Biofilms can act as plasmid reserves in the absence of plasmid specific selection

AbstractPlasmids facilitate rapid bacterial adaptation by shuttling a wide variety of beneficial traits across microbial communities. However, under non-selective conditions, maintaining a plasmid can be costly to the host cell. Nonetheless, plasmids are ubiquitous in nature where bacteria adopt their dominant mode of life - biofilms. Here, we demonstrate that biofilms can act as spatiotemporal reserves for plasmids, allowing them to persist even under non-selective conditions. However, under these conditions, spatial stratification of plasmid-carrying cells may promote the dispersal of cells without plasmids, and biofilms may thus act as plasmid sinks.

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Understanding the evolution of interspecies interactions in microbial communities

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0256 ◽

2020 ◽

Vol 375 (1798) ◽

pp. 20190256 ◽

Cited By ~ 6

Author(s):

Florien A. Gorter ◽

Michael Manhart ◽

Martin Ackermann

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Interaction Strength ◽

Quantitative Model ◽

Systematic Effect ◽

Interspecies Interactions ◽

Fitness Effects ◽

Indirect Fitness ◽

Beneficial Traits ◽

Selection Of

Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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Plant Microbiota Beyond Farming Practices: A Review

Frontiers in Sustainable Food Systems ◽

10.3389/fsufs.2021.624203 ◽

2021 ◽

Vol 5 ◽

Author(s):

Mathieu Delitte ◽

Simon Caulier ◽

Claude Bragard ◽

Nicolas Desoignies

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Agricultural Practices ◽

Farming Practices ◽

Smart Farming ◽

Plant Growth Promoting ◽

Plant Microbiota ◽

Growth Promoting ◽

Chemical Inputs ◽

Beneficial Traits

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

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Understanding the evolution of interspecies interactions in microbial communities

10.1101/770156 ◽

2019 ◽

Author(s):

Florien A. Gorter ◽

Michael Manhart ◽

Martin Ackermann

Keyword(s):

Microbial Communities ◽

Interaction Strength ◽

Quantitative Model ◽

Systematic Effect ◽

Interspecies Interactions ◽

Fitness Effects ◽

Indirect Fitness ◽

Approaches To Study ◽

Beneficial Traits ◽

Selection Of

AbstractMicrobial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood whether and how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of communities. Specifically, we propose that the evolution of interspecies interactions depends crucially on the spatial structure of the environment. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments.

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Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.2920 ◽

2015 ◽

Vol 282 (1806) ◽

pp. 20142920 ◽

Cited By ~ 19

Author(s):

Ville-Petri Friman ◽

Laura Melissa Guzman ◽

Daniel C. Reuman ◽

Thomas Bell

Keyword(s):

Microbial Communities ◽

Evolutionary Dynamics ◽

Environmental Variability ◽

Abundance Ratio ◽

Community Diversity ◽

Resistant Bacteria ◽

Antibiotic Resistant ◽

Bacterial Adaptation ◽

Human Therapy ◽

And Migration

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.

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Bacteriophages Associated with Turkey Coecums in Bluecomb-Infected and Healthy Birds

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100063044 ◽

1969 ◽

Vol 27 ◽

pp. 226-227

Author(s):

A. E. Ritchie

Keyword(s):

Host Cell ◽

Causal Relationship ◽

Cell Cultures ◽

Cell Interaction ◽

Etiologic Agent ◽

Viral Origin ◽

Intestinal Contents ◽

Host Cell Interaction

The cause of bluecomb disease in turkeys is unknown. Filtration of infective intestinal contents suggests a viral origin. To date, it has not been possible to isolate the etiologic agent in various cell cultures. The purpose of this work was to characterize as many virus-like entities as were recognizable in intestines of both healthy and bluecomb-infected turkeys. By a comparison of the viral populations it was hoped that some insight might be gained into the cause of this disease. Studies of turkey hemorraghic enteritis by Gross and Moore (Avian Dis. 11: 296-307, 1967) have suggested that a bacteriophage-host cell interaction may bear some causal relationship to that disease.

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The Infection of Cells by Bullet-Shaped Viruses

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100063779 ◽

1969 ◽

Vol 27 ◽

pp. 372-373

Author(s):

Frederick A. Murphy ◽

Alyne K. Harrison ◽

Sylvia G. Whitfield

Keyword(s):

Electron Microscopy ◽

Physical Properties ◽

Host Cell ◽

Thin Section ◽

Cultured Cells ◽

Cell Infection ◽

Thin Section Electron Microscopy ◽

Section Electron ◽

Section Electron Microscopy

The bullet-shaped viruses are currently classified together on the basis of similarities in virion morphology and physical properties. Biologically and ecologically the member viruses are extremely diverse. In searching for further bases for making comparisons of these agents, the nature of host cell infection, both in vivo and in cultured cells, has been explored by thin-section electron microscopy.

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

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

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.

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