Virus-to-bacteria Ratio Research Articles

Modeling Virus and Bacteria Populations in Europa's Subsurface Ocean.

The search for life in the universe is often informed by the study of “extreme” environments on Earth, which provide analogs for habitable locations in the Solar System, and whose microbial inhabitants may therefore also serve as analogs for potential life forms in extraterrestrial milieus. Recent work has highlighted the ubiquity and importance of viral entities in terrestrial ecosystems, which calls for a greater understanding of the roles that viruses might play in hypothetical extraterrestrial biomes. While some studies have modeled the dynamics of viral and bacterial populations in icy ocean environments on Earth, previous work has yet to apply these findings to icy ocean worlds such as Jupiter’s moon Europa. It is commonly theorized that hydrothermal vents on Europa could produce the necessary reductants for chemosynthesis to take place on the ocean bottom. In the case that Europa’s ocean is a reductant-limited environment, how might reductants and organic matter reach the sub-ice region to power a more easily accessible ecosystem? Here, we propose a ‘viral elevator,’ a mechanism that functions similarly to the ‘viral shunt’ in Earth’s oceans, which could create and shuttle dissolved organic matter (DOM) to a hypothetical sub-ice biosphere through viral carriers. Current models of Europa’s ocean currents and stratification support the movement of DOM to the sub-ice biosphere. We adapt an existing model for bacterial and viral population dynamics in Earth’s Arctic sea ice to Europa and use parameters from various Arctic-based studies as proxies for Europa’s environment. We find that viral burst size has the most significant effect on the virus-to-bacteria ratio (VBR) and system longevity in closed systems (such as brine pockets within Europa’s icy crust), with higher burst sizes clearly increasing both. When applying our model to an open system with an influx of DOM from the viral elevator, we found that a steady-state system is attainable, with resulting sub-ice biofilms on the order of 0.1 mm thick (global equivalent layer). This has implications for future searches for life on Europa, given that life directly under the ice will be easier to detect and observe than life near the ocean bottom.

Disturbed virus-bacteria dynamics in Otsuchi Bay (Japan) after the mega-earthquake and tsunami in March 2011

On 11 March 2011, a mega-earthquake followed by a huge tsunami hit a large area of the Pacific coast of Tohoku, Japan, and caused widespread disturbances in marine ecosystems; however, the impacts on virus-bacteria systems have not yet been elucidated. To investigate whether virus-bacteria interactions were affected by the earthquake and tsunami, we analyzed time series data of viral and bacterial abundances in Otsuchi Bay. Data were collected every 2 mo, from July 2011 to September 2015. Bacterial abundance exhibited a recurrent seasonal cycle with high abundance during the warm season. The seasonal trend of viruses generally followed that of the bacteria, yielding an average virus to bacteria ratio (VBR) of 10.8 ± 3.6 (mean ± SD; n = 432). A notable exception was found at the first 2 sampling times (July and September 2011) when the VBR was consistently low, with an average value of 5.9 ± 1.2 (n = 32). The average VBR during these time periods was substantially lower than the VBR observed in the same season of subsequent years. An analysis of the subset of data collected in the warm season of 2011 and 2012 revealed that the viral abundance and VBR were negatively correlated with turbidity. These results support the hypothesis that viruses were scavenged by non-host particles from the resuspended sediments and damaged catchment. The earthquake and tsunami thus exerted a prolonged impact, over several months, on the virus-bacteria dynamics in Otsuchi Bay.

Viral Abundance and Diversity of Production Fluids in Oil Reservoirs.

Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL−1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL−1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir’s ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.

Temporal variations in the concentrations of bacteria and their lytic phages: an example of an indigenous phage host system in Lake Plußsee, Germany

1. We describe the abundance of an autochthonous alphaproteobacteria Sphingomonas sp. and its lytic phages during a period of about 3 months in Lake Plussee, Northern Germany. This is the first report of a specific autochthonous phage host system of a heterotrophic bacterial strain in a natural freshwater environment. 2. The concentration of bacterial hosts (Sphingomonas sp. strain B18) fluctuated between 20 and 1,150 (median 168) colony-forming units (CFU) mL-1 and the concentration of the specific lytic phages ranged from 20 to 680 (median 110) plaque-forming units (PFU) mL-1. Different Sphingomonas sp. strains were isolated, showing different sensitivity against two phage isolates. The specific virus to bacteria ratio (VBR) varied by a factor of about 280 and ranged from 0.03 to about 8.5 (median 0.6). 3. Encounter rates of 0.0007 to 0.198 d-1 (median 0.03 d-1) were calculated from the measured concentrations of Sphingomonas sp. and its lytic phages. From changes of PFU between two consecutive samplings net phage decay rates in a range between 0.003 and 1.3 d-1 (median 0.26 d-1) were calculated. 4. Concentration factors were calculated which enable sufficient encounter rates to explain the concentrations of bacteria and their phages. 5. The results of Kokjohn et al. (1991) support the suggestion that the explanation of the coexistence of lytic phages and their host bacteria by the used encounter rate model needs to be revised.

Morphology and distribution of phage-like particles in a eutrophic boreal lagoon

In this paper we present the results of direct observations of the morphology and size of phage-like particles by means of transmission electron microscopy (TEM) as a function of their spatial distribution in the shallow highly productive Curonian Lagoon of the Baltic Sea. In total, 26 morphologically different forms of phagelike particles were found. Different trends of distribution in terms of abundance, size and shape of virus-like particles were demonstrated. The total abundance of viruses varied from 1.91×107 ml−1 to 5.06×107 ml−1. The virus to bacteria ratio (VBR) changed from 15.6 to 49 and was negatively associated with total bacterial numbers (r=–0.60; p < 0.05). The phages of family Myoviridae were the most diverse and were dominant at all stations.

Low effect of viruses on bacteria in deep anoxic water and sediment of a productive freshwater reservoir

The seasonal and vertical distribution of freshwater viruses and the related induced bacterial mortality were determined in the water column down to the surface sediments of the thermally stratified reservoir Lake Grangent, France, between March and November 2007 in relation to environmental parameters. Viral abundance (VA, range = 0.9 to 3.5 x 1010 l―1), bacterial abundance (BA), and the frequency of infected cells were significantly higher in the oxic than in the anoxic waters, which was partly related to forcing from the thermal stratification together with vertical changes in dissolved oxygen, ammonia and phytoplankton biomass. BA was the best predictor (R2 = 0.78) for VA in the oxygenated waters only. The virus-to-bacteria ratio (VBR) yielded less variability and did not differ significantly along the water column (mean ± SD value = 5.5 ± 1.3). In the sediments, both VA and BA were one order of magnitude higher than in the water column with a higher variable VBR ratio (10.6 ± 8.9). Paradoxically, the frequency of visibly infected bacterial cells (determined from transmission electron microscopy) in the sediments was significantly lower (on average 3- to 7-fold) compared with the water column, which is in agreement with recent benthic reports in geographically contrasting lake environments. On average, viruses destroyed 23 % of bacterial production in the oxygenated surface waters, but only 9 % in deep anoxic waters and 3 % in the sediments. Overall, there was a remarkably low viral influence on heterotrophic bacteria in the anoxic waters and overlying sediments of Lake Grangent, where recurrent shift from summer planktonic to winter benthic phases in cyanobacterial blooms is typical.

Seasonal and spatial variability of virio-, bacterio-, and picophytoplanktonic abundances in three peri-alpine lakes

Flow cytometry (FCM) was used to assess microbial community abundances and patterns in three natural, large and deep peri-alpine hydrosystems, i.e., lakes Annecy (oligotrophic), Bourget, and Geneva (mesotrophic). Picocyanobacteria, small eukaryotic autotrophs, heterotrophic prokaryotes, and viruses were studied in the 0–50 m surface layers to highlight the impact of both physical and chemical parameters as well as possible biotic interactions on the functioning of microbial communities. Some specificities were recorded according to the trophic status of each ecosystem such as the higher number of viruses and heterotrophic bacteria in mesotrophic environments (i.e., Lakes Geneva and Bourget) or the higher abundance of picocyanobacteria in the oligotrophic Lake Annecy. However, both seasonal (temperature) and spatial (depth) variations were comparatively more important than the trophic status in driving the microbial communities’ abundances in these three lakes, as revealed by principal component analysis (PCA). A strong viral termination of the heterotrophic bacterial blooms could be observed in autumn for each lake, in parallel to the mixing of the upper lit layers. As virus to bacteria ratio (VBR) was indeed very high at this period with values varying between 87 and 114, such important relationships between viruses and bacteria were likely. The magnitudes of seasonal variations in VBR, with the highest values ever reported so far, were largely greater than the magnitude of theoretical variations due to the trophic status, suggesting also a strong seasonality in virioplankton production associated to prokaryotic dynamics. FCM analyses allowed discriminating several viral groups. Virus-Like Particles group 1 (VLP1) and group 2 (VLP2) were always observed and significantly correlated to bacteria for the former and chlorophyll a and picocyanobacteria for the latter, suggesting that most of VLP1 and VLP2 could be bacteriophages and cyanophages, respectively. On the basis of these results, new ways of investigation emerge concerning the study of relationships between specific picoplanktonic groups; and overall these results provide new evidence of the necessity to consider further viruses for a better understanding of lake plankton ecology.

Heterotrophic bacterial and viral dynamics in Arctic freshwaters: results from a field study and nutrient-temperature manipulation experiments

Heterotrophic bacterial and viral concentrations (range, 0.7 × 104 to 206.2 × 104 ml−1 and 0.05 × 106 to 128.9 × 106 ml−1, respectively) were determined in several Arctic freshwater environments, including lakes and glacial ecosystems (78.55°N, 11.56°E). Our bacteria and virus results mirrored trends seen in temperate lakes, with an average virus-to-bacteria ratio (VBR) of 13 (range, 7.3–25.2) and viral concentrations and DOC positively correlated with bacterial concentrations (R = 0.964, P < 0.01 and R = 0.813, P < 0.05, respectively). Lysogenic bacteria, determined by induction with Mitomycin C, were not detected in any of the investigated Arctic freshwater environments. Nutrient-addition experiments at in situ and at elevated temperatures were performed to elucidate the factors which influenced the bacterial growth and the virus–bacteria interactions in Arctic freshwaters. Our results suggest that multiple limiting factors interacted and constrained bacterial growth. Bacterial concentrations and doubling times increased at elevated temperatures and appeared to be co-stimulated by phosphorus and carbon. However, viral concentrations showed a lack of response to nutrient addition thus indicating an uncoupling between bacteria and viruses in the experiment.

Seasonal Variation of Virioplankton in a Eutrophic Shallow Lake

Lake Donghu is a typical eutrophic freshwater lake in which high abundance of planktonic viruses was recently revealed. In this study, seasonal variation of planktonic viruses were observed at three different trophic sites, hypertrophic, eutrophic, and mesotrophic regions, and the correlation between their abundances and other aquatic environmental components, such as bacterioplankton, chlorophyll a, burst size, pH, dissolved oxygen, and temperature, was analyzed for the period of an year. Virioplankton abundance detected by transmission electron microscope (TEM) ranged from 5.48 x 10(8) to 2.04 x 10(9) ml(-1) in all the sites throughout the study, and the high abundances and seasonal variations of planktonic viruses were related to the trophic status at the sampled sites in Lake Donghu. Their annual mean abundances were, the highest at the hypertrophic site (1.23x10(9) ml(-1)), medium at the eutrophic site (1.19x10(9) ml(-1)), and the lowest at the mesotrophic site (1.02x10(9) ml(-1)). The VBR (virus-to-bacteria ratio) values were high, ranging from 49 to 56 on average at the three sampled sites. The data suggested that the high viral abundance and high VBR values might be associated with high density of phytoplankton including algae and cyanobacteria in this eutrophic shallow lake, and that planktonic viruses are important members of freshwater ecosystems.

Dynamic bacterial and viral response to an algal bloom at subzero temperatures

New evidence suggests that cold‐loving (psychrophilic) bacteria may be a dynamic component of the episodic bloom events of high‐latitude ecosystems. Here we report the results of an unusually early springtime study of pelagic microbial activity in the coastal Alaskan Arctic. Heterotrophic bacterioplankton clearly responded to an algal bloom by doubling cell size, increasing the fraction of actively respiring cells (up to an unprecedented 84% metabolically active using redox dye CTC), shifting substrate‐uptake capabilities from kinetic parameters better adapted to lower substrate concentrations to those more suited for higher concentrations, and more than doubling cell abundance. Community composition (determined by polymerase chain reaction/DGGE and nucleotide sequence analysis) also shifted over the bloom. Results support, for the first time with modern molecular methods, previous culture‐based observations of bacterial community succession during Arctic algal blooms and confirm that previously observed variability in pelagic microbial activity can be linked to changes in community structure. During early bloom stages, virioplankton and bacterial abundance were comparable, suggesting that mortality due to phage infection was low at that time. The virus‐to‐bacteria ratio (VBR) increased 10‐fold at the height of the bloom, however, suggesting an increased potential for bacterioplankton mortality resulting from viral infection. The peak in VBR coincided with observed shifts in both microbial activity and community structure. These early‐season data suggest that substrate and virioplankton interactions may control the active microbial carbon cycling of this region.

The distribution and abundance of viruses in the Southern Ocean during spring

The concentrations of viruses, bacteria, chroococcoid cyanobacteria and chlorophyll a were determined in surface waters of the Southern Ocean during spring. Viral concentrations declined southward from around 4 × 106 ml−1 near Tasmania to a minimum of around 1 × 106 ml−1 at the Polar Front. South of the Front, virus concentrations increased again, reaching around 4 × 106 ml−1 in the sea-ice zone south of 60°S. Bacterial concentration decreased southwards across the Southern Ocean from around 6.5 × 105 ml−1 near Tasmania to &lt; 1.0 × 105 ml−1 in the sea-ice zone. Cyanobacteria accounted for &lt; 8% of the prokaryotes. There was no significant relationship between viral abundance and eithercyanobacterial or chl a concentration. Viral and bacterial concentrations were not significantly correlated north (P {0.10 &lt; r &lt; 0.20}) or south (P {0.20 &lt; r &lt; 0.5}) of the Polar Front. The virus to bacteria ratio (VBR) was between 3 and 15 in the open ocean but varied between 15 and 40 in the sea-ice region. These virus concentrations and VBRs indicate that viruses are no less important in Southern Ocean ecosystems than elsewhere in the world's oceans.

Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 16:17-25 (1998) - doi:10.3354/ame016017 Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay, USA Lisa A. Drake1,*, Keun-Hyung Choi1, A. G. Edward Haskell2, Fred C. Dobbs1 1Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, 4600 Elkhorn Avenue, Norfolk, Virginia 23529, USA 2Center for Coastal Physical Oceanography, Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, 768 West 52nd Street, Norfolk Virginia 23529, USA *E-mail: ldrake@odu.edu ABSTRACT: Vertical profiles of virus-like particles (VLPs) and bacteria were determined by near-synoptic sampling through the water column and 15 to 25 cm into the sediment at 5 stations across the mouth of Chesapeake Bay, USA. VLPs were about 10 times more abundant in the pore water (grand mean = 3.6 x 108 VLPs ml-1) than in the water column (grand mean = 3.8 x 107 VLPs ml-1). Similarly, bacteria counts were about 3 times higher in the pore water (grand mean = 6.5 x 106 bacteria ml-1) than in the water column (grand mean = 2.4 x 106 bacteria ml-1). The virus to bacteria ratio (VBR) was greater in the pore water (range = 29 to 85) than in the water column (range = 12 to 17). The VBR was lowest in the water-over-boxcore samples and variable in the pore water. Counts of VLPs and bacteria were positively correlated in the water column, although neither was correlated to chlorophyll a. In the water column, VLP and bacteria counts exhibited significant differences among stations, with the highest values on the southern side of the Bay mouth. In the pore water, VLP abundance varied with depth and was negatively correlated to grain size. Bacteria abundance was highest at the sediment-water interface, decreased in the first cm of sediment, was uniform in the deeper horizons, and showed no significant relationship with grain size. Bacteria counts in pore water were not significantly different among stations. In contrast, VLP abundances in pore water were significantly different among stations, although they did not increase in abundance from north to south across the Bay mouth, as did counts of water-column VLPs. These are the first data indicating the abundance of VLPs below the surface layer of sediment in aquatic systems and demonstrate that VLPs are components of the sedimentary microbial community to at least 25 cm depth. KEY WORDS: Virus abundance · VLP · Sediment pore water · Yo-Pro · Chesapeake Bay Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 16, No. 1. Publication date: October 15, 1998 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 1998 Inter-Research.

Nutritional enrichment of a microbial community: The effects on activity, elemental composition, community structure and virus production

Viruses are active members of the microbial community in natural waters but little is known about the factors that regulate their activity and production. In this study we have investigated the effects of increased availability of organic nutrients and inorganic phosphate on activity, elemental composition, community structure and virus production in a natural bacterial community. The fraction of active cells in the community as estimated from microautoradiography of cells assimilating 3H-labeled thymidine ranged from 0–22%, but changes in the elemental composition of the cells indicated that more than 90% of the cells were active. The increase in carbon and energy availability stimulated virus production more than bacterial biomass production, while the increase in phosphate availability stimulated biomass production rather than virus production. A decrease in morphological diversity of the bacterial community was paralleled by a reduction in the virus-to-bacteria ratio (VBR) but the relationship between bacterial diversity and viral activity is uncertain. Our general conclusion is that nutrient availability, in addition to the bacterial activity, also affects the viral activity, and that both of these may affect the structure and diversity of the bacterial community.

Nutritional enrichment of a microbial community: The effects on activity, elemental composition, community structure and virus production

Viruses are active members of the microbial community in natural waters but little is known about the factors that regulate their activity and production. In this study we have investigated the effects of increased availability of organic nutrients and inorganic phosphate on activity, elemental composition, community structure and virus production in a natural bacterial community. The fraction of active cells in the community as estimated from microautoradiography of cells assimilating 3H-labeled thymidine ranged from 0–22%, but changes in the elemental composition of the cells indicated that more than 90% of the cells were active. The increase in carbon and energy availability stimulated virus production more than bacterial biomass production, while the increase in phosphate availability stimulated biomass production rather than virus production. A decrease in morphological diversity of the bacterial community was paralleled by a reduction in the virus-to-bacteria ratio (VBR) but the relationship between bacterial diversity and viral activity is uncertain. Our general conclusion is that nutrient availability, in addition to the bacterial activity, also affects the viral activity, and that both of these may affect the structure and diversity of the bacterial community.

Viral abundance in aquatic systems:a comparison between marine and fresh waters

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 121:217-226 (1995) - doi:10.3354/meps121217 Viral abundance in aquatic systems: a comparison between marine and fresh waters Maranger R, Bird DF In order to investigate the factors controlling viral abundance, 22 lakes in Quebec were surveyed. We measured viral and bacterial abundance, bacterial production, chlorophyll a, total phosphorus and DOC (dissolved organic carbon) concentrations. Regression models built with these data were compared to models based on literature data, which to date have been collected largely from marine sites. Positive empirical relationships were found between viral abundance and (1) chlorophyll a concentrations, (2) bacterial abundances, (3) bacterial production, and (4) total phosphorus concentration. There was little to no trend in the virus-to-bacteria ratio with increasing trophy. Analysis of covariance revealed significant differences between relations in marine and freshwater systems. The virus-to-bacteria ratio was significantly higher in freshwater (mode = 22.5) than marine environments (mode = 2.5), and there were significantly more bacteria per unit chlorophyll in our freshwater samples. We suggest that this difference is related to the increased dependence of freshwater bacteria on allochthonous material relative to marine systems, as well as the increased relative importance of photosynthetic cyanobacteria in lakes. Virus . Bacteria . Chlorophyll a . Bacterial production . Marine . Freshwater . Empirical relationships Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 121. Publication date: May 25, 1995 Print ISSN:0171-8630; Online ISSN:1616-1599 Copyright © 1995 Inter-Research.