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Title Sum-
Institution Dataset ID
   set  data   graph     files  public Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant,
MA during 2010 (Marine Bacterial Viruses project)
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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Bacteria and viruses were collected from the littoral marine zone at Canoe
Cove, Nahant, MA, USA, on August 22 [ordinal day 222], September 18 [261], and
October 13 [286], 2010.

Bacteria were collected using a previously described size-fractionation
method[1]. Bacterial strain naming convention is described using the example
of 10N.286.54.E5: the first position (here \u201c10N\u201d) indicates the year
(2010) and location (Nahant) of isolation, the second position (here
\u201c286\u201d) indicates the ordinal day of isolation, the third position
(here \u201c54\u201d) is a code representing the size-fraction of origin
(0.2um: 45,46,47; 1um: 48,49,50; 5um: 51,52,53; 63um: 54,55,56), and the
fourth position is the storage plate well identifier. Multiple codes within
the size-fraction identifier reflect independent water samples for the 63um
fraction, and independent water sample fractionation series for the other size
classes (water sample A: 45,51,54; sample B: 46, 52, 55; sample C: 47, 53,

Bacterial genome libraries were prepared for sequencing using a tagmentation-
based approach and 1-2ng input DNA per isolate, as previously described[2].
Genomes were sequenced in multiplexed pools of 50-60 samples per Illumina
HiSeq lane. Accession numbers for all bacterial genomes associated with this
study are provided in Supplementary Table S1.

Bacterial phylogenetic relationships were determined by extracting ribosomal
proteins from 278 genomes with hmmsearch[3] and aligning with MAFFT[4] as
described in Hehemann et al. (2016)[5]. These strains were added to the
Vibrionaceae ribosomal phylogeny used in Hehemann et al., 2016 and taxonomy
was assigned using manual inspection. Full-length hsp60 sequences were also
extracted from these genomes using hmmsearch with default parameters and the
Cpn60 hmm (PF00118) from Pfam[6]. The hsp60 sequences were aligned using the
mafft-fftnsi algorithm. Sanger-sequenced hsp60 fragments from 40 strains
lacking genome sequences were added to this alignment using the mafft-fftnsi
algorithm with the --addfragments option. The hsp60 alignment was concatenated
to the ribosomal protein alignment and used to create a phylogeny using RAxML
under a partitioned general time reversible (GTR) model (options: \u2013q, -m
GTRGAMMAX)[7]. SH-like supports were calculated using RAxML.

Viruses were collected using a previously described iron flocculation
approach[8], using 4L sample volumes, 0.2um pre-filtration to remove bacteria,
0.2um filters for floc-capture, and oxalate solution for resuspension to
maintain virus viability. Isolation of viruses was performed as follows. Iron-
oxalate concentrate volumes equivalent to 15mL of seawater were mixed into
agar overlays of 1,334 potential host Vibrio. The agar overlays were performed
by combining 150uL overnight host culture and virus concentrate directly on a
bottom agar (1% agar, 5% glycerol, 125mL/L of chitin supplement [40g/L
coarsely ground chitin, autoclaved, 0.2um filtered] in 2216MB), directly
pipetting 2mL of molten top agar (52 degrees C, 0.4% agar, 5% glycerol, in
2216MB) onto the bottom agar, and rapidly swirling to mix.\u00a0 Plates were
incubated for 2 weeks, and plaques were archived for later purification.
Sequencing and genome analysis of viruses is described briefly, as follows.
High titer lysates of serially purified viruses were concentrated using 30kD
centrifugal filter units (Millipore, Amicon Ultra Centrifugal Filters,
Ultracel 30K, UFC903024) and washed with 1:100 Marine Broth 2216 to reduce
salts for nuclease treatment. Concentrates were brought to approximately 500uL
using 1:100 diluted 2216MB and then treated with DNase I and RNase A for 65
min at 37 degrees C to digest unencapsidated nucleic acids. Nuclease treated
viral lysates were extracted by addition of 1:10 final volume of SDS mix
(0.25M EDTA, 0.5M Tris-HCl (pH9.0), 2.5% sodium dodecyl sulfate), 30 min
incubation at 65C; addition of 0.125 volumes 8M potassium acetate, 60 min
incubation on ice; addition of 0.5 volumes phenol-chloroform; recovery of
nucleic acids from aqueous phase by isopropanol and ethanol precipitation.
Genomes were sequenced in multiplexed pools using Illumina MiSeq and HiSeq
technologies, assembled using CLC assembly cell, and manually curated to
standardize genome start positions for the Caudovirales.

Viral strain naming convention is described using the example of
1.008.O._10N.286.54.E5, with specific identifiers separated by a period. The
first position (here \u201c1\u201d) represents a unique identifier for each
independent plaque isolated from a given host from the initial exposure of a
given host to an environmental virus concentrate. The second position (here
\u201c008\u201d) represents a unique working ID for a host strain. The third
position (here \u201cO\u201d) indicates a unique sublineage generated from a
single plaque during viral serial purification, for example due to the
emergence of multiple plaque morphologies. Following the underscore is the
full strain ID of the host of isolation, as described above.

Accession numbers for all viral genomes associated with this study are
included under NCBI BioProject PRJNA328102.
attribute NC_GLOBAL awards_0_award_nid String 564675
attribute NC_GLOBAL awards_0_award_number String OCE-1435868
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1435868 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String BioSample Submission Data for NCBI
L. Kelly and M. Polz, PIs
Version 8 September 2016
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2016-09-09T19:11:48Z
attribute NC_GLOBAL date_modified String 2020-01-27T16:38:54Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.658497.1
attribute NC_GLOBAL Easternmost_Easting double -70.906
attribute NC_GLOBAL geospatial_lat_max double 42.419
attribute NC_GLOBAL geospatial_lat_min double 42.419
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -70.906
attribute NC_GLOBAL geospatial_lon_min double -70.906
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/658497 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, biome, bioproject, bioproject_accession, chemical, collection, collection_date, data, dataset, date, day, description, dmo, env, env_biome, erddap, geo, geo_loc_name, host, isolate, isolation, isolation_source, lab, lab_host, latitude, loc, longitude, management, name, oceanography, office, ordinal, ordinal_day_of_isolation, organism, organism_type, preliminary, sample, sample_name, sample_type, source, strain, temperature, type
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/658497/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/658497 (external link)
attribute NC_GLOBAL Northernmost_Northing double 42.419
attribute NC_GLOBAL param_mapping String {'658497': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/658497/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Yeshiva University
attribute NC_GLOBAL people_0_person_name String Dr Libusha Kelly
attribute NC_GLOBAL people_0_person_nid String 564679
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Massachusetts Institute of Technology
attribute NC_GLOBAL people_1_affiliation_acronym String MIT
attribute NC_GLOBAL people_1_person_name String Dr Martin Polz
attribute NC_GLOBAL people_1_person_nid String 564684
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Hannah Ake
attribute NC_GLOBAL people_2_person_nid String 650173
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Marine Bacterial Viruses
attribute NC_GLOBAL projects_0_acronym String Marine Bacterial Viruses
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:
Microbes make up the majority of the biomass in the ocean and viral mortality is one of the main ecological factors determining the diversity, abundance and turnover of microbial taxa. Yet, in spite of the known overall importance of viruses, the dynamics of their interactions with their specific microbial hosts remain poorly understood. This project will characterize viral strategies for survival and interaction with their hosts in the ocean, with the goal of enabling a better understanding of the conditions under which viruses can effectively control bacterial populations. The work will generate and integrate diverse data types, ranging from quantification of specific interactions, environmental dynamics of microbial hosts and their viruses, and comparative genome analysis. While the project focuses on the coastal ocean of New England, the approaches and findings will be applicable to the larger field of marine microbial ecology, to other virus/host systems in nature and to engineered systems. This project will fill a gap in current microbial ecology curricula by creating a bioinformatics module to provide training in large-scale sequence data collection and analysis. The module will be refined through testing during an annual course in Nicaragua and will be broadly accessible in the US and internationally. The close collaboration, throughout this project and its associated outreach, between two laboratories with complementary research strengths will provide highly interdisciplinary training for undergraduate students as well for two graduate students.
Viruses and their microbial hosts have co-evolved over billions of year and shape the ecology of the ocean in many ways. Broadly, understanding the mechanisms and emergent properties of virus-host interactions will allow for better understanding and modeling of biogeochemical cycles and the diversity of microbes at the population and genomic level. The guiding hypothesis of this project is that the prevalence of each of different viral strategies is probabilistic and linked to host availability, environmental parameters, and frequency-dependent competition with other virus strains for available hosts. This research will address four aims that characterize how viruses interact with their hosts in the dilute ocean environment by:
(1) quantification of ecological tradeoffs between specialist and generalist viral strategies,
(2) estimation of the prevalence of dual lytic/lysogenic strategy in marine viruses,
(3) identification of host surface receptors of particular viruses and examination of genetic signatures of distinct viral strategies in virus and host genomes, and
(4) identification of genetic and metabolic interactions between virus and host genomes.
This study takes advantage of a model system with the largest available collection of viruses and hosts for which host range and genome sequences have been determined. This work will provide fine-scale analysis of host and phage genomic diversity and abundance in this model system, while at the same time estimating host-range and co-infection, all of which represent important, poorly constrained parameters in virus-host interactions. Finally, this project complements the large number of studies that have looked at single host-virus interactions, metagenome sequencing, and assessment of viral impact on microbial production.
attribute NC_GLOBAL projects_0_end_date String 2017-08
attribute NC_GLOBAL projects_0_geolocation String Coastal waters off Nahant, MA
attribute NC_GLOBAL projects_0_name String How can bacterial viruses succeed in the marine environment?
attribute NC_GLOBAL projects_0_project_nid String 564676
attribute NC_GLOBAL projects_0_start_date String 2014-09
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 42.419
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String bioproject_accession,env_biome,geo_loc_name
attribute NC_GLOBAL summary String Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project)
attribute NC_GLOBAL title String Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -70.906
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable bioproject_accession   String  
attribute bioproject_accession bcodmo_name String accession number
attribute bioproject_accession description String The accession number of the BioProject(s) to which the BioSample belongs
attribute bioproject_accession long_name String Bioproject Accession
attribute bioproject_accession units String unitless
variable env_biome   String  
attribute env_biome bcodmo_name String site
attribute env_biome description String Descriptor of the broad ecological context of a sample.
attribute env_biome long_name String Env Biome
attribute env_biome units String unitless
variable geo_loc_name   String  
attribute geo_loc_name bcodmo_name String site
attribute geo_loc_name description String Geographical origin of the sample.
attribute geo_loc_name long_name String Geo Loc Name
attribute geo_loc_name units String unitless
variable organism_type   String  
attribute organism_type bcodmo_name String sample
attribute organism_type description String Type of organism described
attribute organism_type long_name String Organism Type
attribute organism_type nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute organism_type units String unitless
variable collection_date   String  
attribute collection_date bcodmo_name String date
attribute collection_date description String Date of sampling; mm/dd/yy
attribute collection_date long_name String Collection Date
attribute collection_date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute collection_date units String unitless
variable isolation_source   String  
attribute isolation_source bcodmo_name String site_descrip
attribute isolation_source description String Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
attribute isolation_source long_name String Isolation Source
attribute isolation_source units String unitless
variable sample_name   String  
attribute sample_name bcodmo_name String sample
attribute sample_name description String Sample name in source database
attribute sample_name long_name String Sample Name
attribute sample_name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_name units String unitless
variable organism   String  
attribute organism bcodmo_name String species
attribute organism description String Organism associated with sample. Identitified to species when possible.
attribute organism long_name String Organism
attribute organism units String unitless
variable strain   String  
attribute strain bcodmo_name String sample
attribute strain description String Microbial or eukaryotic strain name
attribute strain long_name String Strain
attribute strain nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute strain units String unitless
variable isolate   String  
attribute isolate bcodmo_name String sample
attribute isolate description String Identification or description of the specific individual from which this sample was obtained
attribute isolate long_name String Isolate
attribute isolate nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute isolate units String unitless
variable host   String  
attribute host bcodmo_name String sample
attribute host description String The natural (as opposed to laboratory) host to the organism from which the sample was obtained.
attribute host long_name String Host
attribute host nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute host units String unitless
variable lab_host   String  
attribute lab_host bcodmo_name String sample
attribute lab_host description String Scientific name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.
attribute lab_host long_name String Lab Host
attribute lab_host nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute lab_host units String unitless
variable sample_type   String  
attribute sample_type bcodmo_name String sample_type
attribute sample_type description String Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly
attribute sample_type long_name String Sample Type
attribute sample_type units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 42.419, 42.419
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -70.906, -70.906
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable temp   float  
attribute temp _FillValue float NaN
attribute temp actual_range float 13.8, 16.3
attribute temp bcodmo_name String temperature
attribute temp description String Temperature of the sample at time of sampling.
attribute temp long_name String Temperature
attribute temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp units String degrees celsius
variable ordinal_day_of_isolation   short  
attribute ordinal_day_of_isolation _FillValue short 32767
attribute ordinal_day_of_isolation actual_range short 222, 286
attribute ordinal_day_of_isolation bcodmo_name String julian_day_yr0
attribute ordinal_day_of_isolation description String Day of year sample was isolated.
attribute ordinal_day_of_isolation long_name String Ordinal Day Of Isolation
attribute ordinal_day_of_isolation units String unitless
variable description   String  
attribute description bcodmo_name String brief_desc
attribute description description String Description of the sample.
attribute description long_name String Description
attribute description units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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