Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

BACKGROUND

As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS

We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS

Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.

Viruses of Plankton: On the Edge of the Viral Frontier

The field of aquatic viral ecology has continued to evolve rapidly over the last three decades [...].

Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota)

Large DNA viruses in the phylum Nucleocytoviricota, sometimes referred to as "giant viruses" owing to their large genomes and virions, have been the subject of burgeoning interest over the last decade. Here, we describe recently adopted taxonomic updates for giant viruses within the order Imitervirales. The families Allomimiviridae, Mesomimiviridae, and Schizomimiviridae have been created to accommodate the increasing diversity of mimivirus relatives that have sometimes been referred to in the literature as "extended Mimiviridae". In addition, the subfamilies Aliimimivirinae, Megamimivirinae, and Klosneuvirinae have been established to refer to subgroups of the Mimiviridae. Binomial names have also been adopted for all recognized species in the order. For example, Acanthamoeba polyphaga mimivirus is now classified in the species Mimivirus bradfordmassiliense.

Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga

Virophages are small double stranded DNA (dsDNA) viruses that can only replicate in a host by co-infecting with another virus. Marine algae are commonly associated with virophage-like elements such as Polinton-like viruses (PLVs) that remain largely uncharacterized. Here we isolated a PLV that co-infects the alga Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T), a close relative of the "Phaeocystis globosa virus-virophage" genomic sequence. We name this PLV 'Gezel-14T. Gezel is phylogenetically distinct from the Lavidaviridae family where all known virophages belong. Gezel-14T co-infection decreases the fitness of its viral host by reducing burst sizes of PgV-14T, yet insufficiently to spare the cellular host population. Genomic screens show Gezel-14T-like PLVs integrated into Phaeocystis genomes, suggesting that these widespread viruses are capable of integration into cellular host genomes. This system presents an opportunity to better understand the evolution of eukaryotic dsDNA viruses as well as the complex dynamics and implications of viral parasitism.

ICTV Virus Taxonomy Profile: Spinareoviridae 2022

Spinareoviridae is a large family of icosahedral viruses that are usually regarded as non-enveloped with segmented (9–12 linear segments) dsRNA genomes of 23–29 kbp. Spinareovirids have a broad host range, infecting animals, fungi and plants. Some have important pathogenic potential for humans (e.g. Colorado tick fever virus), livestock (e.g. avian orthoreoviruses), fish (e.g. aquareoviruses) and plants (e.g. rice ragged stunt virus and rice black streaked dwarf virus). This is a summary of the ICTV Report on the family Spinareoviridae, which is available at ictv.global/report/spinareoviridae.

ICTV Virus Taxonomy Profile: Sedoreoviridae 2022

Sedoreoviridae is a large family of icosahedral viruses that are usually regarded as non-enveloped with segmented (10-12 linear segments) dsRNA genomes of 18-26 kbp. Sedoreovirids have a broad host range, infecting mammals, birds, crustaceans, arthropods, algae and plants. Some of them have important pathogenic potential for humans (e.g. rotavirus A), livestock (e.g. bluetongue virus) and plants (e.g. rice dwarf virus). This is a summary of the ICTV Report on the family Sedoreoviridae, which is available at ictv.global/report/sedoreoviridae.

Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes

Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixotrophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 - 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell^-1 h^-1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.

Effects of UV Radiation on the Chlorophyte Micromonas polaris Host-Virus Interactions and MpoV-45T Virus Infectivity

Polar seas are under threat of enhanced UV-radiation as well as increasing shipping activities. Considering the ecological importance of marine viruses, it is timely to study the impact of UV-AB on Arctic phytoplankton host-virus interactions and also test the efficacy of ballast water (BW) UV-C treatment on virus infectivity. This study examined the effects of: (i) ecologically relevant doses of UV-AB radiation on Micromonas polaris RCC2258 and its virus MpoV-45T, and (ii) UV-C radiation (doses 25-800 mJ cm-2) on MpoV-45T and other temperate algal viruses. Total UV-AB exposure was 6, 12, 28 and 48 h (during the light periods, over 72 h total). Strongest reduction in algal growth and photosynthetic efficiency occurred for 28 and 48 h UV-AB treatments, and consequently the virus production rates and burst sizes were reduced by more than half (compared with PAR-only controls). For the shorter UV-AB exposed cultures, negative effects by UV (especially Fv/Fm) were overcome without impacting virus proliferation. To obtain the BW desired log-4 reduction in virus infectivity, a UV-C dose of at least 400 mJ cm-2 was needed for MpoV-45T and the temperate algal viruses. This is higher than the commonly used dose of 300 mJ cm-2 in BW treatment.

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.

Spring Accumulation Rates in North Atlantic Phytoplankton Communities Linked to Alterations in the Balance Between Division and Loss

For nearly a century, phytoplankton spring blooms have largely been explained in the context of abiotic factors regulating cellular division rates (e.g., mixed-layer light levels). However, the accumulation of new phytoplankton biomass represents a mismatch between phytoplankton division and mortality rates. The balance between division and loss, therefore, has important implications for marine food webs and biogeochemical cycles. A large fraction of phytoplankton mortality is due to the combination of microzooplankton grazing and viral lysis, however, broad scale simultaneous measurements of these mortality processes are scarce. We applied the modified dilution assay along a West-to-East diagonal transect in the North Atlantic during spring. Our results demonstrate positive accumulation rates with losses dominated by microzooplankton grazing. Considering the dynamic light environment phytoplankton experience in the mixed surface layer, particularly in the spring, we tested the potential for incubation light conditions to affect observed rates. Incubations acted as short-term 'light' perturbations experiments, in which deeply mixed communities are exposed to elevated light levels. These "light perturbations" increased phytoplankton division rates and resulted in proportional changes in phytoplankton biomass while having no significant effect on mortality rates. These results provide experimental evidence for the Disturbance-Recovery Hypothesis, supporting the tenet that biomass accumulation rates co-vary with the specific rate of change in division.

Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H₂O₂) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H₂O₂, little is known about the impacts of these H₂O₂ treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H₂O₂ concentrations (target: 2.5 mg L⁻¹) and in two series of controlled lake incubations. The results show that the H₂O₂ treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H₂O₂ addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H₂O₂ to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer

The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.

An empirical model of carbon flow through marine viruses and microzooplankton grazers

Viruses and microzooplankton grazers represent major sources of mortality for marine phytoplankton and bacteria, redirecting the flow of organic material throughout the world's oceans. Here, we investigate the use of nonlinear population models of interactions between phytoplankton, viruses and grazers as a means to quantitatively constrain the flow of carbon through marine microbial ecosystems. We augment population models with a synthesis of laboratory-based estimates of prey, predator and viral life history traits that constrain transfer efficiencies. We then apply the model framework to estimate loss rates in the California Current Ecosystem (CCE). With our empirically parameterized model, we estimate that, of the total losses mediated by viruses and microzooplankton grazing at the focal CCE site, 22 ± 3%, 46 ± 27%, 3 ± 2% and 29 ± 20% were directed to grazers, sloppy feeding (as well as excretion and respiration), viruses and viral lysate respectively. We identify opportunities to leverage ecosystem models and conventional mortality assays to further constrain the quantitative rates of critical ecosystem processes.

Cyanophage Propagation in the Freshwater Cyanobacterium Phormidium Is Constrained by Phosphorus Limitation and Enhanced by Elevated pCO2

Intensification of human activities has led to changes in the availabilities of CO₂ and nutrients in freshwater ecosystems, which may greatly alter the physiological status of phytoplankton. Viruses require hosts for their reproduction and shifts in phytoplankton host physiology through global environmental change may thus affect viral infections as well. Various studies have investigated the impacts of single environmental factors on phytoplankton virus propagation, yet little is known about the impacts of multiple factors, particularly in freshwater systems. We therefore tested the combined effects of phosphorus limitation and elevated pCO₂ on the propagation of a cyanophage infecting a freshwater cyanobacterium. To this end, we cultured Phormidium in P-limited chemostats under ambient (400 μatm) and elevated (800 μatm) pCO₂ at growth rates of 0.6, 0.3, and 0.05 d^-1. Host C:P ratios generally increased with strengthened P-limitation and with elevated pCO₂. Upon host steady state conditions, virus growth characteristics were obtained in separate infection assays where hosts were infected by the double-stranded DNA cyanophage PP. Severe P-limitation (host growth 0.05 d^-1) led to a 85% decrease in cyanophage production rate and a 73% decrease in burst size compared to the 0.6 d^-1 grown P-limited cultures. Elevated pCO₂ induced a 96% increase in cyanophage production rate and a 57% increase in burst size, as well as an 85% shorter latent period as compared to ambient pCO₂ at the different host growth rates. In addition, elevated pCO₂ caused a decrease in the plaquing efficiency and an increase in the abortion percentage for the 0.05 d^-1 P-limited treatment, while the plaquing efficiency increased for the 0.6 d^-1 P-limited cultures. Together, our results demonstrate interactive effects of elevated pCO₂ and P-limitation on cyanophage propagation, and show that viral propagation is generally constrained by P-limitation but enhanced with elevated pCO₂. Our findings indicate that global change will likely have a severe impact on virus growth characteristics and thereby on the control of cyanobacterial hosts in freshwater ecosystems.

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.

Influence of Irradiance and Temperature on the Virus MpoV-45T Infecting the Arctic Picophytoplankter Micromonas polaris

Arctic marine ecosystems are currently undergoing rapid changes in temperature and light availability. Picophytoplankton, such as Micromonas polaris, are predicted to benefit from such changes. However, little is known about how these environmental changes affect the viruses that exert a strong mortality pressure on these small but omnipresent algae. Here we report on one-step infection experiments, combined with measurements of host physiology and viability, with 2 strains of M. polaris and the virus MpoV-45T under 3 light intensities (5, 60 and 160 μmol quanta m-2 s-1), 2 light period regimes (16:8 and 24:0 h light:dark cycle) and 2 temperatures (3 and 7 °C). Our results show that low light intensity (16:8 h light:dark) delayed the decline in photosynthetic efficiency and cell lysis, while decreasing burst size by 46%. In contrast, continuous light (24:0 h light:dark) shortened the latent period by 5 h for all light intensities, and even increased the maximum virus production rate and burst size under low light (by 157 and 69%, respectively). Higher temperature (7 °C vs 3 °C) led to earlier cell lysis and increased burst size (by 19%), except for the low light conditions. These findings demonstrate the ecological importance of light in combination with temperature as a controlling factor for Arctic phytoplankton host and virus dynamics seasonally, even more so in the light of global warming.

Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance

Cylindrospermopsis (Raphidiopsis) raciborskii is an invasive, filamentous, nitrogen-fixing cyanobacterium that forms frequent blooms in freshwater habitats. While viruses play key roles in regulating the abundance, production and diversity of their hosts in aquatic ecosystems, the role(s) of viruses in the ecology of C. raciborskii is almost unexplored. Progress in this field has been hindered by the absence of a characterized virus-host system in C. raciborskii. To bridge this gap, we sequenced the genome of CrV-01T, a previously isolated cyanosiphovirus, and its host, C. raciborskii strain Cr2010. Analyses suggest that CrV-01T represents a distinct clade of siphoviruses infecting, and perhaps lysogenizing, filamentous cyanobacteria. Its genome contains unique features that include an intact CRISPR array and a 12 kb inverted duplication. Evidence suggests CrV-01T recently gained the ability to infect Cr2010 and recently lost the ability to form lysogens. The cyanobacterial host contains a CRISPR-Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV-01T genome. Examination of metagenomes demonstrates that viruses with high genetic identity to CrV-01T, but lacking the inverted duplication, are present in C. raciborskii blooms in Australia. The unique genomic features of the CrV/Cr2010 system offers opportunities to investigate in more detail virus-host interactions in an ecologically important bloom-forming cyanobacterium.

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

The original publication of this Article included analysis of virus and microbial cell abundances and virus-to-microbial cell ratios. Data in the Article came from 25 studies intended to be exclusively from marine sites. However, 3 of the studies included in the original unified dataset were erroneously classified as marine sites during compilation. The records with mis-recorded longitude and latitude values were, in fact, taken from inland, freshwater sources. The three inland, freshwater datasets are ELA, TROUT and SWAT. The data from these three studies represent 163 of the 5,671 records in the original publication. In the updated version of the Article, all analyses have been recalculated using the same statistical analysis pipeline released via GitHub as part of the original publication. Removal of the three studies reduces the unified dataset to 5,508 records. Analyses involving all grouped datasets have been updated with changes noted in each figure. All key results remain qualitatively unchanged. All data and scripts used in this correction have been made available as a new, updated GitHub release to reflect the updated dataset and figures.

Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change

An 8-year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.

Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses

Global climate change-induced warming of the Artic seas is predicted to shift the phytoplankton community towards dominance of smaller-sized species due to global warming. Yet, little is known about their viral mortality agents despite the ecological importance of viruses regulating phytoplankton host dynamics and diversity. Here we report the isolation and basic characterization of four prasinoviruses infectious to the common Arctic picophytoplankter Micromonas. We furthermore assessed how temperature influenced viral infectivity and production. Phylogenetic analysis indicated that the putative double-stranded DNA (dsDNA) Micromonas polaris viruses (MpoVs) are prasinoviruses (Phycodnaviridae) of approximately 120 nm in particle size. One MpoV showed intrinsic differences to the other three viruses, i.e., larger genome size (205 ± 2 vs. 191 ± 3 Kb), broader host range, and longer latent period (39 vs. 18 h). Temperature increase shortened the latent periods (up to 50%), increased the burst size (up to 40%), and affected viral infectivity. However, the variability in response to temperature was high for the different viruses and host strains assessed, likely affecting the Arctic picoeukaryote community structure both in the short term (seasonal cycles) and long term (global warming).

Immediate ecotoxicological effects of short-lived oil spills on marine biota

Marine environments are frequently exposed to oil spills as a result of transportation, oil drilling or fuel usage. Whereas large oil spills and their effects have been widely documented, more common and recurrent small spills typically escape attention. To fill this important gap in the assessment of oil-spill effects, we performed two independent supervised full sea releases of 5 m(3) of crude oil, complemented by on-board mesocosm studies and sampling of accidentally encountered slicks. Using rapid on-board biological assays, we detect high bioavailability and toxicity of dissolved and dispersed oil within 24 h after the spills, occurring fairly deep (8 m) below the slicks. Selective decline of marine plankton is observed, equally relevant for early stages of larger spills. Our results demonstrate that, contrary to common thinking, even small spills have immediate adverse biological effects and their recurrent nature is likely to affect marine ecosystem functioning.

Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus

The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.

Microscale spatial distributions of microbes and viruses in intertidal photosynthetic microbial mats

Intertidal photosynthetic microbial mats from the Wadden Sea island Schiermonnikoog were examined for microscale (millimetre) spatial distributions of viruses, prokaryotes and oxygenic photoautotrophs (filamentous cyanobacteria and benthic diatoms) at different times of the year. Abundances of viruses and prokaryotes were among the highest found in benthic systems (0.05-5.43 × 10(10) viruses g(-1) and 0.05-2.14 × 10(10) prokaryotes g(-1)). The spatial distribution of viruses, prokaryotes and oxygenic photoautotrophs were highly heterogeneous at mm scales. The vertical distributions of both prokaryotic and viral abundances were related to the depth of the oxygenic photoautotrophic layer, implying that the photosynthetic mat fuelled the microbial processes in the underlying layer. Our data suggest that viruses could make an important component in these productive environments potentially affecting the biodiversity and nutrient cycling within the mat.

Disruption of photoautotrophic intertidal mats by filamentous fungi

Ring-like structures, 2.0-4.8 cm in diameter, observed in photosynthetic microbial mats on the Wadden Sea island Schiermonnikoog (the Netherlands) showed to be the result of the fungus Emericellopsis sp. degrading the photoautotrophic top layer of the mat. The mats were predominantly composed of cyanobacteria and diatoms, with large densities of bacteria and viruses both in the top photosynthetic layer and in the underlying sediment. The fungal attack cleared the photosynthetic layer; however, no significant effect of the fungal lysis on the bacterial and viral abundances could be detected. Fungal-mediated degradation of the major photoautotrophs could be reproduced by inoculation of non-infected mat with isolated Emericellopsis sp., and with an infected ring sector. Diatoms were the first re-colonizers followed closely by cyanobacteria that after about 5 days dominated the space. The study demonstrated that the fungus Emericellopsis sp. efficiently degraded a photoautotrophic microbial mat, with potential implications for mat community composition, spatial structure and productivity.

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.

Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

The aim of this work was to determine the effect of light crude oil on bacterial communities during an experimental oil spill in the North Sea and in mesocosms (simulating a heavy, enclosed oil spill), and to isolate and characterize hydrocarbon-degrading bacteria from the water column. No oil-induced changes in bacterial community (3 m below the sea surface) were observed 32 h after the experimental spill at sea. In contrast, there was a decrease in the dominant SAR11 phylotype and an increase in Pseudoalteromonas spp. in the oiled mesocosms (investigated by 16S rRNA gene analysis using denaturing gradient gel electrophoresis), as a consequence of the longer incubation, closer proximity of the samples to oil, and the lack of replenishment with seawater. A total of 216 strains were isolated from hydrocarbon enrichment cultures, predominantly belonging to the genus Pseudoaltero monas; most strains grew on PAHs, branched and straight-chain alkanes, as well as many other carbon sources. No obligate hydrocarbonoclastic bacteria were isolated or detected, highlighting the potential importance of cosmopolitan marine generalists like Pseudoalteromonas spp. in degrading hydrocarbons in the water column beneath an oil slick, and revealing the susceptibility to oil pollution of SAR11, the most abundant bacterial clade in the surface ocean.

First day of an oil spill on the open sea: early mass transfers of hydrocarbons to air and water

During the first hours after release of petroleum at sea, crude oil hydrocarbons partition rapidly into air and water. However, limited information is available about very early evaporation and dissolution processes. We report on the composition of the oil slick during the first day after a permitted, unrestrained 4.3 m(3) oil release conducted on the North Sea. Rapid mass transfers of volatile and soluble hydrocarbons were observed, with >50% of ≤C17 hydrocarbons disappearing within 25 h from this oil slick of <10 km(2) area and <10 μm thickness. For oil sheen, >50% losses of ≤C16 hydrocarbons were observed after 1 h. We developed a mass transfer model to describe the evolution of oil slick chemical composition and water column hydrocarbon concentrations. The model was parametrized based on environmental conditions and hydrocarbon partitioning properties estimated from comprehensive two-dimensional gas chromatography (GC×GC) retention data. The model correctly predicted the observed fractionation of petroleum hydrocarbons in the oil slick resulting from evaporation and dissolution. This is the first report on the broad-spectrum compositional changes in oil during the first day of a spill at the sea surface. Expected outcomes under other environmental conditions are discussed, as well as comparisons to other models.

Factors affecting virus dynamics and microbial host-virus interactions in marine environments

Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host-virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.

Elevated CO2 and phosphate limitation favor Micromonas pusilla through stimulated growth and reduced viral impact

Growth and viral infection of the marine picoeukaryote Micromonas pusilla was studied under a future-ocean scenario of elevated partial CO2 (pCO2; 750 μatm versus the present-day 370 μatm) and simultaneous limitation of phosphorus (P). Independent of the pCO2 level, the ratios of M. pusilla cellular carbon (C) to nitrogen (N), C:P and N:P, increased with increasing P stress. Furthermore, in the P-limited chemostats at growth rates of 0.32 and 0.97 of the maximum growth rate (μmax), the supply of elevated pCO2 led to an additional rise in cellular C:N and C:P ratios, as well as a 1.4-fold increase in M. pusilla abundance. Viral lysis was not affected by pCO2, but P limitation led to a 150% prolongation of the latent period (6 to 12 h) and an 80% reduction in viral burst sizes (63 viruses per cell) compared to P-replete conditions (4 to 8 h latent period and burst size of 320). Growth at 0.32 μmax further prolonged the latent period by another 150% (12 to 18 h). Thus, enhanced P stress due to climate change-induced strengthened vertical stratification can be expected to lead to reduced and delayed virus production in picoeukaryotes. This effect is tempered, but likely not counteracted, by the increase in cell abundance under elevated pCO2. Although the influence of potential P-limitation-relieving factors, such as the uptake of organic P and P utilization during infection, is unclear, our current results suggest that when P limitation prevails in future oceans, picoeukaryotes and grazing will be favored over larger-sized phytoplankton and viral lysis, with increased matter and nutrient flow to higher trophic levels.

Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa

The release of organic material upon algal cell lyses has a key role in structuring bacterial communities and affects the cycling of biolimiting elements in the marine environment. Here we show that already before cell lysis the leakage or excretion of organic matter by infected yet intact algal cells shaped North Sea bacterial community composition and enhanced bacterial substrate assimilation. Infected algal cultures of Phaeocystis globosa grown in coastal North Sea water contained gamma- and alphaproteobacterial phylotypes that were distinct from those in the non-infected control cultures 5 h after infection. The gammaproteobacterial population at this time mainly consisted of Alteromonas sp. cells that were attached to the infected but still intact host cells. Nano-scale secondary-ion mass spectrometry (nanoSIMS) showed ∼20% transfer of organic matter derived from the infected (13)C- and (15)N-labelled P. globosa cells to Alteromonas sp. cells. Subsequent, viral lysis of P. globosa resulted in the formation of aggregates that were densely colonised by bacteria. Aggregate dissolution was observed after 2 days, which we attribute to bacteriophage-induced lysis of the attached bacteria. Isotope mass spectrometry analysis showed that 40% of the particulate (13)C-organic carbon from the infected P. globosa culture was remineralized to dissolved inorganic carbon after 7 days. These findings reveal a novel role of viruses in the leakage or excretion of algal biomass upon infection, which provides an additional ecological niche for specific bacterial populations and potentially redirects carbon availability.

Dynamics of natural prokaryotes, viruses, and heterotrophic nanoflagellates in alpine karstic groundwater

Seasonal dynamics of naturally occurring prokaryotes, viruses, and heterotrophic nanoflagellates in two hydro-geologically contrasting alpine karst springs were monitored over three annual cycles. To our knowledge, this study is the first to shed light on the occurrence and possible interrelationships between these three groups in karstic groundwater. Hydrological and microbiological standard indicators were recovered simultaneously in order to estimate surface influence, especially during rainfall events. Data revealed a strong dependence of the microbial communities on the prevailing hydrological situation. Prokaryotic numbers averaged 5.1 × 10⁷ and 1.3 × 10⁷ cells L⁻¹, and heterotrophic nanoflagellate abundance averaged 1.1 × 10⁴ and 3 × 10³ cells L⁻¹ in the limestone spring type (LKAS2) and the dolomitic spring type (DKAS1), respectively. Viral abundance in LKAS2 and DKAS1 averaged 9.4 × 10⁸ and 1.1 × 10⁸ viruses L⁻¹. Unlike in DKAS1, the dynamic spring type LKAS2 revealed a clear difference between base flow and high discharge conditions. The virus-to-prokaryotes ratio was generally lower by a factor of 2–3, at higher average water residence times. Furthermore, the high prokaryotes-to-heterotrophic nanoflagellate ratios, namely about 4700 and 5400 for LKAS2 and DKAS1, respectively, pointed toward an uncoupling of these two groups in the planktonic fraction of alpine karstic aquifers.

Seasonal dynamics of naturally occurring prokaryotes, viruses and heterotrophic nanoflagellates in two hydro-geologically contrasting alpine karst springs were monitored over three annual cycles. Data revealed a strong dependence of the microbial communities on the prevailing hydrological situation.

Viral infection of Phaeocystis globosa impedes release of chitinous star-like structures: quantification using single cell approaches

Phaeocystis globosa is an ecologically important bloom-forming phytoplankton, which sequesters substantial amounts of inorganic carbon and can form carbon-enriched chitinous star-like structures. Viruses infecting P. globosa (PgVs) play a significant regulatory role in population dynamics of the host species. However, the extent to which viruses alter host physiology and its carbon assimilation on single cell level is still largely unknown. This study demonstrates for the first time the impact of viral infection on carbon assimilation and cell morphology of individual axenic P. globosa cells using two single cell techniques: high resolution nanometre-scale Secondary-Ion Mass Spectrometry (nanoSIMS) approach and atomic force microscopy (AFM). Up until viral lysis (19 h post infection), the bulk carbon assimilation by infected P. globosa cultures was identical to the assimilation by the non-infected cultures (33 µmol C l(-1)). However, single cell analysis showed that viral infection of P. globosa impedes the release of star-like structures. Non-infected cells transfer up to 44.5 µmol C l(-1) (36%) of cellular biomass in the form of star-like structures, suggesting a vital role in the survival of P. globosa cells. We hypothesize that impediment of star-like structures in infected P. globosa cells may inactivate viral infectivity by forming flocculants after cell lysis. Moreover, we show that substantial amounts of newly produced viruses (≈ 68%) were attached to P. globosa cells prior to cell lysis. Further, we speculate that infected cells become more susceptible for grazing which provides potential reasons for the sudden disappearance of PgVs in the environment. The scenarios of enhanced grazing is at odds to the current perspective that viral infections facilitates microbial mediated processes by diverting host material away from the higher trophic levels.

FLOW CYTOMETRIC APPLICABILITY OF FLUORESCENT VITALITY PROBES ON PHYTOPLANKTON1

The applicability of six fluorescent probes (four esterase probes: acetoxymethyl ester of Calcein [Calcein-AM], 5-chloromethylfluorescein diacetate [CMFDA], fluorescein diacetate [FDA], and 2',7'-dichlorofluorescein diacetate [H₂ DCFDA]; and two membrane probes: bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC₄ (3)] and SYTOX-Green) as vitality stains was tested on live and killed cells of 40 phytoplankton strains in exponential and stationary growth phases, belonging to 12 classes and consisting of four cold-water, 26 temperate, and four warm-water species. The combined live/dead ratios of all six probes indicated significant differences between the 12 plankton classes (P < 0.01) and between individual species (P < 0.05). No specific differences were observed among strains of one species, among species or strains from different origin, nor between cells in exponential and stationary growth phase except for FDA. FDA showed a significant (P < 0.05) drop of <20% in fluorescence intensity in stationary cells. Of the four esterase probes, the live/dead ratios of FDA and CMFDA were not significantly different from each other, and both performed better than Calcein-AM and H₂ DCFDA (P < 0.001). Of the two membrane probes, DIBAC₄ (3) stained rhodophytes and euglenophytes much better than SYTOX-Green. The 13 algal strains best stainable (high live/dead ratios) among all six probes belonged to nine genera from six classes of phytoplankton. In conclusion, FDA, CMFDA, DIBAC₄ (3), and SYTOX-Green represent a wide choice of vitality probes in the study of phytoplankton ecology, applicable in many species from different algal classes, originating from different regions and at different stages of growth.

Enumeration of bacteriophages using flow cytometry

Rapid identification and enumeration of the numerically important bacteriophages has been till recently a major limitation for studies of virus ecology. The development of sensitive nucleic acid stains, in combination with flow cytometric techniques, has changed this. The flow cytometric method allows the detection and discrimination of a wide variety of viruses of different morphology, genome type, and size. The present paper describes an optimized protocol for the enumeration of bacteriophages using a standard benchtop flow cytometer.

INFLUENCE OF IRRADIANCE ON VIRUS-ALGAL HOST INTERACTIONS(1)

The effect of different irradiance levels on the interactions between the algal host and its virus was investigated for two marine phytoplankton, Phaeocystis globosa Scherff. and Micromonas pusilla (Butcher) Manton et Parke. The algal cultures were acclimated at 25, 100, and 250 μmol photons · m(-2)  · s(-1) (LL, ML, and HL, respectively), after which they were infected with a lytic virus (PgV-07T and MpV-02T) and monitored under the appropriate irradiance and in darkness. The effect of irradiance levels on the host-virus interactions differed for the two algal host-virus systems examined. For P. globosa, the LL-acclimated cultures showed a 4 h prolonged latent period (11-16 h), which may be related to the subsaturated growth observed at this irradiance. The burst size was reduced by 50% at LL and HL compared to ML (525 PgV · cell(-1) ). The fraction of infectious viruses, however, remained unchanged. Viral replication was prevented when the LL P. globosa cultures were kept in darkness (up to 48 h) but recovered when placed back into the light. PgV-07T still replicated in the dark for the ML- and HL-acclimated cultures, but viral yield was reduced by 50%-85%. For M. pusilla, the burst size (285-360 MpV · cell(-1) ), the infectivity, and the latent period of MpV-02T (7-11 h) remained unaffected by the incident light. Conversely, darkness not only inhibited MpV replication but also resulted in substantial cell lysis of the noninfected cultures. Our study implies that irradiance level is an important factor controlling algal host-virus interactions and hence the dynamics of phytoplankton populations.

Virus-specific responses of Heterosigma akashiwo to infection

We used flow cytometry to examine the process of cell death in the bloom-forming alga Heterosigma akashiwo during infection by a double-stranded DNA virus (OIs1) and a single-stranded RNA virus (H. akashiwo RNA virus [HaRNAV]). These viruses were isolated from the same geographic area and infect the same strain of H. akashiwo. By use of the live/dead stains fluorescein diacetate and SYTOX green as indicators of cellular physiology, cells infected with OIs1 showed signs of infection earlier than HaRNAV-infected cultures (6 to 17 h versus 23 to 29 h). Intracellular esterase activity was lost prior to increased membrane permeability during infection with OIs1, while the opposite was seen with HaRNAV-infected cultures. In addition, OIs1-infected cells accumulated in the cultures while HaRNAV-infected cells rapidly disintegrated. Progeny OIs1 viruses consisted of large and small morphotypes with estimated latent periods of 11 and 17 h, respectively, and about 1,100 and 16,000 viruses produced per cell, respectively. In contrast, HaRNAV produced about 21,000 viruses per cell and had a latent period of 29 h. This study reveals that the characteristics of viral infection in algae are virus dependent and therefore are variable among viruses infecting the same species. This is an important consideration for ecosystem modeling exercises; calculations based on in situ measurements of algal physiology must be sensitive to the diverse responses of algae to viral infection.

Micromonas pusilla reovirus: a new member of the family Reoviridae assigned to a novel proposed genus (Mimoreovirus)

Micromonas pusilla reovirus (MpRV) is an 11-segmented, double-stranded RNA virus isolated from the marine protist Micromonas pusilla. Sequence analysis (including conserved termini and presence of core motifs of reovirus polymerase), morphology and physicochemical properties confirmed the status of MpRV as a member of the family Reoviridae. Electron microscopy showed that intact virus particles are unusually larger (90–95 nm) than the known size of particles of viruses belonging to the family Reoviridae. Particles that were purified on caesium chloride gradients had a mean size of 75 nm (a size similar to the size of intact particles of members of the family Reoviridae), indicating that they lost outer-coat components. The subcore particles had a mean size of 50 nm and a smooth surface, indicating that MpRV belongs to the non-turreted Reoviridae. The maximum amino acid identity with other reovirus proteins was 21 %, which is compatible with values existing between distinct genera. Based on morphological and sequence findings, this virus should be classified as the representative of a novel genus within the family Reoviridae, designated Mimoreovirus (from Micromonas pusilla reovirus). The topology of the phylogenetic tree built with putative polymerase sequences of the family Reoviridae suggested that the branch of MpRV could be ancestral. Further analysis showed that segment 1 of MpRV was much longer (5792 bp) than any other reovirus segment and encoded a protein of 200 kDa (VP1). This protein exhibited significant similarities to O-glycosylated proteins, including viral envelope proteins, and is likely to represent the additional outer coat of MpRV.

Characterization of different viruses infecting the marine harmful algal bloom species Phaeocystis globosa

Twelve lytic viruses (PgV) infecting the marine unicellular eukaryotic harmful algal bloom species Phaeocystis globosa were isolated from the southern North Sea in 2000-2001 and partially characterized. All PgV isolates shared common phenotypic features with other algal viruses belonging to the family Phycodnaviridae and could be categorized in four different groups. Two main groups (PgV Group I and II) were discriminated based on particle size (150 and 100 nm respectively), genome size (466 and 177 kb) and structural protein composition. The lytic cycle showed a latent period of 10 h for PgV Group I and latent periods of 12 h and 16 h for PgV Group IIA and IIB. Host specificity and temperature sensitivity finally defined a fourth group (PgV Group IIC). Our results imply that viral infection plays an important role not only in P. globosa dynamics but also in the diversity of both host and virus community.

Isolation and phylogenetic analysis of novel viruses infecting the phytoplankton Phaeocystis globosa (Prymnesiophyceae)

Viruses infecting the harmful bloom-causing alga Phaeocystis globosa (Prymnesiophyceae) were readily isolated from Dutch coastal waters (southern North Sea) in 2000 and 2001. Our data show a large increase in the abundance of putative P. globosa viruses during blooms of P. globosa, suggesting that viruses are an important source of mortality for this alga. In order to examine genetic relatedness among viruses infecting P. globosa and other phytoplankton, DNA polymerase gene (pol) fragments were amplified and the inferred amino acid sequences were phylogenetically analyzed. The results demonstrated that viruses infecting P. globosa formed a closely related monophyletic group within the family Phycodnaviridae, with at least 96.9% similarity to each other. The sequences grouped most closely with others from viruses that infect the prymnesiophyte algae Chrysochromulina brevifilum and Chrysochromulina strobilus. Whether the P. globosa viruses belong to the genus Prymnesiovirus or form a separate group needs further study. Our data suggest that, like their phytoplankton hosts, the Chrysochromulina and Phaeocystis viruses share a common ancestor and that these prymnesioviruses and their algal host have coevolved.

Viral Control of Phytoplankton Populations-a Review1

Phytoplankton population dynamics are the result of imbalances between reproduction and losses. Losses include grazing, sinking, and natural mortality. As the importance of microbes in aquatic ecology has been recognized, so has the potential significance of viruses as mortality agents for phytoplankton. The field of algal virus ecology is steadily changing and advancing as new viruses are isolated and new methods are developed for quantifying the impact of viruses on phytoplankton dynamics and diversity. With this development, evidence is accumulating that viruses can control phytoplankton dynamics through reduction of host populations, or by preventing algal host populations from reaching high levels. The identification of highly specific host ranges of viruses is changing our understanding of population dynamics. Viral-mediated mortality may not only affect algal species succession, but may also affect intraspecies succession. Through cellular lysis, viruses indirectly affect the fluxes of energy, nutrients, and organic matter, especially during algal bloom events when biomass is high. Although the importance of viruses is presently recognized, it is apparent that many aspects of viral-mediated mortality of phytoplankton are still poorly understood. It is imperative that future research addresses the mechanisms that regulate virus infectivity, host resistance, genotype richness, abundance, and the fate of viruses over time and space.

Optimization of procedures for counting viruses by flow cytometry

The development of sensitive nucleic acid stains, in combination with flow cytometric techniques, has allowed the identification and enumeration of viruses in aquatic systems. However, the methods used in flow cytometric analyses of viruses have not been consistent to date. A detailed evaluation of a broad range of sample preparations to optimize counts and to promote the consistency of methods used is presented here. The types and concentrations of dyes, fixatives, dilution media, and additives, as well as temperature and length of incubation, dilution factor, and storage conditions were tested. A variety of different viruses, including representatives of phytoplankton viruses, cyanobacteriophages, coliphages, marine bacteriophages, and natural mixed marine virus communities were examined. The conditions that produced optimal counting results were fixation with glutaraldehyde (0.5% final concentration, 15 to 30 min), freezing in liquid nitrogen, and storage at -80 degrees C. Upon thawing, samples should be diluted in Tris-EDTA buffer (pH 8), stained with SYBR Green I (a 5 x 10(-5) dilution of commercial stock), incubated for 10 min in the dark at 80 degrees C, and cooled for 5 min prior to analysis. The results from examinations of storage conditions clearly demonstrated the importance of low storage temperatures (at least -80 degrees C) to prevent strong decreases (occasionally 50 to 80% of the total) in measured total virus abundance with time.

Discovery of a dsRNA virus infecting the marine photosynthetic protist Micromonas pusilla

We report the isolation of the first double-stranded (ds) RNA virus in the family Reoviridae that infects a protist (microalga Micromonas pusilla, Prasinophyceae). The dsRNA genome was composed of 11 segments ranging between 0.8 and 5.8 kb, with a total size of approximately 25.5 kb. The virus (MpRNAV-01B) could not be assigned to the genus level because host type, genome size, and number of segments smaller than 2 kb did not correspond to either of the two existing 11-segmented dsRNA genera Rotavirus and Aquareovirus. MpRNAV-01B has a particle size of 65-80 nm, a narrow host range, a latent period of 36 h, and contains five major proteins (120, 95, 67, 53, and 32 kDa). MpRNAV-01B was stable to freeze-thawing, resistant to chloroform, ether, nonionic detergents, chelating and reducing agents. The virus was inactivated at temperatures above 35 degrees C and by ionic detergent, ethanol, acetone, and acidic conditions (pH 2-5).