ERDDAP > info > bcodmo_dataset_658497

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[Isolation culturing and sequencing of bacteria and viruses] - Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project) (How can bacterial viruses succeed in the marine environment?)		F   I   M	background			BCO-DMO	bcodmo_dataset_658497

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, 56). 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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/658497
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
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] - Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project) (How can bacterial viruses succeed in the marine environment?)
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/
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/
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/
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/
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/
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/
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/
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/
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/
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/
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.