AIMS Geonetwork
Great Barrier Reef Genomics Database: Seawater Illumina Reads
This dataset comprises of microbial metagenomics sequencing reads of seawater collected across 48 reef sites across the Great Barrier Reef. Samples were collected across four Long Term Monitoring Program (LTMP) field trips between November 2019-July 2020, combining water chemistry data, LTMP field surveys and microbial metagenomics data. This data collection was a major part of the QRCIF IMOS GBR microbial genomic database project, which aims to generate a comprehensive open access repositor of microbial genomic data from across the region. Seawater was collected in quadruplicate either by SCUBA or using Niskin Bottles at each reef site, 5L of seawater was pre-filtered using a 5µm filter and applied to a 0.22µm sterivex filter, snap frozen and stored at -20°C in preparation of DNA extraction. DNA was extracted from sterivex filters using phenol:chloroform:Iso-amyl alcolol extraction, ethanol precipitation and cleanup using the Zymo Clean and Concentrator® kit before submission for sequencing at the Australian Centre for Ecogenomics sequencing facility, Illumina. The data presented as illumina paired-end shotgun metagenomics sequencing runs, in fastq format, generated by Microba Life Sciences, Brisbane, QLD, Australia. Each downloadable archive contains forward and reverse reads for all replicate sampling performed at that particular site. Water quality particulate and dissolved nutrient data was generated as previously described ( https://doi.org/10.25845/5c09b551f315b ) from water samples collected simultaneously at each reef site.
Zip files are available through the spatial layer under each site's 'illumina.seawater.zip' - please note these are large downloads (between 6 - 14 GB).
Simple
Identification info
- Date (Revision)
- 2024-10-17T00:00:00
Publisher
Australian Institute of Marine Science (AIMS) - ()
PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE
TOWNSVILLE
Queensland
4810
Australia
Owner
Australian Institute of Marine Science (AIMS) - ()
PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE
TOWNSVILLE
Queensland
4810
Australia
- Website
- AIMS Web Site
- Website
- AIMS Web Site
- Credit
- Yeoh, YK. AIMS, Australia
- Credit
- GBR Microbial Genomic Database project is funded by the Department of Environment and Science, Research Infrastructure Co-investment Fund (RICF) in partnership with Australian Institute of Marine Science (AIMS), Integrated Marine Observing System (IMOS) and University of Queensland
- Credit
- Webster, NS. Australian Antarctic Program, Australia; Australian Centre for Ecogenomics, UQ, Australia; AIMS, Australia
- Credit
- Hugenholtz, P. Australian Centre for Ecogenomics, University of Queensland (UQ), Australia
- Credit
- Robbins, S. Australian Centre for Ecogenomics,UQ, Australia
- Credit
- Australia’s Integrated Marine Observing System (IMOS) is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS). It is operated by a consortium of institutions as an unincorporated joint venture, with the University of Tasmania as Lead Agent.
- Credit
- Laffy, PW. Australian Institute of Marine Science (AIMS), Australia
- Credit
- Bell, SC. AIMS, Australia
- Credit
- Terzin, M. AIMS, Australia, JCU, Australia
- Credit
- Bourne, DG. James Cook University (JCU), Australia; AIMS, Australia
- Status
- Completed
Principal investigator
Australian Institute of Marine Science (AIMS) - Yeoh, YK ()
PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE
TOWNSVILLE
Queensland
4810
Australia
Point of contact
Australian Institute of Marine Science (AIMS) - AIMS Data Centre ()
PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE
TOWNSVILLE
Queensland
4810
Australia
- Temporal resolution
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P1Y0M0DT0H0M0S
- Topic category
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- Oceans
Extent
- Description
- Monsoon Reef
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- 22-084 Reef
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- Rib Reef
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- Chicken Reef
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- 11-049 Reef
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- 11-162 Reef
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- North Reef
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- Grub Reef
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- Mantis Reef
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- Lagoon Reef
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- Sand Bank No 1 Reef
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- St Crispin Reef
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- Davie Reef
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- Corbett Reef
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- 13-124 Reef
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- Fairfax Reef
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- Hoskyn Reef
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- Boult Reef
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- Masthead Reef
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- Erskine Reef
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- Hastings Reef
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- Agincourt Reef
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- John Brewer Reef
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- Fore and Aft Reef
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- Arlington Reef
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- Thetford Reef
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- Moore Reef
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- Hedley Reef
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- McCulloch Reef
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- Peart Reef
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- Helix Reef
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- Feather Reef
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- Farquharson Reef
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- Taylor Reef
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- Little Kelso Reef
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- Kelso Reef
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- Roxburgh Reef
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- Myrmidon Reef
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- Knife Reef
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- Lynch Reef
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- McSweeney Reef
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- Fork Reef
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- Centipede Reef
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- Chinaman Reef
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- 21-580
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- Description
- Small Lagoon Reef
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- Description
- 21-550 Reef
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- Description
- Broomfield Reef
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Extent
- Description
- Collective resources start and end dates
Temporal extent
- Time position
- 2019-11-23
- Time position
- 2020-07-17
- Maintenance and update frequency
- Not planned
- AODN Platform Vocabulary
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- diver
- AODN Organisation Vocabulary
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- Microbial Genomic Database Sub-Facility, Integrated Marine Observing System (IMOS)
- AODN Discovery Parameter Vocabulary
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- Turbidity of the water body
- Fluorescence of the water body
- Concentration of nitrate {NO3} per unit volume of the water body
- Practical salinity of the water body
- Concentration of chlorophyll per unit volume of the water body
- Concentration of pheophytin-a per unit volume of the water body
- Concentration of phosphate {PO4} per unit volume of the water body
- Concentration of suspended particulate material per unit volume of the water body
- Concentration of dissolved nitrite per unit volume of the water body
- Concentration of ammonium {NH4} per unit volume of the water body
- Temperature of the water body
- Concentration of total dissolved phosphorus {TDP} per unit volume of the water body
Resource constraints
- Linkage
-
http://i.creativecommons.org/l/by/3.0/au/88x31.png
License Graphic
- Title
- Creative Commons Attribution 3.0 Australia License
- Website
-
http://creativecommons.org/licenses/by/3.0/au/
License Text
- Other constraints
- Use Limitation: All AIMS data, products and services are provided "as is" and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.
- Other constraints
- Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "Australian Institute of Marine Science (AIMS). (2022). Great Barrier Reef Genomics Database: Seawater Illumina Reads. https://doi.org/10.25845/Q4XH-YN10, accessed[date-of-access]".
- Language
- English
- Character encoding
- UTF8
Content Information
- Content type
- Physical measurement
Identifier
- Description
- Estimate of suspended sediment concentration based on the proportion of a light transmission in the water column that is reflected back to a co-located receiver.
Identifier
- Description
- The amount of radiation generated in the water column in response to higher energy radiation transmission expressed relative to an unspecified baseline
Identifier
- Description
- Concentration of nitrate per unit volume of the water column. Nitrate may be expressed in terms of mass or quantity of substance.
Identifier
- Description
- The quantity of dissolved ions (predominantly salt in seawater) expressed on a scale (PSS-78) based on the conductivity ratio of a seawater sample to a standard KCl solution.
Identifier
- Description
- The mass of all types of chlorophyll per unit volume of the water column held in particles of any size
Identifier
Identifier
- Description
- Concentration of phosphate per unit volume of the water column. Phosphate may be expressed in terms of mass or quantity of substance
Identifier
- Description
- Concentration of ammonium per unit volume of the water column. Ammonium may be expressed in terms of mass or quantity of substance.
Identifier
- Description
- The degree of hotness of the water column expressed against a standard scale. Includes both IPTS-68 and ITS-90 scales.
Distribution Information
Distributor
Distributor
Australian Institute of Marine Science (AIMS) - AIMS Data Centre ()
PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE
TOWNSVILLE
Queensland
4810
Australia
- OnLine resource
-
Data Dictionary - GBR Genomics Database: Seawater Illumina Reads
Data Dictionary - GBR Genomics Database: Seawater Illumina Reads
- OnLine resource
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Access the data via AODN Portal Link
Access the data via AODN Portal Link
- OnLine resource
-
aims:GBR-Genomics-Database_Seawater-Illumina-Reads
GBR-Genomics-Database_Seawater-Illumina-Reads
- OnLine resource
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GeoPackage GBR Genomics Database - Seawater Illumina Reads [gpkg size: 132KB]
GeoPackage GBR Genomics Database - Seawater Illumina Reads [gpkg size: 132KB]
- OnLine resource
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GBR Genomics Database - Seawater Illumina Reads [csv file size: 23KB]
GBR Genomics Database - Seawater Illumina Reads [csv file size: 23KB]
Resource lineage
- Statement
- Water quality particulate and dissolved nutrient data was generated as previously described https://doi.org/10.25845/5c09b551f315b Water quality chlorophyll and turbidity measurements was generated as previously described https://doi.org/10.25845/CMVM-ZT18 Underway Sensors: Enhanced Measurements From Ships Of Opportunity (SOOP)https://apps.aims.gov.au/metadata/view/8af21108-c535-43bf-8dab-c1f45a26088c Underway data were collected throughout the trips and data assembled here are displayed with closest 'Sample Collection Start' times (i.e. <10mins difference), except in two instances, ship sensor readings >30mins time difference occurs (Helix Reef and 21-550 Reef).
- Hierarchy level
- Dataset
- Maintenance and update frequency
- As needed
Metadata
- Metadata identifier
- 5956fd44-f864-4811-9ec3-15499f1863c4
- Language
- English
- Character encoding
- UTF8
Point of contact
Australian Institute of Marine Science (AIMS) - AIMS Data Centre
PRIVATE MAIL BAG 3
TOWNSVILLE MAIL CENTRE
Queensland
4810
Australia
>
- Hours of service
- 0800 to 1640 UTC+10: Monday to Friday
Type of resource
- Resource scope
- Dataset
- Metadata linkage
-
Point of truth URL of this metadata record
Point of truth URL of this metadata record
- Date info (Creation)
- 2022-06-20T00:00:00
- Date info (Revision)
- 2022-12-16T00:00:00
Metadata standard
- Title
- ISO 19115-3:2018
Overviews
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Provided by
Associated resources
Not available