Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

Community responses of testate amoebae (Arcellinida and Euglyphida) to ecological disturbance explained by contrasting assembly mechanisms in two subtropical reservoirs

Mechanisms underlying the effects of ecological disturbance on aquatic ecosystems remain uncertain in subtropical regions. Here, we used a proxy-based approach to explore the community dynamics of testate amoebae (Arcellinida and Euglyphida) in two subtropical deep reservoirs (Tingxi and Shidou) in Xiamen, southeastern China, over a three-year period. Specifically, we employed drought and typhoon events recorded by weather station as proxies for ecological disturbance and chlorophyll-a estimated through fluorometry as a proxy for testate amoeba food. We addressed three questions: (1) Does typhoon-induced ecological disturbance affect the distribution patterns of testate amoebae in subtropical reservoirs? (2) Do typhoon- and drought-induced ecological disturbances affect the testate amoeba community across different water layers of subtropical reservoirs similarly? (3) Do stochastic or deterministic processes shaping the testate amoeba community over time exhibit similar patterns in different water layers of subtropical reservoirs? The typhoon-induced ecological disturbance resulted in pronounced shifts in the distribution patterns of testate amoebae, characterized by lower shell influx in surface waters (11-12 ind. mL-1 d-1) and higher shell influx in middle and bottom waters (12-22 ind. mL-1 d-1). The impact of typhoon-and drought-induced ecological disturbance was more pronounced in surface waters, and its pure explanation accounted for 29.5-35.5 % community variation in a variation partitioning analysis. The effect of stochastic processes revealed by the neutral model increased with water depths, accounting for 63.3-76.5 % of the community variation in the surface, 77.4-82.6 % in the middle, and 82.8-88.1 % in the bottom water. The effect of deterministic processes shown by the null model decreased with water depth and remained relatively low across all water layers. These results suggest contrasting patterns of assembly mechanisms underlying the testate amoeba community responses to ecological disturbance, with the balance perhaps shaped by water depth and the average water residence time in a reservoir.

Stochastic processes driving cyanobacterial temporal succession in response to typhoons in a coastal reservoir

Typhoons associated with heavy rainfall events, potentially triggering harmful algal blooms (cyanoHABs) dominated by cyanobacteria in coastal reservoirs. These blooms deteriorate water quality and produce toxins, posing a threat to aquatic ecosystems. However, the ecological mechanisms driving cyanobacteria communities in response to typhoons remain unclear. To address this gap, we investigated a coastal reservoir with high-frequency sampling during two typhoon seasons. We employed comprehensive statistical methods under neutral and evolutionary theories to analyze environmental dynamics and cyanobacterial genus succession. Our findings revealed a significant increase in nutrient loads following typhoons, with concentrations of total nitrogen (TN), total phosphorus (TP), and ammonia-nitrogen (NH4+-N) rising from 0.4 mg/L to 1.0 mg/L, 0.02 mg/L to 0.63 mg/L, and 0.03 mg/L to 0.26 mg/L, respectively. These changes coincided with fluctuations in other physicochemical parameters under changing hydrometeorological conditions. Despite significant environmental disturbances, the cyanobacterial community exhibited a remarkable recovery within 15-25 days following the typhoons. This recovery progressed through four distinct successional phases, with a notable shift in community composition from Raphidiopsis and Pseudoanabaena to Aphanocapsa, subsequently replaced by Raphidiopsis and Microcystis, before reverting to the pre-typhoon community structure. During the entire successional phase, the availability of TN and the TN/TP ratio played a dominant role, as indicated by PLS-PM analysis (total effects = -0.6; p < 0.05). Pre-typhoon, environmental factors primarily influenced community structure (54 %) based on modified stochasticity ratio. However, following the typhoons, stochastic fluctuations took precedence (71 %-91 %). The rapid recovery of cyanobacterial communities and the shift in driving mechanisms from deterministic to stochastic processes underscore the complex ecological responses to typhoon events. This study provides essential insights for biodiversity preservation and ecosystem restoration, emphasizing the need to consider both stochastic and deterministic processes in ecological management strategies.

Seasonal Dynamics of Eukaryotic Microbial Communities in the Water-Receiving Reservoir of the Long-Distance Water Diversion Project, China

Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving body of YQWD, over a one-year period using 18S rDNA amplicon sequencing. The results showed that the eukaryotic microbial diversity did not exhibit significant seasonal variation (p > 0.05), but there was a notable variance in the community structure (p < 0.05). Arthropoda and Paracyclopina, representing the most dominant phylum and the most dominant genus, respectively, both exhibited the lowest abundance during the winter. The Chlorophyta, as the second-dominant phylum, demonstrates its higher abundance in the spring and winter. The Mantel test and PLS-PM (Partial Least Squares Path Modeling) revealed that water temperature (WT), dissolved oxygen (DO), and pH influenced the seasonal dynamic of eukaryotic microbial communities significantly, of which WT was the primary driving factor. In addition to environmental factors, water diversion is likely to be an important influencing factor. The results of the co-occurrence network and robustness suggested that the spring network is the most complex and exhibits the highest stability. Moreover, keystone taxa within networks have been identified, revealing that these key groups encompass both abundant and rare species, with specificity to different seasons. These insights are vital for understanding the seasonal variation of microbial communities in the Jihongtan Reservoir during ongoing water diversions.

Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.

Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms

The multiple ecological influences and potential microbial degradation of microplastics are generally attributed to the microbial communities colonized on microplastics. Phages play an important role in the composition and function of their bacterial hosts, yet the occurrence and the potential functional characteristics of phages in the biofilms of microplastics have not been known. This study, for the first time, explored the diversity, composition, and potential function characteristics of phage communities living in the biofilms of PP, PE, and PET microplastics and stones, cultured in the same site, via the metagenome method. The results showed that a total of 240 non-redundant virus OTUs (vOTUs), distributed in at least four orders and seven families, were detected from biofilm metagenomes of microplastics. Compared to stones, some phages were selectively enriched by microplastic biofilms, with 13 vOTUs uniquely colonized on three microplastics, and these vOTUs mainly belong to the family Autographiviridae and Podoviridae. Except for the evenness of PP, the richness index, Chao 1 index, and abundance of phage communities of three microplastics were much higher than that of stone. At least 8 bacterial phyla and 72 genera were possibly infected by phages. Compared to the stones, both composition and abundance of the phages and hosts presented significant and strong correlations for three microplastics. Some of the bacterial hosts on microplastics were likely involved in the microplastic degradation, fermenters, nitrogen transformation processes, and so on. A total of 124 encoding auxiliary metabolic genes (AMGs) were detected from viral contigs. The abundance of AMGs in microplastics was much higher than that of stones, which may provide more direct or indirect support for the bacterial degradation of microplastics. This study provides a new perspective on the occurrence and potential functions of phages on microplastic biofilms, thus expanding our understanding of microbial communities on microplastic biofilms.

Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal

Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.

Nutrient levels and prokaryotes affect viral communities in plateau lakes

Viruses are the most abundant organisms in aquatic environments. Recent advances of viral metagenomic have greatly expanded our understanding of aquatic viral communities. However, little is known about the difference of viral communities and driving factors in freshwater lake. This study seeks to understand the spatio-temporal variation, differences, and driving factors of viral communities in two plateau lakes (Dianchi and Fuxian Lakes) with significant nutritional differences. The viral communities exhibited apparent seasonal variation in Dianchi Lake, while seasonal influences on the viral communities were greater than location-based influences. Two-thirds of all detected viral taxa were shared in two lakes, but there was variation in the composition of viral communities. Correlations between prokaryotic communities, environmental factors and viral communities were analyzed. The nutrients, chlorophyll a were primarily environmental parameters affecting viral communities, and the prokaryotic community was significantly correlated with the viral community. In addition, several viruses infecting humans were identified in two lakes, with the most abundant being Herpesviridae and Poxviridae. Overall, these findings provide information on the dynamics, composition, and differences of viral and prokaryotic communities in plateau lakes with different nutrient levels. These results suggest that nutritional levels and prokaryotic communities could play an important role in shaping viral communities in freshwater lakes.

A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use

Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.

Tropical cyclone effects on water and sediment chemistry and the microbial community in estuarine ecosystems

Frequent and intense storm disturbances can have widespread and strong effects on the nitrogen and iron cycles and their associated microbial communities in estuary systems. A three-year investigation was conducted in the Pearl River and Zhanjiang estuaries in Guangdong Province, China through repeated sampling at three timepoints, defined as pre-storm (<1 month before storm), post-storm (<1 month after storm), and non-storm (6-8 months after storm). Increased nutrient concentrations (total organic carbon, nitrate, nitrite, ammonium, and sulfate) in both the sediment and water column were observed immediately after storm. The microbial community experienced extensive and immediate changes determined by an observed composition shift in the nitrogen and iron-cycling microbiomes. Analysis of sediment samples displayed a shift from nitrogen-to sulfur-cycling microorganisms and an increase in microbial interactions that were not observed in the water column. The chemical profile and microbial community components both returned to baseline conditions 6-8 months following storm disturbance. Finally, significant correlations were found between chemical and microbial data, suggesting that niche-sharing microbes may respond similarly to stimuli that impact their ecosystem. Increases in nutrient availability can favor the abundance of specific taxa, as demonstrated by an increase in Acidimicrobium that affect both nitrogen and iron cycling.

Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R² = 0.5065, p < 0.0001; bottom: R² = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.

Microbial Community Resilience across Ecosystems and Multiple Disturbances

The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.

Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa

Background

P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard to cure. One possible alternative to antibiotics is to use phages. However, the isolation of phages suitable for phage therapy— be lytic, be efficient, and have a broad host range —against some target bacteria has proven difficult. To identify the best places to look for these phages against P. aeruginosa we screened hospital sewages, soils, and rivers in two cities.

Results

We isolated eighteen different phages, determined their host range, infection property, and plaque morphology. We found that the sewage and sewage-contaminated environments are the most reliable sources for the isolation of Pseudomonas phages. In addition, phages isolated from hospital sewage showed the highest efficiency in lysing the bacteria used for host range determination. In contrast, phages from the river had larger plaque size and lysed bacteria with higher levels of antibiotic resistance.

Conclusions

Our findings provided additional support for the importance of sewage as the source of phage isolation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02197-z.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Particulate organic matter as causative factor to eutrophication of subtropical deep freshwater: Role of typhoon (tropical cyclone) in the nutrient cycling

Intense storms pose a serious threat to ecosystem functioning and services. However, the effects of typhoons (tropical cyclones) on the biogeochemical processes mediating risk of eutrophication in deep freshwater ecosystems remain unclear. Here, we conducted a three-year study to elucidate linkages between environmental change, stable isotopes and the stoichiometry of particulate organic matter (POM), and nutrient cycling (i.e., carbon, nitrogen and phosphorus) in a subtropical deep reservoir subjected to typhoon events. The typhoons significantly changed the nutrient levels in the deep waters as well as the thermocline position. Increased typhoon-driven organic matter input, algae sinking and heterotrophic decomposition interacted with each other to cause steep and prolonged increases of total nitrogen, ammonium nitrogen and total phosphorus in the bottom waters of the reservoir. Small-sized or pico-sized POM (i.e., 0.2-3 μm) showed a substantial increase in bottom waters, and it exhibited stronger response than large-sized POM (i.e., 3-20, 20-64, 64-200 μm) to the typhoons. Our results also indicated that typhoons boost the nutrient cycling in deep waters mainly through pico-sized POM.

Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal

In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition was similar to that obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8% and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic.

IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Metagenomics revealing new virus species in farm and pet animals and aquaculture

Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.

Charting the diversity of uncultured viruses of Archaea and Bacteria

BACKGROUND

Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.

RESULTS

Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.

CONCLUSIONS

These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.

Charting the diversity of uncultured viruses of Archaea and Bacteria

Background

Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.

Results

Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.

Conclusions

These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.

Metagenomic analysis of viruses, bacteria and protozoa in irrigation water

Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used annually, reclaimed water is a good alternative to reduce dependency on conventional irrigation water sources. European guidelines have established acceptable concentrations of certain pathogens and/or indicators in irrigation water, depending on the irrigation system used and the irrigated crop. However, the incidences of food-borne infections are known to be underestimated and all the different pathogens contributing to these infections are not known. Next-generation sequencing (NGS) enables the determination of the viral, bacterial and protozoan populations present in a water sample, providing an opportunity to detect emerging pathogens and develop improved tools for monitoring the quality of irrigation water. This is a descriptive study of the virome, bacteriome and parasitome present in different irrigation water sources. We applied the same concentration method for all the studied samples and specific metagenomic approaches to characterize both DNA and RNA viruses, bacteria and protozoa. In general, most of the known viral species corresponded to plant viruses and bacteriophages. Viral diversity in river water varied over the year, with higher bacteriophage prevalences during the autumn and winter. Reservoir water contained Enterobacter cloacae, an opportunistic human pathogen and an indicator of fecal contamination, as well as Naegleria australiensis and Naegleria clarki. Hepatitis E virus and Naegleria fowleri, emerging human pathogens, were detected in groundwater. Reclaimed water produced in a constructed wetland system presented a virome and bacteriome that resembled those of freshwater samples (river and reservoir water). Viral, bacterial and protozoan pathogens were occasionally detected in the different irrigation water sources included in this study, justifying the use of improved NGS techniques to get a comprehensive evaluation of microbial species and potential environmental health hazards associated to irrigation water.

Metagenomic Analysis of Virioplankton from the Pelagic Zone of Lake Baikal

This study describes two viral communities from the world’s oldest lake, Lake Baikal. For the analysis, we chose under-ice and late spring periods of the year as the most productive for Lake Baikal. These periods show the maximum seasonal biomass of phytoplankton and bacterioplankton, which are targets for viruses, including bacteriophages. At that time, the main group of viruses were tailed bacteriophages of the order Caudovirales that belong to the families Myoviridae, Siphoviridae and Podoviridae. Annotation of functional genes revealed that during the under-ice period, the “Phages, Prophages, Transposable Elements and Plasmids” (27.4%) category represented the bulk of the virome. In the late spring period, it comprised 9.6% of the virome. We assembled contigs by two methods: Separately assembled in each virome or cross-assembled. A comparative analysis of the Baikal viromes with other aquatic environments indicated a distribution pattern by soil, marine and freshwater groups. Viromes of lakes Baikal, Michigan, Erie and Ontario form the joint World’s Largest Lakes clade.

A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion

Microbial communities are key drivers of ecosystem processes, but their behavior in disturbed environments is difficult to measure. How microbial community composition and function respond disturbances is a common challenge in biomedical, environmental, agricultural, and bioenergy research. A novel way to solve this problem is to use a systems-level perspective and describe microbial communities as networks. Based on a mesophilic anaerobic digestion system of swine manure as a tool, we propose a simple framework to investigate changes in microbial communities via compositions, metabolic pathways, genomic properties and interspecies relationships in response to a long-term temperature disturbance. After temperature disturbance, microbial communities tend towards a competitive interaction network with higher GC content and larger genome size. Based on microbial interaction networks, communities responded to the disturbance by showing a transition from acetotrophic (Methanotrichaceae and Methanosarcinaceae) to methylotrophic methanogens (Methanomassiliicoccaceae and Methanobacteriaceae) and a fluctuation in rare biosphere taxa. To conclude, this study may be important for exploring the dynamic relationships between disturbance and microbial communities as a whole, as well as for providing researchers with a better understanding of how changes in microbial communities relate to ecological processes.

ENVirT: inference of ecological characteristics of viruses from metagenomic data

Background

Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.

Results

In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.

Conclusions

These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2398-5) contains supplementary material, which is available to authorized users.

Occurrence and distribution of viruses and picoplankton in tropical freshwater bodies determined by flow cytometry

This study aimed to examine the drivers in shaping the occurrence and distribution of total viruses and picoplankton in tropical freshwater ecosystems. Flow cytometry was used to quantify the concentrations of total viruses, picoheterotrophs, picophytoplankton, and picocyanobacteria. Three land use patterns (urban-, agriculture- and parkland-dominated) were evaluated using ArcGIS. Significant correlations were observed between water-borne microbial targets and water quality parameters (0.175 ≤ |r| ≤ 0.441), nutrients (0.250 ≤ r ≤ 0.570) and land use factors (0.200 ≤ |r| ≤ 0.460). In particular, the concentrations of total viruses and picoheterotrophic cells were higher in catchments whereas the abundances of picophytoplankton and picocyanobacteria were higher in reservoirs. Total viruses and picoplankton had higher concentrations in urban- and agriculture-dominated areas, probably due to anthropogenic inputs and agricultural inputs, respectively. Although surface water is a complex matrix influenced by niche-based (i.e., physicochemical properties, nutrients, land use impact etc.) and neutral-based factors (i.e., ecological drift, dispersal and species), land use patterns could help to elucidate the occurrence and distribution of the total microbial community at the macroscopic level. Meanwhile, inter-correlations among viruses, picoplankton and picoheterotrophs (0.715 ≤ r ≤ 0.990) also substantiates their mutual interactions in influencing the microbial community. Furthermore, the relationships between total microbial cells and bacterial and viral indicators were also investigated. Concentrations of total viruses, picoplankton and picoheterotrophs were positively correlated with bacterial indicators (0.427 ≤ r ≤ 0.590) and viral indicators (0.201 ≤ r ≤ 0.563). These results indicated that faecal and viral contamination could contribute to the numbers of total viruses and bacteria.

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.

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.

Freshwater Viromes: From Sampling to Evaluation

There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from freshwater samples, specifically targeting dsDNA bacteriophages. We also discuss methods for bioinformatic analysis of the resulting data.

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia

Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.

Geospatial distribution of viromes in tropical freshwater ecosystems

This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

A review on recent progress in the detection methods and prevalence of human enteric viruses in water

Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden–Meyerhof–Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Bacteriophages infecting major groups of freshwater heterotrophic bacteria have been rarely isolated, hampering analyses of freshwater viromes. Here, we report the isolation and genomic characterization of P19250A, the first phage that infects the LD28 clade, an abundant freshwater methylotrophic bacterial group. P19250A was isolated from Lake Soyang, an oligotrophic reservoir, using an LD28 strain as a host. Morphological and genomic analyses revealed that P19250A is a lytic siphovirus with a ∼38.6-kb genome. To analyze the distribution of P19250A genome within its habitat, six seasonal viral metagenome (virome) samples were prepared from Lake Soyang. Through binning analysis of freshwater viromes, P19250A was shown to be the most highly assigned freshwater phage that infects heterotrophic bacteria (up to 8.21%) in five viromes. Furthermore, when freshwater virome data collected worldwide were analyzed, P19250A genome also showed high abundance, especially in Lough Neagh, UK, where P19250A genome was recorded as the most abundant bacteriophage. From metagenome analysis, the proportion of P19250A-assigned reads showed seasonal fluctuation following the abundance of the LD28 clade in Lake Soyang. These results showed that P19250A would be an essential resource for analyses of freshwater viromes, and also suggest that phages of other abundant freshwater bacteria need to be isolated for better understanding of freshwater viruses.

Temporal dynamics of uncultured viruses: a new dimension in viral diversity

Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.

Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)

Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.

The use of informativity in the development of robust viromics-based examinations

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer is pervasive within phage communities. As such, the presence of a particular gene may not be indicative of the presence of a particular viral species. Rather, it is just that: an indication of the presence of a specific gene. To circumvent this limitation, we have developed a new method for the analysis of viral metagenomic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a taxonomic signal, such that each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven freshwater viral metagenomes. While providing a robust method for evaluating viral metagenomic data, the tool is versatile and can easily be customized to investigations of any environment or biome.

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.

Aquatic viral metagenomics: Lights and shadows

Viruses are the most abundant biological entities on Earth, exceeding bacteria in most of the ecosystems. Specially in oceans, viruses are thought to be the major planktonic predators shaping microorganism communities and controlling ocean biological capacity. Plankton lysis by viruses plays an important role in ocean nutrient and energy cycles. Viral metagenomics has emerged as a powerful tool to uncover viral diversity in aquatic ecosystems through the use of Next Generation Sequencing. However, many of the commonly used viral sample preparation steps have several important biases that must be considered to avoid a misinterpretation of the results. In addition to biases caused by the purification of virus particles, viral DNA/RNA amplification and the preparation of genomic libraries could also introduce biases, and a detailed knowledge about such protocols is required. In this review, the main steps in the viral metagenomic workflow are described paying special attention to the potential biases introduced by each one.

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health

The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. From the samples, 110,000 quality-checked bacterial 16S rRNA gene sequences were obtained and analyzed, resulting in an observation of 4500 bacterial operational taxonomic units (OTUs). The most abundant bacteria were Mycobacterium and Arthrobacter of the Actinobacteria (33.2%), Exiguobacterium and Paenisporosarcina of the Firmicutes (23.4%), Planktothrix and Synechococcus of the Cyanobacteria (20.8%), and Methylocystis and Polynucleobacter of the Proteobacteria (16.3%). Considerable spatial and temporal variations were observed in the bacterial community of Actinobacteria, Cyanobacteria, and Firmicutes, where the bacterial community structure was greatly influenced by hydrological and weather conditions. The most influential factors were (1) water inflow for Bacteroidia and Clostridia, (2) turbidity for Gammaproteobacteria, (3) precipitation for Bacilli, and (4) temperature and pH for Cyanobacteria. One noticeable microbial interaction in the bacterial community was a significant negative relationship between Cyanobacteria and Bacilli (P < 0.05). Concerning beach water quality, the level of the genetic markers for cyanobacterial toxin (mcyA) was linked to the abundance of Cyanobacteria. In addition, unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.

Comparison and Interpretation of Taxonomical Structure of Bacterial Communities in Two Types of Lakes on Yun-Gui plateau of China

Bacterial communities from freshwater lakes are shaped by various factors such as nutrients, pH value, temperature, etc. Their compositions and relative abundances would undergo changes to adapt the changing environments, and in turn could affect the environments of freshwater lakes. Analyses of the freshwater lake’s bacterial communities under different environments would be of pivotal importance to monitor the condition of waterbody. In this study, we have collected freshwater samples from two lakes on Yun-Gui plateau of China, Lake Dianchi and Lake Haixihai, and analyzed the bacterial community structures from these samples based on 16S rRNA sequencing. Results have shown that: Firstly, the bacterial community of these samples have very different taxonomical structures, not only between two lakes but also among the intra-groups for samples collected from Dianchi. Secondly, the differences between samples from two lakes are highly associated with the chemical-geographical properties of the two lakes. Thirdly, for samples of Dianchi and Haixihai, analytical results of physicochemical, taxonomical structure and relative abundance of community revealed that extreme physicochemical factors caused by human activities have strongly affected the bacterial ecosystem in Dianchi. These results have clearly indicated the importance of combining biological profiling and chemical-geographical properties for monitoring Chinese plateau freshwater bacterial ecosystem, which could provide clues for Chinese freshwater ecosystem remediation on plateau.

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations.

Transporting Ocean Viromes: Invasion of the Aquatic Biosphere

Studies of marine viromes (viral metagenomes) have revealed that DNA viruses are highly diverse and exhibit biogeographic patterns. However, little is known about the diversity of RNA viruses, which are mostly composed of eukaryotic viruses, and their biogeographic patterns in the oceans. A growth in global commerce and maritime traffic may accelerate spread of diverse and non-cosmopolitan DNA viruses and potentially RNA viruses from one part of the world to another. Here, we demonstrated through metagenomic analyses that failure to comply with mid-ocean ballast water exchange regulation could result in movement of viromes including both DNA viruses and RNA viruses (including potential viral pathogens) unique to geographic and environmental niches. Furthermore, our results showed that virus richness (known and unknown viruses) in ballast water is associated with distance between ballast water exchange location and its nearest shoreline as well as length of water storage time in ballast tanks (voyage duration). However, richness of only known viruses is governed by local environmental conditions and different viral groups have different responses to environmental variation. Overall, these results identified ballast water as a factor contributing to ocean virome transport and potentially increased exposure of the aquatic bioshpere to viral invasion.

Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome

The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga.

Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China

Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% ± 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.

Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

Viruses are the most abundant microorganisms in the aquatic environment, yet the identification of viruses and assessing their diversity still remains a challenge. Here, we present a robust, routinely usable approach to identify viruses from two freshwater lakes of the lower Great Lakes region, Lake Ontario, and Lake Erie. We collected water samples from six different beaches of these two lakes during the summer period of 2012 and 2013, and separated into three distinct fractions, namely a bacterial fraction, a virus like particle (VLP) fraction, and a fraction of eDNA (environmental DNA). DNA extracted from all three fractions was sequenced and bioinformatic analyses of sequences revealed the presence of viruses from major viral families. The analyzed viral sequences were dominated by bacteriophage sequences, but also contained many plant and animal viruses. Within the context of this study, geographic location does not appear to have a major impact on viral abundance and diversity, since virome composition of both lakes were similar. Comparative analyses between eDNA and viral fractions showed that eDNA can be used in combination with VLP fractions to identify viruses from the environment.