Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: May 19, 2020

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged a serious threat pollution. Bioremediation is key to eliminate persistent contaminants from environment. The traditional bioremediation processes showed limitations, therefore, it necessary discover new technologies for best results. Here, in this review, we have provided an outlook on alternative strategies via synthetic biology, including exploring prerequisites analysis research data developing biological models microbial bioremediation. Moreover, cell coordination community, signaling, quorum sensing are engineered enhanced also described along promising gene editing tools obtaining host target sequences responsible degradation compounds. genetic circuit two-component regulatory system (TCRS) based biosensors detection briefly explained. These developments expected increase efficiency

Language: Английский

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Phage mobility is a core determinant of phage–bacteria coexistence in biofilms

The ISME Journal, Journal Year: 2017, Volume and Issue: 12(2), P. 532 - 543

Published: Nov. 10, 2017

Many bacteria are adapted for attaching to surfaces and building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too the exposure ubiquitous viral pathogens, bacteriophages. Although biofilm-phage encounters likely be common nature, little known about how phages might interact with biofilm-dwelling bacteria. It also unclear ecological dynamics their hosts depend on biological physical properties environment. To make headway this area, we develop a simulation framework that captures key mechanistic features growth phage infection. Using these simulations, find equilibrium state interaction between biofilms governed largely by nutrient availability biofilms, infection likelihood per host encounter ability diffuse through populations. Interactions matrix particles thus fundamental importance, controlling extent which can coexist natural contexts. Our results open avenues new questions host-parasite coevolution horizontal gene transfer spatially structured

Language: Английский

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Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Limnology and Oceanography, Journal Year: 2019, Volume and Issue: 65(S1)

Published: Nov. 20, 2019

Abstract Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense a general challenge understand how metabolism interactions single organisms shape community ecosystem‐scale transformations. Metagenomic approaches have developed rapidly, proven be powerful in linking In this review, we provide an overview metagenomic approaches, followed by discussion on some recent insights they provided, including those special issue. These include the discovery new taxa metabolisms microbiomes, into assembly functional ecology as well evolutionary processes shaping genomes influence human activities microbiomes. Given that metagenomics can now considered mature technology where data generation descriptive analyses relatively routine informative, then discuss metagenomic‐enabled research avenues further link integration well‐designed ecological experiments, use inform validate metabolic models, pressing need for ecologically relevant model simple systems better interpret taxonomic information integrated metagenomes. will contribute more mechanistic predictive understanding links between cycles. Owing rapid climate change impacts ecosystems, urgency such has never been greater.

Language: Английский

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Continuum and discrete approach in modeling biofilm development and structure: a review

Journal of Mathematical Biology, Journal Year: 2017, Volume and Issue: 76(4), P. 945 - 1003

Published: July 24, 2017

Language: Английский

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Understanding the evolution of interspecies interactions in microbial communities

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 375(1798), P. 20190256 - 20190256

Published: March 23, 2020

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

Language: Английский

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Bacteriophages benefit from generalized transduction

PLoS Pathogens, Journal Year: 2019, Volume and Issue: 15(7), P. e1007888 - e1007888

Published: July 5, 2019

Temperate phages are bacterial viruses that as part of their life cycle reside in the genome prophages. They found many species including most clinical strains human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate were considered only predators, but mounting evidence point to both antagonistic mutualistic interactions with for example some contributing virulence by encoding factors. Here we show generalized transduction, one type DNA transfer phages, can create conditions where not recipient host also transducing phage benefit. With antibiotic resistance a model trait used individual-based models experimental approaches susceptible cells become resistant antibiotics i) integrating ii) acquiring particles carrying genes obtained from environment. This is observed non-generalized which unable package DNA, nor virulent do form lysogens. Once established, lysogenic prophage benefit existence shuffle between lysogens disseminate antibiotics, encoded phage. facilitates survival leads population growth. We propose transduction function cooperate hosts survive rapidly-changing environments. implies just an error packaging selected ensure survival.

Language: Английский

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Metabolic modelling approaches for describing and engineering microbial communities

Computational and Structural Biotechnology Journal, Journal Year: 2020, Volume and Issue: 19, P. 226 - 246

Published: Dec. 16, 2020

Microbes do not live in isolation but microbial communities. The relevance of communities is increasing due to growing awareness their influence on a huge number environmental, health and industrial processes. Hence, being able control engineer the output both natural synthetic would be great interest. However, most available methods biotechnological applications involving microorganisms, vivo silico, have been developed context isolated microbes. In consortia development extremely difficult costly because it implies replicating suitable environments wet-lab. Computational approaches are thus good, cost-effective alternative study communities, mainly via descriptive modelling, also engineering modelling. this review we provide detailed compilation examples engineered comprehensive, historical revision computational metabolic modelling better understand, rationally wild

Language: Английский

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Rhizosphere Spatiotemporal Organization–A Key to Rhizosphere Functions

Frontiers in Agronomy, Journal Year: 2020, Volume and Issue: 2

Published: July 28, 2020

Resilience of soils, i.e. their ability to maintain functions or recover after disturbance, is closely linked the root-soil interface, soil's power house. However, limited observability key processes at interface has so far our understanding how such resilience emerges. Here, we hypothesise that emerges from self-organised spatiotemporal patterns which are result complex and dynamic feedbacks between physical, chemical biological occurring in rhizosphere. We propose combination modern experimental modelling techniques, with a focus on imaging approaches, allows for plant resource acquisition, microbiome-related health, soil carbon sequestration structure development. A prerequisite identification patterns, underlying feedback loops joint platforms defined investigated true 2D 3D geometry along time. This applies across different scientific disciplines physics/chemistry/microbiology genomics/physiology scales nano/microscopic scale root over radial profiles around single roots, up architecture scale. Thus, can move beyond isolated reductionist approaches have dominated rhizosphere research far.

Language: Английский

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Immunoresponsive microbiota-gut-on-chip reproduces barrier dysfunction, stromal reshaping and probiotics translocation under inflammation

Biomaterials, Journal Year: 2022, Volume and Issue: 286, P. 121573 - 121573

Published: May 17, 2022

Language: Английский

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Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms

eLife, Journal Year: 2017, Volume and Issue: 6

Published: Jan. 13, 2017

Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics Pseudomonas aeruginosa biofilms. Irrespective of initial frequency, competition with mutants, wild-type cells always increase relative abundance planar microfluidic devices under simple regimes. By contrast, microenvironments complex, irregular profiles - common natural environments matrix-producing isogenic non-producing strains can coexist. This result stems from local obstruction producers, generates regions near-zero shear allow mutants locally accumulate. Our findings connect the evolutionary stability production hydrodynamics spatial structure surrounding environment, providing potential explanation for variation biofilm secretion observed among bacteria environments.

Language: Английский

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