Induction of temperate cyanophage AS-1 by heavy metal--copper

Adaptive strategies and ecological roles of phages in habitats under physicochemical stress

Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.

The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Cyanophage technology in removal of cyanobacteria mediated harmful algal blooms: A novel and eco-friendly method

Cyanophages are highly abundant specific viruses that infect cyanobacterial cells. In recent years, the cyanophages and cyanobacteria interactions drew attention to environmental restoration due to their discovery in marine and freshwater systems. Cyanobacterial harmful algal blooms (cyanoHABs) are increasing throughout the world and contaminating aquatic ecosystems. The blooms cause severe environmental problems including unpleasant odors and cyanotoxin production. Cyanotoxins have been reported to be lethal agents for living beings and can harm animals, people, aquatic species, recreational activities, and drinking water reservoirs. Biological remediation of cyanoHABs in aquatic systems is a sustainable and eco-friendly approach to increasing surface water quality. Therefore, this study compiles the fragmented information with the solution of removal of cyanoHABs using cyanophage therapy techniques. To date, scant information exists in terms of bloom formation, cyanophage occurrence, and mode of action to remediate cyanoHABs. Overall, this study illustrates cyanobacterial toxin production and its impacts on the environment, the mechanisms involved in the cyanophage-cyanobacteria interaction, and the application of cyanophages for the removal of toxic cyanobacterial blooms.

The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications

Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles.

Confocal microscopy reveals alterations of thylakoids in Limnospira fusiformis during prophage induction

The alkaliphilic cyanobacterium Limnospira fusiformis is an integral part in food webs of tropical soda lakes. Recently, sudden breakdowns of Limnospira sp. blooms in their natural environment have been linked to cyanophage infections. We studied ultrastructural details and prophage components in the laboratory by means of confocal laser scanning microscopy (CLSM) and transmission electron microscopy (TEM). For a comparison at the subcellular level, we included transmission electron microscopy (TEM) material of infected cells collected during a field survey. Compared to TEM, CLSM has the advantage to rapidly providing results for whole, intact cells. Moreover, many cells can be studied at once. We chemically induced lysogenic cyanophages by means of mitomycin C (MMC) treatments and studied the ultrastructural alterations of host cells. In parallel, the number of cyanophages was obtained by flow cytometry. After treatment of the culture with MMC, flow cytometry showed a strong increase in viral counts, i.e., prophage induction. CLSM reflected the re-organization of L. fusiformis with remarkable alterations of thylakoid arrangements after prophage induction. Our study provides a first step towards 3D visualization of ultrastructure of cyanobacteria and showed the high potential of CLSM to investigate viral-mediated modifications in these groups.

Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host

Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.

Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse

The dissemination of antimicrobial resistance (AMR) is one of the biggest challenges faced by mankind in the public health domains. It is currently favored by a lack of confinement between waste disposal and food production in the environmental compartment. To date, much effort has been devoted into the elucidation and control of cell-associated propagation of AMR. However, substantial knowledge gaps remain on the contribution of cell-free DNA to promote horizontal transfers of resistance genes in wastewater and downstream environments. Cell free DNA, which covers free extracellular DNA (exDNA) as well as DNA encapsulated in vesicles or bacteriophages, can persist after disinfection and promote gene transfer in the absence of physical and temporal contact between a donor and recipient bacteria. The increasing water scarcity associated to climatic change requires developing innovative wastewater reuse practices and, concomitantly, a robust evaluation of AMR occurrence by implementing treatment technologies able to exert a stringent control on AMR propagation in downstream environments exposed to treated or non-treated wastewater. This necessarily implies understanding the fate of ARGs on various forms of cell-free DNA, especially during treatment processes that are permissive to their formation. We propose that comprehensive approaches, investigating both the occurrence of ARGs and their compartmentalization in different forms of cellular or cell-free associated DNA should be established for each treatment technology. This should then allow selecting and tuning technologies for their capacity to limit the propagation of ARGs in any of their forms.

Environmental algal phage isolates and their impact on production potential for food and biofuel applications

AIMS

The United States Department of Energy is aiming to bring microalgal biofuels into commercial use by 2030 at the price of $3 per gasoline gallon equivalent. Large-scale production of biofuel faces many challenges including naturally occurring algal phages; and characterizing this threat is the aim of this study.

METHODS AND RESULTS

Bench-scale experiments were performed to study the impact of viral infectivity on the production of microalgal in bioreactors. All environmental samples were tested positive for algal phages which showed various levels of infectivity against Synechocystis PCC 6803 and the environmental isolates of microalgae. The viral attachment to algal cells was observed under transmission electron microscopy (TEM) and to determine the shape and size of the viral particles. All the viruses detected were c. 50-60 nm icosahedral particles. Viral infection resulted in 48% reduction in the biomass of the infected algal culture in 22 days.

CONCLUSIONS

This study has lead to the conclusion that the microalgal phages prevalent in natural environment may cause infections in broad range of microalgae used for biofuel production.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study has detected and quantified the phages that can infect algal populations in natural freshwater habitats and laboratory cultures of microalgal strains. The impact of viral threat to health of commercial algal production operations has been identified in this study.

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus 'relic' prophage

Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.

Flow Cytometric Analysis of Freshwater Cyanobacteria: A Case Study

Eutrophication is a process that occurs due to the excessive accumulation of nutrients, primarily nitrogen and phosphorus, from natural and anthropogenic sources. This phenomenon causes cyanobacterial overgrowth, which over time leads to cyanobacterial harmful algal blooms (CHABs) that affect public drinking water sources and water sites with recreational usage. The rapid detection of bloom-forming cyanobacteria in freshwater bodies is critical in order to implement prevention strategies. Cyanobacteria contain phycobiliproteins such as phycoerythrin and allophycocyanin as part of the phycobilisome that allows autofluorescence. In this study, samples from 36 freshwater bodies in 14 New Jersey counties were collected and analyzed using flow cytometry with forward-scatter phycoerythrin and allophycocyanin parameters. Pure cultures of Synechococcus sp. IU 625, Cylindrospermum spp. and Microcystis aeruginosa were used as references. The results revealed that 17 out of the 36 analyzed sites contained all three references and related species. Seven sites showed Microcystis and Cylindrospermum-like species, while four sites indicated Microcystis and Cylindrospermum-like species. Six water bodies showed Cylindrospermum-like species, and two sites showed Microcystis-like species. Polymerase chain reaction (PCR)-based assays further confirmed the flow cytometric results. The findings from this study suggest that flow cytometry could potentially serve as a rapid method for freshwater cyanobacteria detection and screening.

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

BACKGROUND

It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations.

RESULTS

Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition.

CONCLUSION

Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.

Contrasting distributions of bacteriophages and eukaryotic viruses from contaminated coastal sediments

Viruses are ubiquitous, abundant and play an important role in all ecosystems. Here, we advance understanding of coastal sediment viruses by exploring links in the composition and abundance of sediment viromes to environmental stressors and sediment bacterial communities. We collected sediment from contaminated and reference sites in Sydney Harbour and used metagenomics to analyse viral community composition. The proportion of phages at contaminated sites was significantly greater than phages at reference sites, whereas eukaryotic viruses were relatively more abundant at reference sites. We observed shifts in viral and bacterial composition between contaminated and reference sites of a similar magnitude. Models based on sediment characteristics revealed that total organic carbon in the sediments explained most of the environmental stress-related variation in the viral dataset. Our results suggest that the presence of anthropogenic contaminants in coastal sediments could be influencing viral community composition with potential consequences for associated hosts and the environment.

Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis

Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge.

This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper treatment on the community structure and functional gene composition, revealing that copper treatment had a selective effect on the functions of the bacterial community in the sponge. These findings suggest that copper pollution has an ecological impact on the sponge symbiont. The analysis showed that the untreated sponges hosted symbiotic autotrophic bacteria as dominant species, and the high-concentration copper treatment enriched for a heterotrophic bacterial community with enrichment for genes important for bacterial motility, supplementary cellular components, signaling and regulation, and virulence. Microscopic observation showed obvious bacterial aggregation and a reduction of sponge cell numbers in treated sponges, which suggested the formation of aggregates to reduce the copper concentration. The enrichment for functions of directional bacterial movement and supplementary cellular components and the formation of bacterial aggregates and phage enrichment are novel findings in sponge studies.

Impact of external forces on cyanophage-host interactions in aquatic ecosystems

Cyanobacterial (algal) blooms have by convention been attributed to the excessive level of nutrients from pollution and runoff, which promotes the rapid growth and multiplication of cyanobacteria or algae. The cyanophage (virus) is the natural predator of cyanobacteria (the host). The aim of this review is to unveil certain pressures that disrupt cyanophage-host interactions and the formation of cyanobacterial blooms. This review focuses principally on the impact of greenhouse gases, ozone depletion, solar ultraviolet radiation (SUR) and the role of recently discovered virophages, which coexist with and in turn are the natural predator of phages. The key findings are that the increase in SUR, the mutation of cyanophages and cyanobacteria, along with changing nutrient levels, have combined with virophages to impede cyanophage-host interactions and the resultant viral infection and killing of the cyanobacterial cell, which is a necessary step in controlling cyanobacterial blooms. Consider this a 'call to action' for researchers interested in corrective action aimed at evolving aquatic ecosystems.

Temperature-induced activation of freshwater Cyanophage AS-1 prophage

Synechococcus sp. IU 625 is one of the freshwater cyanobacteria responsible for harmful algal blooms (HAB). Cyanophages can serve as natural control agents and may be responsible for algal bloom prevention and disappearance. Cyanophage AS-1, which infects Synechococcus sp. IU 625 (Anacystis nidulans) and Synechococcus cedrorum, plays an important role in the environment, significantly altering the numbers of its hosts. Since seasonal (temperature-dependent) lytic induction of cyanobacterial prophage has been proposed to affect seawater algal blooms, we investigated if the AS-1 lytic cycle could be induced by a shift to high temperature. Our hypothesis was confirmed, as more phages were released at 35°C than at 24°C, with maximal induction observed with a shift from 24 to 35°C. Furthermore, transmission electron microscopy (TEM) images provide direct evidence of lysogenic to lytic conversion with temperature shift. Thus, temperature is an important inducer for AS-1 conversion from lysogenic to lytic cycle and could have applications in terms of modulating cyanobacterial populations in freshwater aquatic environments. The study gives insight into the effect of climate change on the interaction between cyanophage and cyanobacteria in freshwater ecosystems.

Epstein-Barr and other viral mimicry of autoantigens, myelin and vitamin D-related proteins and of EIF2B, the cause of vanishing white matter disease: massive mimicry of multiple sclerosis relevant proteins by the Synechococcus phage

The Epstein-Barr virus expresses proteins containing numerous short consensi (identical pentapeptides at least, or longer gapped consensi) that are identical to those in 16 multiple sclerosis autoantigens or in the products of multiple sclerosis susceptibility genes. Other viruses implicated in multiple sclerosis also display such mimicry and the Synechococcus phage was identified as a novel and major contributor to this phenomenon. Cyanobacteria hosts of Synechococcus phage favor temperate climes, in line with multiple sclerosis distribution, and bacterial and phage ecology accords closely with multiple sclerosis epidemiology. Bovine, ovine or canine viral proteins were also identified as autoantigen homologues, in line with epidemiological data linking multiple sclerosis to cattle density, sheep contact and dog ownership. Viral proteins align with known autoantigens, other myelin and vitamin D-related proteins and the translation initiation factor EIF2B, which is implicated in vanishing white matter disease. These data suggest that the autoantigens in multiple sclerosis, which causes demyelination in animal models, may be generated by antibodies raised to viral protein homologues. Multiple autoantibodies may cause multiple sclerosis via protein knockdown and immune activation. Their selective removal may be of clinical benefit as already suggested by promising results using plasmapheresis or immunoadsorption in certain multiple sclerosis patients.