In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation

Couradeau, Estelle; Felde, Vincent J. M. N. L.; Parkinson, Dilworth; Uteau, Daniel; Rochet, Alexis; Cuellar, Charlene; Winegar, Geoffrey; Peth, Stephan; Northen, Trent R.; Garcia-Pichel, Ferran

doi:10.3389/fenvs.2018.00065

Title: In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation

Authors:: Couradeau, Estelle; Felde, Vincent J. M. N. L.; Parkinson, Dilworth; Uteau, Daniel; Rochet, Alexis; Cuellar, Charlene; Winegar, Geoffrey; Peth, Stephan; Northen, Trent R.; Garcia-Pichel, Ferran

Publication Date:: 2018-06-28

Sponsoring Org.:: USDOE

OSTI Identifier:: 1457506

Grant/Contract Number:: AC02-05CH11231; 328530

Resource Type:: Published Article

Journal Name:: Frontiers in Environmental Science

Additional Journal Information:: Journal Name: Frontiers in Environmental Science Journal Volume: 6; Journal ID: ISSN 2296-665X

Publisher:: Frontiers Media SA

Country of Publication:: Switzerland

Language:: English

Citation Formats


                    Couradeau, Estelle, Felde, Vincent J. M. N. L., Parkinson, Dilworth, Uteau, Daniel, Rochet, Alexis, Cuellar, Charlene, Winegar, Geoffrey, Peth, Stephan, Northen, Trent R., and Garcia-Pichel, Ferran. In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation.  Switzerland: N. p., 2018. 
Web.  doi:10.3389/fenvs.2018.00065.

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                    Couradeau, Estelle, Felde, Vincent J. M. N. L., Parkinson, Dilworth, Uteau, Daniel, Rochet, Alexis, Cuellar, Charlene, Winegar, Geoffrey, Peth, Stephan, Northen, Trent R., & Garcia-Pichel, Ferran. In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation.  Switzerland.  https://doi.org/10.3389/fenvs.2018.00065

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                    Couradeau, Estelle, Felde, Vincent J. M. N. L., Parkinson, Dilworth, Uteau, Daniel, Rochet, Alexis, Cuellar, Charlene, Winegar, Geoffrey, Peth, Stephan, Northen, Trent R., and Garcia-Pichel, Ferran. Thu .  
"In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation".  Switzerland.  https://doi.org/10.3389/fenvs.2018.00065.

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@article{osti_1457506,

  title        = {In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation},

  author       = {Couradeau, Estelle and Felde, Vincent J. M. N. L. and Parkinson, Dilworth and Uteau, Daniel and Rochet, Alexis and Cuellar, Charlene and Winegar, Geoffrey and Peth, Stephan and Northen, Trent R. and Garcia-Pichel, Ferran},

  abstractNote = {},

  doi          = {10.3389/fenvs.2018.00065},

  journal      = {Frontiers in Environmental Science},

  number       = ,

  volume       = 6,

  place        = {Switzerland},

  year         = {2018},

  month        = {6}

}

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Title: In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation

Citation Formats

Influence of non-invasive X-ray computed tomography (XRCT) on the microbial community structure and function in soil journal, May 2013

Characterization and Biological Implications of Scytonemin, a Cyanobacterial Sheath Pigment1 journal, June 1991

Assessment of physical and hydrological properties of biological soil crusts using X-ray microtomography and modeling journal, January 2011

Microbial extracellular polymeric substances improve water retention in dryland biological soil crusts journal, January 2018

Functional Genomics of Novel Secondary Metabolites from Diverse Cyanobacteria Using Untargeted Metabolomics journal, September 2013

Dryland photoautotrophic soil surface communities endangered by global change journal, February 2018

Bacteria increase arid-land soil surface temperature through the production of sunscreens journal, January 2016

Localization of soil organic matter in soil aggregates using synchrotron-based X-ray microtomography journal, November 2014

Quantifying coupled deformation and water flow in the rhizosphere using X-ray microtomography and numerical simulations journal, November 2013

BoneJ: Free and extensible bone image analysis in ImageJ journal, December 2010

Pore characteristics in biological soil crusts are independent of extracellular polymeric substances journal, December 2016

Alteration of rocks by endolithic organisms is one of the pathways for the beginning of soils on Earth journal, February 2018

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data journal, October 2015

Water repellency and pore clogging at early successional stages of microbiotic crusts on inland dunes, Brandenburg, NE Germany journal, January 2010

What distinguishes cyanobacteria able to revive after desiccation from those that cannot: the genome aspect: Desiccation Resistance Genes in Cyanobacteria journal, August 2016

Three-Dimensional Quantification of Intra-Aggregate Pore-Space Features using Synchrotron-Radiation-Based Microtomography journal, January 2008

Terrestrial methane fluxes and Proterozoic climate journal, December 2017

Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm: HYDRAULIC PROPERTIES OF BIOFILM AMENDED SOIL journal, August 2016

Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil journal, May 2015

Organic matter from biological soil crusts induces the initial formation of sandy temperate soils journal, November 2014

Evaluation of soil aggregate microstructure and stability under wetting and drying cycles in two Ultisols using synchrotron-based X-ray micro-computed tomography journal, June 2015

Modern Terrestrial Sedimentary Biostructures and Their Fossil Analogs in Mesoproterozoic Subaerial Deposits journal, February 2014

Cyanobacterial crust types, as strategies for survival in extreme habitats journal, March 2009

Complex role of the polymeric matrix in biological soil crusts journal, October 2017

Effects of Root-Induced Compaction on Rhizosphere Hydraulic Properties - X-ray Microtomography Imaging and Numerical Simulations journal, January 2011

Hydrotaxis of Cyanobacteria in Desert Crusts journal, November 2003

The biogenicity of modern terrestrial roll-up structures and its significance for ancient life on land: Roll-ups as biosignatures journal, October 2010

Temperature Drives the Continental-Scale Distribution of Key Microbes in Topsoil Communities journal, June 2013

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust journal, June 2013

Extracellular Polymeric Substances Affecting Pore-Scale Hydrologic Conditions for Bacterial Activity in Unsaturated Soils journal, January 2007

Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils journal, November 2016

Nitrogen cycling in desert biological soil crusts across biogeographic regions in the Southwestern United States journal, March 2011

Exometabolite niche partitioning among sympatric soil bacteria journal, September 2015

TomoPy: a framework for the analysis of synchrotron tomographic data journal, August 2014

Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA journal, May 2007

Microbial secreted exopolysaccharides affect the hydrological behavior of induced biological soil crusts in desert sandy soils journal, January 2014

Water Retention Curves of Biofilm-Affected Soils using Xanthan as an Analogue journal, January 2012

Desiccation Tolerance of Prokaryotes: Application of Principles to Human Cells journal, November 2005

Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands journal, March 2007

The role of the exopolysaccharides in enhancing hydraulic conductivity of biological soil crusts journal, March 2012

Capturing 3D Water Flow in Rooted Soil by Ultra-fast Neutron Tomography journal, July 2017

Exposure to predicted precipitation patterns decreases population size and alters community structure of cyanobacteria in biological soil crusts from the Chihuahuan Desert: Changing rainfall effects on soil cyanobacteria journal, December 2017

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Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land journal, June 2009

A Computational Approach to Edge Detection journal, November 1986

Topological characterization of pore space in soil — sample preparation and digital image-processing journal, September 1996

Quantitative characterization of soil micro-aggregates: New opportunities from sub-micron resolution synchrotron X-ray microtomography journal, November 2017

X-ray micro-tomography at the Advanced Light Source conference, October 2012

The Evolution of a Capacity to Build Supra-Cellular Ropes Enabled Filamentous Cyanobacteria to Colonize Highly Erodible Substrates journal, November 2009

Marching cubes: A high resolution 3D surface construction algorithm conference, January 1987

A Threshold Selection Method from Gray-Level Histograms journal, January 1979

Role of Cyanobacterial Exopolysaccharides in Phototrophic Biofilms and in Complex Microbial Mats journal, April 2015

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics journal, January 2018

Soil stabilization by a prokaryotic desert crust: Implications for Precambrian land biota journal, September 1979

Influence of non-invasive X-ray computed tomography (XRCT) on the microbial community structure and function in soil
journal, May 2013

Characterization and Biological Implications of Scytonemin, a Cyanobacterial Sheath Pigment1
journal, June 1991

Assessment of physical and hydrological properties of biological soil crusts using X-ray microtomography and modeling
journal, January 2011

Microbial extracellular polymeric substances improve water retention in dryland biological soil crusts
journal, January 2018

Functional Genomics of Novel Secondary Metabolites from Diverse Cyanobacteria Using Untargeted Metabolomics
journal, September 2013

Dryland photoautotrophic soil surface communities endangered by global change
journal, February 2018

Bacteria increase arid-land soil surface temperature through the production of sunscreens
journal, January 2016

Localization of soil organic matter in soil aggregates using synchrotron-based X-ray microtomography
journal, November 2014

Quantifying coupled deformation and water flow in the rhizosphere using X-ray microtomography and numerical simulations
journal, November 2013

BoneJ: Free and extensible bone image analysis in ImageJ
journal, December 2010

Pore characteristics in biological soil crusts are independent of extracellular polymeric substances
journal, December 2016

Alteration of rocks by endolithic organisms is one of the pathways for the beginning of soils on Earth
journal, February 2018

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data
journal, October 2015

Water repellency and pore clogging at early successional stages of microbiotic crusts on inland dunes, Brandenburg, NE Germany
journal, January 2010

What distinguishes cyanobacteria able to revive after desiccation from those that cannot: the genome aspect: Desiccation Resistance Genes in Cyanobacteria
journal, August 2016

Three-Dimensional Quantification of Intra-Aggregate Pore-Space Features using Synchrotron-Radiation-Based Microtomography
journal, January 2008

Terrestrial methane fluxes and Proterozoic climate
journal, December 2017

Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm: HYDRAULIC PROPERTIES OF BIOFILM AMENDED SOIL
journal, August 2016

Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil
journal, May 2015

Organic matter from biological soil crusts induces the initial formation of sandy temperate soils
journal, November 2014

Evaluation of soil aggregate microstructure and stability under wetting and drying cycles in two Ultisols using synchrotron-based X-ray micro-computed tomography
journal, June 2015

Modern Terrestrial Sedimentary Biostructures and Their Fossil Analogs in Mesoproterozoic Subaerial Deposits
journal, February 2014

Cyanobacterial crust types, as strategies for survival in extreme habitats
journal, March 2009

Complex role of the polymeric matrix in biological soil crusts
journal, October 2017

Effects of Root-Induced Compaction on Rhizosphere Hydraulic Properties - X-ray Microtomography Imaging and Numerical Simulations
journal, January 2011

Hydrotaxis of Cyanobacteria in Desert Crusts
journal, November 2003

The biogenicity of modern terrestrial roll-up structures and its significance for ancient life on land: Roll-ups as biosignatures
journal, October 2010

Temperature Drives the Continental-Scale Distribution of Key Microbes in Topsoil Communities
journal, June 2013

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
journal, June 2013

Extracellular Polymeric Substances Affecting Pore-Scale Hydrologic Conditions for Bacterial Activity in Unsaturated Soils
journal, January 2007

Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils
journal, November 2016

Nitrogen cycling in desert biological soil crusts across biogeographic regions in the Southwestern United States
journal, March 2011

Exometabolite niche partitioning among sympatric soil bacteria
journal, September 2015

TomoPy: a framework for the analysis of synchrotron tomographic data
journal, August 2014

Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA
journal, May 2007

Microbial secreted exopolysaccharides affect the hydrological behavior of induced biological soil crusts in desert sandy soils
journal, January 2014

Water Retention Curves of Biofilm-Affected Soils using Xanthan as an Analogue
journal, January 2012

Desiccation Tolerance of Prokaryotes: Application of Principles to Human Cells
journal, November 2005

Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands
journal, March 2007

The role of the exopolysaccharides in enhancing hydraulic conductivity of biological soil crusts
journal, March 2012

Capturing 3D Water Flow in Rooted Soil by Ultra-fast Neutron Tomography
journal, July 2017

Exposure to predicted precipitation patterns decreases population size and alters community structure of cyanobacteria in biological soil crusts from the Chihuahuan Desert: Changing rainfall effects on soil cyanobacteria
journal, December 2017

Fiji: an open-source platform for biological-image analysis
journal, June 2012

Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands
journal, November 2011

Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land
journal, June 2009

A Computational Approach to Edge Detection
journal, November 1986

Topological characterization of pore space in soil — sample preparation and digital image-processing
journal, September 1996

Quantitative characterization of soil micro-aggregates: New opportunities from sub-micron resolution synchrotron X-ray microtomography
journal, November 2017

X-ray micro-tomography at the Advanced Light Source
conference, October 2012

The Evolution of a Capacity to Build Supra-Cellular Ropes Enabled Filamentous Cyanobacteria to Colonize Highly Erodible Substrates
journal, November 2009

Marching cubes: A high resolution 3D surface construction algorithm
conference, January 1987

A Threshold Selection Method from Gray-Level Histograms
journal, January 1979

Role of Cyanobacterial Exopolysaccharides in Phototrophic Biofilms and in Complex Microbial Mats
journal, April 2015

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics
journal, January 2018

Soil stabilization by a prokaryotic desert crust: Implications for Precambrian land biota
journal, September 1979