http://lod.bco-dmo.org/id/dataset/565723
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
2015-09-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers from the Bermuda, Red Sea, and Federated States of Micronesia in 2013 (Coral Microbial Relationships project)
2015-09-10
publication
2015-09-10
revision
BCO-DMO Linked Data URI
2015-09-10
creation
http://lod.bco-dmo.org/id/dataset/565723
Amy Apprill
Woods Hole Oceanographic Institution
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: Apprill, A. (2015) Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers from the Bermuda, Red Sea, and Federated States of Micronesia in 2013 (Coral Microbial Relationships project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-09-10) Version Date 2015-09-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/565723 [access date]
Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers Dataset Description: <p><strong>Relevant Reference:</strong></p>
<p>&nbsp;Apprill A, McNally S, Parsons R, Weber L (2015) Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol 75:129-137.&nbsp;doi: 10.3354/ame01753</p> Methods and Sampling: <p><strong>Seawater sample collection</strong></p>
<p>Nucleic acids were collected from surface waters along the coastline of the southeastern Red Sea and from coral reefs surrounding the islands and atolls in the Federated States of Micronesia (Supplementary Table 1). Samples from an aquaria-based experiment housed at the Bermuda Institute of Ocean Sciences (BIOS) were also utilized in this study.&nbsp; Seawater from Ferry Reach, Bermuda (32.37035°N, 64.69545°W) was sampled from a direct inflow line. In addition, this water was also held in separate aerated 30 liter aquaria (similar to de Putron et al. 2011) where it was sampled for nucleic acids (500 ml) and fluorescence <em>in situ</em> hybridization (FISH) analyses (50 ml) over the course of 12 days.</p>
<p><strong>DNA analysis</strong></p>
<p>Seawater collected from the Red Sea (20 liters) and Micronesia (2 liters) was filtered onto 142 mm, 0.22 µm Durapore membrane filters (Millipore, Boston, MA, USA) and 25 mm 0.2 µm polyethersulfone membranes (Supor, Pall, East Hills, NY, USA), respectively, and immediately frozen in liquid nitrogen.&nbsp; Total genomic DNA was extracted from these samples using previously reported methods (Santoro et al. 2010).&nbsp; Similarly, microbial biomass originating from the BIOS seawater inflow line and aquaria seawater was concentrated onto 0.2 µm polyethersulfone membranes (Supor) using a 47 mm support filter and a gelman rig under gentle vacuum (~100mm Hg).&nbsp; Each filter was stored in 1 ml of sterile sucrose lysis buffer (20mM EDTA, 400mM NaCl, 0.75M sucrose, 50mM Tris.HCl) at –80°C. DNA was extracted using the phenol-chloroform method (Giovannoni et al. 1990).&nbsp; Primers targeting the V4 region of the SSU rRNA gene, 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) (Caporaso et al. 2011), were utilized for PCR amplification using unique barcoded primer combinations for each sample.&nbsp; In addition, the same DNA samples were amplified separately with the 515F primer and a modified 806RB primer using the identical barcoding approach. This modified reverse primer replaces the ‘H’ degeneracy in the original 806R primer with a ‘N’, and is designed to enhance SAR11 targets (revised primer 806RB, 5’-GGACTACNVGGGTWTCTAAT-3’).&nbsp; The primers were designed after Kozich and colleagues (2013) and were each equipped with a unique 8-bp barcode, 10-bp pad and 2-bp link that followed the above-mentioned primers (see Supplementary Materials and Methods). Triplicate 25 µl PCR reactions were conducted per sample and each reaction contained 1.25 U of GoTaq Flexi DNA Polymerase (Promega Cooperation, Madison, WI, U.S.A.), 5X Colorless GoTaq Flexi Buffer, 2.5 mM MgCl2, 200 uM dNTP mix (Promega Cooperation, Madison, WI, U.S.A.), 200 nM of each barcoded primer, and 1 - 4 ng of genomic template. The reaction conditions consisted of an initial denaturation step at 95ºC for 2 min, followed by 27-38 cycles of 95ºC for 20 s, 55ºC for 15 s, and 72ºC for 5 min, concluding with an extension step at 72ºC for 10 min. The reactions were carried out on a Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Reaction products (5 µl) were screened on a 1% agarose/TBE gel. The HyperLadder 50bp DNA ladder (generally 5ng µl-1) (Bioline, London, UK) was used to confirm appropriate amplicon size.&nbsp; The number of PCR cycles varied between samples in order to produce similar, minimal yields, but each sample was subjected to nearly identical PCR cycles with both primer sets. The three replicate reactions were pooled and subsequently purified using the QIAquick Purification Kit (Qiagen, Valencia, CA, USA), and quantified using the Qubit 2.0 Fluorometer with the dsDNA High Sensitivity Assay (Life Technologies, Grand Island, NY USA).&nbsp; For each primer set, barcoded amplicons were pooled into equimolar ratios. These amplicon pools were then shipped to the University of Illinois W.M. Keck Center for Comparative and Functional Genomics where they were used for construction of two separate libraries which were subsequently sequenced using 2x250bp paired-end MiSeq (Illumina, San Diego, CA, USA), as detailed previously (similar to Kozich et al. 2013). Control samples included sterile water (negative controls) in which PCR did not yield any detectable amplification with either primer set.&nbsp; A mock community sample (positive control, obtained through BEI Resources, NIAID and NIH as part of the Human Microbiome Project: Genomic DNA from Microbial Mock Community B (even, low concentration), v5.1L, HM-782D) was amplified with the 515F/806RB primers and sequenced to assess amplification and sequencing error rate.</p>
<p><strong>Microbial abundances and FISH</strong></p>
<p>To determine microbial abundances from the BIOS inflow and aquaria samples, the seawater was fixed to 10% formalin and stored at -80°C.&nbsp; Upon analysis, the samples were thawed and filtered onto 0.2µm filters pre-stained with Irgalan black (0.2g in 2% acetic acid) under gentle vacuum (~100mm Hg) and post-stained with 0, 6-diamidino-2-phenyl dihydrochloride (5µg ml-1, DAPI, SIGMA-Aldrich, St. Louis, MO, USA) (Porter and Feig 1980). Slides were then enumerated using an AX70 epifluorescent microscope (Olympus, Tokyo, Japan) under ultraviolet excitation at 100x magnification as previously described (Parsons et al. 2014).&nbsp; At least 500 cells per filter (12 fields) were counted.</p>
<p>Fluorescence in situ hybridization (FISH) was used to quantify the abundance of SAR11 in the BIOS aquaria samples using a probe suite (152R-Cy3, 441R-Cy3, 542R-Cy3, 732R-Cy3) and was conducted as previously described (Morris et al. 2002, Parsons et al. 2012). Image analysis coupled with epifluorescence microscopy was used to process FISH slides excited with Cy3 (550nm) and UV wavelengths. The image capturing was performed using a Retiga Exi CCD digital camera with QCapture software version 2.0 (QImaging, Burnaby, BC, Canada) and processed with Image Pro software (version 7.0; Media Cybernetics, Bethesda, MD, USA) as previously described (Parsons et al. 2014).&nbsp; SAR11 percentages were calculated as SAR11 FISH abundances compared to total cellular abundances.</p>
<p><em>References:</em></p>
<p>Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, C. A. Lozupone, P. J. Turnbaugh, N. Fierer, and R. Knight. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences 108:4516-4522.</p>
<p>Giovannoni, S. J., E. F. DeLong, T. M. Schmidt, and N. R. Pace. 1990. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Applied and Environmental Microbiology 56:2572-2575.</p>
<p>Kozich, J. J., S. L. Westcott, N. T. Baxter, S. Highlander, and P. D. Schloss. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology 79:5112-5120.</p>
<p>Morris, R. M., M. S. Rappé, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson, and S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.</p>
<p>Parsons, R. J., M. Breitbart, M. W. Lomas, and C. A. Carlson. 2012. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J 6:273-284.</p>
<p>Parsons, R. J., C. E. Nelson, C. A. Carlson, C. C. Denman, A. J. Andersson, A. L. Kledzik, K. L. Vergin, S. P. McNally, A. H. Treusch, and S. J. Giovannoni. 2014. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environmental Microbiology:DOI: 10.1111/1462-2920.12445.</p>
<p>Porter, K. G. and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr 25:943-948.</p>
<p>Santoro, A. E., K. L. Casciotti, and C. A. Francis. 2010. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 12:1989-2006.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233612 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233612
completed
Amy Apprill
Woods Hole Oceanographic Institution
508-289-2649
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4
Woods Hole
MA
02543
USA
aapprill@whoi.edu
pointOfContact
asNeeded
Dataset Version: 2015-09-10
Unknown
sample
depth
lat
lon
sample_descrip
pcent_SAR11
SAR11_stdev
primr_806R
primr_806RB
theme
None, User defined
sample identification
depth
latitude
longitude
sample description
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Fluorescence Microscope
Fluorometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Apprill_2013
service
Deployment Activity
Bermuda, Red Sea, Federated States of Micronesia, Florida Keys, and Australia
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.
Fundamental Coral-Microbial Associations
https://osprey.bco-dmo.org/project/564442
Fundamental Coral-Microbial Associations
<p><em>Description from NSF award abstract:</em><br />
Reef-building corals are in decline worldwide due in part to climate change and other human activities, and it is becoming increasingly important to understand what aspects of coral biology are degraded by environmental stress which then leads to coral mortality. It is now widely known that corals harbor communities of bacteria and archaea that are believed to play important roles in maintaining the health of their hosts, but we lack any appreciable understanding about the identity of the microbial associates regularly residing within healthy, reef-building corals. This project asks the central question: do reef-building corals harbor fundamental or persistent microbial associates that are symbiotic within their tissues? In order to address this hypothesis, the investigator will assess the identity of the bacterial and archaeal microbes using a variety of molecular and microscopy approaches that includes the identification and localization of a widespread group of coral bacterial associates belonging to the genus Endozoicomonas. The results of this study will then be used to develop additional questions about the role of these microbial associates in nutrient cycling and how they contribute to the health and survival of corals.</p>
Coral Microbial Relationships
largerWorkCitation
project
eng; USA
biota
oceans
Bermuda, Red Sea, Federated States of Micronesia, Florida Keys, and Australia
2015-09-10
Florida Keys, Federated States of Micronesia, Red Sea, & Bermuda
0
BCO-DMO catalogue of parameters from Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers from the Bermuda, Red Sea, and Federated States of Micronesia in 2013 (Coral Microbial Relationships 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/565735.rdf
Name: sample
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/565736.rdf
Name: depth
Units: meters
Description: <p>sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/565737.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/565738.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/565739.rdf
Name: sample_descrip
Units: unitless
Description: <p>description of location</p>
http://lod.bco-dmo.org/id/dataset-parameter/565740.rdf
Name: pcent_SAR11
Units: percent
Description: <p>percent of SAR11 from FISH counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/565741.rdf
Name: SAR11_stdev
Units: percent
Description: <p>standard deviation of SAR11 from FISH counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/565742.rdf
Name: primr_806R
Units: unitless
Description: <p>Linked sequence data file name of 515F/806R primers; at NCBI SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/565743.rdf
Name: primr_806RB
Units: unitless
Description: <p>Linked sequence data file name of 515F/806RB primers; at NCBI SRA</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
8642
https://datadocs.bco-dmo.org/file/WWW1E26I62yWAM/primers.csv
primers.csv
Primary data file for dataset ID 565723
download
https://osprey.bco-dmo.org/dataset/565723/data/download
download
onLine
dataset
<p><strong>Seawater sample collection</strong></p>
<p>Nucleic acids were collected from surface waters along the coastline of the southeastern Red Sea and from coral reefs surrounding the islands and atolls in the Federated States of Micronesia (Supplementary Table 1). Samples from an aquaria-based experiment housed at the Bermuda Institute of Ocean Sciences (BIOS) were also utilized in this study.&nbsp; Seawater from Ferry Reach, Bermuda (32.37035°N, 64.69545°W) was sampled from a direct inflow line. In addition, this water was also held in separate aerated 30 liter aquaria (similar to de Putron et al. 2011) where it was sampled for nucleic acids (500 ml) and fluorescence <em>in situ</em> hybridization (FISH) analyses (50 ml) over the course of 12 days.</p>
<p><strong>DNA analysis</strong></p>
<p>Seawater collected from the Red Sea (20 liters) and Micronesia (2 liters) was filtered onto 142 mm, 0.22 µm Durapore membrane filters (Millipore, Boston, MA, USA) and 25 mm 0.2 µm polyethersulfone membranes (Supor, Pall, East Hills, NY, USA), respectively, and immediately frozen in liquid nitrogen.&nbsp; Total genomic DNA was extracted from these samples using previously reported methods (Santoro et al. 2010).&nbsp; Similarly, microbial biomass originating from the BIOS seawater inflow line and aquaria seawater was concentrated onto 0.2 µm polyethersulfone membranes (Supor) using a 47 mm support filter and a gelman rig under gentle vacuum (~100mm Hg).&nbsp; Each filter was stored in 1 ml of sterile sucrose lysis buffer (20mM EDTA, 400mM NaCl, 0.75M sucrose, 50mM Tris.HCl) at –80°C. DNA was extracted using the phenol-chloroform method (Giovannoni et al. 1990).&nbsp; Primers targeting the V4 region of the SSU rRNA gene, 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) (Caporaso et al. 2011), were utilized for PCR amplification using unique barcoded primer combinations for each sample.&nbsp; In addition, the same DNA samples were amplified separately with the 515F primer and a modified 806RB primer using the identical barcoding approach. This modified reverse primer replaces the ‘H’ degeneracy in the original 806R primer with a ‘N’, and is designed to enhance SAR11 targets (revised primer 806RB, 5’-GGACTACNVGGGTWTCTAAT-3’).&nbsp; The primers were designed after Kozich and colleagues (2013) and were each equipped with a unique 8-bp barcode, 10-bp pad and 2-bp link that followed the above-mentioned primers (see Supplementary Materials and Methods). Triplicate 25 µl PCR reactions were conducted per sample and each reaction contained 1.25 U of GoTaq Flexi DNA Polymerase (Promega Cooperation, Madison, WI, U.S.A.), 5X Colorless GoTaq Flexi Buffer, 2.5 mM MgCl2, 200 uM dNTP mix (Promega Cooperation, Madison, WI, U.S.A.), 200 nM of each barcoded primer, and 1 - 4 ng of genomic template. The reaction conditions consisted of an initial denaturation step at 95ºC for 2 min, followed by 27-38 cycles of 95ºC for 20 s, 55ºC for 15 s, and 72ºC for 5 min, concluding with an extension step at 72ºC for 10 min. The reactions were carried out on a Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Reaction products (5 µl) were screened on a 1% agarose/TBE gel. The HyperLadder 50bp DNA ladder (generally 5ng µl-1) (Bioline, London, UK) was used to confirm appropriate amplicon size.&nbsp; The number of PCR cycles varied between samples in order to produce similar, minimal yields, but each sample was subjected to nearly identical PCR cycles with both primer sets. The three replicate reactions were pooled and subsequently purified using the QIAquick Purification Kit (Qiagen, Valencia, CA, USA), and quantified using the Qubit 2.0 Fluorometer with the dsDNA High Sensitivity Assay (Life Technologies, Grand Island, NY USA).&nbsp; For each primer set, barcoded amplicons were pooled into equimolar ratios. These amplicon pools were then shipped to the University of Illinois W.M. Keck Center for Comparative and Functional Genomics where they were used for construction of two separate libraries which were subsequently sequenced using 2x250bp paired-end MiSeq (Illumina, San Diego, CA, USA), as detailed previously (similar to Kozich et al. 2013). Control samples included sterile water (negative controls) in which PCR did not yield any detectable amplification with either primer set.&nbsp; A mock community sample (positive control, obtained through BEI Resources, NIAID and NIH as part of the Human Microbiome Project: Genomic DNA from Microbial Mock Community B (even, low concentration), v5.1L, HM-782D) was amplified with the 515F/806RB primers and sequenced to assess amplification and sequencing error rate.</p>
<p><strong>Microbial abundances and FISH</strong></p>
<p>To determine microbial abundances from the BIOS inflow and aquaria samples, the seawater was fixed to 10% formalin and stored at -80°C.&nbsp; Upon analysis, the samples were thawed and filtered onto 0.2µm filters pre-stained with Irgalan black (0.2g in 2% acetic acid) under gentle vacuum (~100mm Hg) and post-stained with 0, 6-diamidino-2-phenyl dihydrochloride (5µg ml-1, DAPI, SIGMA-Aldrich, St. Louis, MO, USA) (Porter and Feig 1980). Slides were then enumerated using an AX70 epifluorescent microscope (Olympus, Tokyo, Japan) under ultraviolet excitation at 100x magnification as previously described (Parsons et al. 2014).&nbsp; At least 500 cells per filter (12 fields) were counted.</p>
<p>Fluorescence in situ hybridization (FISH) was used to quantify the abundance of SAR11 in the BIOS aquaria samples using a probe suite (152R-Cy3, 441R-Cy3, 542R-Cy3, 732R-Cy3) and was conducted as previously described (Morris et al. 2002, Parsons et al. 2012). Image analysis coupled with epifluorescence microscopy was used to process FISH slides excited with Cy3 (550nm) and UV wavelengths. The image capturing was performed using a Retiga Exi CCD digital camera with QCapture software version 2.0 (QImaging, Burnaby, BC, Canada) and processed with Image Pro software (version 7.0; Media Cybernetics, Bethesda, MD, USA) as previously described (Parsons et al. 2014).&nbsp; SAR11 percentages were calculated as SAR11 FISH abundances compared to total cellular abundances.</p>
<p><em>References:</em></p>
<p>Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, C. A. Lozupone, P. J. Turnbaugh, N. Fierer, and R. Knight. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences 108:4516-4522.</p>
<p>Giovannoni, S. J., E. F. DeLong, T. M. Schmidt, and N. R. Pace. 1990. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Applied and Environmental Microbiology 56:2572-2575.</p>
<p>Kozich, J. J., S. L. Westcott, N. T. Baxter, S. Highlander, and P. D. Schloss. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology 79:5112-5120.</p>
<p>Morris, R. M., M. S. Rappé, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson, and S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.</p>
<p>Parsons, R. J., M. Breitbart, M. W. Lomas, and C. A. Carlson. 2012. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J 6:273-284.</p>
<p>Parsons, R. J., C. E. Nelson, C. A. Carlson, C. C. Denman, A. J. Andersson, A. L. Kledzik, K. L. Vergin, S. P. McNally, A. H. Treusch, and S. J. Giovannoni. 2014. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environmental Microbiology:DOI: 10.1111/1462-2920.12445.</p>
<p>Porter, K. G. and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr 25:943-948.</p>
<p>Santoro, A. E., K. L. Casciotti, and C. A. Francis. 2010. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 12:1989-2006.</p>
Specified by the Principal Investigator(s)
<p>Analyses of the data were conducted using mothur version 1.33.3 (Schloss et al. 2009) and included contig construction of the paired ends, quality filtering, amplicon size selection (253bp median size) and alignment to the SSU rRNA gene.&nbsp; Chimera detection was conducted via UCHIME (Edgar et al. 2011) using mothur, and chimeric sequences were removed.&nbsp; Taxonomic classification of sequences was conducted in mothur with the SILVA SSU Ref database (version 117) using the k-nearest neighbor algorithm on sequences sub-sampled to the same depth with each primer pair (10,000, 12,000, or 17,500 sequences per sample for BIOS aquaria, Micronesia, and Red Sea sample sets, respectively). The sequencing error analysis, conducted on the mock community sequences amplified with the 515F/806RB primers, revealed a sequencing error rate of 0.0012%. Raw data are accessible in NCBI’s Short Read Archive under BioProject ID PRJNA279146.</p>
<p><em>References:</em></p>
<p>Edgar, R., B. Haas, J. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200.</p>
<p>Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, C. J. Robinson, J. W. Sahl, B. Stres, G. G. Thallinger, D. J. Van Horn, and C. F. Weber. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-7541.</p>
<p><strong>BCO-DMO Processing:</strong></p>
<p>- 'not available' and 'not determined' changed to nd<br />
- replaced &nbsp;'n/a' with 'NA'<br />
- replaced &nbsp;comma with semicolon<br />
- corrected longitude for BIOS from 64 to -64</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
PI Supplied Instrument Name: PI Supplied Instrument Description:MiSeq (Illumina, San Diego, CA, USA) 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.
PI Supplied Instrument Name: PI Supplied Instrument Description:AX70 epifluorescent microscope (Olympus, Tokyo, Japan) Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
PI Supplied Instrument Name: PI Supplied Instrument Description:Qubit 2.0 Fluorometer with the dsDNA High Sensitivity Assay (Life Technologies, Grand Island, NY USA) Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
PI Supplied Instrument Name: PI Supplied Instrument Description:Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA) 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: Apprill_2013
Apprill_2013
BIOS
BIOS
laboratory
Apprill_2013
Amy Apprill
Woods Hole Oceanographic Institution
BIOS
BIOS
laboratory