument Name: CFX96 Touch Deep Well Real-Time PCR Detection System PI Supplied Instrument Description:CFX96 Touch Deep Well Real-Time PCR Detection System (Bio-Rad, Hercules, CA 94547, USA) Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
NanoDrop ND-1000 UV spectrophotometer
NanoDrop ND-1000 UV spectrophotometer
PI Supplied Instrument Name: NanoDrop ND-1000 UV spectrophotometer PI Supplied Instrument Description:NanoDrop ND-1000 UV spectrophotometer (Thermo Scientific, Wilmington, USA) Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/