Analysis of Metavirome from Bioremediation Culture in R - Statistics Assignment Help

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Background
What is a metavirome?
A metavirome is a metagenome of viral DNA, instead of bacterial DNA. A metavirome is obtained through the isolation of viruses, and extraction and sequencing of the viral DNA. This term was coined by J.H. Paul and M.B. Sullivan in 2005 in reference to their study of the marine virus community (Paul and Sullivan, 2005).
Viruses can parasitize humans, animals, and even bacteria! Viruses that infect bacteria are called bacteriophages, or phages.
In this tutorial, we will analyze a metavirome of phages from bioremediation culture.

Bioremediation
Bioremediation involves the use of a living organism, such as microorganisms, to consume or break down environmental contaminants.
Some of the bioremediation cultures that the Edwards lab studies are mixed microbial communities that degrade chlorinated solvent contamination. Chlorinated solvents are among the most prevalent and recalcitrant soil and groundwater contaminants in industrialized countries (McMurdie et al., 2011). Environmental release of chlorinated solvents is often a result of industrial, military and agricultural practices (Molenda et al., 2016). The two parent compounds, tetrachloroethene (PCE), a dry-cleaning solvent, and trichloroethene (TCE), a metal degreasing agent, and their degradation intermediates are known to be toxic or carcinogenic and so their widespread contamination poses a great concern to human health (McMurdie et al., 2011).

Bioremediation of chlorinated solvents has become a highly successful treatment option since the 1990s when it was discovered that microorganisms were able to completely dechlorinate these contaminants under anaerobic, or oxygen-absent, conditions (Adrian et al., 2016). The only microorganism known to complete dechlorination is Dehalococcoides mccartyi (Jugder et al., 2016).

D. mccartyi genomes are small and highly specialized for their niche of reductive dechlorination, which is the only way these microbes obtain energy for growth, making them obligate organohalide-respiring bacteria. D. mccartyi genomes can be categorized into core regions of “house-keeping” genes, and two regions of high variability called High Plasticity Regions (McMurdie et al., 2009). As the name suggests, these High Plasticity Regions contain evidence of genome plasticity, such as repeat regions, insertion sequences, genomic islands, prophages and phage-related sequences, duplication events, gene loss, etc. (Molenda et al., 2018a).

Horizontal Gene Transfer
As a result of this observation, Molenda et al. (2018b) began to explore the potential of Horizontal Gene Transfer in these microorganisms. They began to study D. mccartyi CRISPR-Cas systems, which are bacterial adaptive defense mechanisms, protecting cells from invading mobile genetic elements, phages, etc. In studying these CRISPR-Cas systems, it was evident that D. mccartyi were actively building immunity against phages and mobile genetic elements. Phages were the most common target, and 18 prophages were identified in D. mccartyi genomes. Mobile genetic elements were the second most common target, and the 20 identified mobile genetic elements were categorized as Integrative and Mobilizable Elements (IMEs).

IMEs encode their own excision, replication and integration machinery, and often use the machinery of a co-resident element to mediate their transfer from cell to cell (Guédon et al., 2017). One group of IMEs, that Molenda et al. called IME1, have site-specific integration in the genome, and some were found in the circularized, extrachromosomal state (Molenda et al., 2018b). The majority of D. mccartyi IME1s, and IME1-like sequences found in other genera, are located directly adjacent to a complete prophage the genome, which may act as a satellite or helper phage to assist in the transfer of IME1s (Molenda et al., 2018b).

Overall, very little additional information is known about these IME1s. It was predicted that these IME1s are involved in Horizontal Gene Transfer by phages, via transduction. So, to characterize these phages, their role in the bioremediation community, and the their potential relationship with IME1s, a metavirome was sequenced.

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