Marine viruses influence host community composition, however, the effect of viruses on communities of phytoplankton is sparsely studied. Natural algal-virus communities which infect and lyse marine primary producers are an abundant and active part of the marine ecosystem.
To understand the dynamics & effects of phytoplankton viruses, the genetic composition of virus communities needs to be understood. Specifically viruses infecting the marine phytoplankton Micromonas pusillla lead to the development of the degenerate algal-virus-specific (AVS) PCR primers AVS1 and AVS2, which amplify a 700 base pair fragment of algal-virus DNA polymerase genes.
Phylogenetic analysis of amplified DNA polymerase fragments showed that cultured algal-viruses formed a monophyletic group, compared to double-stranded DNA viruses.
Algal-virus specific primers were used to amplify unknown algal virus DNA polymerase fragments from natural virus communities, showing that algal-virus diversity can be studied using molecular techniques.
DGGE analysis of PCR products that have been amplified bu AVS PCR primers can be used to examine natural algal-virus community diversity, for example, the banding patterns (fingerprints) in this experiment of samples taken from one location (Salmon Inlet) were identical and easily distinguished from other fingerprints; these samples were collected at the same time and location, but at different depths. However, the temperature and salinity at this site did not vary much with depth, indicating that the water and viruses were mixed well.
On the opposite end of the spectrum, samples taken from a different location (Pendrell Sound) have differing banding patterns at the different depths. This is due to the salinity at depth being double that of surface salinity, meaning that the water and viruses here were had stratification.
The DNA polymerase sequences derived from the PCR and DGGE were closely related to known algal-viruses, and remarkably, some 98% of sequences from samples taken at the Southern Ocean were identical to those from coastal British Columbia, despite how different the environments are.
This paper showed how PCR and DGGE can be used to recover and identify unknown algal-virus DNA polymerase sequences from the natural environment, and that similar sequences can be recovered from different areas worldwide.
I found this paper interesting as it shows how the curiosity sparked by viruses infecting a specific species of marine phytoplankton lead to the development of new primers, and then onto being able to study marine virus community diversity in natural communities.
Sequence analysis of marine virus communities reveals that groups of related algal viruses are widely distributed in nature by Steven M. Short and Curtis A.Suttle, 2002
...here's the link if you'd like to read it http://ukpmc.ac.uk/articles/PMC123764/pdf/1471.pdf
Hi Hannah,
ReplyDeleteAs the importance of viruses in marine environments is only just coming to light, I find this example of the use of molecular techniques to study viral diversity really interesting! I know that in the past, the lack of known specific sequences for viruses have hampered molecular analysis, so I am interested to know how the authors went about finding and creating specific primers for the algae-virus they were interested in.
I wonder if these techniques could be used to created primers that are general enough to amplify the sequences of viruses that infect different, but similar host species; perhaps viruses of all host species in a particular genus?
Jo
Hey Joanna, sorry for the delay in replying. Unfortunately I don't know how they created the primers!
ReplyDeleteThat is an interesting point. I have found a paper from 1999 by Raquel Moron, Ignacio Gonzalez and Olga Genilloud called 'New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora.' which talks about the design of genus-specific probes (here's the link if you would like to look through it: http://ijs.sgmjournals.org/content/49/1/149.full.pdf+html )
Hannah