Seasonal trends in lysogeny in an Appalachian oak-hickory forest soil.

Since 1989, investigations into viral ecology have revealed how bacteriophages can influence microbial dynamics within ecosystems at global scales. Most of the information we know about temperate phages, which can integrate themselves into the host genome and remain dormant via a process called lysogeny, has come from research in aquatic ecosystems. Soil environments remain under-studied, and more research is necessary to fully understand the range of impacts phage infections have on the soil bacteria they infect.

Sequence analysis of Discoknowium, an A5 mycobacteriophage.

Discoknowium is a temperate A5 bacteriophage that infects the bacterial host . Isolated from a rat fecal sample, Discoknowium's genome is 50,222 bp in length, contains 84 genes and 1 tRNA, and shares 82%-98% nucleotide identity with other A5 subcluster phages.

Understanding Viral Impacts in Soil Microbial Ecology Through the Persistence and Decay of Infectious Bacteriophages.

Marine bacteriophages have been well characterized in terms of decay rates, population dynamics in relation to their hosts, and their impacts on biogeochemical cycles in the global ocean. Knowledge in soil bacteriophage ecology lags considerably behind, with few studies documenting population dynamics with hosts and even fewer reporting phage decay rates. By using sterile soil or aquatic microcosms inoculated with single bacteriophage isolates, phage decay rates (loss of infectivity over time) were determined, independent of host interactions, for 5 model phage isolates.

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.

Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems.

Stormwater runoff drives viral community composition changes in inland freshwaters.

Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities.

Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.

Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end.

Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures.

Virtually every study that has used transmission electron microscopy (TEM) to estimate viral diversity has acknowledged that loss of phage tails during sample preparation may have biased the results. However, the magnitude of this potential bias has yet to be constrained. To characterize biases in virus morphological diversity due to tail loss, six phage strains representing the order Caudovirales were inoculated into sterile sediments and soils.

Repeating patterns of virioplankton production within an estuarine ecosystem.

The Chesapeake Bay, a seasonally variable temperate estuary, provides a natural laboratory for examining the fluctuations and impacts of viral lysis on aquatic microorganisms. Viral abundance (VA) and viral production (VP) were monitored in the Chesapeake Bay over 4 1/2 annual cycles, producing a unique, long-term, interannual study of virioplankton production. High and dynamic VP rates, averaging 7.

Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction.

Prophage typically are induced to a lytic cycle under stressful environmental conditions or when the host's survival is threatened. However, stress-independent, spontaneous induction also occurs in nature and may be cell density dependent, but the in vivo signal(s) that can trigger induction is unknown. In the present study, we report that acyl-homoserine lactones (AHL), the essential signaling molecules of quorum sensing in many gram-negative bacteria, can trigger phage production in soil and groundwater bacteria.

Methods for the isolation of viruses from environmental samples.

Viruses are omnipresent and extraordinarily abundant in the microbial ecosystems of water, soil, and sediment. In nearly every reported case for aquatic and porous media environments (soils and sediments) viral abundance exceeds that of co-occurring host populations by 10-100-fold. If current estimates based on metagenome DNA sequence data are correct, then viruses represent the largest reservoir of unknown genetic diversity on Earth.

Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents.

The consequences of viral infection within microbial communities are dependent on the nature of the viral life cycle. Among the possible outcomes is the substantial influence of temperate viruses on the phenotypes of lysogenic prokaryotes through various forms of genetic exchange. To date, no marine microbial ecosystem has consistently shown a predisposition for containing significant numbers of inducible temperate viruses.

Cultivation-based assessment of lysogeny among soil bacteria.

Lysogeny has long been proposed as an important long-term maintenance strategy for autochthonous soil bacteriophages (phages). Whole genome sequence data indicate that prophage-derived sequences pervade prokaryotic genomes, but the connection between inferred prophage sequence and an active temperate phage is tenuous. Thus, definitive evidence of phage production from lysogenic prokaryotes will be critical in determining the presence and extent of temperate phage diversity existing as prophage within bacterial genomes and within environmental contexts such as soils.

Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA.

Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment.

Metagenomic characterization of Chesapeake Bay virioplankton.

Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized.

Incidence of lysogeny within temperate and extreme soil environments.

A companion study indicated that approximately 30% of cultivable soil bacteria may contain inducible prophage; however, the degree to which this cultivation-based estimate applies to autochthonous communities of soil bacteria is unknown. To estimate the prevalence of lysogeny within soil bacterial communities, induction assays were carried out by extracting bacteria from soil and subsequently exposing extracts to mitomycin C (MC; 0.5 microg ml(-1)), or by exposing bacteria to MC (1.

Abundance and diversity of viruses in six Delaware soils.

The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown.

Sampling natural viral communities from soil for culture-independent analyses.

An essential first step in investigations of viruses in soil is the evaluation of viral recovery methods suitable for subsequent culture-independent analyses. In this study, four elution buffers (10% beef extract, 250 mM glycine buffer, 10 mM sodium pyrophosphate, and 1% potassium citrate) and three enumeration techniques (plaque assay, epifluorescence microscopy [EFM], and transmission electron microscopy [TEM]) were compared to determine the best method of extracting autochthonous bacteriophages from two Delaware agricultural soils. Beef extract and glycine buffer were the most effective in eluting viable phages inoculated into soils (up to 29% recovery); however, extraction efficiency varied significantly with phage strain.