vacuuming for virus viromes

Deep sea sediments are one of the largest biomes on earth containing most of the microbial life in the sea. Viruses are one of the most abundant biological components in the oceans. Viruses play a key role in biogeochemical cycles and ecosystem functioning at a global scale by infecting their hosts. However, the diversity of viruses in benthic systems is unknown.

There have been previous studies considering virus diversity but most papers focus on viral assemblages found in the water column. There are four steps taken to investigate the viral diversity in benthic sediments. 1) recovery and concentration of viral particles, 2) extraction and purification of viral DNA, 3) high throughput sequencing of viral DNA and 4) bioinformatic analysis.

Samples were taken from the Black Sea, two sites in the NE Atlantic (NE Atlantic sites 1 & 2), the Arctic ocean and the Mediterranean Sea. Three independent replicates were taken from each site using a multiple corer. Samples were recovered from the sediment using a Physical chemical (PC) treatment. Samples were stained with SYBER Gold and analysed with epifluorescence microscopy to assess the recovery efficiency of the PC procedure and to check for contamination by eukaryote and bacteria cells. Next the viruses were concentrated using a vacuuming step to filter viruses from any contaminants. qPCR was used to check for contamination by looking for 16s rRNA bacteria and 18s rRNA eukaryote genes. Bioinformatic analysis was used to determine the taxonomic annotation of sequences down to the domain level.

The study found that the black sea and NE Atlantic sea site 2 were mostly viral associated sequences. The Mediterranean and Arctic sites had bacterial associated sequences and the NE Atlantic 1 site had the highest amount of eukaryotic sequences. The composition of the viral assemblages at each site showed relationships with environmental factors at those sites. The black sea had viral compositions related to the organic Carbon load in the sediment. The Mediterranean was related to temperature and the Arctic ocean site had assemblages relating to salinity.

 In the deep-sea viromes, viral genotypes belonged mostly to the order Caudovirales (48–66%). The most represented families, from the order Caudovirales, were Siphoviridae, Myoviridae and Podoviridae. The cluster analysis revealed a low similarity among the viromes generated from different benthic deep-sea sites. The fraction of reads annotated in the viromes were highly variable suggesting that a proportion of the viral sequences are still unknown and could be of novel viral genotypes.

The putative viral functions were very different, suggesting that benthic deep-sea ecosystems are characterized by the different ecological settings. Thus, leading to taxonomically diverse viral genotypes with distinct functions which can give viruses advantages when interacting with their hosts.

This paper was difficult to read in places and seemed out of logical order. This paper was only accepted in August of 2017 but was received November 2015 and has yet to be cited. I feel perhaps this paper should have been two separate studies.

The authors used high throughput sequencing and epifluorescence microscopy to evaluate and compare different methods of collecting, purifying and analysing viral assemblages. The washing based (WB) procedure is commonly used to collect microbes from sediments however the physical chemical (PC) procedure created for this study collected up to 2x as much viral particles. Tangential flow filtration (TFF) is commonly used to concentrate viral samples however they found that 80% of viruses were lost in this step compared to using a vacuum procedure which uses a filter to collect viral particles.

When comparing physical chemical (PC) procedure to the washing based (WB) procedure they found a higher level of viral genotypes using the PC procedure. Some families were found only with the PC procedure. The results from this study show that the WB procedure can lead to a major under estimation of viral diversity in deep sea sediments, this means that the efficiency of viral DNA recovery can influence viral genotype richness and assemblage composition. This comparison of the two procedures and the use of sequencing to assess the efficiency of both could be useful for future studies of viral assemblages.

Corinaldesi et al., (2017) ‘From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments’,  Scientific Reports, 7(1). doi:10.1038/s41598-017-08783-4