Advances in viral ecology research (2016)

Viruses are usually composed of a small fragment of nucleic acid (DNA or RNA) surrounded by coat protein, and have been recognized as the simplest living organisms known thus far. Viruses exist only as organic macromolecules when in the environment, because they lack integral enzyme and energy transformation systems. However, once they infect host cells, viruses become active and begin to replicate. Despite their dependence on host cells to reproduce, viruses are the most ubiquitous living organisms, and important drivers influencing microbial communities and ecosystem functioning. However, our understanding of the microbial ecology of viruses in the environment has not kept pace with the rapid advances of studies on bacteria and eukaryotes, owing to the lack of a universal phylogenetic biomarker. Virus particles are widely distributed in the environment, with the abundance of viruses in soils ranging from 1.5×108 g-1 to 109 g-1 soil. Soil-dwelling viruses belong to four morphological types: tailed bacteriophage-like particles, spherical particles, thin filaments, and thick filaments. Most soil virus particles can be identified using electron microscopy. With the rapid development of molecular methodologies, signature genes have been identified in order to investigate the diversity within specific virus groups. These genes include auxiliary metabolism genes and polymerase genes, as well as those encoding structural proteins such as portal protein, major capsid protein, and tail sheath protein, etc. Signature genes have been used in combination with PCR-based fingerprinting and sequencing approaches, in order to investigate the spatial and temporal variations of viruses, as well as their diversity across a wide range of habitats. The development of next-generation sequencing platforms has been followed by a large number of metagenomic studies focusing on bacteria, archaea, and fungi from many environments. A large number of new viruses and genes have also been discovered and identified, which has greatly enriched the virus gene database and contributed significantly to the development of the field of viral ecology; however, our understanding of the soil viruses found in different soil types is still in its infancy. Viruses play several important roles in soil ecology. First, they have the ability to infect soil microorganisms and thus change the functions and nutrients provided by the soils, by altering such factors as nutrient element biogeochemical cycles. Second, viruses acting as shuttle vectors can lead to genetic innovation and bacterial horizontal gene transfer, which facilitates the rapid adaptation of soil bacteria to changing conditions via the transferral of beneficial genes. Thirdly, viruses can affect their host’s metabolism by encoding homologous host genes to modify cell physiology in a way that benefits the infecting virions.Here, we summarize the latest knowledge of the community structure and classification of viruses, their ecological functions, the research methodologies of viral ecology, and in particular, appropriate strategies for surveying the complex biology of soil viruses. Furthermore, we propose several important areas, which should be considered for future study.