They show that the metaviromic islands frequently correspond to genes involved in genome packaging, molecular recognition, and host recognition, the latter of which is suggestive of providing high diversity within lineages to maximize predatory opportunities. Next are two papers that use examples from agriculture to consider the relationship between phages and disturbances at the organismal level. Additional data demonstrate phage-mediated gene transfer by phages induced by this antibiotic.
The piece by Meaden and Koskella is a review on phage therapy, with an emphasis on agricultural examples Meaden and Koskella, Phage therapy is a potential alternative to antibiotic therapy, and the authors thoughtfully explore the potential risks and unknowns associated with phage therapy. The effect of environmental change on viruses is explored here in aquatic ecosystems. Storms are a powerful macro-scale disturbance to any system, and Williamson et al. Unique to this study is consideration of both the planktonic and particle-associated viral communities. The lineages studied showed environment-dependent biogeographic distributions.
A special type of environmental change can occur in host-associated ecosystems, where interaction with hosts adds an additional layer of complexity. The work by Payet et al. They undertook an extended spatiotemporal analysis of viral abundance and lytic activity in the South Pacific Ocean, with the results revealing viral dynamism linked to microbial communities and environmental factors. Next, Yamada presents a hypothesis on the regulation of virulence by filamentous phages of Ralstonia , which is the causative agent of bacterial wilt disease in certain agricultural plants Yamada, The author suggests a phage-encoded open reading frame that is responsible for mediating virulence.
Finally, Santos et al. The use of various probes, including glycans, peptides, and nucleic acids, provides a powerful platform for investigating a wide range of questions in viral ecology. The articles in this Research Topic uniquely and individually address one of the tiniest biological entities on Earth, the viruses of microorganisms, and the enormous role they play in both causing and effecting environmental change.
This collection also provides insights into new techniques and approaches that will be valuable to furthering research on viral ecology. Allen declares that the editing of this volume was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Abedon undertakes paid consulting for phage therapy-associated businesses but was not involved in editing the phage therapy-associated chapter in this volume Meaden and Koskella, United States Department of Agriculture is an equal opportunity provider and employer.
National Center for Biotechnology Information , U. Journal List Front Microbiol v. Published online Dec This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology. Received Oct 30; Accepted Nov The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.
Human enteric pathogenic viruses can enter the environment through discharge of waste materials from infected persons, and be transmitted back to susceptible persons to continue the cycle of disease. Contamination of food with viruses may also promote disease outbreaks. A number of studies have investigated the survival characteristics of several enteric viruses in various environments and foodstuffs, to help explain the transmissibility of these pathogens. This review deals with published work on enteric virus survival on fomites, and in waters, soil, and foods; the results of these studies have illustrated the robust survival of viruses in these environments.
Much information is lacking, however, especially for foodstuffs and soils, and no detailed information is available concerning the survival of noroviruses, the most significant foodborne type. Transmission of a virus is dependent not only on its interaction with a host, but on its interaction with the environment outside of the host.
Viruses outside a host may be regarded as inert particles, and, possessing no intrinsic metabolism, they do not require any nutrients to persist. Nonetheless, they possess a degree of robustness which allows them to remain infectious during the various conditions that they may encounter between one host and another. This is illustrated by the number of outbreaks of enteric viral disease attributable to water- or foodborne transmission [ 1 , 2 ]. The longer a virus can survive outside a host, the greater are its chances for transmission.
These chances will be affected by various environmental conditions and factors as heat, moisture, and pH. These and other factors will vary in presence and extent among different environments. It would be advantageous to have complete knowledge of enteric virus survival in the environment, and the factors which influence it, to comprehend more fully the extent of the risks these pathogens pose, and to ascertain the means to break or curtail the chain of transmission. However, little work appears to have been performed to this end as yet, particularly for soil and food environments, and for fomites.
The following review describes such work as has been published to date. Only studies which have directly involved enteric viruses have been reviewed; no work using potential indicators such as bacteriophage has been included.
In general, studies to determine the potential for survival of viruses have been conducted using basic principles in common. A known number of infectious virus has been artificially introduced into a sample of water, soil, food etc. Then, viruses have been extracted from the sample and enumerated. There are various methods which can be used to extract viruses from food and environmental samples [ 3 , 4 ]; basically, they involve separating virus particles from gross solid material in the sample, and then concentrating them so that they may be delivered to a detection system.
For enumeration of infectious viruses it is necessary to use cell culture in quantal format, e. The number of infectious virus remaining in the sample is compared with the number which was introduced, and statistical procedures can be performed to calculate any degree of decline. Hospitals, homes for the elderly, and institutions housing small children can be subject to outbreaks of virus-associated diarrhea, but the role of surfaces and objects in the transmission of this has not been thoroughly investigated, save for a few studies.
The results of theses studies indicate that enteric viruses can retain infectivity on environmental surfaces over prolonged periods. No precise results or experimental details were given, however. Hands frequently contact environmental surfaces, and the potential for transfer of rotavirus between surfaces and hands was studied by Ansari et al. Sampling times were chosen to mimic the minimum period for inoculum drying 20 min and the maximum period expected min between handwashings for institutional staff and those in their care.
To measure transfer, fingertips inoculated with viruses were kept in contact with stainless steel discs for 10 s, then the discs were washed with buffer to recover any transferred viruses.
When transfer was tested from disc to fingertip, almost identical results were obtained. These findings showed that rotavirus could retain infectivity for several hours on skin, and could transfer in an infectious state to other surfaces.
The moisture levels of the sludge-amended soils were recorded and compared with viral inactivation. Generally HAV was more persistent than poliovirus or echovirus, affected to a lesser extent both by the higher temperature and soil microbial activity. The enteric virus types were reovirus, poliovirus types 1 and 2 and echovirus type 6. This is illustrated by the number of outbreaks of enteric viral disease attributable to water- or foodborne transmission [ 1 , 2 ]. From hairballs to hypotheses—biological insights from microbial networks.
A similar series of experiments was performed by Mbithi et al. They investigated the effect of relative humidity and air temperature on survival of hepatitis A virus on fecally contaminated stainless steel disks .
HAV survival was inversely proportional to the level of relative humidity and temperature. As with the studies performed with rotavirus  , drying appeared to account for the reduction in numbers of infectious virus. The experiments were extended by examining what effect prolonged, increased contact pressure, and friction turning the finger on the surface , had upon virus transfer: Transfer of HAV between hands could also be observed, apparently influenced by moisture.
Moisture would mediate suspension of virus particles, and facilitate their movement between touching surfaces; drying would reduce this effect, as observed in the studies with rotavirus . The persistence of HAV on environmental surfaces, and its ability to transfer to animate environments may be important factors in the spread of this virus, and explain in some part the unidentified mode of transmission in many investigated outbreaks.
Survival of human rotavirus on various non-porous stainless steel, plastic and porous cloth, different types of papers surfaces was studied by Sattar et al. The virus to be used for the contamination of the surfaces was suspended in fecal material, which was placed onto discs of the different materials, and held in glass chambers at various humidities and temperatures. Virus survival on porous surfaces was variable, but virus appeared to survive better on cloth than on paper.
Three sets of environmental conditions were studied: Viruses were inoculated onto the surfaces in phosphate-buffered saline PBS or fecal suspension. Each experiment was conducted over 60 days. Generally, the effect of feces was contradictory, enhancing or reducing virus survival depending on the fomes or virus type; the reason for this is not clear.
It was shown, by drying of samples for a few hours in a flow cabinet, that dessication of viruses produced substantial and differential levels of inactivation of each virus type. Resistance to dessication appears to be significant in determining the ability of enteric viruses to survive on fomites, and may account in some part for the seasonality of infections which has been observed for some virus types [ 11—13 ].
They reviewed information derived from experimental study of the survival of rotavirus in air: Astroviruses exhibited considerable persistence when dried on porous and non-porous materials. When dried on paper at the same temperature, residual astrovirus infectivity was detected after 90 days, with reductions in titer of 4. These results confirmed that astrovirus is able to survive on inert surfaces and fomites may play an important role in the secondary transmission of astrovirus diarrhea.
Noroviruses are a significant cause of outbreaks of gastroenteritis in institutions, and contamination of environmental surfaces may play an important role in the transmission of these agents in such settings. It has been estimated that over 30 million virus particles can be expelled in a single vomiting incident  , and this could result in contamination of surfaces in the immediate area with large numbers of viruses via aerosolization of the vomit.
Noroviruses have been detected on the surfaces of objects around patients during an outbreak of gastroenteritis in a hospital ward  , and there is evidence  to suggest that prolonged survival of noroviruses may occur on fomites. Twelve days after an outbreak of norovirus infection in a hospital ward, two carpet fitters removed a carpet from one of the side rooms. Both men subsequently presented with the symptoms of norovirus infection and their only common exposure appeared to be the carpet, which they had had to handle extensively and vigorously in order to remove it.
It had been vacuumed daily since the ward outbreak, and if it was indeed the source of the two fitters' illness, it would demonstrate considerable robustness in noroviruses. Noroviruses cannot as yet be cultured in any known cell line, and this severely limits any study of their survival characteristics. However, feline calicivirus FCV , a closely related virus which can be grown in cell culture, has been used as a surrogate. Survival was lower at room temperature, but still prolonged, with virus numbers declining to undetectable levels by 21—28 days.
The authors suggested that the effect of temperature on FCV survival may reflect the greater prevalence of norovirus infections in cooler seasons. Feline calicivirus FCV introduced into artificial seawater  exhibited a fold reduction in titer after 1. The initial decline was attributed to the salt content of the water. Other enteric viral types have been shown to survive for many days in seawater. They observed, in both samples, that the virus titer had slightly fallen after 1 day, but thereafter a rapid inactivation occurred, with an approximately 4log 10 reduction after 4 days.
A follow-up study  corroborated this evidence in that the antiviral activity of seawater samples was lost when they were subjected to boiling, autoclaving, or filtration. A comparison of the survival of poliovirus and enteric adenoviruses Ead types 40 and 41 in seawater was performed by Enriquez et al. The survival of poliovirus was shorter than the survival of either adenovirus type: Another comparative survival study was performed using poliovirus and HAV .
A pronounced decline was also observed in numbers of echovirus in these waters. It was considered that antiviral activity was due to bacteria: These studies also found a marked difference in poliovirus survival in waters from Spanish coastal sites and from North Carolina coastal sites, with greater survival in the former waters. The overall antiviral action of waters will generally result from the dominant factors present, and it may have been that the anti-enterovirus factor of the Mediterranean samples was lacking in the North Atlantic samples.
Another series  of experiments, however, did not reveal any differences in the survival of enteric viruses HAV and poliovirus between seawater samples from North Carolina, California, and Hawaiian coastal waters. There was, nonetheless, a different rate of decline in titer for each virus, with poliovirus reducing by 4log 10 in approximately 1 week and HAV reducing by 4log 10 in about 4 weeks.
The authors suggested that reported differences in survival of identical viruses in different seawaters might be a consequence of methodological differences. A standard survival protocol would allow this to be more fully investigated. Microbial predation may not completely account for viral decline in seawater. Schwartzbrod and coworkers [ 27 , 28 ] observed a fall in the infectious titer of hepatitis A virus seeded into artificial seawater, which otherwise would have been sterile.
As free viral RNA is unlikely to persist much more than a few days in seawater  , this indicates that inactivation in seawater might proceed by means other than disruption of the virus particle, possibly through an effect on receptor-binding proteins on the particle surface. Ultraviolet light is highly efficient in the inactivation of poliovirus  , and should strongly influence its and probably all other enteric virus survival in most natural environments.
A series of tests  performed using Hawaiian marine waters seeded with poliovirus plus Cryptosporidium, Giardia and Salmonella and incubated in situ in experimental chambers showed an effect of sunlight on survival. Overall, the order of survival of the microorganisms in sunlight was Cryptosporidium poliovirus Giardia Salmonella. In in situ studies in North Carolina  , experimental chambers inoculated with poliovirus were placed at water depths of 3—10 m, and kept there over 16 week periods which coincided with the seasons e.
Survival times did not differ significantly between the two depths regardless of the season. Kutz and Gerba  reviewed studies of virus survival which had been published over the previous 30 years, which in turn had mostly been reviewed by Akin  and Sattar . These studies had been performed with enteroviruses polio-, echo- and coxsackieviruses. Summarizing the observations from these experiments and grouping them into freshwater sources gave mean viral inactivation rates of: These rates are all less than 1log 10 per day, and indicated that viruses could survive in freshwater sources for prolonged periods of time.
The authors recommended a standard protocol for virus survival studies, so that the effect of environmental conditions such as temperature could be analysed; so far, however, such a protocol has not been produced. The average amount of viral inactivation was 6. Several physical and chemical parameters hardness and conductivity appeared detrimental to virus survival. The turbidity of the water and suspended solids represented a beneficial influence for virus survival.
Rotaviruses may also be able to persist in freshwater for several days. In a study by Raphael et al. The difference was attributed to growth of bacteria and other microorganisms: A more recent experimental study  , using a tangential-flow, hollow-fiber system which allowed a continuous interchange of water through a chamber containing bacteria and viruses, examined their survival in two rivers — the fast-flowing Ottawa and the slower Rideau, which had a higher organic load.
The virus types studied were poliovirus and hepatitis A virus. The authors reported little or no decay of hepatitis A virus in either river over the 48 days experimental period, but stated that poliovirus did show a decline; however, this latter conclusion is not apparent from the figures displayed in the report.
The prolonged persistence of the viruses may have been in part due to the absence of indigenous microorganisms in the chamber itself, as it was unclear whether natural or sterilised water was used in the studies. Land application of sewage effluents and sludges, as well as leachates from septic tanks, pose a risk of viral contamination of groundwater. A series of experiments to determine the potential for survival of enteric viruses in groundwater was performed by workers at the University of North Carolina .
Half of the water samples were sterilised by autoclaving before seeding. There was little inactivation of any virus over the 8 weeks of the experiment, regardless of the sterility of the samples. The different effects at different temperatures might have been due to microbial growth, although the water had been chlorinated. The authors concluded that post-treatment contamination of potable waters with rotaviruses could lead to their widespread dissemination. Overall, they found that the enteric adenoviruses were more stable than the other viral types.
At room temperature the titers of adenovirus types 40 and 41 decreased by nearly 2log 10 after 55 days, and poliovirus and HAV declined by 4 and 3. However, at room temperature, differences in virus survival were very discernible between the two viruses. At this temperature, infectious PV-1 was not detected after days of exposure, while HAV was still infectious.
The authors concluded that this prolonged persistence would increase the risk to consumers following contamination of mineral waters with enteric viruses. They used a combination of infection of cultured CaCo 2 cells and RTPCR detection to compare numbers of infectious astrovirus before and after incubation in the samples for up to 90 days. Because of the increasing emphasis which has been placed upon land application as a means of organic waste disposal, it has been considered important to evaluate the potential for survival of various pathogens in soils.
Few studies however have concerned viruses, possibly because of the complexities involved in handling these agents and developing suitable extraction protocols for them. An early series of experiments was performed by Bagdasaryan  , using small 10 g samples of soil inoculated with enteric viruses poliovirus type 1, echovirus 7, echovirus 9 and coxsackie B3 and incubated under various conditions. Samples were taken at intervals over days.
Two soil types were studied, a sandy and a loamy soil; viruses appeared to survive somewhat longer in the former. The temperature of the soil had some influence on virus persistence: The moisture content of the soils had a marked effect: No appreciable difference was seen in persistence of viruses in sterile and non-sterile soils. Other studies have been performed in field settings. Here, small model vegetable plots were constructed in soil and stone filled boxes, planted with lettuce and radish and irrigated and cultivated as appropriate to normal practice.
The plots were treated with virus-spiked effluent by flooding to a depth of 1 inch, and cultivated with a garden hoe 2 days afterward to till the sewage into the soil. Samples were taken regularly, treated by filtration, and the number of infectious viruses monitored by cell culture assay. The studies covered days, and were conducted in spring, summer and winter seasons; temperature and rainfall were regularly recorded.
The longest period of survival was during the winter, when virus was detected after 96 days. During the summer, the longest survival period was 11 days. In December they added coxsackievirus B3 to municipal sludges which were then placed on lysimeters containing heavy clay, neutral sandy, and acidic sandy soils.
The sludge was dug in by spade, and samples taken each month until May The viral titer fell by 0. Samples were taken over several months. The moisture levels of the sludge-amended soils were recorded and compared with viral inactivation. No viruses were detectable in sludge solids which had been drying in a field for 3 months after land disposal, and results indicated that viral inactivation may have been directly related to loss of moisture in the sludge piles.
The Texas studies were extended  to study the effect of environmental variables and soil characteristics on survival of enteroviruses and rotavirus. Experiments were performed mainly using poliovirus. The main soil type studied was a loamy sand, and viruses were inoculated into 4 g samples of this soil and incubated under various conditions. Samples were assayed by dilution and direct inoculation.
Anaerobic conditions also prolonged virus survival. This may have been due to differences in the extent and mechanisms of virus adsorption to soil under different moisture conditions, or to moisture-dependent differences in microbial growth rates. Survival of the various virus types was studied in nine soil types of differing physicochemical characteristics, and the results were analysed to determine which characteristics had the most marked effect.
Factors such as the levels of organic matter and silt had no significant effect. Decreasing soil pH and phosphorous concentration may have increased adsorption. The authors suggested that a dilemma was posed by the observation that virus adsorption to soil may increase survival, in that adsorptive soils might otherwise be considered as the best sites for application of sewage wastes, as they would minimize virus transport to groundwaters.
Hurst  found that indigenous soil aerobic microorganisms significantly reduced survival of poliovirus, whereas indigenous soil anaerobic microorganisms did not. It was suggested that this may have been due not only to predation but to the production by the microorganisms of substances that interfered with adsorption of virus particles to soil particles.
The samples used were both non-sterile and sterilised through autoclaving.
Generally HAV was more persistent than poliovirus or echovirus, affected to a lesser extent both by the higher temperature and soil microbial activity. They seeded soil samples from freshly amended fields with poliovirus and buried them in containers 10 cm below ground. Samples were taken every day for 7 days. During the winter study, no inactivation of poliovirus was observed; in the summer study there was a 3log 10 reduction in the number of infectious poliovirus after 3 days, and no infectious virus was detected at 7 days.