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

Tools and methodology to in silico phage discovery in freshwater environments

Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.

Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii

Multidrug-resistant (MDR) bacteria are a growing threat to the public health. Among them, the Gram-negative Acinetobacter baumannii is considered today as the most dangerous MDR pathogen. Phage-derived endolysins are peptidoglycan (PG) hydrolytic enzymes that can function as effective tools in the fight against MDR bacteria. In the present work, the viral diversity of a marine environmental sample (biofilm), formed near an industrial zone, was mined for the identification of a putative endolysin (AbLys2) that belongs to the glycoside hydrolase family 24 (GH24, EC 3.2.1.17). The coding sequence of AbLys2 was cloned and expressed in E. coli. The lytic activity and specificity of the recombinant enzyme were evaluated against suspensions of a range of Gram-positive and Gram-negative human pathogens using turbidity assays. AbLys2 displayed enhanced selectivity towards A. baumannii cells, compared to other bacteria. Kinetics analysis was carried out to characterize the dependence of its lytic activity on pH and showed that the enzyme exhibits its maximal activity at pH 5.5. Thermostability analysis showed that AbLys2 displays melting temperature Tm 47.1 °C. Florescence microscopy and cell viability assays established that AbLys2 is active towards live cultures of A. baumannii cells with an inhibitory concentration IC50 3.41 ± 0.09 μM. Molecular modeling allowed the prediction of important amino acid residues involved in catalysis. The results of the present study suggest that AbLys2 provides efficient lytic and antimicrobial activity towards A. baumannii cells and therefore is a promising new antimicrobial against this pathogen.

Deep metagenomic mining reveals bacteriophage sequence motifs driving host specificity

Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where such motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Bacteriophage Library Informed Sequence Scoring (BLISS), to discover sequence motifs in metagenomic datasets governing phage activity. BLISS uses experimental deep mutational scanning data to create sequence profiles to enable deep mining of metagenomes for functional motifs which are otherwise invisible to searches. We experimentally tested 10,073 BLISS-derived sequence motifs for the receptor-binding protein of the T7 phage. The screen revealed hundreds of T7 variants with novel host specificity with functional motifs sourced from distant families besides other major phyla. Position, substitution and location preferences on T7 dictated different specificities. To demonstrate therapeutic utility, we engineered highly active T7 variants against urinary tract pathogens. BLISS is a powerful tool to unlock the functional potential encoded in phage metagenomes.

Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.

Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

BACKGROUND

Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.

RESULTS

Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.

CONCLUSIONS

Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile

Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.

Bacteriophages of the lower urinary tract

The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.

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.

virMine: automated detection of viral sequences from complex metagenomic samples

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.

Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions

While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.

Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.

Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes

Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.

Phages of life - the path to pharma

Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini-review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient-focused pharmaceutical intervention.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

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.