http://lod.bco-dmo.org/id/dataset/882970
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
2022-10-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"
2022-10-25
publication
2022-10-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-03
publication
https://doi.org/10.26008/1912/bco-dmo.882970.1
James Jeffrey Morris
University of Alabama at Birmingham
principalInvestigator
Zhiying Lu
University of Alabama at Birmingham
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: Morris, J. J., Zhiying, L. (2022) Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria". Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-10-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.882970.1 [access date]
Methods and Sampling: <div>
<div><span style="font-size:13px">See "Related Datasets" section for other results and pipelines from this study.</span>
<p><em>Strains</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Six clones each of the open ocean&nbsp;<em>Synechococcus</em>&nbsp;strain WH8102 and the coastal&nbsp;<em>Synechococcus</em>&nbsp;strain CC9311 were obtained by dilution to extinction in SN media&nbsp;[1]. The parent cultures of each organism were obtained from the National Center for Marine Algae (Boothbay Harbor, Maine) and were axenic upon receipt. Six clones of&nbsp;<em>Alteromonas</em>&nbsp;sp. strain EZ55 and&nbsp;<em>Prochlorococcus&nbsp;</em>MIT9312 were also previously obtained and cryopreserved at -80 °C&nbsp;[2]. The EZ55&nbsp;clones used in our&nbsp;<em>Synechococcus</em>&nbsp;co-cultures were the same 6 clones used in our previous transcriptomic study of MIT9312&nbsp;[2]&nbsp;in order to maximize the comparability of results between that study and the present study. Co-cultures were initiated by mixing each of the six clones of CC9311 and WH8102 with one of the EZ55 clones.</p>
<p><em>Culture conditions</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown under similar conditions to those described in our previous experiment with&nbsp;<em>Prochlorococcus&nbsp;</em>[2]. Briefly, all cultures were prepared in acid-washed conical-bottom glass centrifuge tubes containing 13 mL of artificial seawater (ASW) amended with nutrient stocks&nbsp;[1]&nbsp;and with acid and/or base to control pCO<sub>2</sub>. ASW (per L: 28.41 g NaCl, 0.79 g KCl, 1.58 g CaCl2*2H2O, 7.21 g MgSO4*7H2O, 5.18 g MgCl2*6H2O) was sterilized in acid-washed glass bottles, amended with 2.325 mM (final concentration) of filter-sterilized sodium bicarbonate, then bubbled with sterile air overnight.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown in SEv (per L: 32&nbsp;μM NaNO<sub>3</sub>, 2&nbsp;μM NaH<sub>2</sub>PO<sub>4</sub>, 20&nbsp;μL SN trace metal stock, and 20&nbsp;μL F/2 vitamin stock). The primary differences between this medium and the PEv medium used in our earlier&nbsp;<em>Prochlorococcus</em>&nbsp;study are the nitrogen source (NO<sub>3</sub><sup>-</sup>&nbsp;vs. NH<sub>4</sub><sup>+</sup>, with molar concentration of N and N:P ratios identical to PEv) and the addition of F/2 vitamins&nbsp;[1]. Carbonate chemistry of each media batch was determined prior to pCO<sub>2</sub>&nbsp;manipulations by measuring alkalinity and pH by titration and colorimetry, respectively&nbsp;[2, 3]&nbsp;and then using the&nbsp;<em>oa&nbsp;</em>function in&nbsp;<em>seacarb</em>&nbsp;package in R to determine how much hydrochloric acid and bicarbonate (for 800 ppm pCO<sub>2</sub>) or sodium hydroxide (for 400 ppm pCO<sub>2</sub>) was needed to achieve desired experimental conditions&nbsp;[4]. Acid and base amendments were introduced immediately prior to inoculation. Cultures were grown in a Percival growth chamber at 21º C under 150&nbsp;μmol photons m<sup>-2</sup>&nbsp;s<sup>-1</sup>&nbsp;on a 14:10 light:dark cycle.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown on a rotating tissue culture wheel at approximately 60 rpm.<br />
<br />
<span style="font-size:13px">For "EZ55 growth experiments with photorespiration metabolites"&nbsp; and "RNA library preparation and sequencing" details see the related dataset "Synechococcus growth and genetic sequence accessions from pCO2 experiments"&nbsp;https://www.bco-dmo.org/dataset/882390</span></p>
<p><em>Detection of glycolate utilization genes</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Several genes involved in the bacterial glycolate utilization pathway (glycolate/lactate oxidase, the 3 subunits of glycolate dehydrogenase, and tartronate semialdehyde reductase) were not annotated in the reference genomes for our organisms so we specifically sought to detect them using a reciprocal BLAST analysis. We retrieved any sequences from each of the four reference genomes with high similarity (E-value &lt; 0.001) to the relevant genes from&nbsp;<em>Escherichia coli</em>&nbsp;and/or&nbsp;<em>Synechococcus elongatus</em>&nbsp;using blastp&nbsp;[7]&nbsp;and then back-matched each retrieved sequence to the&nbsp;<em>E. coli</em>&nbsp;or&nbsp;<em>S. elongatus</em>&nbsp;reference genome. If the reciprocal match was the same gene used in the original BLAST search, we considered the match significant.</p>
</div>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851085 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851085
completed
James Jeffrey Morris
University of Alabama at Birmingham
205-934-9498
1300 University Blvd CH253
Birmingham
AL
35294
USA
evolve@uab.edu
pointOfContact
Zhiying Lu
University of Alabama at Birmingham
1-252-773-2353
Campbell Hall, Office 474 1300 University Blvd
Birmingham
AL
35233
USA
luzy@uab.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
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: Ecology and Evolution of Microbial Interactions in a Changing Ocean
https://osprey.bco-dmo.org/project/752763
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
<p><em>NSF Award Abstract:</em><br />
Carbon dioxide released from fossil fuels is causing the ocean to become more acidic. Much attention has been given to how this will affect shelled animals like corals, but acidification also affects the algae that form the base of the ocean food chain. It is possible that future algal communities will look very different than they do today, with potentially negative consequences for fisheries, recreation, and climate. Alternatively, it is possible that these algae will be able to adapt rapidly enough to avoid the worst of it. This study looks at algae adapting to acidification in real time in the lab, focusing on "marketplace" interactions between the algae and the bacteria they live alongside. The researchers also go to sea to learn whether adaptations from the lab experiments are beneficial under real-world conditions. Ultimately, this project is helping scientists better understand how the ocean's most important and most overlooked organisms will respond to the changes humans are causing in their habitat. The researchers also use their scientific work to create fun educational opportunities from grade school to college, including agar art classes where students learn about microbial ecology by "painting" with freshly-isolated ocean bacteria.</p>
<p>The effect of ocean acidification on calcifying organisms has been well-studied, but less is known about how changing pH will affect phytoplankton. Previous work showed that the mutualistic interaction between the globally abundant cyanobacterium Prochlorococcus and its "helper" bacterium Alteromonas broke down under projected future CO2 conditions, leading to a strong decrease in the fitness of Prochlorococcus. It is possible that such interspecies interactions between microbes are important for many ecological processes, but a lack of understanding of how these interactions evolve makes it difficult to predict how important they are. This project is using laboratory evolution experiments to discover how evolution shapes the interactions between bacteria and algae like Prochlorococcus, and how these co-evolutionary dynamics might influence the biogeochemical processes that shape Earth's climate. Four research cruises to the Bermuda Atlantic Time Series are also planned to study how natural algal/bacterial communities respond to acidification, and whether evolved microbes from laboratory experiments have a competitive advantage in complex, natural communities exposed to elevated CO2. The ultimate goal of this project is to gain a mechanistic understanding of microbial interactions that can be used to inform models of Earth's oceans and biological feedbacks on global climate.</p>
LTPE
largerWorkCitation
project
eng; USA
oceans
2022-10-25
Lab work: Birmingham, Alabama and New York, New York. Field Work: Bermuda Atlantic Time Series.
0
BCO-DMO catalogue of parameters from Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"
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
197570
https://darchive.mblwhoilibrary.org/bitstream/1912/29466/1/Phylogenetic_analysis.zip
download
https://doi.org/10.26008/1912/bco-dmo.882970.1
download
onLine
dataset
<div>
<div><span style="font-size:13px">See "Related Datasets" section for other results and pipelines from this study.</span>
<p><em>Strains</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Six clones each of the open ocean&nbsp;<em>Synechococcus</em>&nbsp;strain WH8102 and the coastal&nbsp;<em>Synechococcus</em>&nbsp;strain CC9311 were obtained by dilution to extinction in SN media&nbsp;[1]. The parent cultures of each organism were obtained from the National Center for Marine Algae (Boothbay Harbor, Maine) and were axenic upon receipt. Six clones of&nbsp;<em>Alteromonas</em>&nbsp;sp. strain EZ55 and&nbsp;<em>Prochlorococcus&nbsp;</em>MIT9312 were also previously obtained and cryopreserved at -80 °C&nbsp;[2]. The EZ55&nbsp;clones used in our&nbsp;<em>Synechococcus</em>&nbsp;co-cultures were the same 6 clones used in our previous transcriptomic study of MIT9312&nbsp;[2]&nbsp;in order to maximize the comparability of results between that study and the present study. Co-cultures were initiated by mixing each of the six clones of CC9311 and WH8102 with one of the EZ55 clones.</p>
<p><em>Culture conditions</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown under similar conditions to those described in our previous experiment with&nbsp;<em>Prochlorococcus&nbsp;</em>[2]. Briefly, all cultures were prepared in acid-washed conical-bottom glass centrifuge tubes containing 13 mL of artificial seawater (ASW) amended with nutrient stocks&nbsp;[1]&nbsp;and with acid and/or base to control pCO<sub>2</sub>. ASW (per L: 28.41 g NaCl, 0.79 g KCl, 1.58 g CaCl2*2H2O, 7.21 g MgSO4*7H2O, 5.18 g MgCl2*6H2O) was sterilized in acid-washed glass bottles, amended with 2.325 mM (final concentration) of filter-sterilized sodium bicarbonate, then bubbled with sterile air overnight.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown in SEv (per L: 32&nbsp;μM NaNO<sub>3</sub>, 2&nbsp;μM NaH<sub>2</sub>PO<sub>4</sub>, 20&nbsp;μL SN trace metal stock, and 20&nbsp;μL F/2 vitamin stock). The primary differences between this medium and the PEv medium used in our earlier&nbsp;<em>Prochlorococcus</em>&nbsp;study are the nitrogen source (NO<sub>3</sub><sup>-</sup>&nbsp;vs. NH<sub>4</sub><sup>+</sup>, with molar concentration of N and N:P ratios identical to PEv) and the addition of F/2 vitamins&nbsp;[1]. Carbonate chemistry of each media batch was determined prior to pCO<sub>2</sub>&nbsp;manipulations by measuring alkalinity and pH by titration and colorimetry, respectively&nbsp;[2, 3]&nbsp;and then using the&nbsp;<em>oa&nbsp;</em>function in&nbsp;<em>seacarb</em>&nbsp;package in R to determine how much hydrochloric acid and bicarbonate (for 800 ppm pCO<sub>2</sub>) or sodium hydroxide (for 400 ppm pCO<sub>2</sub>) was needed to achieve desired experimental conditions&nbsp;[4]. Acid and base amendments were introduced immediately prior to inoculation. Cultures were grown in a Percival growth chamber at 21º C under 150&nbsp;μmol photons m<sup>-2</sup>&nbsp;s<sup>-1</sup>&nbsp;on a 14:10 light:dark cycle.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown on a rotating tissue culture wheel at approximately 60 rpm.<br />
<br />
<span style="font-size:13px">For "EZ55 growth experiments with photorespiration metabolites"&nbsp; and "RNA library preparation and sequencing" details see the related dataset "Synechococcus growth and genetic sequence accessions from pCO2 experiments"&nbsp;https://www.bco-dmo.org/dataset/882390</span></p>
<p><em>Detection of glycolate utilization genes</em></p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Several genes involved in the bacterial glycolate utilization pathway (glycolate/lactate oxidase, the 3 subunits of glycolate dehydrogenase, and tartronate semialdehyde reductase) were not annotated in the reference genomes for our organisms so we specifically sought to detect them using a reciprocal BLAST analysis. We retrieved any sequences from each of the four reference genomes with high similarity (E-value &lt; 0.001) to the relevant genes from&nbsp;<em>Escherichia coli</em>&nbsp;and/or&nbsp;<em>Synechococcus elongatus</em>&nbsp;using blastp&nbsp;[7]&nbsp;and then back-matched each retrieved sequence to the&nbsp;<em>E. coli</em>&nbsp;or&nbsp;<em>S. elongatus</em>&nbsp;reference genome. If the reciprocal match was the same gene used in the original BLAST search, we considered the match significant.</p>
</div>
</div>
Specified by the Principal Investigator(s)
<div>This .zip package Phylogenetic_analysis.zip contains files and code necessary to replicate our phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes.</div>
<div>&nbsp;</div>
<div>The "Phylogenetic_analysis" folder contains the files necessary to replicate our phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes. Only alignments are provided for glcE and tsar genes, in fasta format, as GlcE.align.faa and tsar.align.faa. For GOX/LOX and glcDF, the following file types are provided:</div>
<div>&nbsp;</div>
<div>.align.faa -- fasta format alignments</div>
<div>.mdsx -- MEGA format files used for sequence alignment</div>
<div>.modelselect.txt -- MEGA output used to determine which model to use for tree formation</div>
<div>.mtsx -- MEGA format tree session files</div>
<div>.nwk -- final trees in Newick format</div>
<div>&nbsp;</div>
<div>Note that glcD, glcD2, glcF, and marine glcDF fusion proteins were analyzed with a single alignment. For organisms with glcD and glcF as separate ORFs, the coding sequences were concatenated with glcD first followed by glcF.</div>
<p><br />
BCO-DMO Data Manager Processing notes:<br />
* Pipeline&nbsp;attached as a zip file bundle&nbsp;to "Data Files" section.<br />
* SRA accessions and related collection and treatment information extracted from NCBI's SRA Run Selector and attached as a supplemental file (SraRunTable_PRJNA377729.csv)</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