Short-term variations of virus-like particles in a tropical lake: relationship with microbial communities (bacteria, ciliates and flagellates)

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado River near Rifle, CO. Virus abundance ranged from 8.0 × 104 to 1.0 × 106 mL-1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 104 to 6.1 × 105 mL-1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.

Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

Recent studies reported comparatively lower heterotrophic bacteria (HB) abundances in tropical regions, indicating that factors involved in bacterial losses could be more relevant in the tropics. Heterotrophic nanoflagellates (HNF) are considered the main predators of HB in aquatic ecosystems, and one should expect higher abundances in the tropics because of differences in the food web configuration (absence of large daphnids). However, there are no comprehensive studies comparing HB and HNF abundances in a latitudinal gradient. We hypothesized that HB abundance would be lower in the tropics because HNF abundance would be higher, resulting in a tighter HNF–HB coupling. To test this hypothesis, we compiled a large dataset of HB and HNF abundances from tropical and temperate freshwater environments. We found that both HB and HNF abundances were lower in the tropical region, and that HNF-HB coupling does not differ between temperate and tropical regions. The lower HNF abundance and lack of coupling may be explained by a strong top-down control on HNF and/or their herbivory preference. Besides, no relationship was found between bacterial specific growth rate and either chlorophyll-a and HB abundance, indicating that bacterial losses may have an important role in tropical freshwaters. Thus, we found that HNF is likely not the main controllers of HB abundance, and that grazing by ciliates and cladocerans, together with the physiological effects of higher temperatures, may explain the high bacterial loss rates in the tropics.

Viruses and bacteria in floodplain lakes along a major Amazon tributary respond to distance to the Amazon River

In response to the massive volume of water along the Amazon River, the Amazon tributaries have their water backed up by 100s of kilometers upstream their mouth. This backwater effect is part of the complex hydrodynamics of Amazonian surface waters, which in turn drives the variation in concentrations of organic matter and nutrients, and also regulates planktonic communities such as viruses and bacteria. Viruses and bacteria are commonly tightly coupled to each other, and their ecological role in aquatic food webs has been increasingly recognized. Here, we surveyed viral and bacterial abundances (BAs) in 26 floodplain lakes along the Trombetas River, the largest clear-water tributary of the Amazon River’s north margin. We correlated viral and BAs with temperature, pH, dissolved inorganic carbon, dissolved organic carbon (DOC), phosphorus, nitrogen, turbidity, water transparency, partial pressure of carbon dioxide (pCO₂), phytoplankton abundance, and distance from the lake mouth until the confluence of the Trombetas with the Amazon River. We hypothesized that both bacterial and viral abundances (VAs) would change along a latitudinal gradient, as the backwater effect becomes more intense with increased proximity to the Amazon River; different flood duration and intensity among lakes and waters with contrasting sources would cause spatial variation. Our measurements were performed during the low water period, when floodplain lakes are in their most lake-like conditions. Viral and BAs, DOC, pCO₂, and water transparency increased as distance to the Amazon River increased. Most viruses were bacteriophages, as viruses were strongly linked to bacteria, but not to phytoplankton. We suggest that BAs increase in response to DOC quantity and possibly quality, consequently leading to increased VAs. Our results highlight that hydrodynamics plays a key role in the regulation of planktonic viral and bacterial communities in Amazonian floodplain lakes.

Environmental influences on virus-host interactions in an Australian subtropical reservoir

Viral and prokaryotic interactions in freshwaters have been investigated worldwide but there are few temporal studies in the tropics and none in the sub-tropics. In this 10-month study, we examined temporal changes in virus-host interactions and viral life cycles (lytic versus lysogenic) in relation to the prevailing environmental conditions in a subtropical water reservoir (Wivenhoe) in southeast Queensland, Australia. Heterotrophic prokaryotes and picocyanobacteria were positively correlated with concentrations of viruses throughout the study, indicating the presence of both bacteriophages and cyanophages in the reservoir. The percentage of heterotrophic prokaryotes and picocyanobacteria containing intracellular viruses (FVIC) ranged between 0.2% and 2.4% and did not vary significantly over the 10-month study, whereas lysogenic heterotrophic prokaryotes were only detected in the drier months of June and July. Spearman rank correlation analysis showed that the oxidative-reduction potential (ORP) of the water reservoir influenced the concentrations of viruses, heterotrophic prokaryotes and picocyanobacteria significantly, with low ORP offering a favourable environment for these components. There was a negative relationship between FVIC and rainfall suggesting the associated run-off altered virus-host interactions. Overall, our study provides novel information and inferences on how virus-host interactions in subtropical freshwaters might respond to changes in precipitation predicted to occur with global climate change.

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

There are an estimated 10(30) virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300 m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100 m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochlorococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean.

Virus silicification under simulated hot spring conditions

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).