Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research

Cell Host & Microbe, Journal Year: 2017, Volume and Issue: 22(2), P. 142 - 155

Published: Aug. 1, 2017

Language: Английский

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Common principles and best practices for engineering microbiomes

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(12), P. 725 - 741

Published: Sept. 23, 2019

Language: Английский

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Emergence of three-dimensional order and structure in growing biofilms

Nature Physics, Journal Year: 2018, Volume and Issue: 15(3), P. 251 - 256

Published: Nov. 16, 2018

Language: Английский

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Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer

Current Opinion in Microbiology, Journal Year: 2017, Volume and Issue: 38, P. 66 - 73

Published: May 17, 2017

Language: Английский

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Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Frontiers in Microbiology, Journal Year: 2018, Volume and Issue: 9

Published: Aug. 27, 2018

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, organic matter and biomass contents) provide insufficient information describe quantitatively activity microorganisms some its outcomes, like emission greenhouse gases. Clearly, new, more appropriate are needed, which reflect better spatial heterogeneity at microscale (i.e., pore scale). For long time, spectroscopic microscopic tools were lacking quantify processes scale, but major technological advances over 15 years made suitable equipment available researchers. In this context, objective present article is review progress achieved date in significant research program has ensued. This can be rationalized as sequence steps, namely quantification modeling physical-, (bio)chemical-, microbiological properties soils, integration these different perspectives into unified theory, upscaling and, eventually, development new approaches measure characteristics. At stage, been on physical front, lesser extent (bio)chemical one well, both terms experiments modeling. microbial aspects, whereas lot work devoted bacterial fungal appropriateness model assumptions cannot readily assessed because relevant extremely scarce. overall move forward, it will crucial make sure components systems does not keep lagging behind Concerning subsequent steps program, very little various disciplinary occurred so far, result, researchers yet able tackle scaling up level. Many challenges, them daunting, remain path ahead.

Language: Английский

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A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Oct. 11, 2021

This paper reviews current knowledge on sources, spread and removal mechanisms of antibiotic resistance genes (ARGs) in microbial communities wastewaters, treatment plants downstream recipients. Antibiotic is the most important tool to cure bacterial infections humans animals. The over- misuse antibiotics have played a major role development, spread, prevalence (AR) microbiomes animals, ecosystems worldwide. AR can be transferred amongst bacteria

Language: Английский

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Ecological modelling approaches for predicting emergent properties in microbial communities

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 855 - 865

Published: May 16, 2022

Language: Английский

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Models predict planned phosphorus load reduction will make Lake Erie more toxic

Science, Journal Year: 2022, Volume and Issue: 376(6596), P. 1001 - 1005

Published: May 26, 2022

Harmful cyanobacteria are a global environmental problem, yet we lack actionable understanding of toxigenic versus nontoxigenic strain ecology and toxin production. We performed large-scale meta-analysis including 103 papers used it to develop mechanistic, agent-based model Microcystis growth microcystin Simulations for Lake Erie suggest that the observed toxigenic-to-nontoxigenic succession during 2014 Toledo drinking water crisis was controlled by different cellular oxidative stress mitigation strategies (protection degradation enzymes) susceptibility those mechanisms nitrogen limitation. This model, as well simpler empirical one, predicts planned phosphorus load reduction will lower biomass but make light more available, which increase production, favor cells, concentrations.

Language: Английский

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How to build the virtual cell with artificial intelligence: Priorities and opportunities

Cell, Journal Year: 2024, Volume and Issue: 187(25), P. 7045 - 7063

Published: Dec. 1, 2024

Cells are essential to understanding health and disease, yet traditional models fall short of modeling simulating their function behavior. Advances in AI omics offer groundbreaking opportunities create an virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent simulate the behavior molecules, cells, tissues across diverse states. This Perspective provides vision on design how collaborative efforts build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, guiding experimental studies, offering new for cellular functions fostering interdisciplinary collaborations open science.

Language: Английский

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Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Feb. 16, 2018

Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests bacterial organization contributes the persistence of anoxic even unsaturated soils. Such processes are difficult observe situ at microscale, hence mechanisms and time scales relevant for remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks mimics resource gradients postulated aggregates fluorescently tagged aerobic facultative anaerobic bacteria. Two initially intermixed species, Pseudomonas putida veronii, segregate into preferential regions promoted by opposing carbon oxygen (such persistent coexistence not possible well-mixed cultures). The study provides quantitative visualization modeling within aggregate-like hotspots, a key step towards developing mechanistic representation community pores.

Language: Английский

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