Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Improved workflow for unguided multiphase image segmentation

(2018) Brendan A. West et al.   COMPUTERS & GEOSCIENCES

Finite-difference method Stokes solver (FDMSS) for 3D pore geometries: Software development, validation and case studies

(2018) Kirill M. Gerke et al.   COMPUTERS & GEOSCIENCES

From Microscopy to Genomic Approach in Soil Biodiversity Assessment

(2018) Lucia Popescu et al.   CURRENT ISSUES IN MOLECULAR BIOLOGY

To what extent do uncertainty and sensitivity analyses help unravel the influence of microscale physical and biological drivers in soil carbon dynamics models?

(2018) L.E. Vogel et al.   ECOLOGICAL MODELLING

The “4 per 1000” initiative: A credibility issue for the soil science community?

(2018) Philippe C. Baveye et al.   GEODERMA

Direct methods to calculate the mass exchange between solutes inside and outside aggregates in macroscopic model for solute transport in aggregated soil

(2018) Zhongyang Li et al.   GEODERMA

A critique of the paper ‘Soil carbon 4 per mille’ by Minasny et al. (2017)

(2018) Robert E. White et al.   GEODERMA

Rejoinder to Comments on Minasny et al., 2017 Soil carbon 4 per mille Geoderma 292, 59–86

(2018) Budiman Minasny et al.   GEODERMA

Quantifying biogeochemical heterogeneity in soil systems

(2018) Thomas Wanzek et al.   GEODERMA

Multifractal analysis of 3D images of tillage soil

(2018) I.G. Torre et al.   GEODERMA

Soil structure as an indicator of soil functions: A review

(2018) E. Rabot et al.   GEODERMA

Rapid soil formation after glacial retreat shaped by spatial patterns of organic matter accrual in microaggregates

(2018) Steffen A. Schweizer et al.   GLOBAL CHANGE BIOLOGY

Representative elementary volume for NMR simulations based on X-ray microtomography of sedimentary rock

(2018) J.L. Gonzalez et al.   JOURNAL OF PETROLEUM SCIENCE AND ENGINEERING

Alive and kicking: Why dormant soil microorganisms matter

(2018) Rainer Georg Joergensen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Anoxic microsites in upland soils dominantly controlled by clay content

(2018) Marco Keiluweit et al.   SOIL BIOLOGY & BIOCHEMISTRY

Evaluating Hydraulic Properties of Biochar-Amended Soil Aggregates by High-Performance Pore-Scale Simulations

(2018) Hongxiang Zhou et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

SoilJ: An ImageJ Plugin for the Semiautomatic Processing of Three-Dimensional X-ray Images of Soils

(2018) John Koestel   VADOSE ZONE JOURNAL

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

(2018) Benedict Borer et al.   Nature Communications

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

(2018) Jared L. Wilmoth et al.   Frontiers in Microbiology

Machine learning for ecosystem services

(2018) Simon Willcock et al.   Ecosystem Services

Quick x-ray microtomography using a laser-driven betatron source

(2018) A. Döpp et al.   Optica

Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage

(2017) Kyle Michelson et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Hexavalent Chromium Generation within Naturally Structured Soils and Sediments

(2017) Debra M. Hausladen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Sequestering Soil Organic Carbon: A Nitrogen Dilemma

(2017) Jan Willem van Groenigen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of Distinct Functional Microstructural Domains Controlling C Storage in Soil

(2017) Markus Steffens et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Soil pores and their contributions to soil carbon processes

(2017) Alexandra N. Kravchenko et al.   GEODERMA

Quantification of the pore size distribution of soils: Assessment of existing software using tomographic and synthetic 3D images

(2017) A.N. Houston et al.   GEODERMA

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

(2017) Marco Voltolini et al.   GEODERMA

Lacunarity of soil macropore space arrangement of CT images: Effect of soil management and depth

(2017) F. San José Martínez et al.   GEODERMA

New segmentation method based on fractal properties using singularity maps

(2017) J.J. Martín-Sotoca et al.   GEODERMA

Build your own soil: exploring microfluidics to create microbial habitat structures

(2017) Kristin Aleklett et al.   ISME Journal

Soil aggregates as massively concurrent evolutionary incubators

(2017) Matthias C Rillig et al.   ISME Journal

Synchrotron-based X-Ray Approaches for Examining Toxic Trace Metal(loid)s in Soil–Plant Systems

(2017) Peter M Kopittke et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Probing the water distribution in porous model sands with two immiscible fluids: A nuclear magnetic resonance micro-imaging study

(2017) Bum Han Lee et al.   JOURNAL OF HYDROLOGY

Accounting for sub-resolution pores in models of water and solute transport in soils based on computed tomography images: Are we there yet?

(2017) Philippe C. Baveye et al.   JOURNAL OF HYDROLOGY

Microaggregates in soils

(2017) Kai Uwe Totsche et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

Modelling three-dimensional fungal growth in response to environmental stimuli

(2017) G. Vidal-Diez de Ulzurrun et al.   JOURNAL OF THEORETICAL BIOLOGY

Conservation Agriculture Had a Poor Impact on the Soil Porosity of Veneto Low-lying Plain Silty Soils after a 5-year Transition Period

(2017) I. Piccoli et al.   LAND DEGRADATION & DEVELOPMENT

ON THE PORE-SCALE MODELING AND SIMULATION OF REACTIVE TRANSPORT IN 3D GEOMETRIES

(2017) Oleg Iliev et al.   Mathematical Modelling and Analysis

FIB/SEM Imaging of Microbial Induced Calcite Precipitation in Sandy Soil

(2017) Lin Li et al.   MICROSCOPY AND MICROANALYSIS

Quantum microscope offers MRI for molecules

(2017) Sara Reardon   NATURE

Hotspots of soil N2O emission enhanced through water absorption by plant residue

(2017) A. N. Kravchenko et al.   Nature Geoscience

Super-resolution imaging goes fast and deep

(2017) Sam Duwé et al.   NATURE METHODS

In vivo imaging of neural activity

(2017) Weijian Yang et al.   NATURE METHODS

A guide to light-sheet fluorescence microscopy for multiscale imaging

(2017) Rory M Power et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

The trajectory of microbial single-cell sequencing

(2017) Tanja Woyke et al.   NATURE METHODS

Adaptive optical fluorescence microscopy

(2017) Na Ji   NATURE METHODS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Roots-eye view: Using microdialysis and microCT to non-destructively map root nutrient depletion and accumulation zones

(2017) Richard Brackin et al.   PLANT CELL AND ENVIRONMENT

Fluid flow in porous media using image-based modelling to parametrize Richards' equation

(2017) L. J. Cooper et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Quantification of soil aggregate microstructure on abandoned cropland during vegetative succession using synchrotron radiation-based micro-computed tomography

(2017) Dong Zhao et al.   SOIL & TILLAGE RESEARCH

Dinner in the dark: Illuminating drivers of soil organic matter decomposition

(2017) Annemieke van der Wal et al.   SOIL BIOLOGY & BIOCHEMISTRY

Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains

(2017) V.L. Bailey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Pore-Size Distributions of Soils Derived using a Geometrical Approach and Multiple Resolution MicroCT Images

(2017) Fabio Augusto Meira Cássaro et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research

(2017) Claire E. Stanley et al.   TRENDS IN MICROBIOLOGY

Pore-scale water dynamics during drying and the impacts of structure and surface wettability

(2017) Brian C. Cruz et al.   WATER RESOURCES RESEARCH

Anaerobic microsites have an unaccounted role in soil carbon stabilization

(2017) Marco Keiluweit et al.   Nature Communications

Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought

(2017) A. Peyton Smith et al.   Nature Communications

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments

(2017) Anja Worrich et al.   Nature Communications

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

(2017) Ali Ebrahimi et al.   Journal of Geophysical Research-Biogeosciences

Biofilm imaging in porous media by laboratory X-Ray tomography: Combining a non-destructive contrast agent with propagation-based phase-contrast imaging tools

(2017) Maxence Carrel et al.   PLoS One

Mapping and predictive variations of soil bacterial richness across France

(2017) Sébastien Terrat et al.   PLoS One

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces

(2017) Robin Tecon et al.   Scientific Reports

Capturing 3D Water Flow in Rooted Soil by Ultra-fast Neutron Tomography

(2017) Christian Tötzke et al.   Scientific Reports

Fungal networks serve as novel ecological routes for enrichment and dissemination of antibiotic resistance genes as exhibited by microcosm experiments

(2017) Rashid Nazir et al.   Scientific Reports

Image-based relative permeability upscaling from the pore scale

(2016) Saeid Norouzi Apourvari et al.   ADVANCES IN WATER RESOURCES

Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution

(2016) S.M. Shah et al.   ADVANCES IN WATER RESOURCES

Biofilm growth in porous media: Experiments, computational modeling at the porescale, and upscaling

(2016) Malgorzata Peszynska et al.   ADVANCES IN WATER RESOURCES

Comment on “An improved gray Lattice Boltzmann model for simulating fluid flow in multi-scale porous media”: Intrinsic links between LBE Brinkman schemes

(2016) Irina Ginzburg   ADVANCES IN WATER RESOURCES

Intercomparison of 3D pore-scale flow and solute transport simulation methods

(2016) Xiaofan Yang et al.   ADVANCES IN WATER RESOURCES

Raman spectroscopy: an evolving technique for live cell studies

(2016) Rachael Smith et al.   ANALYST

Computational challenges in the analyses of petrophysics using microtomography and upscaling: A review

(2016) Jie Liu et al.   COMPUTERS & GEOSCIENCES

Imaging and image-based fluid transport modeling at the pore scale in geological materials: A practical introduction to the current state-of-the-art

(2016) Tom Bultreys et al.   EARTH-SCIENCE REVIEWS

Using computed tomography (CT) images and multi-fractal theory to quantify the pore distribution of reconstructed soils during ecological restoration in opencast coal-mine

(2016) Jinman Wang et al.   ECOLOGICAL ENGINEERING

Characterization of the pore structure and cementing substances of soil aggregates by a combination of synchrotron radiation X-ray micro-computed tomography and scanning electron microscopy

(2016) X. Yu et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Macropores generated during shrinkage in two paddy soils using X-ray micro-computed tomography

(2016) N. Bottinelli et al.   GEODERMA

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model

(2016) Ali Ebrahimi et al.   GLOBAL CHANGE BIOLOGY

Comparative assessment of continuum-scale models of bimolecular reactive transport in porous media under pre-asymptotic conditions

(2016) G.M. Porta et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Review of pore network modelling of porous media: Experimental characterisations, network constructions and applications to reactive transport

(2016) Qingrong Xiong et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Image-based modelling of nutrient movement in and around the rhizosphere

(2016) Keith R. Daly et al.   JOURNAL OF EXPERIMENTAL BOTANY

A Lattice Boltzmann model for simulating water flow at pore scale in unsaturated soils

(2016) Xiaoxian Zhang et al.   JOURNAL OF HYDROLOGY

Near-edge x-ray absorption fine structure spectroscopy at atmospheric pressure with a table-top laser-induced soft x-ray source

(2016) Frank-Christian Kühl et al.   JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A

Soil-on-a-Chip: microfluidic platforms for environmental organismal studies

(2016) Claire E. Stanley et al.   LAB ON A CHIP

Quantifying global soil carbon losses in response to warming

(2016) T. W. Crowther et al.   NATURE

Advancing microbial sciences by individual-based modelling

(2016) Ferdi L. Hellweger et al.   NATURE REVIEWS MICROBIOLOGY

Challenges in imaging and predictive modeling of rhizosphere processes

(2016) T. Roose et al.   PLANT AND SOIL

Applications of laser wakefield accelerator-based light sources

(2016) Félicie Albert et al.   PLASMA PHYSICS AND CONTROLLED FUSION

Microbial competition in porous environments can select against rapid biofilm growth

(2016) Katharine Z. Coyte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

2D visualization captures the local heterogeneity of oxidative metabolism across soils from diverse land-use

(2016) Simonetta Rubol et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model

(2016) Sarah Evans et al.   SOIL BIOLOGY & BIOCHEMISTRY

Functional implications of the pH-trait distribution of the microbial community in a re-inoculation experiment across a pH gradient

(2016) Gema Bárcenas-Moreno et al.   SOIL BIOLOGY & BIOCHEMISTRY

Chemical communication connects soil food webs

(2016) Kristen M. DeAngelis   SOIL BIOLOGY & BIOCHEMISTRY

Rhizosphere shape of lentil and maize: Spatial distribution of enzyme activities

(2016) Bahar S. Razavi et al.   SOIL BIOLOGY & BIOCHEMISTRY

Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity

(2016) Philippe C. Baveye et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ecosystem Engineers in a Self-organized Soil

(2016) Patrick Lavelle et al.   SOIL SCIENCE

New Methods To Unravel Rhizosphere Processes

(2016) Eva Oburger et al.   TRENDS IN PLANT SCIENCE

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

(2016) Martin J. Blaser et al.   mBio

Mycelia as a focal point for horizontal gene transfer among soil bacteria

(2016) Tom Berthold et al.   Scientific Reports

The Munich Compact Light Source: initial performance measures

(2016) Elena Eggl et al.   JOURNAL OF SYNCHROTRON RADIATION

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

(2016) Minsu Kim et al.   PLoS One

Analysis of Soil Structure Turnover with Garnet Particles and X-Ray Microtomography

(2016) Steffen Schlüter et al.   PLoS One

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

(2016) S. M. F. Rabbi et al.   Scientific Reports

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

(2015) V. Pot et al.   ADVANCES IN WATER RESOURCES

Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

(2015) Laure E. Vogel et al.   ADVANCES IN WATER RESOURCES

Two decades of chemical imaging of solutes in sediments and soils – a review

(2015) Jakob Santner et al.   ANALYTICA CHIMICA ACTA

Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil

(2015) Andreas O. Wagner et al.   APPLIED SOIL ECOLOGY

Fungal communities are more sensitive indicators to non-extreme soil moisture variations than bacterial communities

(2015) A. Kaisermann et al.   APPLIED SOIL ECOLOGY

Aggregate size and their disruption affect 14C-labeled glucose mineralization and priming effect

(2015) Jing Tian et al.   APPLIED SOIL ECOLOGY

Lattice Boltzmann Modeling of Thermal Conduction in Composites with Thermal Contact Resistance

(2015) Chiyu Xie et al.   Communications in Computational Physics

Simulating flows in multi-layered and spatially-variable permeability media via a new Gray Lattice Boltzmann model

(2015) A. Yehya et al.   COMPUTERS AND GEOTECHNICS

Moving away from the geostatistical lamppost: Why, where, and how does the spatial heterogeneity of soils matter?

(2015) Philippe C. Baveye et al.   ECOLOGICAL MODELLING

Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers

(2015) Rainer U. Meckenstock et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Protist-Facilitated Particle Transport Using Emulated Soil Micromodels

(2015) Rebecca L. Rubinstein et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Soil aggregate geometry: Measurements and morphology

(2015) F. San José Martínez et al.   GEODERMA

Using time of flight secondary ion mass spectrometry and field emission scanning electron microscopy with energy dispersive X-ray spectroscopy to determine the role of soil components in competitive copper and cadmium migration and fixation in soils

(2015) B. Cerqueira et al.   GEODERMA

Laboratory-based characterization of plutonium in soil particles using micro-XRF and 3D confocal XRF

(2015) K. G. McIntosh et al.   JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils

(2015) Glade Dlott et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Moving across scales: a quantitative assessment of X-ray CT to measure the porosity of rocks

(2015) Ronny Pini et al.   JOURNAL OF POROUS MATERIALS

Soil-Borne Microbiome: Linking Diversity to Function

(2015) Lucas W. Mendes et al.   MICROBIAL ECOLOGY

Multi-scale characterization of porosity in Boom Clay (HADES-level, Mol, Belgium) using a combination of X-ray μ-CT, 2D BIB-SEM and FIB-SEM tomography

(2015) Susanne Hemes et al.   MICROPOROUS AND MESOPOROUS MATERIALS

Combining effective media and multi-phase methods of Lattice Boltzmann modelling for the characterisation of liquid-vapour dynamics in multi-length scale heterogeneous structural materials

(2015) P J McDonald et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Deep learning

(2015) Yann LeCun et al.   NATURE

Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics

(2015) Kwangmin Son et al.   NATURE REVIEWS MICROBIOLOGY

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Analysis and improvement of Brinkman lattice Boltzmann schemes: Bulk, boundary, interface. Similarity and distinctness with finite elements in heterogeneous porous media

(2015) Irina Ginzburg et al.   PHYSICAL REVIEW E

Tomography of human trabecular bone with a laser-wakefield driven x-ray source

(2015) J M Cole et al.   PLASMA PHYSICS AND CONTROLLED FUSION

Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images

(2015) Simona Hapca et al.   PLoS One

Socially mediated induction and suppression of antibiosis during bacterial coexistence

(2015) Monica I. Abrudan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lattice Boltzmann-Based Approaches for Pore-Scale Reactive Transport

(2015) Hongkyu Yoon et al.   Reviews in Mineralogy & Geochemistry

Impact of no-till and reduced tillage on aggregation and aggregate-associated carbon in Northern European agroecosystems

(2015) Jatta Sheehy et al.   SOIL & TILLAGE RESEARCH

Aggregate-related changes in network patterns of nematodes and ammonia oxidizers in an acidic soil

(2015) Yuji Jiang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Metabolising old soil carbon: Simply a matter of simple organic matter?

(2015) N. Nunan et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2015) Hannes Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Synergistic effects of soil microstructure and bacterial EPS on drying rate in emulated soil micromodels

(2015) Jinzi Deng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities

(2015) Weibing Xun et al.   SOIL BIOLOGY & BIOCHEMISTRY

Measuring biogeochemical heterogeneity at the micro scale in soils and sediments

(2015) Lasse L. Pedersen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Upscaling Diffusion and Nonlinear Reactive Mass Transport in Homogeneous Porous Media

(2015) Helen D. Lugo-Méndez et al.   TRANSPORT IN POROUS MEDIA

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities

(2015) Stephane Uroz et al.   TRENDS IN MICROBIOLOGY

Using X-ray Computed Tomography to Describe the Dynamics of Nitrous Oxide Emissions during Soil Drying

(2015) E. Rabot et al.   VADOSE ZONE JOURNAL

Application of Reactive Transport Modeling to Growth and Transport of Microorganisms in the Capillary Fringe

(2015) P. Hron et al.   VADOSE ZONE JOURNAL

Persistent questions of heterogeneity, uncertainty, and scale in subsurface flow and transport

(2015) Peter K. Kitanidis   WATER RESOURCES RESEARCH

Pore-scale and multiscale numerical simulation of flow and transport in a laboratory-scale column

(2015) Timothy D. Scheibe et al.   WATER RESOURCES RESEARCH

Three-dimensional quantification of soil hydraulic properties using X-ray Computed Tomography and image-based modeling

(2015) Saoirse R. Tracy et al.   WATER RESOURCES RESEARCH

Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

(2015) Ali Ebrahimi et al.   WATER RESOURCES RESEARCH

Quantitative X-ray phase-contrast microtomography from a compact laser-driven betatron source

(2015) J. Wenz et al.   Nature Communications

3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

(2015) C. K. Egan et al.   Scientific Reports

Protection of soil carbon within macro-aggregates depends on intra-aggregate pore characteristics

(2015) Alexandra N. Kravchenko et al.   Scientific Reports

Laser-wakefield accelerators as hard x-ray sources for 3D medical imaging of human bone

(2015) J. M. Cole et al.   Scientific Reports

Wiretapping into microbial interactions by single cell genomics

(2015) Ramunas Stepanauskas   Frontiers in Microbiology

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

(2015) Wakene C. Negassa et al.   PLoS One

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

(2015) Marina V. Karsanina et al.   PLoS One

Microscale Heterogeneity Explains Experimental Variability and Non-Linearity in Soil Organic Matter Mineralisation

(2015) Ruth E. Falconer et al.   PLoS One

Measuring gene expression in single bacterial cells: recent advances in methods and micro-devices

(2014) Xu Shi et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

X-ray microtomography: A porosity-based thresholding method to improve soil pore network characterization?

(2014) E. Beckers et al.   GEODERMA

Probing bacterial–fungal interactions at the single cell level

(2014) Claire E. Stanley et al.   Integrative Biology

Sub-continuum thermal transport modeling using diffusion in the Lattice Boltzmann Transport Equation

(2014) Cheng Chen et al.   INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER

Resolution effect in X-ray microcomputed tomography imaging and small pore’s contribution to permeability for a Berea sandstone

(2014) Sheng Peng et al.   JOURNAL OF HYDROLOGY

Quantitative comparison of segmentation algorithms for FIB-SEM images of porous media

(2014) M. SALZER et al.   JOURNAL OF MICROSCOPY

Transmission–Reflection Coefficient in the Lattice Boltzmann Method

(2014) Hiroaki Yoshida et al.   JOURNAL OF STATISTICAL PHYSICS

Advances in 3D focused ion beam tomography

(2014) Marco Cantoni et al.   MRS BULLETIN

Table-top soft x-ray microscope using laser-induced plasma from a pulsed gas jet

(2014) Matthias Müller et al.   OPTICS EXPRESS

Soil water availability strongly alters the community composition of soil protists

(2014) Geisen Stefan et al.   PEDOBIOLOGIA

Bacterial community structure in soil microaggregates and on particulate organic matter fractions located outside or inside soil macroaggregates

(2014) Aimeric Blaud et al.   PEDOBIOLOGIA

Lattice Boltzmann modeling of permeability in porous materials with partially percolating voxels

(2014) Ruru Li et al.   PHYSICAL REVIEW E

Pore-scale dynamics of salt transport and distribution in drying porous media

(2014) Nima Shokri   PHYSICS OF FLUIDS

Laser wakefield accelerator based light sources: potential applications and requirements

(2014) F Albert et al.   PLASMA PHYSICS AND CONTROLLED FUSION

Impact of Matric Potential and Pore Size Distribution on Growth Dynamics of Filamentous and Non-Filamentous Soil Bacteria

(2014) Alexandra B. Wolf et al.   PLoS One

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Soil macro- and microstructure as affected by different tillage systems and their effects on maize root growth

(2014) N. Dal Ferro et al.   SOIL & TILLAGE RESEARCH

Localization of soil organic matter in soil aggregates using synchrotron-based X-ray microtomography

(2014) Stephan Peth et al.   SOIL BIOLOGY & BIOCHEMISTRY

Early season dynamics of soil nitrogen fluxes in fertilized and unfertilized boreal forests

(2014) Erich Inselsbacher et al.   SOIL BIOLOGY & BIOCHEMISTRY

New Approach to Measure Soil ParticulateOrganic Matter in Intact Samples Using X-ray Computed Microtomography

(2014) A. N. Kravchenko et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Intra-aggregate Pore Structure Influences Phylogenetic Composition of Bacterial Community in Macroaggregates

(2014) Alexandra N. Kravchenko et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Numerical Calculation of Effective Diffusion in Unsaturated Porous Media by the TRT Lattice Boltzmann Method

(2014) Alain Genty et al.   TRANSPORT IN POROUS MEDIA

Research Efforts Involving Several Disciplines: Adherence to a Clear Nomenclature Is Needed

(2014) Philippe C. Baveye et al.   WATER AIR AND SOIL POLLUTION

Image processing of multiphase images obtained via X-ray microtomography: A review

(2014) Steffen Schlüter et al.   WATER RESOURCES RESEARCH

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

(2014) Ali N. Ebrahimi et al.   WATER RESOURCES RESEARCH

Printing soil: a single-step, high-throughput method to isolate micro-organisms and near-neighbour microbial consortia from a complex environmental sample

(2014) Bradley R. Ringeisen et al.   Methods in Ecology and Evolution

Comment on “Averaging theory for description of environmental problems: What have we learned?” by William G. Gray, Cass T. Miller, and Bernhard A. Schrefler

(2013) Philippe C. Baveye   ADVANCES IN WATER RESOURCES

Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

(2013) Yohan Davit et al.   ADVANCES IN WATER RESOURCES

Three-Dimensional Chemical Mapping with a Confocal XRF Setup

(2013) Lars Lühl et al.   ANALYTICAL CHEMISTRY

Pore morphology and distribution in the Shaly facies of Opalinus Clay (Mont Terri, Switzerland): Insights from representative 2D BIB–SEM investigations on mm to nm scale

(2013) M.E. Houben et al.   APPLIED CLAY SCIENCE

Relationships between intra-aggregate pore structures and distributions of Escherichia coli within soil macro-aggregates

(2013) A. Kravchenko et al.   APPLIED SOIL ECOLOGY

Addressing key challenges to interdisciplinary research on water-related issues: Biologists’ engagement and funding structure

(2013) Philippe Baveye   BIOLOGIA

Lattice Boltzmann modeling and evaluation of fluid flow in heterogeneous porous media involving multiple matrix constituents

(2013) Jinfang Gao et al.   COMPUTERS & GEOSCIENCES

Neutron imaging of hydrogen-rich fluids in geomaterials and engineered porous media: A review

(2013) E. Perfect et al.   EARTH-SCIENCE REVIEWS

Applications of X-ray computed tomography for examining biophysical interactions and structural development in soil systems: a review

(2013) J. R. Helliwell et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescencein situhybridization

(2013) Hannes Schmidt et al.   FEMS MICROBIOLOGY ECOLOGY

Regulation of soil organic C mineralisation at the pore scale

(2013) Léo S. Ruamps et al.   FEMS MICROBIOLOGY ECOLOGY

Effects of permeability fields on fluid, heat, and oxygen isotope transport in extensional detachment systems

(2013) Raphaël Gottardi et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Effect of scanning and image reconstruction settings in X-ray computed microtomography on quality and segmentation of 3D soil images

(2013) A.N. Houston et al.   GEODERMA

Evaluation of X-ray computed tomography for quantifying macroporosity of loamy pasture soils

(2013) M.A. Rab et al.   GEODERMA

Contrast agents for soil investigation with X-ray computed tomography

(2013) Denis Van Loo et al.   GEODERMA

Soil organic carbon mineralization rates in aggregates under contrasting land uses

(2013) S.M. Fazle Rabbi et al.   GEODERMA

Identification of pore spaces in 3D CT soil images using PFCM partitional clustering

(2013) B. Ojeda-Magaña et al.   GEODERMA

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Dependence of Arsenic Fate and Transport on Biogeochemical Heterogeneity Arising from the Physical Structure of Soils and Sediments

(2013) Yoko Masue-Slowey et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Hydrology and the looming water crisis: It is time to think, and act, outside the box

(2013) Philippe C. Baveye   Journal of Hydrology and Hydromechanics

Bacteria with ACC deaminase can promote plant growth and help to feed the world

(2013) Bernard R. Glick   MICROBIOLOGICAL RESEARCH

A 3D lattice Boltzmann effective media study: understanding the role of C-S-H and water saturation on the permeability of cement paste

(2013) M Zalzale et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Single-cell sequencing in its prime

(2013) Roger S Lasken   NATURE BIOTECHNOLOGY

The future is fibre accelerators

(2013) Gerard Mourou et al.   Nature Photonics

Zero-field nuclear magnetic resonance

(2013) Micah P. Ledbetter et al.   PHYSICS TODAY

Real-time 3D imaging of Haines jumps in porous media flow

(2013) S. Berg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale modelling of hydraulic conductivity in vuggy porous media

(2013) K. R. Daly et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Pore Scale Processes Associated with Subsurface CO2 Injection and Sequestration

(2013) C. I. Steefel et al.   Reviews in Mineralogy & Geochemistry

Fungal–bacterial consortia increase diuron degradation in water-unsaturated systems

(2013) Lea Ellegaard-Jensen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Texture and organic carbon contents do not impact amount of carbon protected in Malagasy soils

(2013) Tantely Razafimbelo et al.   SCIENTIA AGRICOLA

Soil zymography – A novel in situ method for mapping distribution of enzyme activity in soil

(2013) Marie Spohn et al.   SOIL BIOLOGY & BIOCHEMISTRY

Green Water and Global Food Security

(2013) Garrison Sposito   VADOSE ZONE JOURNAL

New Local Thresholding Method for Soil Images by Minimizing Grayscale Intra-Class Variance

(2013) Simona M. Hapca et al.   VADOSE ZONE JOURNAL

Biophysics of the Vadose Zone: From Reality to Model Systems and Back Again

(2013) Paul D. Hallett et al.   VADOSE ZONE JOURNAL

A tomographic imagery segmentation methodology for three-phase geomaterials based on simultaneous region growing

(2013) Mir Amid Hashemi et al.   Acta Geotechnica

Resolution enhancement techniques in microscopy

(2013) Christoph Cremer et al.   European Physical Journal H

Carbon mineralisation and pore size classes in undisturbed soil cores

(2013) Liesbeth Bouckaert et al.   Soil Research

X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems

(2012) Dorthe Wildenschild et al.   ADVANCES IN WATER RESOURCES

Microbial cultivation and the role of microbial resource centers in the omics era

(2012) Om Prakash et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Permeability of a growing biofilm in a porous media fluid flow analyzed by magnetic resonance displacement-relaxation correlations

(2012) Sarah J. Vogt et al.   BIOTECHNOLOGY AND BIOENGINEERING

Micro- and nano-environments of carbon sequestration: Multi-element STXM–NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations

(2012) Dawit Solomon et al.   CHEMICAL GEOLOGY

Developing Extensible Lattice-Boltzmann Simulators for General-Purpose Graphics-Processing Units

(2012) Stuart D. C. Walsh et al.   Communications in Computational Physics

Soil porosity resulting from the assemblage of silt grains with a clay phase: New perspectives related to utilization of X-ray synchrotron computed microtomography

(2012) Olivier Rozenbaum et al.   COMPTES RENDUS GEOSCIENCE

On the aptitude of the lattice Boltzmann approach for the treatment of the transient heat transfer with crack resistance

(2012) M. El Ganaoui et al.   COMPTES RENDUS MECANIQUE

Adaptive-window indicator kriging: A thresholding method for computed tomography images of porous media

(2012) A.N. Houston et al.   COMPUTERS & GEOSCIENCES

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

A combination of cellular automata and agent-based models for simulating the root surface colonization by bacteria

(2012) Adrialy L. Muci et al.   ECOLOGICAL MODELLING

Soil fungal dynamics: Parameterisation and sensitivity analysis of modelled physiological processes, soil architecture and carbon distribution

(2012) K. Cazelles et al.   ECOLOGICAL MODELLING

Linking environmental processes to thein situfunctioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM)

(2012) Sebastian Behrens et al.   ENVIRONMENTAL MICROBIOLOGY

NanoSIMS Study of Organic Matter Associated with Soil Aggregates: Advantages, Limitations, and Combination with STXM

(2012) Laurent Remusat et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Biofilm Detection in Natural Unconsolidated Porous Media Using a Low-Field Magnetic Resonance System

(2012) Alexis B. Sanderlin et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Multifractal properties of porosity as calculated from computed tomography (CT) images of a sandy soil, in relation to soil gas diffusion and linked soil physical properties

(2012) J. A. Lafond et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)

(2012) Sünje J. Pamp et al.   GENOME RESEARCH

Quantification of Grain, Pore, and Fluid Microstructure of Unsaturated Sand from X-Ray Computed Tomography Images

(2012) Clinton S. Willson et al.   GEOTECHNICAL TESTING JOURNAL

Soil organic matter turnover is governed by accessibility not recalcitrance

(2012) Jennifer A. J. Dungait et al.   GLOBAL CHANGE BIOLOGY

Evaluation of tyramide solutions for an improved detection and enumeration of single microbial cells in soil by CARD-FISH

(2012) Hannes Schmidt et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Three dimensional quantification of biological samples using micro-computer aided tomography (microCT)

(2012) Osu Lilje et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Comparison of commercial kits for the extraction of DNA from paddy soils

(2012) S. Knauth et al.   LETTERS IN APPLIED MICROBIOLOGY

Are Uncultivated Bacteria Really Uncultivable?

(2012) Indun Dewi Puspita et al.   MICROBES AND ENVIRONMENTS

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

Arbuscular mycorrhizal fungi - short-term liability but long-term benefits for soil carbon storage?

(2012) Erik Verbruggen et al.   NEW PHYTOLOGIST

In-Situ Observation of Cracks in Frozen Soil using Synchrotron Tomography

(2012) Á. Ní Bhreasail et al.   PERMAFROST AND PERIGLACIAL PROCESSES

Prominent Effect of Soil Network Heterogeneity on Microbial Invasion

(2012) F. J. Pérez-Reche et al.   PHYSICAL REVIEW LETTERS

X-ray imaging detectors

(2012) Sol M. Gruner   PHYSICS TODAY

Two methods for full-length RNA sequencing for low quantities of cells and single cells

(2012) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Confocal micro-x-ray fluorescence spectrometer for light element analysis

(2012) S. Smolek et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Bad News for Soil Carbon Sequestration?

(2012) G. A. Kowalchuk   SCIENCE

Arbuscular Mycorrhizal Fungi Increase Organic Carbon Decomposition Under Elevated CO2

(2012) L. Cheng et al.   SCIENCE

Soil physics meets soil biology: Towards better mechanistic prediction of greenhouse gas emissions from soil

(2012) Sergey Blagodatsky et al.   SOIL BIOLOGY & BIOCHEMISTRY

Compatibility of X-ray micro-Computed Tomography with soil biological experiments

(2012) Liesbeth Bouckaert et al.   SOIL BIOLOGY & BIOCHEMISTRY

Synthesis analysis of the temperature sensitivity of soil respiration from laboratory studies in relation to incubation methods and soil conditions

(2012) Salwa Hamdi et al.   SOIL BIOLOGY & BIOCHEMISTRY

Can intra-aggregate pore structures affect the aggregate's effectiveness in protecting carbon?

(2012) K. Ananyeva et al.   SOIL BIOLOGY & BIOCHEMISTRY

Emergent Behavior of Soil Fungal Dynamics

(2012) Ruth E. Falconer et al.   SOIL SCIENCE

Gold-FISH: A new approach for the in situ detection of single microbial cells combining fluorescence and scanning electron microscopy

(2012) Hannes Schmidt et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Numerical Simulation of 3D Liquid–Gas Distribution in Porous Media by a Two-Phase TRT Lattice Boltzmann Method

(2012) Alain Genty et al.   TRANSPORT IN POROUS MEDIA

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Roots, water, and nutrient acquisition: let's get physical

(2012) Nick Chapman et al.   TRENDS IN PLANT SCIENCE

Soil Architecture and Physicochemical Functions: An Introduction

(2012) L.W. de Jonge et al.   VADOSE ZONE JOURNAL

Three-Dimensional Multiphase Segmentation of X-Ray CT Data of Porous Materials Using a Bayesian Markov Random Field Framework

(2012) Ramaprasad Kulkarni et al.   VADOSE ZONE JOURNAL

A Review of Micromodels and Their Use in Two-Phase Flow Studies

(2012) N. K. Karadimitriou et al.   VADOSE ZONE JOURNAL

Pore-scale simulation of mixing-induced calcium carbonate precipitation and dissolution in a microfluidic pore network

(2012) Hongkyu Yoon et al.   WATER RESOURCES RESEARCH

Characterising the chemistry of micropores in a sodic soil with strong texture-contrast using synchrotron X-ray techniques and LA-ICP-MS

(2012) Laurence Jassogne et al.   Soil Research

Advantages of functional single-cell isolation method over standard agar plate dilution method as a tool for studying denitrifying bacteria in rice paddy soil

(2012) Tomoyasu Nishizawa et al.   AMB Express

Hybrid models of reactive transport in porous and fractured media

(2011) Ilenia Battiato et al.   ADVANCES IN WATER RESOURCES

Comparison of organic versus mineral resource effects on short-term aggregate carbon and nitrogen dynamics in a sandy soil versus a fine textured soil

(2011) P. Chivenge et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Coherent Nonlinear Optical Imaging: Beyond Fluorescence Microscopy

(2011) Wei Min et al.   Annual Review of Physical Chemistry

Culture-independent methods for studying environmental microorganisms: methods, application, and perspective

(2011) Can Su et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Compact and high-quality gamma-ray source applied to 10 μm-range resolution radiography

(2011) A. Ben-Ismaïl et al.   APPLIED PHYSICS LETTERS

Application of X-ray computed tomography to soil science: A literature review

(2011) I A Taina et al.   CANADIAN JOURNAL OF SOIL SCIENCE

Soil microbial diversity: Methodological strategy, spatial overview and functional interest

(2011) Pierre-Alain Maron et al.   COMPTES RENDUS BIOLOGIES

3D shape extraction segmentation and representation of soil microstructures using generalized cylinders

(2011) Ndèye Fatou Ngom et al.   COMPUTERS & GEOSCIENCES

Single cell genome sequencing

(2011) Suzan Yilmaz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Single cell Raman spectroscopy for cell sorting and imaging

(2011) Mengqiu Li et al.   CURRENT OPINION IN BIOTECHNOLOGY

Individual-based modelling of carbon and nitrogen dynamics in soils: Parameterization and sensitivity analysis of microbial components

(2011) Anna Gras et al.   ECOLOGICAL MODELLING

A reactive transport modeling approach to simulate biogeochemical processes in pore structures with pore-scale heterogeneities

(2011) Mehdi Gharasoo et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Wavelet analysis of soil variation at nanometre- to micrometre-scales: an example of organic carbon content in a micro-aggregate

(2011) A. E. Milne et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Soil carbon sequestration to mitigate climate change: a critical re-examination to identify the true and the false

(2011) D. S. Powlson et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Mycelial response to spatiotemporal nutrient heterogeneity: A velocity-jump mathematical model

(2011) Steven Hopkins et al.   Fungal Ecology

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils

(2011) Simona M. Hapca et al.   GEODERMA

Characterization of peat structure using X-ray computed tomography and its control on the ebullition of biogenic gas bubbles

(2011) Nicholas Kettridge et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Characterization of refractory organic substances by NEXAFS using a compact X-ray source

(2011) Julia Sedlmair et al.   JOURNAL OF SOILS AND SEDIMENTS

Advanced spectroscopic, microscopic, and tomographic characterization techniques to study biogeochemical interfaces in soil

(2011) Thilo Rennert et al.   JOURNAL OF SOILS AND SEDIMENTS

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

(2011) Haluk Resat et al.   MICROBIAL ECOLOGY

Highly specific label-free molecular imaging with spectrally tailored excitation-stimulated Raman scattering (STE-SRS) microscopy

(2011) Christian W. Freudiger et al.   Nature Photonics

Imaging mass spectrometry in microbiology

(2011) Jeramie D. Watrous et al.   NATURE REVIEWS MICROBIOLOGY

Submicron scale imaging of soil organic matter dynamics using NanoSIMS – From single particles to intact aggregates

(2011) Carsten W. Mueller et al.   ORGANIC GEOCHEMISTRY

From Dust Bowl to Dust Bowl: Soils are Still Very Much a Frontier of Science

(2011) Philippe C. Baveye et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Evaluation of an Advanced Benchtop Micro-Computed Tomography System for Quantifying Porosities and Pore-Size Distributions of Two Brazilian Oxisols

(2011) Carlos M. P. Vaz et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Long-term Differences in Tillage and Land Use Affect Intra-aggregate Pore Heterogeneity

(2011) A.N. Kravchenko et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

How Succolarity could be used as another fractal measure in image analysis

(2011) R. H. C. de Melo et al.   TELECOMMUNICATION SYSTEMS

Representative elementary volume estimation for porosity, moisture saturation, and air-water interfacial areas in unsaturated porous media: Data quality implications

(2011) Molly S. Costanza-Robinson et al.   WATER RESOURCES RESEARCH

Imaging biofilm architecture within porous media using synchrotron-based X-ray computed microtomography

(2011) Gabriel C. Iltis et al.   WATER RESOURCES RESEARCH

Hydrologic and biogeochemical functioning of intensively managed catchments: A synthesis of top-down analyses

(2011) Nandita B. Basu et al.   WATER RESOURCES RESEARCH

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

(2011) Sébastien Terrat et al.   Microbial Biotechnology

Modeling non-equilibrium mass transport in biologically reactive porous media

(2010) Yohan Davit et al.   ADVANCES IN WATER RESOURCES

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Low Pore Connectivity Increases Bacterial Diversity in Soil

(2010) J. K. Carson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell analysis and isolation for microbiology and biotechnology: methods and applications

(2010) Satoshi Ishii et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Variations in microbial isotopic fractionation during soil organic matter decomposition

(2010) T. Z. Lerch et al.   BIOGEOCHEMISTRY

Segmentation of X-ray microtomography images of soil using gradient masks

(2010) Steffen Schlüter et al.   COMPUTERS & GEOSCIENCES

Quantification of soil structure based on Minkowski functions

(2010) H.-J. Vogel et al.   COMPUTERS & GEOSCIENCES

Threshold Fine-Tuning and 3D Characterisation of Porous Media Using X-ray Nanotomography

(2010) Hossein Ostadi et al.   Current Nanoscience

Single cell metabolomics

(2010) Matthias Heinemann et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes

(2010) Alexandra Kravchenko et al.   ECOLOGICAL APPLICATIONS

Aqueous films limit bacterial cell motility and colony expansion on partially saturated rough surfaces

(2010) Gang Wang et al.   ENVIRONMENTAL MICROBIOLOGY

Transport Implications Resulting from Internal Redistribution of Arsenic and Iron within Constructed Soil Aggregates

(2010) Yoko Masue-Slowey et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Aggregate-scale spatial heterogeneity in reductive transformation of ferrihydrite resulting from coupled biogeochemical and physical processes

(2010) C. Pallud et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data

(2010) Philippe C. Baveye et al.   GEODERMA

Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses

(2010) E. ATTARD et al.   GLOBAL CHANGE BIOLOGY

Soil architecture and preferential flow across scales

(2010) Henry Lin et al.   JOURNAL OF HYDROLOGY

Quantification of 3-D soil macropore networks in different soil types and land uses using computed tomography

(2010) Lifang Luo et al.   JOURNAL OF HYDROLOGY

Imaging biofilm in porous media using X-ray computed microtomography

(2010) Y. DAVIT et al.   JOURNAL OF MICROSCOPY

A new phase for X-ray imaging

(2010) Henry N. Chapman   NATURE

Ptychographic X-ray computed tomography at the nanoscale

(2010) Martin Dierolf et al.   NATURE

Spatially resolved 3D micro-XANES by a confocal detection scheme

(2010) Geert Silversmit et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantitative x-ray dark-field computed tomography

(2010) M Bech et al.   PHYSICS IN MEDICINE AND BIOLOGY

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

Twenty-five years of computed tomography in soil physics: A literature review of the Brazilian contribution

(2010) Luiz F. Pires et al.   SOIL & TILLAGE RESEARCH

Loss of low molecular weight dissolved organic carbon (DOC) and nitrogen (DON) in H2O and 0.5M K2SO4 soil extracts

(2010) Johannes Rousk et al.   SOIL BIOLOGY & BIOCHEMISTRY

Priming effects: Interactions between living and dead organic matter

(2010) Yakov Kuzyakov   SOIL BIOLOGY & BIOCHEMISTRY

Microbial biogeography at the soil pore scale

(2010) Léo Simon Ruamps et al.   SOIL BIOLOGY & BIOCHEMISTRY

Hitchhikers on the fungal highway: The helper effect for bacterial migration via fungal hyphae

(2010) J.A. Warmink et al.   SOIL BIOLOGY & BIOCHEMISTRY

Individual-Based Modeling of Carbon and Nitrogen Dynamics in Soils

(2010) Anna Gras et al.   SOIL SCIENCE

3D chemical imaging based on a third-generation synchrotron source

(2010) Pierre Bleuet et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Single cell analysis: the new frontier in ‘omics’

(2010) Daojing Wang et al.   TRENDS IN BIOTECHNOLOGY

Noninvasive Observations of Flow Patterns in Locally Heterogeneous Mine Soils using Neutron Radiation

(2010) Annika Badorreck et al.   VADOSE ZONE JOURNAL

Integrating 3D images using laboratory-based micro X-ray computed tomography and confocal X-ray fluorescence techniques

(2010) Brian M. Patterson et al.   X-RAY SPECTROMETRY

Upscaling microbial chemotaxis in porous media

(2009) Francisco J. Valdés-Parada et al.   ADVANCES IN WATER RESOURCES

Upscaling of the advection–diffusion–reaction equation with Monod reaction

(2009) F. Heße et al.   ADVANCES IN WATER RESOURCES

Comment on “The role of scaling laws in upscaling” by B.D. Wood

(2009) Philippe Baveye   ADVANCES IN WATER RESOURCES

Reply to comment by Philippe Baveye on“The role of scaling laws in upscaling”

(2009) Brian D. Wood   ADVANCES IN WATER RESOURCES

Practical methods for measuring the tortuosity of porous materials from binary or gray-tone tomographic reconstructions

(2009) Cedric J. Gommes et al.   AICHE JOURNAL

Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria

(2009) Naoaki Ashida et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Do soil aggregates really protect encapsulated organic matter against microbial decomposition?

(2009) Marc-O. Goebel et al.   BIOLOGIA

Using pore space 3D geometrical modelling to simulate biological activity: Impact of soil structure

(2009) Olivier Monga et al.   COMPUTERS & GEOSCIENCES

Molecular characterization of copper in soils using X-ray absorption spectroscopy

(2009) Daniel G. Strawn et al.   ENVIRONMENTAL POLLUTION

Linking hyphal growth to colony dynamics: Spatially explicit models of mycelia

(2009) Graeme P. Boswell et al.   Fungal Ecology

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis

(2009) C. R. Woese et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Three-Dimensional X-Ray Imaging and Analysis of Fungi on and in Wood

(2009) Jan Van den Bulcke et al.   MICROSCOPY AND MICROANALYSIS

To sequence or not to sequence the whole-soil metagenome?

(2009) Philippe C. Baveye   NATURE REVIEWS MICROBIOLOGY

TerraGenome: a consortium for the sequencing of a soil metagenome

(2009) Timothy M. Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial growth and motility in sub-micron constrictions

(2009) J. Mannik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of soil water in macropores of undisturbed soil using microfocus X-ray tube computerized tomography (μCT)

(2009) Rolf Tippkötter et al.   SOIL & TILLAGE RESEARCH

Exploiting plant–microbe partnerships to improve biomass production and remediation

(2009) Nele Weyens et al.   TRENDS IN BIOTECHNOLOGY

Combining Spatial Resolutions in the Multiscale Analysis of Soil Pore-Size Distributions

(2009) Apostolos Papadopoulos et al.   VADOSE ZONE JOURNAL

Segmentation of X-ray computed tomography images of porous materials: A crucial step for characterization and quantitative analysis of pore structures

(2009) Pavel Iassonov et al.   WATER RESOURCES RESEARCH

A study of the upper limit of solid scatters density for gray Lattice Boltzmann Method

(2008) Yongli Chen et al.   ACTA MECHANICA SINICA

Unsaturated water flow across soil aggregate contacts

(2008) A. Carminati et al.   ADVANCES IN WATER RESOURCES

Biofilms in porous media: Development of macroscopic transport equations via volume averaging with closure for local mass equilibrium conditions

(2008) Fabrice Golfier et al.   ADVANCES IN WATER RESOURCES

The role of scaling laws in upscaling

(2008) Brian D. Wood   ADVANCES IN WATER RESOURCES

Comment on “Conservation of protists: Is it needed at all?” by Cotterill et al.

(2008) Philippe C. Baveye   BIODIVERSITY AND CONSERVATION

A new partial-bounceback lattice-Boltzmann method for fluid flow through heterogeneous media

(2008) Stuart D.C. Walsh et al.   COMPUTERS & GEOSCIENCES

Genomic sequencing of single microbial cells from environmental samples

(2008) Thomas Ishoey et al.   CURRENT OPINION IN MICROBIOLOGY

Modelling of thermal contact resistance within the framework of the thermal lattice Boltzmann method

(2008) K. Han et al.   INTERNATIONAL JOURNAL OF THERMAL SCIENCES

A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale

(2008) Paul G. Dennis et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Near-edge x-ray absorption fine structure measurements using a laboratory-scale XUV source

(2008) Christian Peth et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

An integrative approach of organic matter stabilization in temperate soils: Linking chemistry, physics, and biology

(2008) Ingrid Kögel-Knabner et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY

Spatial complexity of soil organic matter forms at nanometre scales

(2008) Johannes Lehmann et al.   Nature Geoscience

Principles and applications of compact laser–plasma accelerators

(2008) Victor Malka et al.   Nature Physics

A fungal growth model fitted to carbon-limited dynamics ofRhizoctonia solani

(2008) M. J. Jeger et al.   NEW PHYTOLOGIST

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aggregate associated-C and physical protection in a tropical clayey soil under Malagasy conventional and no-tillage systems

(2008) Tantely M. Razafimbelo et al.   SOIL & TILLAGE RESEARCH

Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

(2008) Thilo Eickhorst et al.   SOIL BIOLOGY & BIOCHEMISTRY

The metagenomics of disease-suppressive soils – experiences from the METACONTROL project

(2008) Jan Dirk van Elsas et al.   TRENDS IN BIOTECHNOLOGY

Estimation of a Critical Spatial Discretization Limit for Solving Richards' Equation at Large Scales

(2008) H.-J. Vogel et al.   VADOSE ZONE JOURNAL

Computational pore network modeling of the influence of biofilm permeability on bioclogging in porous media

(2007) Martin Thullner et al.   BIOTECHNOLOGY AND BIOENGINEERING

X-ray computed tomography of frozen soil

(2007) J.K. Torrance et al.   COLD REGIONS SCIENCE AND TECHNOLOGY

Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods

(2007) Thilo Eickhorst et al.   SOIL BIOLOGY & BIOCHEMISTRY