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      Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates

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          Abstract

          Particulate carbon (C) degradation in soils is a critical process in the global C cycle governing greenhouse gas fluxes and C storage. Millimeter-scale soil aggregates impose strong controls on particulate C degradation by inducing chemical gradients of e.g. oxygen, as well as limiting microbial mobility in pore structures. To date, experimental models of soil aggregates have incorporated porosity and chemical gradients but not particulate C. Here, we demonstrate a proof-of-concept encapsulating microbial cells and particulate C substrates in hydrogel matrices as a novel experimental model for soil aggregates. Ruminiclostridium cellulolyticum was co-encapsulated with cellulose in millimeter-scale polyethyleneglycol-dimethacrylate (PEGDMA) hydrogel beads. Microbial activity was delayed in hydrogel-encapsulated conditions, with cellulose degradation and fermentation activity being observed after 13 days of incubation. Unexpectedly, hydrogel encapsulation shifted product formation of R. cellulolyticum from an ethanol-lactate-acetate mixture to an acetate-dominated product profile. Fluorescence microscopy enabled simultaneous visualization of the PEGDMA matrix, cellulose particles, and individual cells in the matrix, demonstrating growth on cellulose particles during incubation. Together, these microbe-cellulose-PEGDMA hydrogels present a novel, reproducible experimental soil surrogate to connect single cells to process outcomes at the scale of soil aggregates and ecosystems.

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          Biofilms: an emergent form of bacterial life.

          Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.
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            Scientists’ warning to humanity: microorganisms and climate change

            In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial ‘unseen majority’. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
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              Mineral protection of soil carbon counteracted by root exudates

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                Author and article information

                Contributors
                Journal
                ISME Commun
                ISME Commun
                ismecommun
                ISME Communications
                Oxford University Press
                2730-6151
                2730-6151
                January 2024
                04 May 2024
                04 May 2024
                : 4
                : 1
                : ycae068
                Affiliations
                Civil and Environmental Engineering, University of Washington , 201 More Hall, Seattle, WA 98195-2700, United States
                Laboratory of Systems and Synthetic Biology, Wageningen University & Research , 6708 WE, Wageningen, The Netherlands
                Laboratory of Systems and Synthetic Biology , Wageningen University & Research, 6708 WE, Wageningen, The Netherlands. E-mail: pieter.candry@ 123456wur.nl
                Civil and Environmental Engineering, University of Washington , 201 More Hall, Seattle, WA 98195-2700, United States
                Civil and Environmental Engineering, University of Washington , 201 More Hall, Seattle, WA 98195-2700, United States
                Author notes
                Corresponding author: Pieter Candry, Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA 98195-2700, United States. Email: pcandry@ 123456uw.edu
                Article
                ycae068
                10.1093/ismeco/ycae068
                11126157
                38800124
                27a83e68-35af-4337-8a8a-c0ff8da2eee1
                © The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 11 January 2024
                : 12 April 2024
                : 03 May 2024
                : 22 May 2024
                Page count
                Pages: 9
                Funding
                Funded by: US Department of Energy, Office of Science, Office of Biological & Environmental Research;
                Award ID: #DE-SC0020356
                Categories
                Original Article
                AcademicSubjects/SCI00010
                AcademicSubjects/SCI00960
                AcademicSubjects/SCI01150
                AcademicSubjects/SCI02281

                experimental model,carbon cycling,soil microbiology
                experimental model, carbon cycling, soil microbiology

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