Virus genes in Arctic marine bacteria identified by metagenomic analysis
In the Arctic Ocean, heterotrophic Bacteria play a major role in the energy availability as they are important components of the food web. Even though bacteria are adapted to the conditions in the Arctic Ocean, the primary production in proportion to biomass is lower than in more temperate regions. Therefore, it is assumed that the overall food web structure differs as a result of this. As a general rule, the richness of bacteria and viruses was found to be poorer in the Arctic which suggests that contact between these two groups is less regular. Studies on the rate of viral infections on Arctic surface waters indicate that the viral reproduction rate is relatively low and similar to the growth rate of bacteria.
Uncultivated bacteria were metagenomically analysed and there were indications of actively replicating viruses present in these host cells. The Global Ocean Survey (GOS) has identified many virus genes that originated from actively replicating viruses rather than prophages, i.e. viral DNA incorporated into bacterial genomes. It is assumed that viral genomes are widespread in uncultivated bacteria as in around 60 – 70% of cultivated bacteria viral DNA was found when the genome was sequenced. However there have not been many studies on virus DNA in genomes of uncultivated bacteria.
The Arctic Ocean was not sampled as part of the GOS, and the purpose of this research was to investigate whether virus genes occurred in uncultivated bacteria from this extreme ecosystem. Genomic fragments consisting of 40 kilobases from bacteria were analysed and genomic parts were cloned into fosmid vectors (fosmid DNA; DNA sequences equivalent to the bacterial F-plasmid which is responsible for sexual functions) and sequenced after to detect viral DNA in the bacterial genomes.
Fosmid clones (as identified from the Arctic fosmid library, 2004) were amplified in PCR and screened for 16S rRNA genes in a denaturing gradient gel electrophoresis (DGGE), and fosmids containing 16S rRNA genes were fully sequenced. They were then compared to the data base of Arctic 16S rRNA gene tags in order to determine which groups of bacteria were present in the fosmid clones. A fluorescence in situ analysis (FISH) was also used in order to determine the overall bacterial community of the Arctic seawater. The majority of the fosmids contained DNA from Bacteriodetes and Gammaproteobacteria.
The fosmids sequences were scanned for virus genes using the viral metagenome sequences which were gathered from Arctic Ocean seawater. For this analysis, the seawater had to be filtered to remove bacterial sequences which had a close match to known bacterial sequences in the data base. Comparing the bacterial genomes from different two other environments, phage genes in were more abundant in samples from the Arctic Ocean.
Against previous findings of lowest viral mortality in the Arctic Ocean as determined for any aquatic system, this study has shown a high frequency of virus DNA in bacterial metagenomes. Although previous studies showed that bacteria and viruses are less common in the Arctic Ocean, interactions between host and phage are more extensive than assumed. It was hypothesized that this might be due to the high abundance of temperate rather than virulent viruses in this ecosystem. Temperate viruses in the host don't lyse and infect it, and hence are longer present in the host than virulent phages which have lethal effects to the host. Different habitats such as the Antarctic waters show a much higher bacterial mortality than the Arctic indicating a different ecological impact of viruses in different ecosystems. This means that the ecology viruses has a major role in the overall primary production of bacteria in these ecosystems…
Cottrell, M. T. & Kirchman, D. L. (2012). Virus genes in Arctic marine bacteria identified by metagenomic analysis. Aquatic Microbial Ecology, 66, pp.107-112.