Bacterial Communities of S Alligator River Floodplain (Kakadu)

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: 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.