Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

Abstract

Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history. Bacteriophages are the dark matter of the biological world (1); a vastness of ill-defined genetic variation whose impacts we observe on the microbial population but of which we have little understanding. The phage population is estimated to contain approximately 10 31 particles and is highly dynamic, with the population turning over every few days. Moreover, this rolling boil of evolution has been churning away for perhaps two billion years or more, giving rise to fantastic genetic diversity (2, 3).It is noteworthy that these estimations of phage population size and turnover emerged primarily from observations made with water samples that are simple to collect and quantify (4). Although terrestrial environments may contribute a relatively minor part of the total numbers of phage particles in the biosphere, prokaryotic diversity in soil samples is very high (5), which is anticipated to be reflected in the companion phage populations. Quantifying the phage populations in soil and terrestrial samples can be tricky, but phages are estimated to be present at levels approaching 10 9 particles per gram of soil (6).Two key approaches to defining viral diversity are metagenomics of total concentrated phage samples collected from the environment and a genome-by-genome strategy of analyzing individually isolated phages. The two approaches are compatible but have distinct outcomes. Metagenomics generates a large amount of sequence data and provides good indicators of diversity. Analysis of individually isolated phages generates smaller data sets, but they are structured into whole genomes. Because phage genomes are architecturally mosaic, the availability of complete genomes contextualizes the complexities of the relationships among phages (7). Moreover, individual phages are available for genetic, biochemical, and microbiological analyses, a critical resource given the evident functional and regulatory novelty within the phage population. Metagenomics typically does not offer a confident linkage between viral sequences and potential bacterial hosts, although methods for enrichment with particular hosts have been described (8). For individually recovered phages, host ranges can be defined empirically.Perhaps not surprisingly, phage diversity is sufficiently high that phages infecting phylogenetically distant hosts share little genetic information (9). The question then arises as to what is the diversity of viruses that infect a single host strain, in which they can be assumed to be ...

Diversity and Ecology of Viruses in Hyperarid Desert Soils

“…The use of these methods to study virus diversity and biogeography in desert soils is relatively new and most commonly involves the sequencing of whole metaviromes (37)(38)(39). However, metaviromic approaches generally result in a large number of unknown sequences (43). In addition, we warn that the taxonomic affiliation of single genes and/or virus genome fragments (using BLAST analysis of public databases) in metavirome data sets may not be evidence for the presence of these viruses in the sample (80), and results should be carefully inspected by additional read mapping to a reference genome.…”

“…With the advances in next-generation-sequencing (NGS) technologies, culture-independent methods have become the standard for determinations of viral diversity (41). However, the rapidly growing volume of viral environmental sequence data has revealed that most sequences (ϳ70%) have no homologs in public databases, and such sequences are typically labeled "viral dark matter" (42,43). Here, we discuss the current understanding of hot and cold desert soil virus diversity and function, propose alternative technical approaches to virus concentration methods, and identify key areas of future research.…”

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

“…Each architectural type defines the structural basis of a lineage. Whether this approach can ultimately succeed has been discussed previously at length, but with no clear resolution (14–19), leading us to seek further support from sequence-based analysis and to compare our results with the structural data, although the identification of viral proteins from sequences alone is known to be very challenging due to the overwhelming size and diversity of the virosphere (1, 3, 20, 21). Here, our primary focus will be on the two most established structure-based viral lineages, roughly corresponding to the two supermodules recently identified using gene and genome network analysis (22).…”

Mycobacteriophages

“…Comparative genomic analysis of phages clearly shows them to have modular structures, with segments assembled to form distinct genomes (35, 75). This is evident at the nucleotide sequence level when comparing phages grouped within particular clusters or subclusters, where otherwise closely related segments are interspersed with regions that are unrelated or more distantly related.…”