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      Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments


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          Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.

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          Additive manufacturing (3D printing): A review of materials, methods, applications and challenges

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            A functional perspective on phenotypic heterogeneity in microorganisms.

            Most microbial communities consist of a genetically diverse assembly of different organisms, and the level of genetic diversity plays an important part in community properties and functions. However, biological diversity also arises at a lower level of biological organization, between genetically identical cells that reside in the same microenvironment. In this Review, I outline the molecular mechanisms responsible for phenotypic heterogeneity and discuss how phenotypic heterogeneity allows genotypes to persist in fluctuating environments. I also describe how it promotes interactions between phenotypic subpopulations in clonal groups, providing microbial groups with new functionality.
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              Interactions and self-organization in the soil-microbe complex.

              Soil is the most complicated biomaterial on the planet. As with any material, the physical habitat is of prime importance in determining and regulating biological activity. However, until recently the opaque nature of soil has meant that any interrogation of its interior architecture has been relatively rudimentary, restricted to simple qualitative expressions of the physical heterogeneity that fail to relate to any specific function. However, new techniques and insights into the biophysical and biochemical processes of this inner space are leading to the developments of theoretical frameworks and experimental approaches that will allow us to sustainably manage Earth's most important resource. We introduce the concept that the soil-microbe system is self-organized and suggest new priorities for research based on an integrative approach that combines biochemistry and biophysics.

                Author and article information

                Comput Struct Biotechnol J
                Comput Struct Biotechnol J
                Computational and Structural Biotechnology Journal
                Research Network of Computational and Structural Biotechnology
                01 October 2020
                01 October 2020
                : 18
                : 2860-2866
                [a ]School of Life Sciences, University of Nottingham, Nottingham, UK
                [b ]Faculty of Engineering, University of Nottingham, Nottingham, UK
                [c ]School of Biosciences, University of Nottingham, Nottingham, UK
                Author notes
                [* ]Corresponding author. Simon.Avery@ 123456nottingham.ac.uk
                © 2020 The Author(s)

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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