Abundance Of Virus-like Particles Research Articles

Компоненты микробной пищевой сети в пелагиали фьордов о. Западный Шпицберген в современных климатических условиях

The spatial variability of quantitative indicators of prokaryotes and virus-like particles in the waters of three Arctic fjords was studied in connection with the structure of their dominant water masses in the summer. A comparison of the abundance and biomass of prokaryotes showed that their average value in mesotrophic surface waters (0.60 million cells/ml and 28.64 mg/m3, respectively) exceeded the values in deeper oligotrophic waters – intermediate (0.33 million cells/ml and 16.82 mg/m3) and winter (0.32 million cells/ml and 19.72 mg/m3). The abundance of virus-like particles in different trophic conditions positively correlated with the parameters of prokaryotic communities and in the isolated water masses averaged 1.01 million, 0.09 million and 1.31 million per ml respectively. The factors determining the distribution of the most abundant representatives of the microbial food web and the nature of their interaction are considered.

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick

Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.

Viruses direct carbon cycling in lake sediments under global change

Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.

Distribution Characteristics of Soil Viruses Under Different Precipitation Gradients on the Qinghai-Tibet Plateau.

Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.

Effect of the Presence of Virus-like Particles on Bacterial Growth in Sunlit Surface and Dark Deep Ocean Environments in the Southern East China Sea

Virus-like particles (VLPs) are thought to increase the dissolved organic carbon by releasing the contents of the host cell, which, in turn, can affect bacterial growth in natural aquatic environments. Yet, experimental tests have shown that the effect of VLPs on the bacterial growth rate at different depths has seldom been studied. Bacteria–VLP interaction and the effect of VLPs on bacterial growth rate in the sunlit surface (3 m) and dark, deep ocean (130 m) environments were first explored at a test site in the southern East China Sea of the northwest Pacific. Our experimental results indicated that bacterial and virus-like particle (VLP) abundance decreased with depth from 0.8 ± 0.3 × 105 cells mL−1 and 1.8 ± 0.4 × 106 VLPs mL−1 at 3 m to 0.4 ± 0.1 × 105 cells mL−1 and 1.4 ± 0.3 × 106 VLPs mL−1 at 130 m. We found that the abundance of VLPs to Bacteria Ratio (VBR) in the dark deep ocean (VBR = 35.0 ± 5.6) was higher than in the sunlit surface environment (VBR = 22.5 ± 2.1). The most interesting finding is that in the dark, deep ocean region the bacterial growth rate in the presence of VLPs was higher (0.05 h−1) than that in virus-diluted treatments (0.01 h−1). However, there was no significant difference in the bacterial growth rates between the treatments in the sunlit surface ocean region. Deep-sea ecosystems are dark and extreme environments that lack primary photosynthetic production, and our estimates imply that the contribution of recycled carbon by viral lysis is highly significant for bacterial growth in the dark, deep ocean environment. Further work for more study sites is needed to identify the relationship of VLPs and their hosts to enable us to understand the role of VLPs at different depths in the East China Sea.

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome

SummaryChanges in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales. Notably, phage richness and diversity of individuals with O and OMS tended to increase, while the VLP abundance remained the same among all groups. Of the 4,611 phage contigs composing the phageome, 48 contigs were highly prevalent in ≥80% of individuals, suggesting high inter-individual phage diversity. The abundance of several contigs correlated with gut bacterial taxa; and with anthropometric and biochemical parameters altered in O and OMS. To our knowledge, this gut phageome represents one of the largest datasets and suggests disease-specific phage alterations.

Viral abundance, community structure and correlation with bacterial community in soils of different cover plants

Microbial abundance, diversity, metabolic activities, and interactions are central to the ecosystem functions and biogeochemical processes in soil. Viruses can impose top-down control over microbial communities and thus regulate the microbial-mediated processes of the system. However, the understanding of the linkage between viral community, virus-host interactions and environmental conditions of soil is still lacking which imposes a major knowledge gap in microbial ecology of this complex environmental system. Here, we investigated the viral and bacterial communities under different plant cover types. Soil properties such as organic matter and nitrate content showed significant correlations with virus-like particles (VLPs) abundance, bacterial abundance, and inducible lysogenic fractions (LF) suggesting that the environmental factors might be influencing viral/bacterial abundance and reproduction strategy in soils. The bacterial communities were shaped by the land management, i.e., cover plants and agricultural practices. Soil physicochemical properties, VLP abundance, and LF were significant factors accounting for the difference of bacterial community composition in soils. The variances of the viral community composition were closely related to cover plants corresponding to similar patterns in bacterial community composition suggesting that viral and bacterial community composition are tightly linked. Our study provides insight in the ways how environmental factors shape virus-host interactions and further influence soil viruses in soil ecosystems.

Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.

ABSTRACTDuring the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment.IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.

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.

Femtoplankton: What's New?

Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010–2020) of high abundances of biomimetic mineral–organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.

Changes of viral and prokaryote abundances in a high rate algal pond using flow cytometry detection.

High rate algal ponds (HRAPs) are shallow, mixed systems for wastewater treatment, which use sunlight exposure for disinfection. Little is known regarding the relationships between the bacteria and viruses within HRAP systems. Uniquely, flow cytometry permits the rapid identification of bacterial and viral populations in wastewater samples, separating populations based on genome and particle size. Treated wastewater samples were collected from an HRAP at Kingston on Murray, South Australia. Flow cytometry analysis detected bacterial populations and discriminated virus-like particles (VLP) and large VLP (LVLP). Rapid, short term, fluctuations in the abundance of all three populations were observed. Changes in the abundance of these populations was compared; wastewater composition was used as metadata for the comparisons. Linear regression determined relationships in abundances between bacteria and LVLP (R2 0.2985); LVLP and VLP (R2 0.5829) and bacteria and VLP (R2 0.5778) all with p-values of <0.001. Bacterial, LVLP and VLP abundance positively correlated with each other, indicating potential microbial interactions. Overall, the results suggest a parasitic relationship was occurring and driving the abundances of bacteria and viruses within the system.

Seasonal variation in estuarine phytoplankton viability and its relationship with carbon dynamics in the Baltic Sea

Cell death drives the magnitude and community composition of phytoplankton and can result in the conversion of particulate organic carbon to dissolved organic carbon (DOC), thereby affecting carbon cycling in the aquatic food web. We used a membrane integrity probe (Sytox Green) to study the seasonal variation in the percentage of viable cells in the phytoplankton population in an estuary in the northern Baltic Sea for 21 months. The associated dissolved and particulate organic matter concentrations were also studied. The viable fraction of phytoplankton cells varied from < 20% to almost 100%, with an average of 62%. Viability was highest when a single phytoplankton group (diatoms or dinoflagellates) dominated the community. Viability of sinking phytoplankton cells, including some motile species, was in general as high as in surface water. Changes in viability were not closely related to nutrient concentrations, virus-like particle abundance, seawater temperature or salinity. There was a weak but significant negative correlation between viability and DOC, although at this location, the DOC pool was mainly influenced by the inflow of riverine water. This study demonstrates that cell viability, and its relationship with carbon export, is highly variable in the complex microbial populations common within estuarine and coastal marine ecosystems.

Virioplankton distribution in the tropical western Pacific Ocean in the vicinity of a seamount.

The shallow Caroline Seamount is located in the tropical western Pacific Ocean. Its summit is 57 m below the surface and penetrates the euphotic zone. Therefore, it is ideal for the study of the influence of seamount on plankton distribution. Here, virioplankton abundance and distribution were investigated by flow cytometry (FCM) in the Caroline Seamount in August and September 2017. The total abundance of virus‐like particles (VLP) was in the range of 0.64 × 106–18.77 × 106 particles/ml and the average was 5.37 ± 3.75 × 106 particles/ml. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensities were identified. Above the deep chlorophyll maximum (DCM), two medium fluorescence virus (MFV) subclusters were discriminated. Between the DCM and the deeper layers, only one MFV subcluster was resolved. In general, low fluorescence viruses (LFV) comprised the most abundant subclusters. In the 75–150 m water column, however, the MFV abundance was higher than the LFV abundance. High fluorescence viruses (HFV) constituted the least abundant subcluster throughout the entire water column. Virioplankton abundance was significantly enhanced at the seamount stations. Environmental factors including water temperature and nitrate concentration were the most correlated with the variation in virioplankton abundance at the seamount stations. Interactions between shallow seamounts and local currents can support large virus standing stocks, causing a so‐called indirect “seamount effect” on the virioplankton.

Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity

Increased awareness of the abundance and diversity of viruses in soils has led to a growing interest in soil virus ecology. This interest is in part fueled by a need to understand the mechanisms behind the transformation of carbon and nutrient elements within soil ecosystems and what role if any viruses play in these biologically mediated processes. To explore the virus-host distribution and diversity patterns in soil profiles, bacterial community composition and structure, viral and bacterial abundances, and the lysogenic fractions (LF) of bacterial communities were assessed. Enumeration of virus-like particles (VLPs) by epifluorescence microscopy, prophage-induction assays (mitomycin C-based), and bacterial 16S rRNA gene amplicon sequencing were used in this study. The abundances of both extractable VLPs and bacterial cells decreased with soil depth, but VLP abundances decreased more rapidly than bacterial abundances leading to an overall decreasing virus-to-bacteria ratio with depth. In contrast, LF increased with soil depth, indicating lysogeny became a more important reproduction strategy for autochthonous soil bacteriophages in subsurface soil. Significant shifts in bacterial community composition and diversity with soil depth were closely correlated with VLP abundance, virus-to-bacteria ratio, and LF. The results suggest that the viral abundance and replication strategies vary significantly in different soil depths and are linked to microbial host community composition in soil.

Analysis of the seasonal impact of three marine bivalves on seston particles in water column

Suspension-feeding bivalves are the keystone species that affect the abundance and composition of phytoplankton communities. This study compares the food selectivity of oysters Crassostrea gigas (Thunberg, 1973), mussels Mytilus galloprovincialis (Lamarck, 1819), and cockles Katelysia rhytiphora (Lamy, 197) on natural particle assemblages in the laboratory using water collected from Coffin Bay, South Australia, in spring, summer, autumn and winter. The phytoplankton community was dominated by Bacillariophyceae (diatoms), Dinophyceae (dinoflagellates), Synechococcus (cyanobacteria), and picophytoplankton (2–5 μm) from September 2016 to August 2017. Diatoms and picoplankton, including cyanobacteria, were dominant in spring and summer, while dinoflagellates were dominant in autumn and winter. Oysters and mussels selectively fed on large food particles (e.g., diatom, dinoflagellate and large picoplankton > 2 μm) regardless of season, but mussels could access a wider size spectrum of food particles compared to oysters. In contrast, cockles selected for both large and small food particles (e.g., Synechococcus and small picoeukaryotes < 2 μm) and fed more efficiently on small particles than both oysters and mussels. Bacteria were more abundant in warmer seasons, but mussels and cockles selectively reduced bacterial abundance. The abundance of virus-like particles was not affected by season nor by filtration of any molluscan species. This study demonstrates that oysters and mussels utilise similar food sources, whereas cockles consume a large range of food particles. Additionally, these three molluscan species do not necessarily compete for food; hence, stocking multiple filter-feeding species in an ecosystem could exploit a wider spectrum of food particle size and increase system productivity.

Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics.

This study reports the discovery of Aster-Like Nanoparticles (ALNs) in pelagic environments. ALNs are pleomorphic, with three dominant morphotypes which do not fit into any previously defined environmental entities [i.e., ultramicro-prokaryotes, controversed nanobes, and non-living particles (biomimetic mineralo-organic particles, natural nanoparticles or viruses)] of similar size. Elemental composition and selected-area electron diffraction patterns suggested that the organic nature of ALNs may prevail over the possibility of crystal structures. Likewise, recorded changes in ALN numbers in the absence of cells are at odds with an affiliation to until now described viral particles. ALN abundances showed marked seasonal dynamics in the lakewater, with maximal values (up to 9.0 ± 0.5 × 107 particles·mL−1) reaching eight times those obtained for prokaryotes, and representing up to about 40% of the abundances of virus-like particles. We conclude that (i) aquatic ecosystems are reservoirs of novel, abundant, and dynamic aster-like nanoparticles, (ii) not all virus-like particles observed in aquatic systems are necessarily viruses, and (iii) there may be several types of other ultra-small particles in natural waters that are currently unknown but potentially ecologically important.

Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands

Studies investigating viral ecology have mainly been conducted in temperate marine and freshwater habitats. Fewer reports are available on the often less accessible “extreme environments” such as hot springs. This study investigated prokaryotic- and virus-like particles (VLP) associated to hot springs, themselves situated in cold environments of the Southern Hemisphere (i.e. in the French Southern and Antarctic Lands). This was performed by examining their abundance in hot springs and surrounding temperate seawater using both epifluorescence microscopy (EFM) and flow cytometry (FCM), which was applied for the first time to such ecosystems. On one hand, prokaryotic abundances of 4.0 × 105–2.2 × 106 cell mL−1 and 7.0 × 104–2.8 × 106 cell mL−1 were measured using EFM and FCM, respectively. The abundances of virus-like particles (VLP), on the other hand, ranged between 9.8 × 105 and 7.5 × 106 particles mL−1 when using EFM, and between 1.3 × 105 and 6.2 × 106 particles mL−1 when FCM was applied. A positive correlation was found between VLP and prokaryotic abundances, while the virus-to-prokaryote ratio was generally low and ranged between 0.1 and 6. In parallel, samples and culture supernatants were also visualised using transmission electron microscopy. For this, enrichment cultures were prepared using environmental samples. Both raw sample and enrichment culture—supernatants were analysed for the presence of VLPs. Observations revealed the presence of Caudovirales, membrane vesicles and possibly a new type of virion morphology, associated to members of the order Thermotogales, a thermophilic and anaerobic bacterium.

The first known virus isolates from Antarctic sea ice have complex infection patterns.

Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0°C and 4°C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.

Abundance of virus-like particles (VLPs) and microbial plankton community composition in a Mediterranean Sea coastal area

Abundance of virus-like particles (VLPs) and microbial plankton community composition in a Mediterranean Sea coastal area

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD).

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.