Occurrence record: MGYA00167670_Bacteria::Firmicutes:Clostridia:Clostridiales:Clostridiaceae:Clostridium

MaterialSample of Clostridium recorded on 2009-11-21

API

Dataset

Data partner	GBIF
Data resource	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.
Occurrence ID	MGYA00167670_Bacteria::Firmicutes:Clostridia:Clostridiales:Clostridiaceae:Clostridium
Basis of record	MaterialSample Supplied basis "MATERIAL_SAMPLE"
License	CC-BY 4.0 (Int) Supplied as CC_BY_4_0
Organism quantity type	DNA sequence reads
Dynamic properties	"{""temperature"":""18.142626"",""project name"":""Tara Oceans expedition (2009-2013)"",""geographic location (longitude)"":""17.9348"",""collection date"":""2009-11-21"",""environment (biome)"":""marine biome (ENVO:00000447)"",""environment (feature)"":""surface water layer (ENVO:00002042)"",""environment (material)"":""""particulate matter, including plankton (ENVO:xxxxxxxx)"""",""environmental package"":""water"",""sample collection device or method"":""PUMP (High Volume Peristaltic Pump)"",""salinity"":""38.114216"",""geographic location (latitude)"":""42.4552"",""instrument model"":""Illumina Genome Analyzer IIx"",""ENA checklist"":""ERC000030""}"
Occurrence status	present Supplied as PRESENT
Organism quantity	1.0
Identification references	https://www.ebi.ac.uk/metagenomics/pipelines/4.1
Abcd identification qualifier	Not provided
Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00167670#taxonomic.

Event

Event ID	MGYA00167670
Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00167670#taxonomic.
Occurrence date	2009-11-21 Supplied as year:2009 month:11 day:21
Date precision	Day
Event remarks	"""This sample (TARA_A100000362) was collected during the Tara Oceans expedition (2009-2013) at station TARA_024 (latitudeN=42.4552, longitudeE=17.9348) on date/time=2009-11-21T11:10, using a PUMP (High Volume Peristaltic Pump). The sample material (particulate matter, including plankton (ENVO:xxxxxxxx)) was collected at a depth of 3-7 m, targeting a surface water layer (ENVO:00002042) in the marine biome (ENVO:00000447). The sample was size-fractionated (0.8-20 micrometres), and stored in liquid nitrogen for later detection of unicellular eukaryote (protist) nucleic acid sequences by pyrosequencing methods, and for later metagenomics/transcriptomics analysis."""
End day of year	325
Start day of year	325

Taxonomy

Scientific name	Clostridium Supplied scientific name "Clostridium Prazmowski, 1880"
Taxon rank	genus
Kingdom	Bacteria
Phylum	Firmicutes Supplied as "Firmicutes_A"
Class	Clostridia
Order	Clostridiales
Family	Clostridiaceae
Genus	Clostridium
Taxonomic issue	No issues
Name match metric	Exact match The supplied name matched the name exactly.
Name parse type	SCIENTIFIC
Taxonomic status	ACCEPTED

Geospatial

Country	Croatia
latitude	42.4552
longitude	17.9348
Geodetic datum	EPSG:4326
Coordinate precision	Unknown
Verbatim depth	5.0
Country code	HR

Additional properties

Accepted scientific name	Clostridium Prazmowski, 1880
Accepted taxon key	3226206
Class key	304
Dataset key	d596fccb-2319-42eb-b13b-986c932780ad
depth accuracy	0.0
Family key	7797
Gbif id	2019465859
Gbif region	EUROPE
Generic name	Clostridium
Genus key	3226206
Has coordinate	true
Has geospatial issues	false
Is sequenced	false
Kingdom key	3
Last crawled	2025-02-15T14:53:27.275Z
Last interpreted	2025-02-15T15:06:57.232Z
Last parsed	2025-02-15T15:06:57.232Z
Material sample ID	https://www.ebi.ac.uk/metagenomics/samples/ERS488476
Order key	1211
Phylum key	11371390
Protocol	DWC_ARCHIVE
Published by gbif region	EUROPE
Publishing country	GB
relative organism quantity	3.652813250653123E-7
Repatriated	true
Sample size unit	DNA sequence reads
Sample size value	2737616.0
Taxon key	3226206
Verbatim scientific name	Clostridium

Ostali atributi

User flagged issues

Data quality tests

Test name	Result
Geodetic datum assumed WGS84	Warning
Country inferred from coordinates	Warning
Show/Hide 26 passed properties
Basis of record not supplied	Passed
Basis of record badly formed	Passed
Invalid collection date	Passed
Incomplete collection date	Passed
First of the month	Passed
Missing identification references	Passed
Data are generalised	Passed
Missing taxonomic rank	Passed
Name not supplied	Passed
Kingdom not recognised	Passed
Name not recognised	Passed
Invalid scientific name	Passed
Name not in national checklists	Passed
Decimal coordinates not supplied	Passed
Depth out of range	Passed
Depth value non-numeric	Passed
Depth value supplied in feet	Passed
Coordinates are transposed	Passed
Coordinates are out of range for species	Passed
Supplied coordinates are zero	Passed
Zero latitude	Passed
Zero longitude	Passed
Location not supplied	Passed
Supplied coordinates centre of state	Passed
Coordinates centre of country	Passed
Missing geodetic datum	Passed
Show/Hide 11 missing properties
Missing an identification qualifier	Missing
Missing name of person who identified the specimen/observation	Missing
Missing identification date	Missing
Missing catalogue number	Missing
Missing coordinate precision	Missing
Coordinate uncertainty not specified	Missing
Missing name of person who georeferenced the occurrence	Missing
Missing georeferenced protocol	Missing
Missing georeferenced sources	Missing
Missing georeferenced verification status	Missing
Missing georeference date	Missing
Show/Hide 47 tests that have not been run
Coordinates dont match supplied state	Unchecked (lack of data)
Habitat incorrect for species	Unchecked (lack of data)
Outside expert range for species	Unchecked (lack of data)
Altitude out of range	Unchecked (lack of data)
Identification date before occurrence date	Unchecked (lack of data)
Min and max altitude reversed	Unchecked (lack of data)
Invalid geodetic datum	Unchecked (lack of data)
Georeferenced after occurrence date	Unchecked (lack of data)
Cultivated / escapee	Unchecked (lack of data)
Higher taxonomy missing	Unchecked (lack of data)
Badly formed altitude	Unchecked (lack of data)
Media unrepresentative	Unchecked (lack of data)
Day and month transposed	Unchecked (lack of data)
Coordinates converted to WGS84	Unchecked (lack of data)
Date precision invalid	Unchecked (lack of data)
Coordinates converted from UTM	Unchecked (lack of data)
Supplied country not recognised	Unchecked (lack of data)
Latitude Longitude calculated from grid reference	Unchecked (lack of data)
Precision / range mismatch	Unchecked (lack of data)
Possible duplicate record	Unchecked (lack of data)
Altitude value supplied in feet	Unchecked (lack of data)
Coordinates dont match supplied country	Unchecked (lack of data)
Latitude is negated	Unchecked (lack of data)
Occurrence status assumed to be present	Unchecked (lack of data)
unrecognisedOccurrenceStatus	Unchecked (lack of data)
Decimal latitude/longitude conversion failed	Unchecked (lack of data)
Min and max depth reversed	Unchecked (lack of data)
Homonym issues with supplied name	Unchecked (lack of data)
Altitude value non-numeric	Unchecked (lack of data)
Media unrepresentative for taxon	Unchecked (lack of data)
Resource taxonomic scope mismatch	Unchecked (lack of data)
No collection date supplied	Unchecked (lack of data)
First of the year	Unchecked (lack of data)
Coordinate precision and uncertainty transposed	Unchecked (lack of data)
Unable to convert UTM coordinates	Unchecked (lack of data)
Coordinate precision not valid	Unchecked (lack of data)
Institution code not recognised	Unchecked (lack of data)
Longitude is negated	Unchecked (lack of data)
Collection code not recognised	Unchecked (lack of data)
Unparseable verbatim coordinates	Unchecked (lack of data)
First of the century	Unchecked (lack of data)
Coordinate uncertainty not valid	Unchecked (lack of data)
Collector name unparseable	Unchecked (lack of data)
Type status not recognised	Unchecked (lack of data)
Coordinates derived from verbatim coordinates	Unchecked (lack of data)
Image URL invalid	Unchecked (lack of data)
Unrecognized geodetic datum	Unchecked (lack of data)

Additional information about political and environmental boundaries

Biogeoregije	Mediteranska
Država	Hrvatska
Županije	Dubrovačko-neretvanska županija

Group	Field Name	Original Value	Processed Value
Classification	Name parse type		SCIENTIFIC
	Name match metric		exactMatch
	Scientific name	Clostridium Prazmowski, 1880	Clostridium
	Class	Clostridia	Clostridia
	Genus id		3226206
	Taxon concept ID		3226206
	Kingdom id		3
	Left		6410504
	Phylum	Firmicutes_A	Firmicutes
	Kingdom	Bacteria	Bacteria
	Class id		304
	Genus	Clostridium	Clostridium
	Phylum id		11371390
	Order	Clostridiales	Clostridiales
	Taxon rank	GENUS	genus
	Order id		1211
	Taxonomic issue		["noIssue"]
	Family id		7797
	Taxonomic status	ACCEPTED
	Family	Clostridiaceae	Clostridiaceae
	Taxon rank id		6000
	Right		6410870
Event	Date precision		Day
	Event date	2009-11-21	2009-11-21
	Year	2009	2009
	Event remarks	"""This sample (TARA_A100000362) was collected during the Tara Oceans expedition (2009-2013) at station TARA_024 (latitudeN=42.4552, longitudeE=17.9348) on date/time=2009-11-21T11:10, using a PUMP (High Volume Peristaltic Pump). The sample material (particulate matter, including plankton (ENVO:xxxxxxxx)) was collected at a depth of 3-7 m, targeting a surface water layer (ENVO:00002042) in the marine biome (ENVO:00000447). The sample was size-fractionated (0.8-20 micrometres), and stored in liquid nitrogen for later detection of unicellular eukaryote (protist) nucleic acid sequences by pyrosequencing methods, and for later metagenomics/transcriptomics analysis."""
	End day of year	325
	Day	21	21
	Start day of year	325
	Month	11	11
	Event ID	MGYA00167670
Identification	Identification references	https://www.ebi.ac.uk/metagenomics/pipelines/4.1
	Determinacijski kvalifikator Abcd		Not provided
	Identification qualifier		Not provided
	Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00167670#taxonomic.
Occurrence	Occurrence ID	MGYA00167670_Bacteria::Firmicutes:Clostridia:Clostridiales:Clostridiaceae:Clostridium
	Basis of record	MATERIAL_SAMPLE	MaterialSample
	Organism quantity type	DNA sequence reads
	Dynamic properties	"{""temperature"":""18.142626"",""project name"":""Tara Oceans expedition (2009-2013)"",""geographic location (longitude)"":""17.9348"",""collection date"":""2009-11-21"",""environment (biome)"":""marine biome (ENVO:00000447)"",""environment (feature)"":""surface water layer (ENVO:00002042)"",""environment (material)"":""""particulate matter, including plankton (ENVO:xxxxxxxx)"""",""environmental package"":""water"",""sample collection device or method"":""PUMP (High Volume Peristaltic Pump)"",""salinity"":""38.114216"",""geographic location (latitude)"":""42.4552"",""instrument model"":""Illumina Genome Analyzer IIx"",""ENA checklist"":""ERC000030""}"
	Occurrence status	PRESENT	present
	Organism quantity	1.0
Attribution	Data resource		Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.
	Data provider uid		dp8
	License	CC_BY_4_0	CC-BY 4.0 (Int)
	Data resource uid	dr81
	Data partner		GBIF
Location	Decimal latitude	42.4552	42.4552
	Country		Croatia
	Decimal longitude	17.9348	17.9348
	Verbatim depth	5.0	5.0
	Geodetic datum		EPSG:4326
	Country code	HR

Occurrence record: MGYA00167670_Bacteria::Firmicutes:Clostridia:Clostridiales:Clostridiaceae:Clostridium

Dataset

Event

Taxonomy

Geospatial

Additional properties

Ostali atributi

User flagged issues

Data quality tests

Additional information about political and environmental boundaries

- flagged by