scholarly journals Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Felipe Hernandes Coutinho ◽  
Riccardo Rosselli ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Real Life ◽  
Host Density ◽  
Marine Ecosystems ◽  
Microbial Evolution ◽  
Evolutionary Strategies ◽  
Host Recognition ◽  
Replication Proteins ◽  
Viral Genes ◽  
Viral Communities ◽  
Depth Gradients

ABSTRACT The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which is very removed from real-life situations. Few studies have addressed trends of microdiversity in marine viral communities throughout depth gradients. We analyzed metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zones at depths of 15, 45, 60, and 2,000 m during the summer stratification of the water column. We evaluated microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations in viral genes. Our results demonstrated clear depth-dependent trends in the frequency of polymorphic sites and nonsynonymous mutations among genes encoding metabolic, structural, and replication proteins. These differences were linked to changes in energy availability, host and viral densities, and the proportions of actively replicating viruses. We propose the hypothesis that in the energy-rich, high-host-density, euphotic depths, selection acts to favor diversity of the host recognition machinery to increase host range, while in energy-depleted aphotic waters, selection acts on viral replication fitness, enhancing diversity in auxiliary metabolic genes. IMPORTANCE Viruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance, few studies have addressed trends of mutation accumulation in marine viral communities across depth gradients. By investigating these trends, we show that mutation frequencies differ among viral genes according to their molecular functions, with the highest microdiversity occurring among proteins related to host metabolism, followed by structural proteins and, lastly, genome replication proteins. This is in agreement with evolutionary theory that postulates that housekeeping genes are under strong purifying selection. We also observed a positive association between depth and microdiversity. One exception to this trend was the host recognition proteins from the deep chlorophyll maximum, which displayed strikingly high microdiversity, which we hypothesize to be associated with intraspecies competition for hosts. Finally, our data allowed us to propose a theoretical model for viral microdiversity across the depth gradient. These discoveries are of special relevance because many of the viral genomic sequences discovered here were predicted to infect some of the most abundant bacteria in marine ecosystems, such as “Candidatus Pelagibacter,” Puniceispirillum, and Prochlorococcus.

scholarly journals Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

2019 ◽  
Author(s):  
FH Coutinho ◽  
R Rosselli ◽  
F Rodríguez-Valera
Keyword(s):  
Marine Ecosystems ◽  
Replication Proteins ◽  
Synonymous Mutations ◽  
Genes Encoding ◽  
Marine Viruses ◽  
Viral Communities ◽  
Depth Gradients ◽  
Seawater Samples ◽  
Biological Entities ◽  
Bathypelagic Zone

AbstractViruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance no studies have addressed trends of micro-diversity in marine viral communities across depth gradients. To fill this gap we obtained metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zone at 15, 45, 60 and 2000 meters deep. The majority of viral genomic sequences obtained were derived from bacteriophages of the order Caudovirales, and putative host assignments suggested that they infect some of the most abundant bacteria in marine ecosystems such as Pelagibacter, Puniceispirillum and Prochlorococcus. We evaluated micro-diversity patterns by measuring the accumulation of synonymous and non-synonymous mutations in viral genes. Our results demonstrated that the degree of micro-diversity differs among genes encoding metabolic, structural, and replication proteins and that the degree of micro-diversity increased with depth. These trends of micro-diversity were linked to the changes in environmental conditions observed throughout the depth gradient, such as energy availability, host densities and proportion of actively replicating viruses. These observations allowed us to generate hypotheses regarding the selective pressures acting upon marine viruses from the epipelagic to the bathypelagic zones.

Epilogue

2021 ◽  
pp. 148-156
Author(s):  
Thomas E. Schindler
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Engineering ◽  
Significant Role ◽  
Living Cells ◽  
Microbial Evolution ◽  
Tree Of Life ◽  
Dna Structures ◽  
Viral Genes ◽  
Biochemical Systems

This chapter reveals the importance of bacterial sex in evolution. After scientists realized that antibiotic resistance and the development of MDR pathogens were caused by bacterial sex, some evolutionary biologists began to wonder about the potential role of HGT in evolution. Scientists speculated that mobile genes might have played a significant role in microbial evolution. James Shapiro has argued genome change in evolution results from a natural genetic engineering process utilizing the biochemical systems for reorganizing DNA structures present in living cells. For billions of years—from the beginning of evolution—bacteria have been transferring genes horizontally, between species and therefore between lineages, interconnecting the branches on the tree of life. The promiscuous process that has scrambled the tree of life is bacterial sex, discovered by Joshua and Esther Lederberg as a laboratory curiosity that helped uncover the molecular secretes of bacterial and viral genes.

Disease can shape marine ecosystems

2020 ◽  
pp. 61-70
Author(s):  
Joseph P. Morton ◽  
Brian R. Silliman ◽  
Kevin D. Lafferty
Keyword(s):  
Species Diversity ◽  
Structure Function ◽  
Food Web ◽  
Species Coexistence ◽  
Host Density ◽  
Marine Ecosystems ◽  
Ecosystem Engineers ◽  
Ecosystem Structure ◽  
Ecosystem Stability ◽  
Ecosystem Models

This chapter reviews how marine ecosystems respond to parasites. Evidence from several marine ecosystems shows that parasites can wield control over ecosystem structure, function, and dynamics by regulating host density and phenotype. Like predators, parasites can generate or modify trophic cascades, regulate important foundational species and ecosystem engineers, and mediate species coexistence by affecting competitive outcomes. Sometimes the parasites have clear positive impacts within ecosystems, such as increasing species diversity or maintaining ecosystem stability. Other times, parasites may have destabilizing effects that signal an ecosystem out of balance. But it is now clear that some (but not all) parasites can have strong and, at times, predictable effects, and should thus be incorporated into food web and ecosystem models

scholarly journals Pathology and Epizootiology of Entomophaga maimaiga Infections in Forest Lepidoptera

1999 ◽  
Vol 63 (4) ◽  
pp. 814-835 ◽  
Author(s):  
Ann E. Hajek
Keyword(s):  
Biological Control ◽  
North America ◽  
Species Complex ◽  
Plasma Membranes ◽  
Dna Analysis ◽  
Production Systems ◽  
Host Density ◽  
Host Recognition ◽  
Density Prediction ◽  
Entomophaga Maimaiga

SUMMARY The insect-pathogenic fungal pathogen Entomophaga maimaiga is endemic to northeastern Asia and was first found in North America in 1989. Due to repeated epizootics and spread within populations of the major forest defoliator in northeastern North America, the gypsy moth (Lymantria dispar), this pathogen has gained much notoriety. Although this pathogen was purposely introduced to North America for biological control of L. dispar in 1910 to 1911, it is questionable whether it became established at the time of release and then remained at innocuous levels until relatively recently. Alternatively, the fungal strain present in North America today could be a more recent accidental introduction. DNA analysis demonstrates that this pathogen differs significantly from North American members of the same species complex (the Lepidoptera-specific Entomophaga aulicae species complex), and, to date, isolates of this introduced pathogen display little heterogeneity in North America. Nonsusceptible lepidopteran larvae have been identified, and either E. maimaiga is unable to penetrate the cuticle or the fungus cannot survive within the hemocoel. In the latter case, although E. maimaiga grows as protoplasts lacking cell walls in the host hemolymph, glycoproteins on plasma membranes of the protoplasts could lead to host recognition. Epizootiological studies demonstrate a clear association between fungal activity and environmental moisture but little association with host density under hypothesized conditions of high fungal density. Prediction of the occurrence of epizootics is not yet possible. E. maimaiga is easily established in new areas by releasing azygospores, but the ability to use this pathogen further for biological control will depend, in large part, on the development of mass production systems.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

The Speech-Language Pathologist in the Public Schools: Preparation for Real Life Practices From the Perspective of a Speech-Language Pathology Program Coordinator

2010 ◽  
Vol 11 (2) ◽  
pp. 60-65
Author(s):  
Francine Wenhardt
Keyword(s):  
Public Schools ◽  
School Setting ◽  
Real Life ◽  
Effective School ◽  
Program Coordinator ◽  
Educational Preparation ◽  
The Public ◽  
Speech Language Pathologist ◽  
New Graduate ◽  
Language Pathology

Abstract The speech-language pathologist (SLP) working in the public schools has a wide variety of tasks. Educational preparation is not all that is needed to be an effective school-based SLP. As a SLP currently working in the capacity of a program coordinator, the author describes the skills required to fulfill the job requirements and responsibilities of the SLP in the school setting and advises the new graduate regarding the interview process and beginning a career in the public schools.

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