Observing root growth and signalling responses to stress gradients and pathogens using the bi-directional dual-flow RootChip

Claudia Allan, Yiling Sun, Stephen C. Whisson, Michael Porter, Petra C. Boevink, Volker Nock and Claudia-Nicole Meisrimler

Lab Chip, 2024, 24, 5360
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Exploring the intricacies of plant growth promoting rhizobacteria interactions: an omics review

Kamogelo Mmotla, Nompumelelo R. Sibanyoni, Farhahna Allie, Lungile Sitole, Thendo Mafuna, Manamele D. Mashabela and Msizi I. Mhlongo

Ann Microbiol, 2025, 75
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Controlling matric potential in microfluidics to examine microbial dynamics in unsaturated porous media

Shane M. Franklin, Scott T. Retterer, Amber N. Bible and Jennifer L. Morrell-Falvey

Soil Biology and Biochemistry, 2025, 210, 109916
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Fabricated devices for performing bacterial-fungal interaction experiments across scales

Julia M. Kelliher, Leah Y. D. Johnson, Aaron J. Robinson, Reid Longley, Buck T. Hanson, Guillaume Cailleau, Saskia Bindschedler, Pilar Junier and Patrick S. G. Chain

Front. Microbiol., 2024, 15
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Advances in Microfluidics: Technical Innovations and Applications in Diagnostics and Therapeutics

Guillaume Aubry, Hyun Jee Lee and Hang Lu

Anal. Chem., 2023, 95, 444
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Studying root–environment interactions in structured microdevices

Christian-Frederic Kaiser, Alessia Perilli, Guido Grossmann, Yasmine Meroz and Ivan Reyna-Llorens

Journal of Experimental Botany, 2023, 74, 3851
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Hierarchical Structure of the Program Used by Filamentous Fungi to Navigate in Confining Microenvironments

Gala Montiel-Rubies, Marie Held, Kristi L. Hanson, Dan V. Nicolau, Radu C. Mocanasu, Falco C. M. J. M. van Delft and Dan V. Nicolau

Biomimetics, 2025, 10, 287
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Dynamic in situ detection in iRhizo-Chip reveals diurnal fluctuations of Bacillus subtilis in the rhizosphere

Hengyi Dai, Binbin Wu, Yajuan Zhuang, Hao Ren, Yanbo Chen, Fangzhou Zhang, Chiheng Chu, Xiaofei Lv, Jianming Xu and Bin Ma

Proc. Natl. Acad. Sci. U.S.A., 2024, 121
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Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Bruce J. Palmer, Connah G. M. Johnson, Ann S. Almgren, Andrew T. Myers and William R. Cannon

Phys. Rev. E, 2025, 112
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Spatiotemporal control of root immune responses during microbial colonization

Huei-Hsuan Tsai, Jiachang Wang, Niko Geldner and Feng Zhou

Current Opinion in Plant Biology, 2023, 74, 102369
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Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Is Required in Bradyrhizobium diazoefficiens for Efficient Soybean Root Colonization and Competition for Nodulation

Rocío S. Balda, Carolina Cogo, Ornella Falduti, Florencia M. Bongiorno, Damián Brignoli, Tamara J. Sandobal, María Julia Althabegoiti and Aníbal R. Lodeiro

Plants, 2024, 13, 2362
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Emerging sensing, imaging, and computational technologies to scale nano-to macroscale rhizosphere dynamics – Review and research perspectives

Amir H. Ahkami, Odeta Qafoku, Tiina Roose, Quanbing Mou, Yi Lu, Zoe G. Cardon, Yuxin Wu, Chunwei Chou, Joshua B. Fisher, Tamas Varga, Pubudu Handakumbura, Jayde A. Aufrecht, Arunima Bhattacharjee and James J. Moran

Soil Biology and Biochemistry, 2024, 189, 109253
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Achieving Extra-High-Quality Images in ToF-SIMS Molecular Imaging of Insulating Samples Using a Low Current O2+ Auxiliary Beam and Back Side Au Coating

Yadong Zhou, Jeffrey A. Dhas, Mengxue Xia, Vidya Suseela, Hsin-Mei Kao, R. Matthew Asmussen, Arunima Bhattacharjee, Courtney A. Creamer, Min Liu, Jun-Gang Wang and Zihua Zhu

Anal. Chem., 2025, 97, 8755
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Dynamic nitrogen fixation in an aerobic endophyte of Populus

Andrew W Sher, Jayde A Aufrecht, Daisy Herrera, Amy E Zimmerman, Young-Mo Kim, Nathalie Munoz, Jesse B Trejo, Vanessa L Paurus, John B Cliff, Dehong Hu, William B Chrisler, Robert J Tournay, Emma Gomez-Rivas, Galya Orr, Amir H Ahkami and Sharon L Doty

The ISME Journal, 2024, 18
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Smart soils track the formation of pH gradients across the rhizosphere

Daniel Patko, Qizhi Yang, Yangminghao Liu, Panagiotis Falireas, Benoit Briou, Bhausaheb V. Tawade, Timothy S. George, Tim J. Daniell, Michael P. MacDonald, Vincent Ladmiral, Bruno Ameduri and Lionel X. Dupuy

Plant Soil, 2024, 500, 91
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Insight into industrial hemp (Cannabis sativa L.) root exudation composition in a simulated soil environment: a rhizosphere-on-a-chip study

Idowu A. Atoloye, Daisy Herrera, Dusan Veličković, Chaevien S. Clendinen, Kylee Tate, Arunima Bhattacharjee, Jayde Aufrecht, Ting Zeng, Dipti Rai and Arnab Bhowmik

Rhizosphere, 2025, 34, 101099
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Synthetic soil microcosms as emerging model systems to study the rhizosphere

Andrew Mair, Daniel Patko, Yangminghao Liu, Ilonka Engelhardt and Lionel X. Dupuy

Plant Soil, 2025
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Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpa

Manasa R. Appidi, Sameer Mudbhari, Kevin Cope, Sara S. Jawdy, Dana L. Carper, Edanur Öksüz, Xianghu Wang, Timothy Tschaplinski, Mingxun Wang, Robert L. Hettich, Udaya Kalluri and Paul E. Abraham

Plant Cell & Environment, 2025
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Spatiotemporal dynamics of reactive oxygen species and its effect on beta-blockers’ degradation in aquatic plants’ rhizosphere

He Ji, Jingwen Li, Diga Gang, Hongwei Yu, Hanzhong Jia, Chengzhi Hu and Jiuhui Qu

Journal of Hazardous Materials, 2024, 476, 135146
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Legacy effects of rhizodeposits on soil microbiomes: A perspective

Paolo Nannipieri, S. Emilia Hannula, Giacomo Pietramellara, Michael Schloter, Tom Sizmur and Shamina Imran Pathan

Soil Biology and Biochemistry, 2023, 184, 109107
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Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Laura K Quinn, Kriti Sharma, Katherine T Faber, Victoria J Orphan and Peter Fratzl

PNAS Nexus, 2025, 4
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Harnessing the plant microbiome for environmental sustainability: From ecological foundations to novel applications

Jing-Ru Hao, Yan Li and Yuan Ge

Science of The Total Environment, 2024, 951, 175766
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Advances in microfluidic plant biotechnology: From single cells to mature plants

Víctor Marín-Lizarraga, Luis F. Núñez-Becerril and Clelia De-la-Peña

Process Biochemistry, 2024, 146, 560
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Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments

Emily M. Lacroix, Meret Aeppli, Kristin Boye, Eoin Brodie, Scott Fendorf, Marco Keiluweit, Hannah R. Naughton, Vincent Noël and Debjani Sihi

ACS Earth Space Chem., 2023, 7, 1592
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RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere

Dušan Veličković, Tanya Winkler, Vimal Balasubramanian, Thomas Wietsma, Christopher R. Anderton, Amir H. Ahkami and Kevin Zemaitis

Plant Methods, 2024, 20
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Microbial drivers of root plasticity

Francisco Dini‐Andreote, Darren M. Wells, Jonathan A. Atkinson, Brian S. Atkinson, Omri M. Finkel and Gabriel Castrillo

New Phytologist, 2025, 248, 52
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From rhizosphere to detritusphere – Soil structure formation driven by plant roots and the interactions with soil biota

Carsten W. Mueller, Vera Baumert, Andrea Carminati, Amandine Germon, Maire Holz, Ingrid Kögel-Knabner, Stephan Peth, Steffen Schlüter, Daniel Uteau, Doris Vetterlein, Pedro Teixeira and Alix Vidal

Soil Biology and Biochemistry, 2024, 193, 109396
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In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry

Courtney L. Walton, Muneeba Khalid, Amber N. Bible, Vilmos Kertesz, Scott T. Retterer, Jennifer Morrell-Falvey and John F. Cahill

J. Am. Soc. Mass Spectrom., 2022, 33, 1615
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Spatial and temporal detection of root exudates with a paper-based microfluidic device

Daniel Patko, Udara Bimendra Gunatilake, Belen Gonzalez-Gaya, Lionel X. Dupuy, Lourdes Basabe-Desmonts and Fernando Benito-Lopez

Soil Biology and Biochemistry, 2024, 195, 109456
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Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots

Shwetha M Acharya, Mon Oo Yee, Spencer Diamond, Peter F Andeer, Nameera F Baig, Omolara T Aladesanmi, Trent R Northen, Jillian F Banfield and Romy Chakraborty

ISME Communications, 2023, 3
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Probing Mineral-Organic Interfaces in Soils and Sediments Using Optical Photothermal Infrared Microscopy

Floriane Jamoteau, Mustafa Kansiz, Miriam Unger and Marco Keiluweit

Environ. Sci. Technol., 2025, 59, 501
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Microcosm fabrication platform for live microscopy of plant-soil systems

Yangminghao Liu, Daniel Patko, Alberto Lora de la Mata, Xingshui Dong, Emma Gomez Peral, Xinhua He, Bruno Ameduri, Vincent Ladmiral, Michael P. MacDonald and Lionel X. Dupuy

Biosystems Engineering, 2025, 252, 105
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Automated high-content image-based characterization of microorganism behavioral diversity and distribution

Carlotta Aurora Lupatelli, Agnes Attard, Marie-Line Kuhn, Celine Cohen, Philippe Thomen, Xavier Noblin and Eric Galiana

Computational and Structural Biotechnology Journal, 2023, 21, 5640
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