Article
Chemistry, Multidisciplinary
Haoqiang Feng, Shitao Shen, Mingliang Jin, Qilin Zhang, Mengjun Liu, Zihao Wu, Jiamei Chen, Zichuan Yi, Guofu Zhou, Lingling Shui
Summary: This work proposes a method for rapid formation of uniform droplet array called electro-coalescence droplet array (ECDA). The electro-coalescence of droplets is achieved by polarization induced electrostatic and dielectrophoretic forces, and the dielectrowetting effect. Photolithographically fabricated microwells ensure identical volume and physical confinement to achieve uniform droplet array, and microwell isolation protects the paired water droplets from fusion. The optimized ECDA is successfully applied for various microwell geometries and functional materials, and shows potential for high-throughput screening and analysis.
Article
Ecology
Anette Teittinen, Jianjun Wang, Janne Soininen
Summary: Knowledge of elevational and beta diversity patterns in microorganisms in sensitive aquatic ecosystems at high latitudes is limited. This study investigated elevational and beta diversity patterns for three biofilm microbial groups in subarctic freshwater ponds. The results showed that community dissimilarities increased with increasing environmental or elevational distances, with pH being the most important variable. Mean community dissimilarities generally decreased with elevation. The communities were influenced by both deterministic and stochastic processes, with the influence of deterministic processes being stronger at higher elevations.
FRESHWATER BIOLOGY
(2023)
Article
Biodiversity Conservation
Yuan Xu, Xinyi Chen, Caio Graco-Roza, Janne Soininen
Summary: This study found that the assembly processes of bacterial communities are scale-dependent, with deterministic processes dominating at the local scale and dispersal limitation dominating at regional and subcontinental scales. In contrast, fungal community assembly is consistently driven by drift across all spatial scales. These findings highlight the importance of adopting a multi-scale approach to understanding the complex spatial patterns of microbial communities.
Article
Microbiology
Nana Liu, Huifeng Hu, Wenhong Ma, Ye Deng, Qinggang Wang, Ao Luo, Jiahui Meng, Xiaojuan Feng, Zhiheng Wang
Summary: This study investigates the deterministic and stochastic processes shaping the taxonomic and phylogenetic beta-diversity of soil microbes in temperate grasslands in northern China. The results indicate that soil microbial beta-diversity is influenced by various factors such as soil depth, species abundance, and phylogenetic turnover.
Article
Microbiology
Kristin Aleklett, Daniel Rosa, Brian John Pickles, Miranda M. Hart
Summary: Little is known about the impact of plant life events on the composition of the plant microbiome. This study manipulated the timing of microbial exposure and the priority effects of early colonizers to investigate their effects on the root microbiota in mature plants. The results showed that the timing of soil exposure in the early life stages of a plant plays an important role in the development of the root microbiota in mature plants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Madison D. Bygd, Kelly G. Aukema, Jack E. Richman, Lawrence P. Wackett
Summary: Thousands of organofluorine chemicals are known to be persistent and toxic environmental pollutants, but few bacteria biodegrade fluorinated chemicals. A rapid screening method was developed to discover new organofluoride biodegradation, revealing 21 new microbial defluorination reactions. A general mechanism was delineated for the biodegradation of trifluoromethylphenyl groups that are increasingly being used in drugs and pesticides.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Lloyd D. Potts, Alex Douglas, Luis J. Perez Calderon, James A. Anderson, Ursula Witte, James Prosser, Cecile Gubry-Rangin
Summary: Acute environmental perturbations cause changes in microbial community composition and selection of different phylotypes, while chronic perturbations maintain community stability and can lead to the establishment of alternative stable states. This study also demonstrates the functional resilience of ecosystem following environmental perturbations.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Microbiology
Chuntao Yin, Juan M. Casa Vargas, Daniel C. Schlatter, Christina H. Hagerty, Scot H. Hulbert, Timothy C. Paulitz
Summary: Successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes, which may help address agronomic concerns associated with plant diseases and crop productivity.
Article
Environmental Sciences
Min Zhang, Teng Zhang, Lei Zhou, Wei Lou, Weiai Zeng, Tianbo Liu, Huaqun Yin, Hongwei Liu, Xueduan Liu, Krishnamurthy Mathivanan, Loganathan Praburaman, Delong Meng
Summary: This study found that heavy metal pollution significantly affected the diversity and composition of soil microbial communities. As heavy metal concentration increased, microbial community assembly tended to be more deterministic. The effects of heavy metal stress on the assembly process of different microbial groups were distinct.
ENVIRONMENTAL RESEARCH
(2022)
Article
Ecology
Zhang Gefei, Zhao Wenzhi, Wang Xiaofen
Summary: This study explores the impact of benefactor species on the assembly processes along a drought gradient. It found that functional diversity responds differently to benefactor species under drought stress. The microenvironment and soil moisture conditions created by shrub plants played a significant role in shaping trait distributions. However, these effects became less significant under extreme drought stress, coinciding with decreased positive interactions assessed by plant density and species diversity.
FUNCTIONAL ECOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Xin Lv, Songhe Zhang, Lisha Zhang, Shaozhuang Guo, Yu Ma, Tiantian Zhou
Summary: This study investigated nutrient transfer and microbial community shift during the decomposition of submerged macrophyte Hydrillaverticillata in flowing water and static water environments. The results showed that water flow stimulated cellulase activity and influenced nutrient transfer. Turnover affected microbial diversity, and water flow improved microbial community stability and altered the microbial food web.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Microbiology
Daniela F. Soto, Ivan Gomez, Pirjo Huovinen
Summary: The study investigates the ecological mechanisms governing the assembly of microbial communities during the formation of snow algae blooms in the West Antarctic Peninsula. The microbial composition and abundance were examined using metabarcoding techniques, and the contribution of different ecological processes to the microbial community assembly was quantified. The results show differences in microbial assembly between bacteria and eukaryotes in snow algae blooms and propose a model to integrate both assembly processes.
Article
Environmental Sciences
Jingjing Cui, Zhihao Yi, Dengbo Chen, Yuming Fu, Hong Liu
Summary: Under simulated microgravity, the bacterial community diversity and network complexity decreased during seed germination of wheat varieties. The relative abundance of certain bacterial families changed, and the levels of certain metabolites also showed significant changes. This study provides valuable insights into the effects of microgravity on bacterial assembly during seed germination and suggest potential strategies for improving plant adaptation to space cultivation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Soil Science
Laibin Huang, Junhong Bai, Junjing Wang, Guangliang Zhang, Wei Wang, Xin Wang, Ling Zhang, Yaqi Wang, Xinhui Liu, Baoshan Cui
Summary: This study investigated the assembly processes of bacterial and fungal communities in the topsoil of a wetland transect in the Yellow River Estuary, China. The results showed that stochastic processes primarily shaped the two communities, with bacterial assembly being controlled by homogenizing dispersal and dispersal limitation, and fungal assembly being mostly regulated by undominated processes.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Ecology
Janne Soininen
Summary: This study aimed to investigate the variation of stream diatom community assembly processes at different spatial scales. It was found that environmental filtering dominated the assembly of diatom communities, especially at small scales, while stochastic factors such as random dispersal and ecological drift became more influential at larger scales.
FRESHWATER BIOLOGY
(2023)
Article
Biochemical Research Methods
Jayde Aufrecht, Muneeba Khalid, Courtney L. Walton, Kylee Tate, John F. Cahill, Scott T. Retterer
Summary: The rhizosphere is a complex ecosystem with diverse characteristics, making it challenging to study. Microfluidic platforms have provided an alternative approach to studying rhizosphere organisms under reduced-complexity conditions. However, reducing complexity can lead to biases in laboratory data compared to real-life experiments. To restore some complexity, a rhizosphere-on-a-chip platform mimicking soil structure was developed.
Article
Polymer Science
Bin Hu, Jan-Michael Carrillo, Liam Collins, Kevin S. Silmore, Jong Keum, Peter Bonnesen, Yangyang Wang, Scott Retterer, Rajeev Kumar, Bradley S. Lokitz
Summary: A strategy for facile synthesis of bottlebrush block copolymers with flexible backbones was developed. The utility of this strategy was demonstrated by grafting end-functionalized PMMA and PS onto the dually reactive block copolymer PGMA-b-PVDMA. Experimental and computational analysis showed a relationship between glass transition temperature and chain end fraction, highlighting the potential of this method to tailor polymer properties. The study also revealed multiscale structures in the samples using X-ray scattering methods and molecular dynamics simulations. The modular approach can be extended to other grafts, providing a powerful tool for synthesizing novel bottlebrush block copolymers with desired properties.
Article
Chemistry, Multidisciplinary
Dong Zhou, Gang Feng, Henna Khosla, Scott T. Retterer, Bo Li
Summary: This study demonstrates a new strategy to suspend and test polymer single crystals by stacking them on a 2D material and suspending them over microholes. The in-plane moduli of the polymer single crystal and the 2D material are experimentally measured for the first time. This research provides key insights for accurately measuring the mechanical properties of polymer single crystals and their composites, as well as designing composite structures.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Biochemical Research Methods
Courtney L. Walton, Muneeba Khalid, Amber N. Bible, Vilmos Kertesz, Scott T. Retterer, Jennifer Morrell-Falvey, John F. Cahill
Summary: The plant rhizosphere is a complex environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the biological system. Exogenous compounds in the rhizosphere play a crucial role in plant-microbe interactions, growth and development, and the spatiotemporal distribution of molecular components. A methodology for in situ measurement of amino acids from bacterial biofilms and plant roots using liquid microjunction-surface sampling probe-mass spectrometry was successfully developed.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Physics, Applied
Dayne Y. Sasaki, Rajesh Chopdekar, Scott T. Retterer, Daniel Y. Jiang, Jeremy K. Mason, Michael S. Lee, Yayoi Takamura
Summary: This study investigates the stabilization of complex spin textures in thermally demagnetized artificial spin ice arrays through an appropriate selection of nanoisland width and interisland spacing. Micromagnetic simulations reveal the role of interisland dipolar interactions in the formation of these spin textures.
PHYSICAL REVIEW APPLIED
(2022)
Article
Chemistry, Multidisciplinary
Luoxi Tan, Haden L. Scott, Micholas Dean Smith, Sai Venkatesh Pingali, Hugh M. O'Neill, Jennifer L. Morrell-Falvey, John Katsaras, Jeremy C. Smith, Brian H. Davison, James G. Elkins, Jonathan D. Nickels
Summary: Biofuels are crucial for sustainable energy and optimizing their production is a societal and economic imperative. Reducing the toxicity of co-solvents can improve the efficiency of biofuel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Microbiology
Connor Robertson, Jared L. L. Wilmoth, Scott Retterer, Miguel Fuentes-Cabrera
Summary: The recent advancement in machine learning technologies has allowed for new analytical capabilities in microbiology, particularly in the field of predictive microbial growth. This paper introduces the use of a Recurrent Neural Network (RNN) trained on experimental data to accurately predict the growth of two Pseudomonas aeruginosa mutants. The accuracy of the predictions was evaluated using various metrics, such as image comparison and colony size, showing promising results but indicating a need for more comprehensive data in the literature for further validation.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Andrea C. C. Timm, Bryan Brensinger, Meaghan Hart, Collin Timm, David Karig
Summary: The assembly and function of microbial communities are influenced by various factors, including the local environment and the metabolic properties of the colonizing organisms. Chemical communication and secreted factors also play a role in the cooperative and competitive interactions between different microbial strains. The secretions of microbes can have both positive and negative effects on their respective hosts, and understanding these effects can provide insights into microbiome function and lead to new intervention strategies. A microfluidic device is developed to enable high-content screening of microbial secretion effects on adherent cell types, allowing for scalable analysis of complex microbial communities and diverse host tissues.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Jaime Lorenzo N. Dinglasan, Tien T. Sword, J. William Barker, Mitchel J. Doktycz, Constance B. Bailey
Summary: Lysate-based cell-free expression systems provide a means to express complex proteins, such as nonribosomal peptide synthetases (NRPSs), which are difficult to synthesize in vivo. This study describes a reporter system for optimizing NRPS expression in E. coli lysate reactions. The optimized conditions enable higher product yield and improved expression of other monomodular NRPSs. Tailored reporters for specific enzyme classes are necessary for optimizing expression in lysate-based systems. These findings have important implications for complex enzyme synthesis and natural product discovery.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Samuel G. V. Charlton, Amber N. Bible, Eleonora Secchi, Jennifer L. Morrell-Falvey, Scott T. Retterer, Thomas P. Curtis, Jinju Chen, Saikat Jana
Summary: Biofilms are bacterial communities structured within an extracellular matrix, which plays a role in controlling their architecture and mechanical resistance. The research investigates the correlation between biofilm structure and viscoelastic response by comparing biofilms of Pantoea sp. (WT) and a mutant (& UDelta;UDP) with reduced exopolysaccharide production.
Article
Biochemical Research Methods
Jaime Lorenzo N. Dinglasan, Mitchel J. Doktycz
Summary: Cell-free systems can expedite biomanufacturing processes by bypassing troublesome requirements associated with live cells. The lack of survival objectives and the open nature of cell-free reactions allow for purposeful direction of metabolic flux. However, pathway crosstalk within endogenous lysate metabolism can compromise conversion yields by diverting carbon flow away from desired products.
Article
Microbiology
Daniel J. Wieczynski, Kristin M. Yoshimura, Elizabeth R. Denison, Stefan Geisen, Jennifer M. DeBruyn, A. Jonathan Shaw, David J. Weston, Dale A. Pelletier, Steven W. Wilhelm, Jean P. Gibert
Summary: We provide a roadmap for understanding the impact of viral infections within microbial food webs on ecosystem carbon and nutrient cycling in the context of global warming. Microorganisms play a crucial role in carbon and nutrient cycles and act as a link between ecosystems and climate. However, viral infections within complex microbial food webs pose a significant challenge in predicting and understanding ecosystem responses to warming. We highlight the need for further research on virus-microbe-temperature interactions and their effects on ecosystem functioning in the face of climate change.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Microbiology
Michelle C. Halsted, Amber N. Bible, Jennifer L. Morrell-Falvey, Scott T. Retterer
Summary: This study utilizes functionalized silanes and an image processing algorithm to quantitatively investigate early biofilm propagation. The results show that Pantoea sp. YR343 forms honeycomb-shaped biofilms on hydrophobic surfaces, with the morphology displaying logarithmic growth over time. The fliR mutant with flagella deficiency has reduced surface attachment, and the image processing algorithm effectively captures quantifiable differences between Pantoea WT and Delta fliR biofilm morphologies.
Article
Polymer Science
Bin Hu, Jan-Michael Carrillo, Liam Collins, Kevin S. Silmore, Jong Keum, Peter Bonnesen, Yangyang Wang, Scott Retterer, Rajeev Kumar, Bradley S. Lokitz
Summary: A strategy for facile synthesis of bottlebrush block copolymers with flexible backbones was developed, which demonstrated the potential to tailor polymer properties. By analyzing and simulating various copolymers, the relationship between the glass transition temperature and the fraction of chain ends was highlighted.
