Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Bhattacharjee, Arunima; Velickovic, Dusan; Wietsma, Thomas W.; Bell, Sheryl L.; Jansson, Janet K.; Hofmockel, Kirsten S.; Anderton, Christopher R.; Wilmes, ed., Paul

doi:10.1128/mSystems.00645-19

Title: Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Abstract

Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.

Authors:

Bhattacharjee, Arunima; Velickovic, Dusan; Wietsma, Thomas W.; Bell, Sheryl L.; Jansson, Janet K.; Hofmockel, Kirsten S.;

; Wilmes, ed., Paul

Publication Date:: 2020-02-11

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1598721

Alternate Identifier(s):: OSTI ID: 1600533

Report Number(s):: PNNL-SA-147223
Journal ID: ISSN 2379-5077; e00645-19

Grant/Contract Number:: AC05-76RL01830

Resource Type:: Published Article

Journal Name:: mSystems

Additional Journal Information:: Journal Name: mSystems Journal Volume: 5 Journal Issue: 1; Journal ID: ISSN 2379-5077

Publisher:: American Society for Microbiology

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Bhattacharjee, Arunima, Velickovic, Dusan, Wietsma, Thomas W., Bell, Sheryl L., Jansson, Janet K., Hofmockel, Kirsten S., Anderton, Christopher R., and Wilmes, ed., Paul. Visualizing Microbial Community Dynamics via a Controllable Soil Environment.  United States: N. p., 2020. 
Web.  doi:10.1128/mSystems.00645-19.

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                    Bhattacharjee, Arunima, Velickovic, Dusan, Wietsma, Thomas W., Bell, Sheryl L., Jansson, Janet K., Hofmockel, Kirsten S., Anderton, Christopher R., & Wilmes, ed., Paul. Visualizing Microbial Community Dynamics via a Controllable Soil Environment.  United States.  https://doi.org/10.1128/mSystems.00645-19

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                    Bhattacharjee, Arunima, Velickovic, Dusan, Wietsma, Thomas W., Bell, Sheryl L., Jansson, Janet K., Hofmockel, Kirsten S., Anderton, Christopher R., and Wilmes, ed., Paul. Tue .  
"Visualizing Microbial Community Dynamics via a Controllable Soil Environment".  United States.  https://doi.org/10.1128/mSystems.00645-19.

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@article{osti_1598721,

  title        = {Visualizing Microbial Community Dynamics via a Controllable Soil Environment},

  author       = {Bhattacharjee, Arunima and Velickovic, Dusan and Wietsma, Thomas W. and Bell, Sheryl L. and Jansson, Janet K. and Hofmockel, Kirsten S. and Anderton, Christopher R. and Wilmes, ed., Paul},

  abstractNote = {Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.},

  doi          = {10.1128/mSystems.00645-19},

  journal      = {mSystems},

  number       = 1,

  volume       = 5,

  place        = {United States},

  year         = {2020},

  month        = {2}

}

Copy to clipboard

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Title: Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Abstract

Citation Formats

Fluorescence microscopy for visualization of soil microorganisms?a review journal, April 2004

Assessing the Relative Effects of Geographic Location and Soil Type on Microbial Communities Associated with Straw Decomposition journal, March 2013

Imaging mass spectrometry in microbiology journal, August 2011

Enhanced Drought Stress Tolerance by the Arbuscular Mycorrhizal Symbiosis in a Drought-Sensitive Maize Cultivar Is Related to a Broader and Differential Regulation of Host Plant Aquaporins than in a Drought-Tolerant Cultivar journal, June 2017

Challenges and Approaches in Microbiome Research: From Fundamental to Applied journal, August 2018

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device journal, December 2006

Impacts of Carbon and Flooding on Soil Microbial Communities: Phospholipid Fatty Acid Profiles and Substrate Utilization Patterns journal, May 1998

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development journal, May 2017

Selection, Succession, and Stabilization of Soil Microbial Consortia journal, May 2019

Characterization of Chitin and Its Hydrolysis to GlcNAc and GlcN journal, July 2008

The hydrolysis of chitin by concentrated hydrochloric acid, and the preparation of low-molecular-weight substrate for lysozyme journal, November 1964

Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification journal, February 2019

Bacterial chitin degradation—mechanisms and ecophysiological strategies journal, January 2013

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil journal, November 2005

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Mass Spectrometry Imaging of Complex Microbial Communities journal, December 2016

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale journal, June 2009

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A facile bottom-up route to self-assembled biogenic chitin nanofibers journal, January 2010

Oxygen diffusion in soils: Understanding the factors and processes needed for modeling journal, January 2015

Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy journal, March 2014

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway) journal, February 2016

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments journal, June 2017

Complementary analysis of lipids in whole bacteria cells by thermally assisted hydrolysis and methylation-GC and MALDI-MS combined with on-probe sample pretreatment journal, October 2006

The soil microbiome — from metagenomics to metaphenomics journal, June 2018

Histology-Compatible MALDI Mass Spectrometry Based Imaging of Neuronal Lipids for Subsequent Immunofluorescent Staining journal, April 2017

Influence of Arbuscular mycorrhiza fungi (AMF) on drought tolerance and charcoal rot disease of cowpea journal, March 2017

Bacterial chitinases and chitin-binding proteins as virulence factors journal, March 2013

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression journal, May 2018

Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry journal, September 2016

New insights into the structural and spatial variability of cell-wall polysaccharides during wheat grain development, as revealed through MALDI mass spectrometry imaging journal, March 2014

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A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples journal, January 2017

Chitinolytic Microorganisms and Their Possible Application in Environmental Protection journal, August 2013

Fluorescence microscopy for visualization of soil microorganisms?a review
journal, April 2004

Assessing the Relative Effects of Geographic Location and Soil Type on Microbial Communities Associated with Straw Decomposition
journal, March 2013

Imaging mass spectrometry in microbiology
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Enhanced Drought Stress Tolerance by the Arbuscular Mycorrhizal Symbiosis in a Drought-Sensitive Maize Cultivar Is Related to a Broader and Differential Regulation of Host Plant Aquaporins than in a Drought-Tolerant Cultivar
journal, June 2017

Challenges and Approaches in Microbiome Research: From Fundamental to Applied
journal, August 2018

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device
journal, December 2006

Impacts of Carbon and Flooding on Soil Microbial Communities: Phospholipid Fatty Acid Profiles and Substrate Utilization Patterns
journal, May 1998

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development
journal, May 2017

Selection, Succession, and Stabilization of Soil Microbial Consortia
journal, May 2019

Characterization of Chitin and Its Hydrolysis to GlcNAc and GlcN
journal, July 2008

The hydrolysis of chitin by concentrated hydrochloric acid, and the preparation of low-molecular-weight substrate for lysozyme
journal, November 1964

Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification
journal, February 2019

Bacterial chitin degradation—mechanisms and ecophysiological strategies
journal, January 2013

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil
journal, November 2005

Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures
journal, January 2016

METLIN: A Metabolite Mass Spectral Database
journal, January 2005

Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces
journal, September 2017

Rapid Microbial Identification and Antibiotic Resistance Detection by Mass Spectrometric Analysis of Membrane Lipids
journal, November 2018

Matrix Optical Absorption in UV-MALDI MS
journal, November 2017

Mass Spectrometry Imaging of Complex Microbial Communities
journal, December 2016

Soil oxygen availability and biogeochemistry along rainfall and topographic gradients in upland wet tropical forest soils
journal, March 1999

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
journal, June 2009

Spatio-temporal microbial community dynamics within soil aggregates
journal, May 2019

Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities
journal, February 2013

Visualization and quantification of the cellular and extracellular components of Salmonella Agona biofilms at different stages of development
journal, July 2018

A facile bottom-up route to self-assembled biogenic chitin nanofibers
journal, January 2010

Oxygen diffusion in soils: Understanding the factors and processes needed for modeling
journal, January 2015

Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy
journal, March 2014

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway)
journal, February 2016

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments
journal, June 2017

Complementary analysis of lipids in whole bacteria cells by thermally assisted hydrolysis and methylation-GC and MALDI-MS combined with on-probe sample pretreatment
journal, October 2006

The soil microbiome — from metagenomics to metaphenomics
journal, June 2018

Histology-Compatible MALDI Mass Spectrometry Based Imaging of Neuronal Lipids for Subsequent Immunofluorescent Staining
journal, April 2017

Influence of Arbuscular mycorrhiza fungi (AMF) on drought tolerance and charcoal rot disease of cowpea
journal, March 2017

Bacterial chitinases and chitin-binding proteins as virulence factors
journal, March 2013

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression
journal, May 2018

Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry
journal, September 2016

New insights into the structural and spatial variability of cell-wall polysaccharides during wheat grain development, as revealed through MALDI mass spectrometry imaging
journal, March 2014

Primer on Agar-Based Microbial Imaging Mass Spectrometry
journal, July 2012

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples
journal, January 2017

Chitinolytic Microorganisms and Their Possible Application in Environmental Protection
journal, August 2013