Ecology of prokaryotic viruses

Abstract

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

Re-examination of the relationship between marine virus and microbial cell abundances

“…Observations accumulating over the past 25 years have observed wide variation in VPR, yet there is an emergent census that a suitable first-approximation is that VPR is 10 (see Table I). This ratio also reflects a consensus that typical prokaryote abundances are approximately 10 6 per ml and typical virus abundances are approximately 10 7 per ml [50,57]. Yet, the use of a fixed ratio carries with it another assumption: that of linearity, i.e., if prokaryote abundance were to double, then viruses are expected to double as well.…”

“…Viruses measured in these methods are generally thought to represent bacteriophage, consistent with the numerical dominance of bacteria in seawater [50]. Yet, currently available methods have potential limitations.…”

“…Weinbauer [50] 2004 Chibani-Chennoufi and colleagues advance the notion that VBR is 10:1 in the ocean and that this is justified by the claim that each prokaryote species can be infected by 10 different phage.…”

Mixing alters the lytic activity of viruses in the dark ocean

“…1998, De Paepe and Taddei 2006) and consequently also among aquatic environments (Wommack and Colwell 2000, Weinbauer 2004, Parada et al. 2006) harboring different viral communities.…”

Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis

“…In this regard, the necessity of the research into the role of viruses-bacteriophages in the functioning of microbial communities in various aquatic ecosystems is obvious. Today there is a large amount of publications devoted to the study of biodiversity of viruses in fresh and marine waters and the study of influence on their composition of the season, trophic status of the water reservoir, depth of sampling of material for research and anthropogenic influences [9][10][11]. They have revealed that the composition of viruses is affected not only by the geographical location of the water body but also by the variety of microorganisms inhabiting it [12].…”