The rbcL gene, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), has been used to barcode algae. Because RuBisCO is a key enzyme in photosynthesis, the rbcL gene is a molecular marker linked to the ecosystem function of algae (Paul et al. 2000). Most algae have one of three subtypes of RuBisCO Form I (Badger and Bek 2008). Sets of primers have been developed to amplify genes coding for a region of the IA and IB Forms, which are found in green algae and cyanobacteria, and for a region of the ID Form, which is found in non-green algae (Paul et al. 2000).
Figure 1-PCR results (run on a 1.2% agarose gel) from amplification of a region of the rbcL gene in Aliquot B using primers for rbcL Forms IA and IB. DNA amounts were 0 ng (negative control, NC), 1 ng, 5 ng, 10 ng, and 40 ng. Reaction volume was 25Ál.
Figure 2-Table 1: Community composition of each aliquot, expressed as a percentage of the total sequences in each aliquot matching a particular genotype. % NT indicates the range of percent similarity of the sequences in each genotype to the closest match for that genotype in GenBank.
Previous studies have designed primers for regions of the rbcL gene for use in whole-community analyses of phytoplankton. The purpose of this study was to determine if the rbcL gene can be used to assess the biodiversity of green algae and cyanobacteria in two aliquots of an environmental sample of periphyton. Each of the aliquots had a genotype richness of seven, and the most common genotype in both was Ulothrix zonata. The community compositions of the aliquots were significantly different. Future studies may identify more rbcL sequences from periphyton species, increasing the resolution and precision of whole-community analysis.
I would like to thank Dr. Rubin, Bo Liu, and Xie Xie for their help with the techniques associated with this project. I thank Dr. Rubin, Dr. Wehr, Bo Liu, and Xie Xie for their help in designing this project; Sarah Whorley and Kam Truhn for their help in algae collection and processing, and Rosalind Becker for providing materials and advice. I would like to thank Dr. Plunkett, Dr. Karol, and especially Robin Sleith of the New York Botanical Gardens for use of their machine and expertise in lysing the cells. I also thank Dr. Wehr and Daniel Grubaugh for their help in analyzing the data. This work was supported by the Biological Sciences Department at Fordham University.
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