Amplification of DNA in sediment cores to detect historic Planktothrix occurrence in three Norwegian lakes

• Published in: Journal of paleolimnology 2015-01, Vol.53 (1), p.61-72
• Main Authors: Kyle, Marcia, Haande, Sigrid, Sønstebø, Jørn, Rohrlack, Thomas
• Format: Article
• Language: English
• Subjects: Aluminum; Climate Change; Cores; Deoxyribonucleic acid; DNA; DNA primers; Earth and Environmental Science; Earth Sciences; Freshwater; Freshwater & Marine Ecology; genes; Geology; History; human health; Lake sediments; Lakes; Magnesium; Organic matter; Original Paper; Paleontology; Physical Geography; Phytoplankton; Planktothrix; sediment deposition; Sedimentation; Sedimentology; Sediments; Water management; watersheds
• ISSN: 0921-2728; 1573-0417
• DOI: 10.1007/s10933-014-9807-1

The past 50 years have been marked by overabundance of cyanobacteria in many lakes. One cyanobacterium in particular, Planktothrix, produces large blooms that affect phytoplankton diversity and presents human health concerns. Historical information on Planktothrix, however, is limited. More background information on this taxon would be useful for water management. Archival DNA in lake sediment has shown increasing promise for providing insights into historical lake conditions. In an effort to identify Planktothrix DNA in sediments, we developed a set of primers to amplify the DNA, using sequences from the non-ribosomal peptide synthetase gene cluster, ociB, which codes for the oligopeptide class cyanopeptolin. Four primer sets were designed, using a single forward primer and four separate reverse primers that span a specific sequence fragment between 50 and 383 base pairs in length. This enabled us to assess the recovery of Planktothrix DNA in sediment cores from three lakes that differed with respect to watershed characteristics, sedimentation rate, chemistry and organic matter content. The method proved to be sensitive for detection of Planktothrix ociB in sediment from these lakes. Long fragments were found in sediment deposited over the last 20 years, whereas shorter DNA fragments were amplified from samples taken over the entire length of the cores. Highest DNA concentrations were found in the lake with highest levels of aluminum and magnesium in the sediment, suggestive of clay-rich deposits. The lake with the highest organic matter content and lowest sedimentation rate also had the lowest concentrations of Planktothrix DNA. In this organic-rich sediment, however, the shortest fragment primers amplified Planktothrix DNA from sediment deposited over the last 300 years. This research shows the potential for DNA in sediment archives to yield information about past cyanobacteria presence in a variety of lakes, and indicates that it is a useful tool for identifying the presence of Planktothrix, an important nuisance cyanobacterium in some lakes.