Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments

The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.

Persistence of poliovirus types 2 and 3 in waste-impacted water and sediment

Eradication of poliovirus (PV) is a global public health priority, and as clinical cases decrease, the role of environmental surveillance becomes more important. Persistence of PV and the environmental factors that influence it (such as temperature and sample type) are an important part of understanding and interpreting positive environmental surveillance samples. The objective of this study was to evaluate the persistence of poliovirus type 2 (PV2) and type 3 (PV3) in wastewater and sediment. Microcosms containing either 1) influent wastewater or 2) influent wastewater with a sediment matrix were seeded with either PV2 or PV3, and stored for up to 126 days at three temperatures (4°C, room temperature [RT], and 30°C). Active PV in the liquid of (1), and the sediment and liquid portions of (2) were sampled and quantified at up to 10 time points via plaque assay and RT-qPCR. A suite of 17 models were tested for best fit to characterize decay of PV2 and PV3 over time and determine the time points at which >90% (T90) and >99% (T99) reduction was reached. Linear models assessed the influence of experimental factors (matrix, temperature, virus type and method of detection) on the predicted T90 and T99 values. Results showed that when T90 was the dependent variable, virus type, matrix, and temperature significantly affected decay, and there was a clear interaction between the sediment matrix and temperature. When T99 was the dependent variable, only temperature and matrix type significantly influenced the decay metric. This study characterizes the persistence of both active and molecular PV2 and PV3 in relevant environmental conditions, and demonstrates that temperature and sediment both play important roles in PV viability. As eradication nears and clinical cases decrease, environmental surveillance and knowledge of PV persistence will play a key role in understanding the silent circulation in endemic countries.

Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

BACKGROUND

The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.

RESULTS

We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts' nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.

CONCLUSION

Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.

Revealing the Viral Community in the Hadal Sediment of the New Britain Trench

Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.

An Advanced Protocol for the Quantification of Marine Sediment Viruses via Flow Cytometry

Viruses are highly abundant, diverse, and active components of marine environments. Flow cytometry has helped to increase the understanding of their impact on shaping microbial communities and biogeochemical cycles in the pelagic zone. However, to date, flow cytometric quantification of sediment viruses is still hindered by interference from the sediment matrix. Here, we developed a protocol for the enumeration of marine sediment viruses by flow cytometry based on separation of viruses from sediment particles using a Nycodenz density gradient. Results indicated that there was sufficient removal of background interference to allow for flow cytometric quantification. Applying this new protocol to deep-sea and tidal-flat samples, viral abundances enumerated by flow cytometry correlated well (R² = 0.899) with counts assessed by epifluorescence microscopy over several orders of magnitude from marine sediments of various compositions. Further optimization may be needed for sediments with low biomass or high organic content. Overall, the new protocol enables fast and accurate quantification of marine sediment viruses, and opens up the options for virus sorting, targeted viromics, and single-virus sequencing.

Quantitative Detection of Human Adenovirus and Human Rotavirus Group A in Wastewater and El-Rahawy Drainage Canal Influencing River Nile in the North of Giza, Egypt

Environmental monitoring is critical in a developing country like Egypt where there is an insufficient framework for recording and tracking outbreaks. In this study, the prevalence of human adenovirus (HAdV), rotavirus group A (RVA) was determined in urban sewage, activated sludge, drainage water, drainage sediment, Nile water, and Nile sediment, using quantitative polymerase chain reaction (qPCR) analysis. HAdV was detected in 50% of urban sewage with viral concentrations ranging from 10³ to 10⁷ genome copies/liter (GC/L), 33% of activated sludge with viral concentrations ranging from 10³ to 10⁷ GC/kilogram (GC/kg), 95% of drainage water with viral concentrations ranging from 10³ to 10⁷ GC/L, 75% of drainage sediment with viral concentrations ranging from 10³ to 10⁷ GC/L, 50% of Nile water with viral concentrations ranging from 10³ to 10⁷ GC/L, and 45% of Nile sediment with viral concentrations ranging from 10³ to 10⁷ GC/kg. RVA was detected in 50% of urban sewage with viral concentrations ranging from 10³ to 10⁷ GC/L, 75% of activated sludge with viral concentrations ranging from 10³ to 10⁷ GC/L, 58% of drainage water with viral concentrations ranging from 10³ to 10⁷ GC/L, 50% of drainage sediment with viral concentrations ranging from 10³ to 10⁷ GC/L, and 45% of Nile water with viral concentrations ranging from 10³ to 10⁷ GC/kg. In conclusion, Abu-Rawash WWTP acts as a source of HAdV and RVA, releasing them into El-Rahawy drain then to the River Nile Rosetta branch.

Sediment re-suspension as a potential mechanism for viral and bacterial contaminants

Pathogenic enteric viruses and bacteria tend to occur in higher concentrations and survive longer in aquatic sediments than suspended in the water column. Re-suspension of these organisms can result in a significant degradation of overlying water quality. Additionally, the re-suspension of microbial pathogens in artificial irrigation canals could endanger the consumption of fresh and ready-to-eat produce. Irrigation water has been implicated in numerous fresh produce outbreaks over the last 30 years. This study aimed to quantify the proportions of bacterial and viral re-suspension from sediment in a recirculating flume with varying velocities. MS2 coliphage and Escherichia coli were found to re-suspend at rates that were not significantly different, despite organism size differences. However, E. coli re-suspension rates from sand and clay were significantly different. This suggests that likely sediment-associated particles were recovered with the organisms attached. Similar re-suspension rates are hypothesized to be due to the dynamics of sediment transport, rather than that of the organisms themselves. This study also indicated that the re-suspension of sediment at very low velocities (e.g., less than 10 cm/s), could impact the microbiological quality of the overlaying water. Results from this study conclude that sediment could be a viable mechanism for irrigation water contamination.

TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE

Surveillance methods for avian influenza virus (AIV) based upon collecting and testing samples from individual wild birds have several significant limitations primarily related to the difficulties associated with obtaining samples. Because AIVs are shed in waterfowl feces, the use of environmental substrates where waterfowl feces accumulate may overcome some of these limitations. However, these substrates are difficult to analyze using traditional diagnostic techniques, such as virus culture and PCR, because of virus inactivation, RNA degradation, low concentration of target RNA, microbial complexity, presence of inhibitory substances, and other factors. We investigated the use of a genomics-based approach called targeted resequencing to detect and characterize AIVs in wetland sediments during the 2014-15 North American highly pathogenic avian influenza outbreak. We identified AIV in 20.6% (71/345) sediment samples obtained from wetlands (n=15) and outdoor waterbodies on AIV-infected poultry farms (n=10) in British Columbia, Canada (the first area affected during the outbreak). Thirteen hemagglutinin (HA) and nine neuraminidase (NA) subtypes were detected, including H5, N1, and N8 sequences that clustered with other sequences associated with the North American outbreak. Additionally, as many as eight HA and eight NA subtypes could be detected in a single sediment sample. This proof-of-concept study shows the potential utility of sediment sampling coupled with genomics-based analysis as a tool for AIV surveillance.

eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population

The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs (Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species' activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.

Critical Evaluation of CrAssphage as a Molecular Marker for Human-Derived Wastewater Contamination in the Aquatic Environment

The discharge of human-derived wastewater represents a major threat to water quality with the potential for waterborne disease outbreaks mainly associated with enteric viruses. To prevent illnesses, indicators associated with fecal contamination are monitored in polluted areas, however, their prevalence often does not correlate well with viral pathogens. In this study, we used crAssphage, a recently discovered human-specific gut-associated bacteriophage, for the surveillance of wastewater-derived viral contamination. Untreated and treated wastewater, surface water, sediment and mussel samples were collected monthly over 1 year from the Conwy River and estuary (UK) and were analyzed for crAssphage marker by quantitative PCR. This is the first long-term catchment-to-coast scale study of environmental crAssphage concentrations. CrAssphage was detected in all sample types and showed no distinct seasonal pattern. CrAssphage concentrations were 2 × 105-109 genome copies (gc)/L in all untreated wastewater influent and 107-108 gc/L in secondary treated effluent samples, 3 × 103 gc/L-3 × 107 gc/L in surface water samples (94% positive) and 2 × 102-104 gc/g sediment (68% positive) and mussel digestive tissue (79% positive). CrAssphage concentrations were 1-5 log10 higher than human enteric virus titers (norovirus, sapovirus, adenovirus, polyomavirus). Our results indicate that crAssphage is well suited to tracking human wastewater contamination and pollution risk assessment in aquatic environments.

Recovery of influenza A viruses from lake water and sediments by experimental inoculation

Influenza A viruses (IAV) are zoonotic pathogens relevant to human, domestic animal and wildlife health. Many avian IAVs are transmitted among waterfowl via a faecal-oral-route. Therefore, environmental water where waterfowl congregate may play an important role in the ecology and epidemiology of avian IAV. Water and sediment may sustain and transmit virus among individuals or species. It is unclear at what concentrations waterborne viruses are infectious or remain detectable. To address this, we performed lake water and sediment dilution experiments with varying concentrations or infectious doses of four IAV strains from seal, turkey, duck and gull. To test for infectivity of the IAV strains in a concentration dependent manner, we applied cultivation to specific pathogen free (SPF) embryonated chicken eggs and Madin-Darby Canine Kidney (MDCK) cells. IAV recovery was more effective from embryonated chicken eggs than MDCK cells for freshwater lake dilutions, whereas, MDCK cells were more effective for viral recovery from sediment samples. Low infectious dose (1 PFU/200 μL) was sufficient in most cases to detect and recover IAV from lake water dilutions. Sediment required higher initial infectious doses (≥ 100 PFU/200 μL).

Human mastadenovirus in water, sediment, sea surface microlayer, and bivalve mollusk from southern Brazilian beaches

Anthropogenic contamination of beaches in the south of Brazil was assessed by detection of Escherichia coli, human mastadenovirus species C (HAdV-C) and F (HAdV-F) and hepatitis E virus (HEV). Sampling was carried out in October (2016), and in January, April and July (2017). Water, sediment, sea surface microlayer (SML), bivalves, and air sentinel samples were evaluated. Quantitative microbiological risk assessment (QMRA) was used to estimate the probability of swimmer infection. HAdV-C was present in 26% of the samples, for both qPCR and viral isolation. The highest rates of detection in genomic copies (GC) were in water (2.42E+10 GC/L), SML (2.08E+10 GC/L), sediment (3.82E+08 GC/g) and bivalves (3.91E+07 GC/g). QMRA estimated daily and annual risks with a maximum value (9.99E-01) in almost all of the samples. Viable HAdV-C was often detected in the SML, pointing that this is a source of infection for people bathing in these waters.

Sediments from Arctic Tide-Water Glaciers Remove Coastal Marine Viruses and Delay Host Infection

Over the past few decades, the Arctic region has been strongly affected by global warming, leading to increased sea surface temperatures and melting of land and sea ice. Marine terminating (tide-water) glaciers are expected to show higher melting and calving rates, with an increase in the input of fine sediment particles in the coastal marine environment. We experimentally investigated whether marine viruses, which drive microbial interactions and biogeochemical cycling are removed from the water column through adsorption to glacier-delivered fine sediments. Ecologically relevant concentrations of 30, 100 and 200 mg·L-1 sediments were added to filtered lysates of 3 cultured algal viruses and to a natural marine bacterial virus community. Total virus removal increased with sediment concentration whereby the removal rate depended on the virus used (up to 88% for an Arctic algal virus), suggesting a different interaction strength with the sediment. Moreover, we observed that the adsorption of viruses to sediment is a reversible process, and that desorbed viruses are still able to infect their respective hosts. Nonetheless, the addition of sediment to infection experiments with the Arctic prasinovirus MpoV-45T substantially delayed host lysis and the production of progeny viruses. We demonstrate that glacier-derived fine sediments have the potency to alter virus availability and consequently, host population dynamics.

A 1,000-Year-Old RNA Virus

Only a few RNA viruses have been discovered from archaeological samples, the oldest dating from about 750 years ago. Using ancient maize cobs from Antelope house, Arizona, dating from ca. 1,000 CE, we discovered a novel plant virus with a double-stranded RNA genome. The virus is a member of the family Chrysoviridae that infect plants and fungi in a persistent manner. The extracted double-stranded RNA from 312 maize cobs was converted to cDNA, and sequences were determined using an Illumina HiSeq 2000. Assembled contigs from many samples showed similarity to Anthurium mosaic-associated virus and Persea americana chrysovirus, putative species in the Chrysovirus genus, and nearly complete genomes were found in three ancient maize samples. We named this new virus Zea mays chrysovirus 1. Using specific primers, we were able to recover sequences of a closely related virus from modern maize and obtained the nearly complete sequences of the three genomic RNAs. Comparing the nucleotide sequences of the three genomic RNAs of the modern and ancient viruses showed 98, 96.7, and 97.4% identities, respectively. Hence, in 1,000 years of maize cultivation, this virus has undergone about 3% divergence.IMPORTANCE A virus related to plant chrysoviruses was found in numerous ancient samples of maize, with nearly complete genomes in three samples. The age of the ancient samples (i.e., about 1,000 years old) was confirmed by carbon dating. Chrysoviruses are persistent plant viruses. They infect their hosts from generation to generation by transmission through seeds and can remain in their hosts for very long time periods. When modern corn samples were analyzed, a closely related chrysovirus was found with only about 3% divergence from the ancient sequences. This virus represents the oldest known plant virus.

Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability

Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. Turbidity was measured on combinations of virus and each sediment type at low concentration to determine aggregation rates. Aggregation of sediment with virus occurred regardless of mineral type, and larger fraction of virus is expected to aggregate with increasing sediment concentration leading to higher deposition rates. The negatively charged sediments, aggregated with φ6 (also negatively charged at neutral pH) at a faster rate than the positively charged sediments, yielding turbidity slopes of 4.94 × 10-3 s-1 and 7.50 × 10-4 s-1 for φ6-montmorillonite and φ6-illite aggregates, respectively, and 2.98 × 10-5 s-1 and 2.84 × 10-5 s-1, for φ6-goethite and φ6-kaolinite, respectively. This indicates that the interaction between sediments and virus is hydrophobic, rather than electrostatic. Large numbers of virions remained viable post-aggregation, despite the fragility of the viral envelope, indicating that small-sized aggregates, which may travel more readily through porous media, may pose an infection risk. The fraction of φ6 that remained viable varied with sediment type, with montmorillonite-φ6 aggregates experiencing the greatest reduction in infectivity at 35%. TEM analyses reveal that in all sediment-φ6 combinations, infectivity loss was likely due to disassembly of the viral envelope as a result of aggregation.

Transport of Escherichia coli phage through saturated porous media considering managed aquifer recharge

Virus is one of the most potentially harmful microorganisms in groundwater. In this paper, the effects of hydrodynamic and hydrogeochemical conditions on the transportation of the colloidal virus considering managed aquifer recharge were systematically investigated. Escherichia coli phage, vB_EcoM-ep3, has a broad host range and was able to lyse pathogenic Escherichia coli. Bacteriophage with low risk to infect human has been found extensively in the groundwater environment, so it is considered as a representative model of groundwater viruses. Laboratory studies were carried out to analyze the transport of the Escherichia coli phage under varying conditions of pH, ionic strength, cation valence, flow rate, porous media, and phosphate buffer concentration. The results indicated that decreasing the pH will increase the adsorption of Escherichia coli phage. Increasing the ionic strength, either Na⁺ or Ca²⁺, will form negative condition for the migration of Escherichia coli phage. A comparison of different cation valence tests indicated that changes in transport and deposition were more pronounced with divalent Ca²⁺ than monovalent Na⁺. As the flow rate increases, the release of Escherichia coli phage increases and the retention of Escherichia coli phage in the aquifer medium reduces. Changes in porous media had a significant effect on Escherichia coli phage migration. With increase of phosphate buffer concentration, the suspension stability and migration ability of Escherichia coli phage are both increased. Based on laboratory-scale column experiments, a one-dimensional transport model was established to quantitatively describe the virus transport in saturated porous medium.

Wastewater contamination in Antarctic melt-water streams evidenced by virological and organic molecular markers

Human activities in the Antarctica including tourism and scientific research have been raised substantially in the last century with the concomitant impact on the Antarctic ecosystems through the release of wastewater mainly from different scientific stations activities. The aim of this study was to assess the wastewater contamination of surface waters and sediments of three melt-water streams (11 sites) by leaking septic tanks located in the vicinity of the Uruguayan Scientific Station in the Fildes Peninsula, King George Island, Antarctica, during summer 2015. For this purpose, we combined the analysis of fecal steroids in sediments by using gas chromatography and six enteric viruses in surface waters by quantitative and qualitative PCR. Coprostanol concentrations (from 0.03 to 3.31μgg^-1) and fecal steroids diagnostic ratios indicated that stations C7 and C8 located in the kitchen stream presented sewage contamination. Rotavirus was the only enteric virus detected in five sites with concentration ranging from 1.2×10⁵gcL^-1 to 5.1×10⁵gcL^-1 being three of them located downstream from the leaking AINA and Kitchen septic tanks. This study shows for the first time the presence of both virological and molecular biomarkers of wastewater pollution in surface waters and sediments of three melt-water streams in the vicinity of a scientific station in the Antarctica. These results highlight the importance of the complementation of these biomarkers in two different matrices (surface waters and sediments) to assess wastewater pollution in an Antarctic environment related to anthropogenic activities in the area.

Evaluation of Two Triplex One-Step qRT-PCR Assays for the Quantification of Human Enteric Viruses in Environmental Samples

Human enteric viruses are responsible for waterborne and shellfish-associated disease outbreaks worldwide. Quantitative reverse transcription PCR (qRT-PCR) is often used to assess the health risks associated with shellfish and environmental water, but viral titres in sediments are less commonly investigated. In this study, we developed and validated two multiplex qRT-PCR assays for aquatic sediment and shellfish samples targeting viruses that are a common cause of gastroenteritis (norovirus GI, GII and hepatitis A virus), two emerging viruses (sapovirus and hepatitis E virus), along with mengovirus (MgV), which is often used as a sample process control for the assessment of RNA extraction efficiency. Singleplex and multiplex assays demonstrated comparable PCR efficiencies and gave reliable results over a wide concentration range. The multiplex assays showed remarkable sensitivity with a limit of detection of 1 RNA copy/µL nucleic acid extract for all target viruses and limits of quantification of 3-18 RNA copies/µL for the targeted human pathogenic viruses and 20-40 RNA copies/µL for MgV. The results demonstrated the veracity of multiplex qRT-PCR for the estimation of viral titres in sediment and shellfish, allowing the rapid assessment of viral infection risks associated with environments exposed to wastewater contamination.

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.

The occurrence of antibiotic resistance genes in a Mediterranean river and their persistence in the riverbed sediment

The spread of antibiotic resistance genes (ARGs) in the environment is a serious concern. Bacterial ARGs can spread via different mobile genetic elements as phage particles, which thereby emerge as novel vectors for environmental dissemination. To assess how climate events, such as heavy rains or water scarcity, could affect the spread of ARGs, it is necessary to know their prevalence and abundance in aquatic environments as well as the potential reservoirs from which they could become mobile. This study evaluates the occurrence of ARGs in the water and sediment of a Mediterranean river. Six clinically relevant ARGs (bla_TEM, bla_CTX-M, qnrA, qnrS, mecA and sul1) were quantified by qPCR in the bacterial and phage fractions of 69 water and 70 sediment samples from the River Llobregat (NE Spain), collected during both dry and rainy periods. bla_TEM and sul1 were the most prevalent and abundant ARGs; the others were more variable. Significant seasonal differences in ARG prevalences and abundances were observed. Since ARGs were detected in the sediment, the persistence of the most abundant ARGs naturally occurring in that sediment (bla_TEM and sul1) was evaluated under three conditions. No ARG inactivation occurred in fresh sediment over 14 days; while the ARGs declined by less than 2 log₁₀ units over 35 days in semi-dry and dry sediment. The occurrence of ARGs in water and sediment is influenced by seasonal conditions and they can be mobilized by bacteria and phage particles. In sediment, ARGs persist for long periods and hence sediment can be a natural reservoir of ARGs, from where they can spread and cause the emergence of new resistant strains.

Hepatitis E Virus in Surface Water, Sediments, and Pork Products Marketed in Southern Brazil

Hepatitis E virus (HEV) is an emerging causative agent of food and waterborne hepatitis in human beings. HEV circulates among human populations and swine herds, and may be found in water contaminated by swine feces, as well as in pork. In the present study, 68 sediment samples and 250 water samples collected from the Sinos River tributaries, as well as 50 samples of pork products (pâté and blood sausage) marketed in the Sinos River watershed region, Brazil, were tested for the presence of HEV genome. Reverse-transcriptase polymerase chain reaction followed by nucleotide sequencing was used for detection and characterization of HEV genomes. Overall, 36 % of food samples tested positive for HEV (genotype 3). No sediment or water samples were positive. These results suggest that contaminated pork products may be a source of HEV infection within this region and indicate a need for better monitoring of food safety and swine herds.

Contribution of hydrological data to the understanding of the spatio-temporal dynamics of F-specific RNA bacteriophages in river water during rainfall-runoff events

Heavy rainfall events were previously reported to bring large amounts of microorganisms in surface water, including viruses. However, little information is available on the origin and transport of viral particles in water during such rain events. In this study, an integrative approach combining microbiological and hydrological measurements was investigated to appreciate the dynamics and origins of F-specific RNA bacteriophage fluxes during two distinct rainfall-runoff events. A high frequency sampling (automatic sampler) was set up to monitor the F-specific RNA bacteriophages fluxes at a fine temporal scale during the whole course of the rainfall-runoff events. A total of 276 rainfall-runoff samples were collected and analysed using both infectivity and RT-qPCR assays. The results highlight an increase of 2.5 log10 and 1.8 log10 of infectious F-specific RNA bacteriophage fluxes in parallel of an increase of the water flow levels for both events. Faecal pollution was characterised as being mainly from anthropic origin with a significant flux of phage particles belonging to the genogroup II. At the temporal scale, two successive distinct waves of phage pollution were established and identified through the hydrological measurements. The first arrival of phages in the water column was likely to be linked to the resuspension of riverbed sediments that was responsible for a high input of genogroup II. Surface runoff contributed further to the second input of phages, and more particularly of genogroup I. In addition, an important contribution of infectious phage particles has been highlighted. These findings imply the existence of a close relationship between the risk for human health and the viral contamination of flood water.

Transport and retention of bacteria and viruses in biochar-amended sand

The transport and retention of Escherichia coli and bacteriophages (PRD1, MS2 and ФX174), as surrogates for human pathogenic bacteria and viruses, respectively, were studied in the sand that was amended with several types of biochar produced from various feedstocks. Batch and column studies were conducted to distinguish between the role of attachment and straining in microbe retention during transport. Batch experiments conducted at various solution chemistries showed negligible attachment of viruses and bacteria to biochar before or after chemical activation. At any given solution ionic strength, the attachment of viruses to sand was significantly higher than that of biochar, whereas bacteria showed no attachment to either sand or biochar. Consistent with batch results, biochar addition (10% w/w) to sand reduced virus retention in the column experiments, suggesting a potential negative impact of biochar application to soil on virus removal. In contrast, the retention of bacteria was enhanced in biochar-amended sand columns. However, elimination of the fine fraction (<60μm) of biochar particles in biochar-amended sand columns significantly reduced bacteria retention. Results from batch and column experiments suggest that land application of biochar may only play a role in microbe retention via straining, by alteration of pore size distribution, and not via attachment. Consequently, the particle size distribution of biochar and sediments is a more important factor than type of biochar in determining whether land application of biochar enhances or diminishes microbial retention.

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication

Viruses are ubiquitous drivers of microbial ecology and evolution and contribute to biogeochemical cycling. Attention to these attributes has been more substantial for marine viruses than viruses of other environments. Microscopy-based investigation of the viral communities from two cold, hypersaline Arctic springs was undertaken to explore the effects of these conditions on microbe-viral ecology. Sediments and water samples were collected along transects from each spring, from anoxic spring outlets through oxygenated downstream channels. Viral abundance, virus-microbe ratios and modelled virus-microbe contact rates were lower than comparable aqueous and sedimentary environments and most similar to deep subsurface sediments. No individual cell from either spring was visibly infected. Viruses in these springs appear to play a smaller role in controlling microbial populations through lytic activity than in marine water column or surface sedimentary environments. Relief from viral predation indicates the microbial communities are primarily controlled by nutrient limitation. The similarity of these springs to deep subsurface sediments suggests a biogeographic divide in viral replication strategy in marine sediments.

Enteric viruses in surface water and sediment samples from the catchment area of Peri Lagoon, Santa Catarina State, Brazil

This paper aims to quantify human adenovirus (HAdV), rotavirus species A (RVA), and hepatitis A virus (HAV) in surface water and sediments and to determine the viability of HAdV in these samples. Water and sediment samples were collected, and HAdV, RVA, and HAV were quantified by real-time polymerase chain reaction (PCR); HAdV was also evaluated for infectivity by a plaque assay (PA). For the water samples, HAdV was detected in 70.8% of the summer collections, with 82.4% containing infectious HAdV; the HAdV incidence in winter was 62.5%. For the sediment samples, the incidence of HAdV was 37.5% in the summer collections, with 66.7% containing infectious HAdV; the HAdV incidence in winter was 37.5%. RVA was detected in 20.8 and 45.8% of surface water samples collected in summer and winter, respectively, and 8.3 and 12.5% of sediment samples collected in summer and winter, respectively. HAV was detected only in surface waters, with 54.8 and 12.5% positivity in summer and winter samples, respectively. This study demonstrated that enteric viruses are present in water and sediments and that the presence of infectious viruses should be investigated whenever possible for quantitative microbial risk assessment studies. Combined analyses of water and sediments are important for reliable public health risk analysis of recreational and lagoon waters.

Viral activities and life cycles in deep subseafloor sediments

Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60-97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage-host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus-host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass.

Behaviour and recovery of human adenovirus from tropical sediment under simulated conditions

This study assessed the contributions of pH and organic matter (OM) on the recovery of infectious human adenovirus 5 (HAdV-5) and genome copies (GCs) in waters that were artificially contaminated with tropical soil. The use of a mathematical equation was proposed based on the flocculation index of clay to assess the recovery of total GCs in these controlled assays. The results suggest that solids in the water reduced the viral genome copy loads per millilitre (GC · mL(-1)) and viral infectivity. OM did not influence the GC · mL(-1) recovery rate (p > 0.05) but led to a 99% (2 log10) reduction in plaque-forming unit counts per millilitre (PFU/mL), which indicates that infectivity and gene integrity were non-related parameters. Our findings also suggest that acidic pH levels hinder viral inactivation and that clay is the main factor responsible for the interactions of HAdV-5 with soil. These findings may be useful for future eco-epidemiological investigations and studies of viral inactivation or even as parameters for future research into water quality analysis and water treatment.

[Diversity of virus-like particles from salt mines in Yunnan, China]

OBJECTIVE

For exploring and characterizing the diversity of virus-like particles from salt mines in Yunnan, China.

METHODS

Virus-like particles were identified from enriched brine or saline soil samples by transmission electronic microscopy and double-layer plate, and their morphological properties were further characterized.

RESULTS

Three types of virus-like particles, head-tailed virus, linear virus and spherical virus, were observed by using transmission electronic microscopy. Then, two Halomonas viruses and one Chromohalobacter virus were subsequently isolated from Qiaohou salt mine and Yipinglang salt mine. According to the sample sources, their morphological characteristics and the character of host strains, those viruses were named as Qiaohou Halomonas Siphoviridae Virus 1 ( QHHSV-1), Yipinglang Halomonas Siphoviridae Virus 1 (YPHSV-1) and Yipinglang Chromohalobacter Pleomorphic Virus 1 (YPCPV-1). QHHSV-1 was head-tailed virus with a diameter of 47 nm icosahedrons-like head, and an easily broken 75 nm length tail. YPHSV-1 was head-tailed virus with a diameter of 50 nm icosahedrons-like head, and a 140 nm length tail. YPCPV-1 was a pleomorphic, variable-sized (20 -50 nm) virus, which possessed protuberances on the virus particles.

Attenuation and colloidal mobilization of bacteriophages in natural sediments under anoxic as compared to oxic conditions

Redox conditions are known to affect the fate of viruses in porous media. Several studies report the relevance of colloid-facilitated virus transport in the subsurface, but detailed studies on the effect of anoxic conditions on virus retention in natural sediments are still missing. Therefore, we investigated the fate of viruses in natural flood plain sediments with different sesquioxide contents under anoxic conditions by considering sorption to the solid phase, sorption to mobilized colloids, and inactivation in the aqueous phase. Batch experiments were conducted under oxic and anoxic conditions at pH values between 5.1 and 7.6, using bacteriophages MS2 and PhiX174 as model viruses. In addition to free and colloid-associated bacteriophages, dissolved and colloidal concentrations of Fe, Al and organic C as well as dissolved Ca were determined. Results showed that regardless of redox conditions, bacteriophages did not adsorb to mobilized colloids, even under favourable charge conditions. Under anoxic conditions, attenuation of bacteriophages was dominated by sorption over inactivation, with MS2 showing a higher degree of sorption than PhiX174. Inactivation in water was low under anoxic conditions for both bacteriophages with about one log10 decrease in concentration during 16 h. Increased Fe/Al concentrations and a low organic carbon content of the sediment led to enhanced bacteriophage removal under anoxic conditions. However, even in the presence of sufficient Fe/A-(hydr)oxides on the solid phase, bacteriophage sorption was low. We presume that organic matter may limit the potential retention of sesquioxides in anoxic sediments and should thus be considered for the risk assessment of virus breakthrough in the subsurface.

Counting viruses and bacteria in photosynthetic microbial mats

Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures typically used in benthic viral ecology were applied to the complex matrix of microbial mats but were found to inefficiently extract viruses. Here, we present a method for extraction and quantification of viruses from photosynthetic microbial mats using epifluorescence microscopy (EFM) and flow cytometry (FCM). A combination of EDTA addition, probe sonication, and enzyme treatment applied to a glutaraldehyde-fixed sample resulted in a substantially higher viral (5- to 33-fold) extraction efficiency and reduced background noise compared to previously published methods. Using this method, it was found that in general, intertidal photosynthetic microbial mats harbor very high viral abundances (2.8 × 10(10) ± 0.3 × 10(10) g(-1)) compared with benthic habitats (10(7) to 10(9) g(-1)). This procedure also showed 4.5- and 4-fold-increased efficacies of extraction of viruses and bacteria, respectively, from intertidal sediments, allowing a single method to be used for the microbial mat and underlying sediment.

Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with (13)C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, (13)CO2 production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r(2)=0.6252, P<0.05) and (13)CO2 production (r(2)=0.6572, P<0.05); whereas change in cell abundance was not correlated to acetate consumption or (13)CO2 production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r(2)=0.5036, P<0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r(2)=0.5368, P<0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.

Prospective epidemiological pilot study on the morbidity of bathers exposed to tropical recreational waters and sand

A prospective cohort epidemiological pilot study was performed at three tropical beaches with point- and non-point-sources of fecal pollution to characterize the risk of illness among swimmers and non-swimmers. There was an increased risk of illness in swimmers as compared to non-swimmers, even when waters met current microbial standards for recreational water quality. Illnesses included gastrointestinal (GI), skin and respiratory symptoms, earache and fever. Odds ratios (ORs) ranged from 0.32 to 42.35 (GI illness), 0.69 to 3.12 (skin infections), 0.71 to 3.21 (respiratory symptoms), 0.52 to 15.32 (earache) and 0.80 to 1.68 (fever), depending on the beach sampled. The indicators that better predicted the risks of symptoms (respiratory) in tropical recreational waters were total (somatic and male-specific) coliphages (OR = 1.56, p < 0.10, R(2) = 3.79%) and Escherichia coli (OR = 1.38, p < 0.10, R(2) = 1.97%). The present study supports the potential of coliphages as good predictors of risks of respiratory illness in tropical recreational waters. This is the first study that has determined risks of illness after exposure to tropical recreational waters with point- and non-point sources of fecal contamination. The results give an opportunity to perform epidemiological studies in tropical recreational waters in Puerto Rico which can include more participants and other indicators and detection techniques.

Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments

We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems.

Fecal pathogen pollution: sources and patterns in water and sediment samples from the upper Cook Inlet, Alaska ecosystem

Fecal pathogens are transported from a variety of sources in multi-use ecosystems such as upper Cook Inlet (CI), Alaska, which includes the state's urban center and is highly utilized by humans and animals. This study used a novel water quality testing approach to evaluate the presence and host sources of potential fecal pathogens in surface waters and sediments from aquatic ecosystems in upper CI. Matched water and sediment samples, along with effluent from a municipal wastewater treatment facility, were screened for Salmonella spp., Vibrio spp., Cryptosporidium spp., Giardia spp., and noroviruses. Additionally, Bacteroidales spp. for microbial source tracking, and the fecal indicator bacteria Enterococcus spp. as well as fecal coliforms were evaluated. Overall, Giardia and Vibrio were the most frequently detected potential pathogens, followed by Cryptosporidium and norovirus, while Salmonella was not detected. Sample month, matrix type, and recent precipitation were found to be significant environmental factors for protozoa or host-associated Bacteroidales marker detection, whereas location and water temperature were not. The relative contribution of host-associated markers to total fecal marker concentration was estimated using a Monte Carlo method, with the greatest relative contribution to the Bacteroidales marker concentration coming from human sources, while the remainder of the universal fecal host source signal was uncharacterized by available host-associated assays, consistent with wildlife fecal sources. These findings show how fecal indicator and pathogen monitoring, along with identifying contributing host sources, can provide evidence of coastal pathogen pollution and guidance as to whether to target human and/or animal sources for management.

Metagenomic analysis of viral communities in (hado)pelagic sediments

In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth = 9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 10(6) to 10(11) viruses/cm(3) of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24-30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10(-3) in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95-99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including Microviridae, Circoviridae, and Geminiviridae. A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.

An investigation into occasional White Spot Syndrome Virus outbreak in traditional paddy cum prawn fields in India

A yearlong (September 2009-August 2010) study was undertaken to find out possible reasons for occasional occurrence of White Spot Syndrome Virus (WSSV) outbreak in the traditional prawn farms adjoining Cochin backwaters. Physicochemical and bacteriological parameters of water and sediment from feeder canal and four shrimp farms were monitored on a fortnightly basis. The physicochemical parameters showed variation during the two production cycles and between the farms studied. Dissolved oxygen (DO) content of water from feeder canal showed low oxygen levels (as low as 0.8 mg/L) throughout the study period. There was no disease outbreak in the perennial ponds. Poor water exchange coupled with nutrient loading from adjacent houses resulted in phytoplankton bloom in shallow seasonal ponds which led to hypoxic conditions in early morning and supersaturation of DO in the afternoon besides considerably high alkaline pH. Ammonia levels were found to be very high in these ponds. WSSV outbreak was encountered twice during the study leading to mass mortalities in the seasonal ponds. The hypoxia and high ammonia content in water and abrupt fluctuations in temperature, salinity and pH might lead to considerable stress in the shrimps triggering WSSV infection in these traditional ponds.

Mechanisms for parasites removal in a waste stabilisation pond

A waste stabilisation pond (WSP) system formed by two anaerobic ponds, a facultative pond and a maturation pond was studied from December 2003 to September 2004 in north-western Spain in order to evaluate its efficiency in the removal of faecal indicator bacteria (total coliforms, Escherichia coli, faecal streptococci), coliphages, helminth eggs and protozoan (oo)cysts (Cryptosporidium and Giardia). Furthermore, sediment samples were collected from the bottom of the ponds to assess the settling rates and thus determine the main pathogen removal mechanisms in the WSPs system. The overall removal ranged from 1.4 log units for coliphages in the cold period to 5.0 log units for E. coli in the hot period. Cryptosporidium oocysts were reduced by an average of 96%, Giardia cysts by 98% and helminth eggs by 100%. The anaerobic ponds showed significantly higher surface removal rates (4.6, 5.2 and 3.7 log (oo)cysts/eggs removed m(-2) day(-1), respectively) than facultative and maturation ponds. Sunlight and water physicochemical conditions were the main factors influencing C. parvum oocysts removal both in the anaerobic and maturation ponds, whereas other factors like predation or natural mortality were more important in the facultative pond. Sedimentation, the most commonly proposed mechanism for cyst removal had, therefore, a negligible influence in the studied ponds.

Vulnerability of unconfined aquifers to virus contamination

An empirical formula was developed for determining the vulnerability of unconfined sandy aquifers to virus contamination, expressed as a dimensionless setback distance r(s)(*). The formula can be used to calculate the setback distance required for the protection of drinking water production wells against virus contamination. This empirical formula takes into account the intrinsic properties of the virus and the unconfined sandy aquifer. Virus removal is described by a rate coefficient that accounts for virus inactivation and attachment to sand grains. The formula also includes pumping rate, saturated thickness of the aquifer, depth of the screen of the pumping well, and anisotropy of the aquifer. This means that it accounts also for dilution effects as well as horizontal and vertical virus transport. Because the empirical model includes virus source concentration it can be used as an integral part of a quantitative viral risk assessment.

Characterisation of virus transport and attenuation in epikarst using short pulse and prolonged injection multi-tracer testing

Attenuation processes controlling virus fate and transport in the vadose zone of karstified systems can strongly influence groundwater quality. This research compares the breakthrough of two bacteriophage tracers (H40/1 and T7), with contrasting properties, at subsurface monitoring points following application onto an overlying composite sequence of thin organic soil and weathered limestone (epikarst). Short pulse multi-tracer test results revealed that T7 (Source concentration, Co=1.8x10(6)pfu/mL) and H40/1 (Co=5.9x10(6)pfu/mL) could reach sampling points 10 m below ground less than 30 min after tracer application. Contrasting deposition rates, determined from simulated tracer responses, reflected the potential of the ground to differentially attenuate viruses. Prolonged application of both T7 (Co=2.3x10(4)pfu/mL) and H40/1 (Co=1.3x10(5)pfu/mL) over a five hour period during a subsequent test, in which ionic strength levels observed at monitoring points rose consistently, corresponded to a rapid rise in T7 levels, followed by a gradual decline before the end of tracer injection; this reflected reaction-limited deposition in the system. T7's response contrasted with that of H40/1, whose concentration remained constant over a three hour period before declining dramatically prior to the end of tracer injection. Subsequent application of lower ionic strength tracer-free flush water generated a rapid rise in H40/1 levels and a more gradual release of T7. Results highlight the benefits of employing prolonged injection multi-tracer tests for identifying processes not apparent from conventional short pulse tests. Study findings demonstrate that despite rapid transport rates, the epikarst is capable of physicochemical filtration of viruses and their remobilization, depending on virus type and hydrochemical conditions.

Application of real-time PCR assays to genotyping of F-specific phages in river water and sediments in Japan

Genotyping of F-specific RNA phages is currently one of the most promising approaches to differentiate between human and animal fecal contamination in aquatic environments. In this study, a total of 18 river water and sediment samples were collected from the Tonegawa River basin, Japan, in order to describe the genogroup distribution of F-specific RNA and DNA phages using genogroup-specific real-time PCR assays. F-specific phages were detected in nine (100%) river water and six (67%) sediment samples. Eighty-five phage plaques were isolated from these samples and subjected to real-time PCR assays specific for the phages. F-specific RNA phages of human genogroups (II and III) were detected in 32 (38%) plaques, whereas those of animal genogroups (I and IV) were detected in 17 (20%) plaques. No correlation was observed between the genogroup distribution of F-specific RNA phages and the occurrence of human adenovirus genomes, suggesting that genotyping of the phages alone is inadequate for the evaluation of the occurrence of viruses in aquatic environments. SYBR Green-based real-time PCR assay revealed the presence of F-specific DNA phages in four (5%) plaques, which were further classified into two genogroups (fd- and f1-like phages) by sequence analysis. Thirty-two (38%) plaques were not classified as the F-specific phage genogroups, indicating the limited applicability of these real-time PCR assays to a wide range of aquatic environmental samples worldwide.

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. Microscopy and molecular genetic tools have been critical in demonstrating that viruses are a dynamic component of microbial ecosystems capable of significantly influencing the productivity and population biology of their host communities. Moreover, these approaches have begun to describe and constrain the immense genetic diversity of viral communities. A critical first step in the application of many cultivation-independent approaches to virus ecology is obtaining a concentrate of viruses from an environmental sample. Culture-dependent methods also rely on viruses being present at a high enough abundance to detect. Here, methodological details for the isolation and concentration of viruses from water, soil, and aquatic sediment samples are covered in detail.

Accumulation of Tobacco mosaic virus (TMV) at different depths clay and loamy sand textural soils due to tobacco waste application

The effects of tobacco waste (TW) application to the soil surface on the accumulation of Tobacco mosaic virus (TMV) in clay and loamy sand textural soils at various depths were investigated in two different fields. The tobacco waste had been found to be infected with TMV. Eighteen months after TW application to the soil surface, soils were sampled at 20 cm intervals through to 80 cm depth. The DAS-ELISA method was performed to determine infection of soil with TMV. The viruses persisted in clay soil for a long period compared with loamy sand soil. There was no accumulation of TMV at any depth of loamy sand soil in Experimental Field 2. TMV adsorption to soil particles in 0-60 cm depth of clay soil was determined in all TW treatments in Experimental Field 1. The highest ELISA Absorbance (A405) values in all treatments were determined in the 20-40 cm soil depth that had the highest clay content. ELISA A405 values of TMV at different depths of clay soil gave significant correlations with clay content (r = 0.793**), EC values (r = 0.421**) and soil pH (r = -0.405**). Adsorption of TMV to net negatively charged clay particle surfaces increased with increasing EC values of soil solution. Decreasing soil pH and infiltration rate increased adsorption of TMV to clay particles. Higher infiltration rate and lower clay content in loamy sand soil caused leaching of TMV from the soil profile.

Effects of deposit-feeding macrofauna on benthic bacteria, viruses, and protozoa in a silty freshwater sediment

In microcosm experiments, we simultaneously tested the effects of increased numbers of deposit-feeding macrofauna (chironomids, oligochaetes and cladocerans) on the standing stock, activities and interactions of heterotrophic bacteria, viruses, and bacterivorous protozoa (heterotrophic nanoflagellates and ciliates) in the aerobic layer of a silty littoral freshwater sediment. On average, bacterial secondary production was stimulated between 11 and 29% by all macrofaunal groups compared to control experiments without macrofauna addition. Bacterial standing stock increased significantly by 8 and 13% in case of chironomids and cladocerans, respectively. Oligochaetes and chironomids produced significant negative effects on viral abundance while the results with cladocerans were inconsistent. The addition of oligochaetes and chironomids resulted in a significant decrease by on average 68 and 32% of viral decay rates, respectively, used as a measure of viral production. The calculated contribution of virus-induced lysis to benthic bacterial mortality was low, with 2.8 to 11.8% of bacterial secondary production, and decreased by 39 to 81% after the addition of macrofauna compared to the control. The abundances of heterotrophic nanoflagellates were significantly reduced by 20% by all tested macrofauna groups, while ciliates showed inconsistent results. The importance of heterotrophic nanoflagellate grazing on benthic bacteria was very low (<1% of bacterial secondary production) and was further reduced by elevated numbers of macrofauna. Thus, the selected deposit feeding macrofauna groups seem to have several direct and indirect and partly antagonistic effects on the benthic bacterial compartment through the enhancement of bacterial production and the reduction of virus-induced cell lysis and protozoan grazing.

Genetic analysis of infectious pancreatic necrosis virus from Scotland

Infectious pancreatic necrosis (IPN) is a highly contagious disease of young salmonid fish, and is one of the most serious economic diseases in aquaculture. In Scotland, an increase in IPN virus (IPNV) outbreaks in seawater Atlantic salmon, Salmo salar, has been reported in recent years. The aim of this study was to analyse the VP2 gene from recent IPNV isolates from Scotland, to determine whether there are epidemiological links between IPNV isolates from farms (13), wild fish (17) and the environment (6) in order to investigate potential wild and farmed fish interactions. Comparison of the nucleotide sequence of the VP2 gene revealed that 34 of 36 isolates were 97.1-100% similar and the deduced amino acid sequences showed 97-100% identity. Two isolates from wild fish exhibited the most divergence at 85-87.3% similarity to the other isolates at the nucleotide level and 88.2-90.8% identity at the deduced amino acid level. Phylogenetic analyses revealed that 34 of 36 of the isolates from Scotland were genetically closely related to the A2 (Sp) serotype of IPNV. The two wild isolates from seatrout, Salmo trutta, and flounder, Platichthys flesus, were most closely related to the European A5 (Te) serotype. This study represents a comprehensive IPNV phylogenetic study that indicates that there are closely related or identical isolates in circulation in the marine environment, which adds evidence that disease interactions between wild and farmed fish may occur. This type of analysis is a useful tool in the management and control of fish diseases because it can assist in the identification of epidemiological links and highlight potential risks to aquaculture.

Detection of infectious pancreatic necrosis virus (IPNV) from the environment in the vicinity of IPNV-infected Atlantic salmon farms in Scotland

Infectious pancreatic necrosis virus (IPNV) has been isolated from mussels, sediment and surface water in the vicinity of clinically infected salmon farms, at shore bases supplying the farms and for several hundred metres distance from farms in the direction of current flow. There was evidence of decreasing prevalence of IPNV in mussels from Shetland once IPN outbreaks subsided, indicating they are an unlikely source of re-infection on farms. There was little evidence of persistence in the environment, although conclusions were complicated by the presence of IPNV on neighbouring farms 1 year after the outbreak.

Techniques for the recovery of enteric viruses from artificially contaminated marine sediments

Viruses are an important component of aquatic microbial communities and marine sediments may represent an optimal means for their survival. The aim of this study was to evaluate different methods for virus recovery from marine sediments. Three methods were used for virus recovery from artificially contaminated sediments: elution and centrifugation technique, sonication technique, and mechanical disgregation followed by elution and centrifuge technique. The sonication technique obtained the highest virus recovery percentages (94,25%). Eluent 2 provided more efficient recovery of enteric viruses than eluent 1 presumably due to the presence, in eluent 2, of NANO3, a chaotropic agent that enhances the solubilization of hydrophobic compounds in water. Finally, the authors confirm the importance of searching for viruses in sediments, which protect them from inactivation by biological, chemical and physical factors and allow them to survive longer than in the overlaying water column.

Virus attachment to transparent exopolymeric particles along trophic gradients in the southwestern lagoon of New Caledonia

Viruses on organic aggregates such as transparent exopolymeric particles (TEP) are not well investigated. The number of TEP-attached viruses was assessed along trophic gradients in the southwestern lagoon of New Caledonia by determining the fraction of viruses removed after magnetic isolation of TEP. In order to isolate TEP magnetically, TEP were formed in the presence of magnetic beads from submicrometer precursors collected along the trophic gradients. The mixed aggregates of TEP-beads-viruses were removed from solution with a magnetic field. The percentage of viruses associated with newly formed TEP averaged 8% (range, 3 to 13%) for most of the stations but was higher (ca. 30%) in one bay characterized by the low renewal rate of its water mass. The number of viruses (N) attached to TEP varied as a function of TEP size (d [in micrometers]) according to the formulas N = 100d(1.60) and N = 230d(1.75), respectively, for TEP occurring in water masses with short (i.e., <40 days) and long (i.e., >40 days) residence times. These two relationships imply that viral abundance decreases with TEP size, and they indicate that water residence time influences viral density and virus-bacterium interactions within aggregates. Our data suggest that the fraction of viruses attached to TEP is highest in areas characterized by a low renewal rate of the water mass and can constitute at times a significant fraction of total virus abundance. Due to the small distance between viruses and hosts on TEP, these particles may be hot spots for viral infection.

Viral abundance and genome size distribution in the sediment and water column of marine and freshwater ecosystems

The size distribution of viral DNA in natural samples was investigated in a number of marine, brackish and freshwater environments by means of pulsed field gel electrophoresis (PFGE). The method was modified to work with both water and sediment samples, with an estimated detection limit for individual virus genome size groups of 1-2 x 10(4) virus-like particles (VLP) mL(-1) water and 2-4 x 10(5) VLP cm(-3) sediment in the original samples. Variations in the composition and distribution of dominant virus genome sizes were analyzed within and between different habitats that covered a range in viral density from 0.4 x 10(7) VLP mL(-1) (sea water) to 300 x 10(7) VLP cm(-3) (lake sediment). The PFGE community fingerprints showed a number of cross-system similarities in the genome size distribution with a general dominance of genomes in the 30-48, 50-70 and 145-200 kb size fractions, and with many of the specific genome sizes detected in all the investigated habitats. However, large differences in community fingerprints were also observed between the investigated sites, and some virus genome sizes were found only in specific biotopes (e.g. lake water), in specific ecosystems (e.g. a particular lake) or even in specific microhabitats (e.g. a particular sediment stratum).

Virus-bacterium interactions in water and sediment of West African inland aquatic systems

The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water.

Ranavirus in wood frogs (Rana sylvatica): potential sources of transmission within and between ponds

Members of the genus Ranavirus (family Iridoviridae) can cause catastrophic mortality of pond-breeding amphibians and are associated with an emerging infectious disease that may be contributing to amphibian declines. We conducted three experiments to examine factors that may affect transmission both within and between local breeding populations of the wood frog (Rana sylvatica). In a laboratory study, when exposed to moribund tadpoles collected during a local ranaviral die-off, uninfected tadpoles died as soon as 4 days after exposure. The onset of death was accelerated when tadpoles were allowed to scavenge on carcasses of infected tadpoles. In a mesocosm experiment that was conducted in outdoor wading pools, die-offs of tadpoles began approximately 19 days after infected tadpoles were added to pools containing uninfected tadpoles. Mass die-offs with greater than 98% mortality occurred in all pools, regardless of the initial tadpole density. In a second mesocosm experiment, the addition of water and bottom sediments that were collected from a pond during a ranaviral die-off did not result in lower tadpole survival or growth relative to controls. Only a small percentage of tadpoles appeared to be sick, and most tadpoles survived until the first individuals began metamorphosing within a pool. However, tests for ranavirus using polymerase chain reaction were positive for most pools that received contaminated sediment, suggesting that some infections were sublethal. Our results indicate that transmission within ponds is enhanced by scavenging and that spread between local ponds could occur via the transport of contaminated sediment by animals or humans.