Review
Physics, Multidisciplinary
Ethan Levien, Jiseon Min, Jane Kondev, Ariel Amir
Summary: Phenotypic variability in isogenic populations has significant effects on population dynamics and the relationship between cell-to-cell variability and population dynamics is closely linked. Models of bet-hedging and phenotypic switching can help populations survive in uncertain environments through switching between phenotypes at the single-cell level. Fine-grained models of phenotypic variability show that even in a constant environment, traits like single-cell growth rates, generation times, and cell sizes can have significant effects on population dynamics.
REPORTS ON PROGRESS IN PHYSICS
(2021)
Article
Microbiology
Keith Arora-Williams, Christopher Holder, Maeve Secor, Hugh Ellis, Meng Xia, Anand Gnanadesikan, Sarah P. Preheim
Summary: The number, size and severity of aquatic low-oxygen dead zones are increasing worldwide. Microbial processes in low-oxygen environments have important ecosystem-level consequences. This study analyzed the microbial populations in the low-oxygen bottom waters of the Chesapeake Bay and found that sulfur-oxidizing microorganisms can serve as indicators of hypoxic conditions. Additionally, the study revealed connections between the sulfur, nitrogen, and oxygen cycles.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Water Resources
Moein Jahanbani Veshareh, Hamidreza M. Nick
Summary: The research focuses on the impact of microbial communities in subsurface porous environments on ecosystem functions, proposing an equivalent strain model to estimate the rate of community-derived metabolisms. By simulating four different scenarios, it is demonstrated that the model can efficiently characterize community behavior in cases of limited electron donor availability.
ADVANCES IN WATER RESOURCES
(2021)
Article
Biology
Sylvie Estrela, Alicia Sanchez-Gorostiaga, Jean C. C. Vila, Alvaro Sanchez
Summary: The study found that while the family-level community composition can generally be predicted using the null, naturally additive model, there are systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance. Pairs of more similar nutrients tend to be more additive than pairs of dissimilar nutrients, and sugar-acid communities are generally more similar to sugar communities than acid communities, possibly due to family-level asymmetries in nutrient benefits. Overall, the study suggests that regularities in how nutrients interact may help predict community responses to dietary changes.
Article
Multidisciplinary Sciences
Youness Azimzade
Summary: This study developed a model to investigate the invasion of cooperative/competitive populations in the presence of a physical barrier. The results showed that population interactions and environmental barrier intensity influenced the position and morphology of the invasion front. Additionally, competition among subpopulations led to more irregular invasion fronts.
SCIENTIFIC REPORTS
(2022)
Article
Physics, Multidisciplinary
Jayabrata Dhar, Anh L. P. Thai, Arkajyoti Ghoshal, Luca Giomi, Anupam Sengupta
Summary: This study explores the self-regulation of phenotypic noise and its coordination with collective structural organization, topological defects kinetics, and active transport emergence in bacterial colonies. Despite noise in cell geometry and colony area, there is a statistically precise critical time for the transition from a monolayer biofilm to a multilayer biofilm. By rectifying phenotypic noise, the study reveals an emergent strategy of confluent systems to tune active transport and buffer inherent heterogeneities.
Article
Biochemical Research Methods
Ting Lu, Congjian Ni
Summary: This study presents an individual-based, biophysical computational framework for simulating the spatiotemporal dynamics of microbial populations. The framework successfully validates single-cell chemotaxis simulations and reveals spatial patterns of different microbial populations. This study provides insights into microbial spatial ecology and offers a tool for designing spatial patterns in synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Microbiology
Wen-Sheng Shu, Li-Nan Huang
Summary: This article explores the diversity, functions, and evolution of bacteria and archaea inhabiting Earth's major extreme environments. Marker gene surveys and omics studies have played a crucial role in revealing the structure, function, and evolution of extremophile microbial communities, uncovering vast uncultured microbial diversity and the predominance of archaea in extreme conditions.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biophysics
Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani, Daniele De Martino, Andrea De Martino
Summary: Despite high single-cell variability, the fitness of microbial populations is influenced by the theoretically optimal boundary defined by minimal reduction of metabolic variability, indicating a trade-off between growth and heterogeneity within bacterial metabolism.
BIOPHYSICAL JOURNAL
(2022)
Article
Engineering, Environmental
Chunxiao Wang, Yu Yang, Yulin Wang, Dou Wang, Xiaoqing Xu, Yubo Wang, Liguan Li, Chao Yang, Tong Zhang
Summary: This study developed an absolute quantification method to investigate microbial community variations and population dynamics in anaerobic digesters. The results revealed decaying and growing microbial populations during the AD process. Functional analysis assigned some populations to specific niches related to hydrolysis, short-chain fatty acids metabolism, and methane generation.
Article
Green & Sustainable Science & Technology
Juan B. Garcia Martinez, Joseph Egbejimba, James Throup, Silvio Matassa, Joshua M. Pearce, David C. Denkenberger
Summary: The current food production system of human civilization is unprepared for global catastrophes that could reduce food production by 10% or more. Alternative food solutions, such as microbial food from SCP, have been proposed as a cost-effective option in case of such catastrophic events. Further research and investment in SCP production may help mitigate the negative impact of potential food-related global catastrophic risks.
SUSTAINABLE PRODUCTION AND CONSUMPTION
(2021)
Article
Chemistry, Physical
Monochura Saha, Subhajit Bandyopadhyay
Summary: Radical anions play important roles in various applications, but their generation and stabilization under ambient conditions can be challenging. This study reports a photogenerated NDI-based radical-anion that remains stable in water for over a month, forming a stacked supramolecular structure and conducting electricity with a linear I-V curve. The system exhibits a photoresponsive turn-on behavior with a high response ratio compared to its neutral precursor.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Yiliang Lin, Xiang Gao, Jiping Yue, Yin Fang, Jiuyun Shi, Lingyuan Meng, Clementene Clayton, Xin-Xing Zhang, Fengyuan Shi, Junjing Deng, Si Chen, Yi Jiang, Fabricio Marin, Jingtian Hu, Hsiu-Ming Tsai, Qing Tu, Eric W. Roth, Reiner Bleher, Xinqi Chen, Philip Griffin, Zhonghou Cai, Aleksander Prominski, Teri W. Odom, Bozhi Tian
Summary: In this study, a soil-inspired chemical system was developed to modulate microbial communities and impact biogeochemical cycles and homeostasis in human health. The composite material showed potential in rectifying gut microbiome dysbiosis and inflammatory symptoms.
Article
Physics, Multidisciplinary
Pierre A. Haas, Maria A. Gutierrez, Nuno M. Oliveira, Raymond E. Goldstein
Summary: Recent theoretical work has shown that clonal microbes can stabilize microbial communities by switching between different phenotypes. This switching can be stochastic or in response to environmental factors. The study explores the ecological effects of responsive switching and shows that it can stabilize coexistence, even when stochastic switching does not affect community stability.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Astronomy & Astrophysics
Aurelien Barrau, Killian Martineau, Cyril Renevey
Summary: Using the Schwarzschild metric as a toy model, this article revisits and explores the prediction that the mass of a classical black hole in a constant temperature thermal bath either diverges or vanishes in a finite amount of time. The study considers the behavior of this instability when the temperature of the bath varies with time and shows that the competition between the effects of temperature and Hawking radiation is subtle and not entirely determined by temperature hierarchy. The results are also extended to spaces with extra dimensions and the implications for bouncing models are discussed.
Review
Ecology
Stefanie Widder, Rosalind J. Allen, Thomas Pfeiffer, Thomas P. Curtis, Carsten Wiuf, William T. Sloan, Otto X. Cordero, Sam P. Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J. Flint, Andreas F. Haas, Beatrice Laroche, Jan-Ulrich Kreft, Paul B. Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R. van der Meer, Tobias Grosskopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F. Smets, Harris Wang, Orkun S. Soyer
Article
Multidisciplinary Sciences
Gavin Melaugh, Jaime Hutchison, Kasper Norskov Kragh, Yasuhiko Irie, Aled Roberts, Thomas Bjarnsholt, Stephen P. Diggle, Vernita D. Gordon, Rosalind J. Allen
Article
Multidisciplinary Sciences
D. Schneidereit, H. Vass, B. Reischl, R. J. Allen, O. Friedrich
Article
Microbiology
Kasper N. Kragh, Jaime B. Hutchison, Gavin Melaugh, Chris Rodesney, Aled E. L. Roberts, Yasuhiko Irie, Peter O. Jensen, Stephen P. Diggle, Rosalind J. Allen, Vernita Gordon, Thomas Bjarnsholt
Article
Microbiology
Yasuhiko Irie, Aled E. L. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle
Review
Physics, Multidisciplinary
Rosalind J. Allen, Bartlomiej Waclaw
REPORTS ON PROGRESS IN PHYSICS
(2019)
Article
Ecology
Catherine G. Mills, Rosalind J. Allen, Richard A. Blythe
THEORETICAL ECOLOGY
(2020)
Article
Biochemical Research Methods
Martin Carballo-Pacheco, Michael D. Nicholson, Elin E. Lilja, Rosalind J. Allen, Bartlomiej Waclaw
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Daniel Taylor, Nia Verdon, Peter Lomax, Rosalind J. Allen, Simon Titmuss
Summary: In this study, a microfluidic device and imaging protocol were introduced for high-resolution imaging and automatic counting of bacteria within microdroplets. The researchers successfully tracked the stochastic growth of replicate Escherichia coli populations and found that the growth trajectories in early times followed the predictions of the Bellman-Harris model.
Article
Physics, Multidisciplinary
Patrick Sinclair, Chris A. Brackley, Martin Carballo-Pacheco, Rosalind J. Allen
Summary: Surface-attached bacterial biofilms can lead to disease and industrial biofouling, and are widespread in natural environments. Quorum sensing is an important mechanism for biofilm initiation. We present and analyze a model that suggests a stochastic transition from loosely attached bacteria near the surface to a growing biofilm.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biotechnology & Applied Microbiology
Ellen Young, Gavin Melaugh, Rosalind J. Allen
Summary: The emergence of spatial organisation in biofilm growth is investigated using individual-based simulations. It is found that the transition from smooth to rough interface morphologies is associated with dynamical changes in the active layer. The fluctuations in the active layer thickness play a central role in controlling the pinning of the biofilm interface and the resulting biofilm morphology.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Biotechnology & Applied Microbiology
Gavin Melaugh, Vincent A. Martinez, Perrin Baker, Preston J. Hill, P. Lynne Howell, Daniel J. Wozniak, Rosalind J. Allen
Summary: Researchers have found that Pseudomonas aeruginosa forms suspended multicellular aggregates in liquid media, and these aggregates may play important roles in disease and biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have been implicated in aggregation, but their roles vary depending on the growth stage of the bacterial cultures. Cell-associated Psl mediates aggregation in exponentially growing cultures, while both eDNA and Psl mediate cohesion in stationary phase cultures. These findings suggest that the properties of multicellular aggregates change throughout the growth cycle of P. aeruginosa.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Biochemistry & Molecular Biology
Patrick Sinclair, Martin Carballo-Pacheco, Rosalind J. Allen