Abstract
Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
Highlights
The majority of genomic diversity is contained in viral genomes, yet only a fraction of this diversity has been described (Hatfull, 2008; Thurber, 2009; Clokie et al, 2011)
Due to the high level of recombination or intermediate forms in the Circoviridae and Geminiviridae families, all of the genomes that appeared similar to the Circoviridae or Geminiviridae families were combined together as one group (Fig. 1)
The capsid gene was annotated as hypothetical for 30 of the Circo/Geminiviridae genotypes as only the replication gene had a match on GenBank
Summary
The majority of genomic diversity is contained in viral genomes, yet only a fraction of this diversity has been described (Hatfull, 2008; Thurber, 2009; Clokie et al, 2011). Advanced knowledge of the natural mutational landscape, along with other viral genes present in the environment for potential recombination, could provide background information should related viral genotypes cause outbreaks (Hambly & Suttle, 2005). Viral genomes have already provided us with many genes that we can use for our benefit, including capsid genes for drug delivery systems and bacteriophage lysis genes as antibiotics (Kovacs et al, 2007; Schmitz, Schuch & Fischetti, 2010). Increasing our knowledge of their diversity is necessary to discover new ways in which we can use their genes and gene products (Hatfull, 2008; Godzik, 2011)
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