Minimum information about marine microbial sampling

The Micro B3 checklist is a multi-disciplinary standard developed by the Micro B3 Consortium for description of marine microbial sampling. Content of the standard is grouped into six categories covering various aspects of marine microbial sampling. These categories are environment, measurement, sampling, event, sample and organism. Full adoption of the standard allows generation of data records, which are MIxS compliant but also compliant to minimal reporting requirements of the oceanographic and marine biodiversity community, i.e. respectively the Common Data Index (CDI) and the OBIS schema, advancing the metadata interoperability across research domains. Nucleotide sequences of marine microbial samples described according to the Micro B3 checklist can be placed into a very rich environmental context.

The MicroB3 checklist will facilitate description of samples collected during the Ocean Sampling Day OSD, a simultaneous sampling campaign of the world’s oceans to reveal a marine microbial diversity.

MicroB3 checklist

MANDATORY information

The Micro B3 checklist is schematically shown in the figure below. Mandatory information is placed in colour-coded triangles representing the above mentioned six categories of marine microbial sampling. Detailed description of the mandatory information can be found here. Marine microbial samples described with these mandatory fields are Micro B3 compliant.

MicroB3 checklist mandatory attributes

RECOMMENDED information

In order to reach compliance with standards of all three scientific communities, the genomic (MIxS), oceanographic (CDI) and marine biodiversity (OBIS), Micro B3-recommended information needs to be provided for each sample. The Micro B3-recommended information should be submitted to the appropriate National Oceanographic Data Centre and for the OSD data to the PANGAEA. A comprehensive description of the Micro B3-recommended information for reaching full cross-domain compliance can be found here.

The Micro B3 consortium identified in close collaboration with the oceanographic and marine ecosystem biology communities a number of environmental parameters particularly valuable for description of the environmental context of marine microbial samples. A comprehensive description of these environmental parameters can be found here.

OPTIONAL information

Optional contextual data of marine microbial samples are generally reported depending on scientific interests of the submitting group. The MIxS standard provides a broad range of optional parameters describing environmental context of marine microbial samples associated with genomic data.

Micro B3 data submission

Submission of NON-GENOMIC data

The European Nucleotide Archive can accept molecular data and contextual data of marine microbial samples associated with genomic data.

Non-genomic data, i.e. oceanographic environmental data and morphology-based biodiversity data, should be submitted to the appropriate National Oceanographic Data Centre (NODC) according to established reporting practices maintained by oceanographic community experts. Major National Oceanographic Data Centres from countries bordering the North-East Atlantic, and its adjacent seas: the Mediterranean, the Black Sea, the Baltic, the North Sea and the Arctic are listed here.

For the Ocean Sampling Day campaign, non-genomics data should be reported to the PANGAEA.

Submission of GENOMIC data

Instructions for submissions of raw reads from marine microbial samples can be found here. Instructions for submissions of assembled and annotated sequences of marine microbial samples can be found here.

Contextual data of marine microbial samples associated with genomic data can be submitted to the European Nucleotide Archive using the ENA Micro B3 checklist available from the Webin submission tool.

Webin submission of an environmental Micro B3-compliant sample metadata is in detail described in the online video tutorial available here.

Submitters using the ENA Micro B3 checklist will need to provide the Micro B3 mandatory information but can also add user-defined attributes or use the optional MIxS terms clustered in the checklist into the following groups, (1) environmental conditions, (2) concentration measurements, (3) MIxS sample collection terms, (4) MIxS non-sample terms, (5) MIxS other attributes.

MANDATORY Micro B3 sample checklist

Recommendation applies to microbial sampling in the pelagic zone.

Field Description Controlled vocabulary/format* Example
SAMPLING_ Campaign Refers to a finite or indefinite activity aiming at collecting data/samples, e.g. a cruise, a time series, a mesocosm experiment. Free text OSD-SS2014
SAMPLING_Site Refers to the unique identifier and name of the site/station where the data/sample collection is performed. Format: <Site ID from OSD Site Registry>, <Site name from OSD Site Registry> OSD5, Poseidon-E1-M3A Time Series Station
SAMPLING_Platform Refers to the specific unique stage from which the sampling device was deployed; includes the platform category and platform name. Format:<Platform category from SDN:L06>,<Platform name> research vessel, FILIA
EVENT_Date/Time Date and time when the sampling event started and ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Date and time in UTC;
Format: yyyy-mm-ddThh:mm:ssZ
2013-06-21T14:05:00Z/2013-06-21T14:46:00Z
EVENT_Longitude Longitude of the location where the sampling event started and ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event Format: ###.######
Decimal degrees; East= +, West= - 
Format: Use WGS 84 for GPS data
035.666666 035.670200
EVENT_Latitude Latitude of the location where the sampling event started and ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event Format: ##.######
Decimal degrees; North= +, South= - 
Format: Use WGS 84 for GPS data
-24.666666 -24.664300
SAMPLE_Depth The distance below the surface of the water at which a measurement was made or a sample was collected. Format: ##.#
Positive below the sea surface. SDN:P06:46:ULAA for m
1.7 m
SAMPLE_Protocol_Label Identifies the protocol used to produce the sample, e.g. filtration and preservation. Term list; For details see the SAMPLE_Protocol_Short_Label in the OSD Protocols Section of the OSD Handbook. NP0223
SAMPLE_Title A short informative description of the sample. Must be unique for each sample, (i.e. for each filter generated during sampling). Free text Crete_2m_2
ENVIRONMENT_Biome Descriptor of the broad ecological context of a sample. Terms list: EnvO ENVO:01000023 for “marine pelagic biome”
ENVIRONMENT_Feature Compared to biome, feature is a descriptor of a geographic aspect or a physical entity that strongly influences the more local environment of a sample. Terms list: EnvO ENVO:01000080 for “pelagic isothermal surface”
ENVIRONMENT_Material Descriptor of the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Terms list: EnvO ENVO:00002225 for “mesotrophic water”
ENVIRONMENT_Temperature Temperature of water at the time of taking the sample. Format: ##.# 
SDN:P02:75:TEMP
SDN:P06:46:UPAA for °C
16.2 °C
ENVIRONMENT_Salinity Salinity of water at the time of taking the sample. Format: ##.#
SDN:P02:75:PSAL
SDN:P06:46:UGKG for PSU
39.1 psu
ORGANISM_Taxon_ID An identifier for the nomenclatural (not taxonomic) details of a scientific name. Term list: WoRMS;
Format: LSID
urn:lsid:marinespecies.org:taxname: 345516
ORGANISM_Taxon_Scientific_Name The full name of the lowest level taxon. Term list: WoRMS;
Format: Taxon name
Prochlorococcus marinus
PARAMETER_ID Unique ID from a controlled vocabulary. SDN:P011:353:xxxxxxxx SDN:P011:353: OSEDZZZZ for Concentration of suspended particulate material (organic) per unit volume of water

* SDN:L06::XX is a controlled Terms list describing “CATEGORIES” of platforms. (http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=L06 for human interface)

* SDN:P02:75:XXXX is a controlled Terms list describing “WHAT” is measured. (http://www.seadatanet.org/urnurl/SDN:P02:75:XXXX for XML response; http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P02 for human interface)

* SDN:P06:46:XXXX is a controlled Terms list describing “UNITS” of measurements. (http://www.seadatanet.org/urnurl/SDN:P06:46:XXXX for XML response; http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P06 for human interface)

* OSD Sites Registry is a controlled register for OSD sampling Sites maintained by the Micro B3 IS (http://mb3is.megx.net/osd-registry)

* EnvO is Environment Ontology (http://www.environmentontology.org/Browse-EnvO)

* WoRMS is a World Register of Marine Species (http://www.marinespecies.org/aphia.php?p=search)

* SDN:P011 is a BODC parameter usage vocabulary (http://seadatanet.maris2.nl/v_bodc_vocab/welcome.aspx)

RECOMMENDED Micro B3 sample checklist

Recommendation applies to microbial sampling in the pelagic zone.

Field Description Controlled vocabulary/format* Example
SAMPLING_Investigators List of people who will appear in the citation of data publications. Please order the list according to authorship. The first author is the contact person. Format: <LASTNAME>, <FirstName>, <Institution>, <email> JONES, Peter, Institute1, pjones@institute1.eu; SMITH, Mary, Institute2, msmith@institute2.eu
SAMPLING_Project Refers to the project that organised/funded the data/sample collection. Free text Micro B3
SAMPLING_Objective Describes the scientific context/interest of the sampling activity. This information is useful to generate a short abstract as part of the data set citation. Free text; 100-500 words A short abstract
EVENT_Device Refers to the instrument/gear used to collect the sample or the sensor used to measure environmental parameters. Free text 10L-Niskins or 5L-Bucket
EVENT_Method Refers to the deployment procedure of the Device. Free text 12 Niskins were deployed on a Rosette
EVENT_Comment Report any deviation. Free text Lots of Jellyfish in the water
SAMPLE_Quantity Refers to the quantity of environment that was sampled, most often with dimensions Length, Amount, Mass or Time. Format: ###.### in litres 100 L
SAMPLE_Container Refers to the container in which the sample is stored prior to analysis. Term list; See the SAMPLE_Container in the OSD Protocols Section of the OSD Handbook for details Cryovial, 5 mL
SAMPLE_Content Refers to the content of the sample container. While the sample might target bacteria, the sample content might be a filter or a volume of water. Term list; See the SAMPLE_Material in the OSD Protocols Section of the OSD Handbook for details. (=Investigation_type @ ENVO) Particulate matter on a 142mm PC membrane
SAMPLE_Size-Fraction_Upper-Threshold Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample. Term list; See the SAMPLE_Size-Fraction_Upper-Threshold in the OSD Protocols Section of the OSD Handbook for details 3 µm
SAMPLE_Size-Fraction_Lower-Threshold Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are exclude from the sample. Term list; See the SAMPLE_Size-Fraction_Lower-Threshold in the OSD Protocols Section of the OSD Handbook for details 0.22 µm
SAMPLE_Treatment_Chemicals Refers to the chemicals added to the sample, in the container, preservatives. Terms list: www; See the SAMPLE_Treatment_Chemicals in the OSD Protocols Section of the OSD Handbook for details None
SAMPLE_Treatment_Storage Refers to the conditions in which the sample is stored, e.g. temperature, light conditions, time. Term list; See the SAMPLE_Treatment_Storage in the OSD Protocols Section of the OSD Handbook for details Liquid nitrogen
ENVIRONMENT_Marine_Region It characterises the environment, based on the latitude and longitude, by reference to geographic, political, economic or ecological boundaries. Terms list: Marine Regions Crete Sea
ENVIRONMENT_Other_Parameters Add as many fields as there are other environments parameters measured. See the Micro B3 checklist of environmental parameters. Define the parameter using fields marked with ∆.
ORGANISM_Sex The sex of a specimen or collected/observed individual(s). Terms list: M=Male; F=Female; H=Hermaphrodite; I=Indeterminate (examined but could not be determined; U=Unkown (not examined); T=Transitional (between sexes; useful for sequential hermaphrodites); B = Both Male and Female M
ORGANISM_Life-Stage Indicates the life stage present. Free text ND
ORGANISM_Measurement_Size Refers to size measurements that are made concurrently to the enumeration and identification of organisms. Define the parameter using fields marked with ∆ .
ORGANISM_Measurement_Biovolume Refers to volume measurements/calculations that are made concurrently to the enumeration and identification of organisms. Define the parameter using fields marked with ∆ .
ORGANISM_Measurement_Biomass Refers to biomass measurements/calculations that are made concurrently to the enumeration and identification of organisms. Define the parameter using fields marked with ∆
PARAMETER_Name ∆ Common name for the parameter. Free text Biomass
QUANTITY ∆ Describes the quantity measured using terms from the Système International of units. Free text; SI of units Mass concentration
DIMENSIONS ∆ Describes the quantity measured using dimension terms from the Système International of units. Free text; SI of units M^1 L^-3
CURRENCY ∆ May often refer to a TAXONOMY_ID or a CHEMICAL_ID. Free text; Terms list: Marine Species; Terms list: www; Organic carbon
UNITS ∆ Describes the units of the quantity measured using terms from the Système International of units. SDN:P06:46:xxxx SDN:P06:46:UMGL for mg/L
METHOD ∆ Describes the method used. Equivalent to methodological details provided in a paper. Free text; Mass spectrometry
COMMENT ∆ Any comment about the measurement. Free text Inorganic carbon removed by acidification

* Marine Regions is a standard list of marine georeferenced place names (http://www.marineregions.org/)

* www is an ontological classification and dictionary of small chemical compounds (http://wwwdev.ebi.ac.uk/www/init.do)

Micro B3 checklist of ENVIRONMENTAL PARAMETERS

Recommendation applies to microbial sampling in the pelagic zone. Parameters in bold are part of the MANDATORY Micro B3 checklist

Category Parameter Description Controlled vocabulary/format *
CTD Conductivity Electrical conductivity of water SDN:P02:75:CNDC
SDN:P06:46:UECA for mS/cm
Temperature Temperature of water SDN:P02:75:TEMP
SDN:P06:46:UPAA for °C
Depth (m) Vertical spatial coordinates SDN:P02:75:AHGT
SDN:P06:46:ULAA for m
Salinity Salinity of water SDN:P02:75:PSAL
SDN:P06:46:UGKG for PSU
Fluorescence Raw (volts) or converted (mg Chla/m^3) fluorescence of the water SDN:P02:75:FVLT
SDN:P06:46:UVLT for volts
Seawater Nutrients Concentration Nitrate Nitrate concentration parameters in the water column SDN:P02:75:NTRA
SDN:P06:46:UPOX for µmol/L
Nitrite Nitrite concentration parameters in the water column SDN:P02:75:NTRI
SDN:P06:46:UPOX for µmol/L
Phosphate Phosphate concentration parameters in the water column SDN:P02:75:PHOS
SDN:P06:46:UPOX for µmol/L
Silicate Silicate concentration parameters in the water column SDN:P02:75:SLCA
SDN:P06:46:UPOX for µmol/L
Ammonium Ammonium concentration parameters in the water column SDN:P02:75:AMON
SDN:P06:46:UPOX for µmol/L
Seawater Chemical Properties pH Alkalinity, acidity and pH of the water column SDN:P02:75:ALKY
Dissolved oxygen concentration Dissolved oxygen parameters in the water column SDN:P02:75:DOXY
SDN:P06:46:KGUM for µmol/kg
Seawater Optical Properties Downward PAR Visible waveband radiance and irradiance measurements in the water column SDN:P02:75:VSRW
SDN:P06:46:UMES for µE/m^2/s
Turbidity Transmittance and attenuance of the water column SDN:P02:75:ATTN
SDN:P06:46:USTU for FTU or NTU
Organic Matter Concentration (Amount or Mass) Carbon organic particulate (POC) Particulate organic carbon concentration in the water column SDN:P02:75:CORG
SDN:P06:46:UGPL for µg/L
Nitrogen organic particulate (PON) Particulate organic nitrogen concentration in the water column SDN:P02:75:NTOT
SDN:P06:46:UGPL for µg/L
Carbon organic dissolved (DOC) Dissolved organic carbon concentration in the water column SDN:P02:75:DOCC
SDN:P06:46:UPOX for µmol/L
Nitrogen organic dissolved (DON) Dissolved organic nitrogen concentration in the water column SDN:P02:75:TDNT
SDN:P06:46:UMGL for mg/L
Organism Concentration (Amount, Volume or Mass) Pigment concentrations Concentration of pigments (e.g. chlorophyll a) extracted and analysed by fluorometry or HPLC SDN:P02:75:CPWC
SDN:P06:46:UMMC for mg/m^3
Picoplankton (Flow Cytometry) Abundance of cells in the water column (+other avail. cell properties) SDN:P02:75:BATX
SDN:P06:46:UPMM for #/m^3
Nano/Microplankton Abundance of cells in the water column (+other avail. cell properties) SDN:P02:75:MATX or PATX
SDN:P06:46:UPMM for #/m^3
Meso/Macroplankton Abundance of individuals in the water column (+other avail. properties) SDN:P02:75:ZATX
SDN:P06:46:UPMM for #/m^3
Community Production Rate Primary Production (isotope uptake) Primary Production in the water column SDN:P02:75:PPRD
SDN:P06:46:UGDC for mg/m^3/d
Primary Production (oxygen) Primary Production in the water column SDN:P02:75:PPRD
SDN:P06:46:UGDC for mg/m^3/d
Bacterial production (isotope uptake) Bacterial production in the water column SDN:P02:75:UPTH
SDN:P06:46:UGDC for mg/m^3/d
Bacterial production (respiration) Bacterial production in the water column SDN:P02:75:UPTH
SDN:P06:46:UGDC for mg/m^3/d

* SDN:P02:75:XXXX is a controlled Terms list describing “WHAT” is measured. (http://www.seadatanet.org/urnurl/SDN:P02:75:XXXX for XML response; http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P02 for human interface)

* SDN:P06:46:XXXX is a controlled Terms list describing “UNITS” of measurements. (http://www.seadatanet.org/urnurl/SDN:P06:46:XXXX for XML response; http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P06 for human interface)

Latest ENA news

09 Dec 2014: ENA release 122
Release 122 of ENA's assembled/annotated sequences is now available

12 Nov 2014: Simplification of data release procedures
The European Nucleotide Archive will couple the public release of sequence records and the release of study records that contain these sequence records, with immediate effect.

11 Nov 2014: ENA/EMG Sample Record Annotation Workshop
European Nucleotide Archive (ENA) and EBI Metagenomics Portal (EMG), are organising the ENA/EMG Sample Record Annotation Workshop on the 1-5 December 2014 to enrich the environmental sample records.