About Open Access
Development of Alternate ssu-rRNA Probing Strategies for Characterizing Aquatic Microbial Communities
Lookup NU author(s)
Dr Charles Knapp
Professor David Graham
Knapp CW, Graham DW
Journal of Microbiological Methods
Full text for this publication is not currently held within this repository. Alternative links are provided below where available.
Plastids in phytoplankton retain prokaryote-like DNA sequences that may generate false-positive signals from eubacterial small-subunit (ssu) rRNA oligonucleotide probes resulting in the overestimation of bacterial activity in aquatic microbial communities. To assess the extent of possible plastid-associated binding to eubacterial signals, we performed an extensive database search, flask experiments using algal and cyanobacterial pure cultures, and field trials on five common eubacterial probes: S-D-Bact-008-a-A-19, S-D-Bact-338-a-A-18, S-D-Bact-785-a-A-19, S-D-Bact-927-a-A-17, and S-D-Bact-1088-a-A-20. The database search and laboratory tests showed significant potential for binding among most bacterial probes and organelle ssu-rRNA. However, we propose two probing strategies to overcome this problem. First, one could use Bact-785 and Bact-338 in tandem, with the plastid component being estimated as the difference between the two signals (Bact-338 has ~70% overlap with known plastid sequences). Alternately, one might use Bact-338 as the primary eubacterial probe, but then use Cyan-785-a-A-19 (a probe that binds significantly to plastid rRNA) to correct for the plastid-associated false-positive signal. Both strategies would use a eukaryotic probe (S-D-Euca-1379-a-A-16) and Cyan-785-b-A-19 (a probe for most cyanobacteria) to further segregate rRNA signals. Trials were successfully performed using the strategies on samples from a recent field study.
Altmetrics provided by
Newcastle University Library, NE2 4HQ, United Kingdom. Tel: 0044 (191) 222 7657
©2016 Newcastle University Library