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© 1989Nature Publishing Group
© 1989Nature Publishing Group
High abundance of viruses found in aquatic environments
Abstract
The concentration of bacteriophages in natural unpolluted waters is in general believed to be low, and they have therefore been considered ecologically unimportant. Using a new method for quantitative enumeration, we have found up to 2.5 x 10(8) virus particles per millilitre in natural waters. These concentrations indicate that virus infection may be an important factor in the ecological control of planktonic micro-organisms, and that viruses might mediate genetic exchange among bacteria in natural aquatic environments.
... Accordingly, microorganisms, including pathogenic ones, are more abundant in marine environments [29,30]. However, despite being continuously exposed to these microbialrich challenging environments, marine organisms keep healthy under normal circumstances through a complex network of defense mechanisms that have had to co-evolve under such conditions of selective pressure. ...
The high proliferation of microorganisms in aquatic environments has allowed their coevolution for billions of years with other living beings that also inhabit these niches. Among the different existing types of interaction, the eternal competition for supremacy between the susceptible species and their pathogens has selected, as part of the effector division of the immune system of the former ones, a vast and varied arsenal of efficient antimicrobial molecules, which is highly amplified by the broad biodiversity radiated, above any others, at the marine habitats. At present, the great recent scientific and technological advances already allow the massive discovery and exploitation of these defense compounds for therapeutic purposes against infectious diseases of our interest. Among them, antimicrobial peptides and antimicrobial metabolites stand out because of the wide dimensions of their structural diversities, mechanisms of action, and target pathogen ranges. This revision work contextualizes the research in this field and serves as a presentation and scope identification of the Special Issue from Marine Drugs journal “The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases”.
... In the last decades, the role of viruses as major drivers for microbial ecology and biogeochemical cycles in the ocean became increasingly apparent (Bergh et al., 1989;Wilhelm and Suttle, 1999;Zimmerman et al., 2020). Every year, up to ∼10 32 prokaryotic cells are infected by viruses in the ocean (Suttle, 2007), releasing an estimated 150 Gt of C, 27.6 Gt of N, and 4.6 Gt of P to the environment (Wilhelm and Suttle, 1999;Suttle, 2005;Lara et al., 2017). ...
Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.
... Phages are viruses that infect specific bacteria and are the most abundant organisms on Earth (up to 2.5 × 10 8 phages per mL in water) (Bergh et al., 1989). Phages need bacteria to replicate and survive; thus, naturally, they work as bacteria controllers. ...
With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii , Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.
... Phages are the most abundant entities in the biosphere (Bergh et al., 1989), and as such, they impose a tremendous selective pressure upon their bacterial hosts. Phages attach to a specific host, inject their genetic material, and utilize the host's enzymes and energy stores to replicate exponentially in a process that typically leads to cell lysis and death. ...
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve antiphage defense. However, the prevalence and effectiveness of minimal, single-component systems that cleave DNA remain unknown. Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity). This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates. Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in antiphage defense.
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 ‘life below water’. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals. Studying the ocean microbiome can inform international policies related to ocean governance, tackling climate change, ocean acidification and pollution, and can help promote achievement of multiple Sustainable Development Goals.
We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample.
Viruses are key members of Earth’s microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.
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.
It's about applications of bacteriophages in microbiology and biotechnology
A method is proposed which provides a minimum estimate of the rate of bacterial mortality in growing natural populations of planktonic bacteria. This estimate is given by the rate of decrease of radioactivity from the DNA of a [H]thymidine-labeled natural assemblage of bacteria after all added thymidine has been exhausted from the medium. Results obtained from river water, estuarine water, and seawater show overall bacterial mortality rates in the range 0.010 to 0.030 h, in good agreement with the range of growth rates measured in the same environments. Use of selective filtration through Nuclepore filters (pore size, 2 mum) allowed us to determine the contribution of microzooplankton grazing to overall bacterial mortality. Grazing rates estimated by this method ranged from 0 to 0.02 h.
Knowledge of the rates of bacterial mortality, particularly predatory mortality, is important in determining the fate of bacterial
production. Communities of planktonic bacteria have specific growth rates on the order of 1 d−1, but there is relatively little variation in bacterial abundance, implying that growth and mortality are closely coupled.
A review of the mechanisms of bacterial mortality suggests that predation and parasitism are the most likely factors balancing
the rapid rates of bacterial growth on daily time-scales. Experiments done in two-stage continuous cultures partially support
this notion. At bacterial growth rates of 1 d−1, predatory mortality was on the order of 1.5–2 d−1 and nonpredatory mortality was undetectable. On the other hand, a review of existing field studies indicates that neither
predation by metazoans nor protists balances rates of bacterial growth. Improved methods for measuring bacterial growth and
mortality and studies of the nonpredatory mechanisms of bacterial mortality are required to resolve this paradox.
The morphology of 75 bacteriophage strains isolated from water samples collected in the North Sea or in the northern Atlantic
was studied by electron microscopy. Only tailed phages were observed (bradley groups A, B, and C). According to structural
similarities, the strains are ascribed to 12 groups, 5 of which comprise types of marine phages not reported before. Four
of these 5 groups include phage types that have not been detected from any other source. Among the phages isolated from northern
Atlantic water a high incidence was observed of strains the particles of which have long appendages. Certain types of the
northern Atlantic phages investigated were derived only from samples collected either east or west of the Azores. This finding
agrees with former observations pointing to the existence of different populations of closely related bacteria east and west,
respectively, of the northern Mid-Atlantic Ridge.
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Bacteriophage 80 alpha did not increase in number in cultures containing less than about 1.0 X 10(4) to 1.5 X 10(4) CFU of Staphylococcus aureus per ml, but bacteriophage replication did occur when the number of bacteria exceeded this density, either initially or as a result of host cell multiplication. The minimum density of an asporogenous strain of Bacillus subtilis required for an increase in the number of bacteriophage SP beta cI was about 3 X 10(4) CFU/ml. The threshold density of Escherichia coli for the multiplication of bacteriophage T4 was about 7 X 10(3) CFU/ml. In the presence of montmorillonite, bacteriophage T4 did not increase in number until the E. coli population exceeded 10(4) CFU/ml. The mineralization of glucose was not affected in E. coli cultures inoculated with a low number of bacteriophage T4, but it could not be detected in cultures inoculated with a large number of phage. The numbers of bacteriophage T4 and a bacteriophage that lyses Pseudomonas putida declined rapidly after being added to lake water or sewage. We suggest that bacteriophages do not affect the number or activity of bacteria in environments where the density of the host species is below the host cell threshold of about 10(4) CFU/ml.
Up to 60 percent of the total marine primary production (or about one-fourth of the total global carbon dioxide fixation) passes through the free-living bacterioplankton. Grazing by bacteriovores is probably the predominant fate of the bacteria, although data are scarce. Evidence is presented that previously uncharacterized, small eukaryotes that are able to pass even 0.6-micrometer filters may be responsible for a large fraction (more than 50 percent) of the total grazing in coastal waters. These organisms have not yet been observed microscopically.