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      Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations

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          Abstract

          Microbial populations often experience fluctuations in nutrient complexity in their natural environment such as between high molecular weight polysaccharides and simple monosaccharides. However, it is unclear if cells can adopt growth behaviors that allow individuals to optimally respond to differences in nutrient complexity. Here, we directly control nutrient complexity and use quantitative single-cell analysis to study the growth dynamics of individuals within populations of the aquatic bacterium Caulobacter crescentus. We show that cells form clonal microcolonies when growing on the polysaccharide xylan, which is abundant in nature and degraded using extracellular cell-linked enzymes; and disperse to solitary growth modes when the corresponding monosaccharide xylose becomes available or nutrients are exhausted. We find that the cellular density required to achieve maximal growth rates is four-fold higher on xylan than on xylose, indicating that aggregating is advantageous on polysaccharides. When collectives on xylan are transitioned to xylose, cells start dispersing, indicating that colony formation is no longer beneficial and solitary behaviors might serve to reduce intercellular competition. Our study demonstrates that cells can dynamically tune their behaviors when nutrient complexity fluctuates, elucidates the quantitative advantages of distinct growth behaviors for individual cells and indicates why collective growth modes are prevalent in microbial populations.

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          Most cited references40

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          Physiological heterogeneity in biofilms.

          Biofilms contain bacterial cells that are in a wide range of physiological states. Within a biofilm population, cells with diverse genotypes and phenotypes that express distinct metabolic pathways, stress responses and other specific biological activities are juxtaposed. The mechanisms that contribute to this genetic and physiological heterogeneity include microscale chemical gradients, adaptation to local environmental conditions, stochastic gene expression and the genotypic variation that occurs through mutation and selection. Here, we discuss the processes that generate chemical gradients in biofilms, the genetic and physiological responses of the bacteria as they adapt to these gradients and the techniques that can be used to visualize and measure the microscale physiological heterogeneities of bacteria in biofilms.
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            Bacteria and archaea on Earth and their abundance in biofilms

            Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.
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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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                Author and article information

                Contributors
                glengeralddsouza@gmail.com
                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group UK (London )
                1751-7362
                1751-7370
                17 March 2021
                17 March 2021
                September 2021
                : 15
                : 9
                : 2614-2626
                Affiliations
                [1 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Department of Environmental Systems Sciences, Microbial Systems Ecology Group, Institute of Biogeochemistry and Pollutant Dynamics, , ETH-Zurich, ; Zurich, Switzerland
                [2 ]Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf, Switzerland
                [3 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Department of Civil, Environmental and Geomatic Engineering, , Institute of Environmental Engineering, ETH Zurich, ; Zurich, Switzerland
                Author information
                http://orcid.org/0000-0002-9123-101X
                http://orcid.org/0000-0002-8877-4881
                http://orcid.org/0000-0002-3199-0508
                Article
                953
                10.1038/s41396-021-00953-7
                8397785
                33731836
                b7030001-b576-4a2b-aa99-0089b58b15a0
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 September 2020
                : 18 February 2021
                : 25 February 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000893, Simons Foundation;
                Award ID: 542395
                Award ID: 542389
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100003006, Eidgenössische Technische Hochschule Zürich (Federal Institute of Technology Zurich);
                Funded by: FundRef https://doi.org/10.13039/501100011718, Federal Institute of Technology Zurich | Eidgenössische Anstalt für Wasserversorgung Abwasserreinigung und Gewässerschutz (Swiss Federal Institute of Aquatic Science and Technology);
                Funded by: FundRef https://doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation);
                Award ID: 310030_188642
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s), under exclusive licence to International Society for Microbial Ecology 2021

                Microbiology & Virology
                microbial ecology,water microbiology,biofilms
                Microbiology & Virology
                microbial ecology, water microbiology, biofilms

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