{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T19:47:33Z","timestamp":1782416853107,"version":"3.54.5"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":148,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"SNSF Sinergia","award":["CRSII5_213522"],"award-info":[{"award-number":["CRSII5_213522"]}]},{"name":"SNSF Scientific Exchange","award":["IZSEZ0_221465"],"award-info":[{"award-number":["IZSEZ0_221465"]}]},{"name":"Matterhorn"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Microorganisms in nature are often found in porous confined environments (soils, sediments, or plant and animal tissues), self-organized in heterogeneous communities. Such an organization, resulting from complex interactions and self-generated steep chemical gradients, controls the emergent microbial community\u2019s ecological functions. The combination of microfluidics, fluorescent bacteria, and optical sensing can constitute a powerful tool to achieve new insights into these microbial dynamics. However, such a combination has remained challenging so far due to the limited compatibility of the current sensing approaches and fluorescent reporters. Here, we present a sensing microfluidic platform that enables simultaneous, real-time visualization of microscale oxygen gradients and multi-strain microbial community organization under flow. The approach combines transparent microfluidic devices, genetically encoded fluorescent bacteria, and the latest generation of near-infrared (NIR) luminescent oxygen sensors. We demonstrate that NIR oxygen sensing allows interference-free mapping of oxygen concentrations alongside GFP and mScarlet-I-labeled bacteria. Applying this platform to a heterogeneous porous geometry, we track the co-development of oxygen gradients and spatial organization in a two-strain Pseudomonas community under flowing conditions. The two strains exhibit distinct microscale spatial patterns consistent with known shape-dependent attachment and growth dynamics, while inducing sharp oxygen gradient formation. This work establishes a broadly accessible experimental framework for quantitatively linking microbial self-organization to chemical microenvironments in real time. This platform is cost-effective, customizable, and adaptable to sense different analytes, while being compatible with a range of spectrometry techniques. Therefore, this methodology opens new avenues for investigating microscale ecological processes in soils, sediments, and other confined habitats.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag146","type":"journal-article","created":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T11:41:01Z","timestamp":1779882061000},"source":"Crossref","is-referenced-by-count":0,"title":["Simultaneous real-time imaging of oxygen gradients and in vivo microbial community spatial organization in confined environments"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4998-7921","authenticated-orcid":false,"given":"Giulia","family":"Ceriotti","sequence":"first","affiliation":[{"name":"Institute of Earth Surface Dynamics, Faculty of Geoscience and Environment, University of Lausanne , 1015 Lausanne ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9318-8273","authenticated-orcid":false,"given":"Sergey M","family":"Borisov","sequence":"additional","affiliation":[{"name":"Institute of Analytical Chemistry and Food Chemistry , Faculty of Technical Chemistry, Chemical and Process Engineering and Biotechnology, Graz University of Technology, 8010 Graz ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"2026062515064300900_ref1","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/s42254-025-00849-x","article-title":"On the growth and form of bacterial colonies","volume":"7","author":"Porter","year":"2025","journal-title":"Nature Reviews Physics"},{"key":"2026062515064300900_ref2","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/s41579-019-0158-9","article-title":"Bacteria and archaea on earth and their abundance in biofilms","volume":"17","author":"Flemming","year":"2019","journal-title":"Nat Rev 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