Data

Bacterial Communities of the South Alligator River Floodplain (Kakadu) 2012

Australian Ocean Data Network
CSIRO (Associated with) CSIRO O&A, Information & Data Centre (Point of contact) CSIRO Oceans & Atmosphere - Hobart (Associated with) Chariton, Anthony (principalInvestigator)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://marlin.csiro.au/geonetwork/srv/eng/catalog.search#/metadata/c193c71c-1ff6-4860-9b70-8dc31808c285&rft.title=Bacterial Communities of the South Alligator River Floodplain (Kakadu) 2012&rft.identifier=c193c71c-1ff6-4860-9b70-8dc31808c285&rft.publisher=Australian Ocean Data Network&rft.description=Bacterial survey of the S Alligator River Floodplain (Kakadu). The study was designed to examine how history to saltwater exposure alters microbial assemblages. The research was part of the NERP Northern Australian Hub. Data includes 90 samples taken from three different areas of energy (low, medium and high) and three areas of the floodplain (lower, upper and backwaters). The data includes processed 16S rDNA amplicons, GPS co-ordinates and soil chemistry.Progress Code: completedStatement: Oligonucleotide barcoded primers were used to PCR amplify a ~600 base pair (bp) product spanning the V4 and V6 hyper variable region of the 16S rRNA gene 563F, 5’-ccatctcatccctgcgtgtctccgactcag-AYTGGGYDTAAAGNG-3’ (Claesson, et al., 2010) and 1046R, 5’-cctatcccctgtgtgccttggcagtctcag-CGACAGCCATGCANCACCT- 3’ (Sogin, et al., 2006). Data were analysed using the Mothur v.1.30.1. Sequences were aligned to the SILVA database (Pruesse et al. 2007) and those that did not align were removed. Alignments were trimmed so that all sequences covered the entire alignment length. Sequences were clustered at a similarity cut-off of 97%. Representatives of resultant operational taxonomic units (OTUs) were identified using the SILVA taxonomy tool. The final dataset comprised 939,511 sequences.&rft.creator=Anonymous&rft.date=2015&rft.coverage=westlimit=132.35; southlimit=-12.77; eastlimit=132.56; northlimit=-12.36; projection=WGS 84 (EPSG:4326)&rft.coverage=westlimit=132.35; southlimit=-12.77; eastlimit=132.56; northlimit=-12.36; projection=WGS 84 (EPSG:4326)&rft_rights=The data have been released under the CSIRO Data Licence.&rft_rights=All Rights (including copyright) Australian Institute of Marines Sciences, Charles Darwin University, CSIRO Australia, Department of the Enviroment 2015.&rft_rights=The metadata and data are available to the public.&rft_subject=biota&rft_subject=environment&rft_subject=Earth Science | Biological Classification | Bacteria/Archaea&rft_subject=Earth Science | Land Surface | Erosion/Sedimentation | Sediments&rft_subject=Earth Science | Solid Earth | Geomorphic Landforms/Processes | Fluvial Landforms | Flood Plain&rft.type=dataset&rft.language=English Access the data
Cite Saved to MyRDA Save to MyRDA

Licence & Rights:

view details

The data have been released under the CSIRO Data Licence.

All Rights (including copyright) Australian Institute of Marines Sciences, Charles Darwin University, CSIRO Australia, Department of the Enviroment 2015.

The metadata and data are available to the public.

Access:

Other

Full description

Bacterial survey of the S Alligator River Floodplain (Kakadu). The study was designed to examine how history to saltwater exposure alters microbial assemblages. The research was part of the NERP Northern Australian Hub. Data includes 90 samples taken from three different areas of energy (low, medium and high) and three areas of the floodplain (lower, upper and backwaters). The data includes processed 16S rDNA amplicons, GPS co-ordinates and soil chemistry.

Lineage

Progress Code: completed
Statement: Oligonucleotide barcoded primers were used to PCR amplify a ~600 base pair (bp) product spanning the V4 and V6 hyper variable region of the 16S rRNA gene 563F, 5’-ccatctcatccctgcgtgtctccgactcag-AYTGGGYDTAAAGNG-3’ (Claesson, et al., 2010) and 1046R, 5’-cctatcccctgtgtgccttggcagtctcag-CGACAGCCATGCANCACCT- 3’ (Sogin, et al., 2006). Data were analysed using the Mothur v.1.30.1. Sequences were aligned to the SILVA database (Pruesse et al. 2007) and those that did not align were removed. Alignments were trimmed so that all sequences covered the entire alignment length. Sequences were clustered at a similarity cut-off of 97%. Representatives of resultant operational taxonomic units (OTUs) were identified using the SILVA taxonomy tool. The final dataset comprised 939,511 sequences.

Notes

Credit
This research was funded under the NERP Northern Australia Hub, Project 5.4. The research was a collaboration between the Federal Government, CSIRO, AIMS and Charles Darwin University.
Credit
Contributors: Anthony Chariton, Claire Streten, Karen Gibb

This dataset is part of a larger collection

Click to explore relationships graph
Help

Related People

132.56,-12.36 132.56,-12.77 132.35,-12.77 132.35,-12.36 132.56,-12.36

132.455,-12.565

text: westlimit=132.35; southlimit=-12.77; eastlimit=132.56; northlimit=-12.36; projection=WGS 84 (EPSG:4326)

Subjects
Earth Science | Biological Classification | Bacteria/Archaea | Earth Science | Land Surface | Erosion/Sedimentation | Sediments | Earth Science | Solid Earth | Geomorphic Landforms/Processes | Fluvial Landforms | Flood Plain | biota | environment |

User Contributed Tags    

Login to tag this record with meaningful keywords to make it easier to discover

Other Information
Data Link (DOI) (Data Link)

url : https://dx.doi.org/10.4225/08/551B48D79701C

Link to the data (CSIRO Data Access Portal) (Data Link (DOI))

url : https://dx.doi.org/10.4225/08/551B48D79701C

Identifiers
  • global : c193c71c-1ff6-4860-9b70-8dc31808c285