Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Nature Communications
Benedict BorerDani Or

Abstract

Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests that bacterial spatial organization contributes to the persistence of anoxic hotspots even in unsaturated soils. Such processes are difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks that mimics resource gradients postulated in soil aggregates to observe spatial organization of fluorescently tagged aerobic and facultative anaerobic bacteria. Two initially intermixed bacterial species, Pseudomonas putida and Pseudomonas veronii, segregate into preferential regions promoted by opposing gradients of carbon and oxygen (such persistent coexistence is not possible in well-mixed cultures). The study provides quantitative visualization and modeling of bacterial spatial organization within aggregate-like hotspots, a key step towards developing a mechanistic representation of bacterial community organization in soil pores.

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Citations

Dec 30, 2018·Proceedings of the National Academy of Sciences of the United States of America·Nick Vallespir Lowery, Tristan Ursell
May 30, 2020·Proceedings of the National Academy of Sciences of the United States of America·Joris HeymanTanguy Le Borgne
Mar 24, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Davide CiccareseDavid R Johnson
Mar 27, 2020·Journal of the Royal Society, Interface·David ScheidweilerPietro de Anna
May 23, 2019·The ISME Journal·Anja WorrichHauke Harms
Oct 10, 2020·Physical Biology·Ghazaleh OstovarJames Q Boedicker
Nov 3, 2020·Computational and Structural Biotechnology Journal·Harry J HarveySimon V Avery
Jan 26, 2021·Current Opinion in Biotechnology·Benedict Borer, Dani Or
Mar 19, 2019·Biotechnology Advances·Ryan TsoiLingchong You
Apr 24, 2021·Communications Biology·Manupriyam DubeyJan R van der Meer
May 1, 2021·Environmental Microbiome·Marian MoralesJan Roelof van der Meer
May 6, 2021·MSystems·Nana Y D AnkrahAngela E Douglas
Jul 22, 2021·Communications Biology·Paola Micaela Mafla-EndaraEdith C Hammer
Jul 6, 2021·FEMS Microbiology Ecology·Darian N SmercinaKirsten S Hofmockel
Nov 5, 2021·The ISME Journal·Dasith PereraMatthew Ramsey
Jan 6, 2022·Environmental Science & Technology·Xiangyu ZhuBaoliang Chen

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Methods Mentioned

BETA
fluorescence microscopy

Software Mentioned

AnalytiCal
Matlab
KNIME
KNIME Analytics platform
LAS
Leica Application Suite ( LAS )
KNIME Image Processing toolbox ( KNIP )
Mathematica
Leica Application Suite

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