Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales
Abstract
Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as “microbial villages” that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. Here, we describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining “model system” approaches (e.g., developing mock community artificial aggregates), field observations of natural communities,more »
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- The Ohio State Univ., Columbus, OH (United States)
- Goethe Univ., Frankfurt am Main (Germany)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1542240
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Applied and Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 85; Journal Issue: 14; Journal ID: ISSN 0099-2240
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; 54 ENVIRONMENTAL SCIENCES; microbial communities; soil; soil aggregate; virus
Citation Formats
Wilpiszeski, Regina L., Aufrecht, Jayde A., Retterer, Scott T., Sullivan, Matthew B., Graham, David E., Pierce, Eric M., Zablocki, Olivier D., Palumbo, Anthony V., Elias, Dwayne A., and Müller, Volker. Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. United States: N. p., 2019.
Web. doi:10.1128/AEM.00324-19.
Wilpiszeski, Regina L., Aufrecht, Jayde A., Retterer, Scott T., Sullivan, Matthew B., Graham, David E., Pierce, Eric M., Zablocki, Olivier D., Palumbo, Anthony V., Elias, Dwayne A., & Müller, Volker. Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. United States. https://doi.org/10.1128/AEM.00324-19
Wilpiszeski, Regina L., Aufrecht, Jayde A., Retterer, Scott T., Sullivan, Matthew B., Graham, David E., Pierce, Eric M., Zablocki, Olivier D., Palumbo, Anthony V., Elias, Dwayne A., and Müller, Volker. Fri .
"Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales". United States. https://doi.org/10.1128/AEM.00324-19. https://www.osti.gov/servlets/purl/1542240.
@article{osti_1542240,
title = {Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales},
author = {Wilpiszeski, Regina L. and Aufrecht, Jayde A. and Retterer, Scott T. and Sullivan, Matthew B. and Graham, David E. and Pierce, Eric M. and Zablocki, Olivier D. and Palumbo, Anthony V. and Elias, Dwayne A. and Müller, Volker},
abstractNote = {Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as “microbial villages” that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. Here, we describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining “model system” approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.},
doi = {10.1128/AEM.00324-19},
journal = {Applied and Environmental Microbiology},
number = 14,
volume = 85,
place = {United States},
year = {Fri May 10 00:00:00 EDT 2019},
month = {Fri May 10 00:00:00 EDT 2019}
}
Web of Science
Works referenced in this record:
Viruses in Soil Systems
journal, January 1979
- Duboise, Samuel Monroe; Moore, Barbara E.; Sorber, Charles A.
- CRC Critical Reviews in Microbiology, Vol. 7, Issue 3
Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals
journal, January 2010
- Vincent, Meghan E.; Liu, Weishan; Haney, Elizabeth B.
- Chemical Society Reviews, Vol. 39, Issue 3
Rising to the challenge: accelerated pace of discovery transforms marine virology
journal, February 2015
- Brum, Jennifer R.; Sullivan, Matthew B.
- Nature Reviews Microbiology, Vol. 13, Issue 3
Micrometer-scale physical structure and microbial composition of soil macroaggregates
journal, October 2013
- Bailey, Vanessa L.; McCue, Lee Ann; Fansler, Sarah J.
- Soil Biology and Biochemistry, Vol. 65
Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS
journal, March 2008
- Behrens, S.; Losekann, T.; Pett-Ridge, J.
- Applied and Environmental Microbiology, Vol. 74, Issue 10
Stable-isotope probing as a tool in microbial ecology
journal, February 2000
- Radajewski, Stefan; Ineson, Philip; Parekh, Nisha R.
- Nature, Vol. 403, Issue 6770, p. 646-649
Measuring Porosity at the Nanoscale by Quantitative Electron Tomography
journal, December 2010
- Biermans, E.; Molina, L.; Batenburg, K. J.
- Nano Letters, Vol. 10, Issue 12
Host-linked soil viral ecology along a permafrost thaw gradient
journal, July 2018
- Emerson, Joanne B.; Roux, Simon; Brum, Jennifer R.
- Nature Microbiology, Vol. 3, Issue 8
Aggregate hierarchy in soils
journal, January 1991
- Oades, Jm; Waters, Ag
- Soil Research, Vol. 29, Issue 6
Geostatistical analysis of the distribution of NH4+ and NO2â-oxidizing bacteria and serotypes at the millimeter scale along a soil transect
journal, October 2000
- Grundmann, G. L.; Debouzie, D.
- FEMS Microbiology Ecology, Vol. 34, Issue 1
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
journal, October 2013
- Embree, Mallory; Nagarajan, Harish; Movahedi, Narjes
- The ISME Journal, Vol. 8, Issue 4
Synergistic effects of soil microstructure and bacterial EPS on drying rate in emulated soil micromodels
journal, April 2015
- Deng, Jinzi; Orner, Erika P.; Chau, Jessica Furrer
- Soil Biology and Biochemistry, Vol. 83
Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?
journal, February 2016
- Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas
- Frontiers in Microbiology, Vol. 7
Combining X-ray CT and 3D printing technology to produce microcosms with replicable, complex pore geometries
journal, August 2012
- Otten, W.; Pajor, R.; Schmidt, S.
- Soil Biology and Biochemistry, Vol. 51
Soil dry aggregate size distribution: effects of soil type and land use
journal, January 2012
- Ciric, V.; Manojlovic, M.; Nesic, Lj
- Journal of soil science and plant nutrition, Issue ahead
NanoSIMS Study of Organic Matter Associated with Soil Aggregates: Advantages, Limitations, and Combination with STXM
journal, March 2012
- Remusat, Laurent; Hatton, Pierre-Joseph; Nico, Peter S.
- Environmental Science & Technology, Vol. 46, Issue 7
High-resolution X-ray computed tomography in geosciences: A review of the current technology and applications
journal, August 2013
- Cnudde, V.; Boone, M. N.
- Earth-Science Reviews, Vol. 123
Pore size determination in modified micro- and mesoporous materials. Pitfalls and limitations in gas adsorption data analysis
journal, June 2003
- Groen, Johan C.; Peffer, Louk A. A.; Pérez-Ramı́rez, Javier
- Microporous and Mesoporous Materials, Vol. 60, Issue 1-3
The ‘Neglected’ Soil Virome – Potential Role and Impact
journal, August 2018
- Pratama, Akbar Adjie; van Elsas, Jan Dirk
- Trends in Microbiology, Vol. 26, Issue 8
Submicron scale imaging of soil organic matter dynamics using NanoSIMS – From single particles to intact aggregates
journal, January 2012
- Mueller, Carsten W.; Kölbl, Angelika; Hoeschen, Carmen
- Organic Geochemistry, Vol. 42, Issue 12
Build your own soil: exploring microfluidics to create microbial habitat structures
journal, November 2017
- Aleklett, Kristin; Kiers, E. Toby; Ohlsson, Pelle
- The ISME Journal, Vol. 12, Issue 2
Denitrification in Soil Aggregate Analogues-Effect of Aggregate Size and Oxygen Diffusion
journal, April 2018
- Schlüter, Steffen; Henjes, Sina; Zawallich, Jan
- Frontiers in Environmental Science, Vol. 6
Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site
journal, February 2011
- Kerkhof, Lee J.; Williams, Ken H.; Long, Philip E.
- Environmental Science & Technology, Vol. 45, Issue 4
Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria
journal, October 2014
- Hol, Felix J. H.; Dekker, Cees
- Science, Vol. 346, Issue 6208
Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)
journal, July 2008
- Eickhorst, Thilo; Tippkötter, Rolf
- Soil Biology and Biochemistry, Vol. 40, Issue 7
Sampling Natural Viral Communities from Soil for Culture-Independent Analyses
journal, November 2003
- Williamson, K. E.; Wommack, K. E.; Radosevich, M.
- Applied and Environmental Microbiology, Vol. 69, Issue 11
Internal Domains of Natural Porous Media Revealed: Critical Locations for Transport, Storage, and Chemical Reaction
journal, February 2016
- Zachara, John; Brantley, Sue; Chorover, Jon
- Environmental Science & Technology, Vol. 50, Issue 6
Embracing the unknown: disentangling the complexities of the soil microbiome
journal, August 2017
- Fierer, Noah
- Nature Reviews Microbiology, Vol. 15, Issue 10
Soil mineral–organic matter–microbe interactions: Impacts on biogeochemical processes and biodiversity in soils
journal, November 2005
- Huang, Pan-Ming; Wang, Ming-Kuang; Chiu, Chih-Yu
- Pedobiologia, Vol. 49, Issue 6
The Spread of VA Mycorrhizal Fungal Hyphae in the Soil: Inoculum Types and External Hyphal Architecture
journal, July 1991
- Friese, Carl F.; Allen, Michael F.
- Mycologia, Vol. 83, Issue 4
Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought
journal, November 2017
- Smith, A. Peyton; Bond-Lamberty, Ben; Benscoter, Brian W.
- Nature Communications, Vol. 8, Issue 1
Syntrophy in anaerobic global carbon cycles
journal, December 2009
- McInerney, Michael J.; Sieber, Jessica R.; Gunsalus, Robert P.
- Current Opinion in Biotechnology, Vol. 20, Issue 6
Isolation and characterization of phage–host systems from the Baltic Sea ice
journal, December 2013
- Luhtanen, Anne-Mari; Eronen-Rasimus, Eeva; Kaartokallio, Hermanni
- Extremophiles, Vol. 18, Issue 1
Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA
journal, November 2007
- Ghosh, D.; Roy, K.; Williamson, K. E.
- Applied and Environmental Microbiology, Vol. 74, Issue 2
Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants
journal, January 2014
- Neumann, Dominik; Heuer, Anke; Hemkemeyer, Michael
- The ISME Journal, Vol. 8, Issue 6
Promotion and Inhibition of Soil Aggregate Stabilization by Micro-organisms
journal, October 1981
- Lynch, J. M.
- Microbiology, Vol. 126, Issue 2
Uncovering Earth’s virome
journal, August 2016
- Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
- Nature, Vol. 536, Issue 7617
Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model
journal, February 2016
- Evans, Sarah; Dieckmann, Ulf; Franklin, Oskar
- Soil Biology and Biochemistry, Vol. 93
Phage as agents of lateral gene transfer
journal, August 2003
- Canchaya, Carlos; Fournous, Ghislain; Chibani-Chennoufi, Sandra
- Current Opinion in Microbiology, Vol. 6, Issue 4
Lytic to temperate switching of viral communities
journal, March 2016
- Knowles, B.; Silveira, C. B.; Bailey, B. A.
- Nature, Vol. 531, Issue 7595
Abundance and Diversity of Viruses in Six Delaware Soils
journal, June 2005
- Williamson, K. E.; Radosevich, M.; Wommack, K. E.
- Applied and Environmental Microbiology, Vol. 71, Issue 6
Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments
journal, January 2010
- Miller, Lance D.; Mosher, Jennifer J.; Venkateswaran, Amudhan
- BMC Microbiology, Vol. 10, Issue 1
The distribution of nitrifying bacteria in soil aggregates
journal, January 1970
- Nishio, Michinori; Furusaka, Choseki
- Soil Science and Plant Nutrition, Vol. 16, Issue 1
Incidence of lysogeny within temperate and extreme soil environments
journal, October 2007
- Williamson, Kurt E.; Radosevich, Mark; Smith, David W.
- Environmental Microbiology, Vol. 9, Issue 10
Phage-host interactions in soil
journal, November 1994
- Marsh, P.; Wellington, E. M. H.
- FEMS Microbiology Ecology, Vol. 15, Issue 1-2
NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction
journal, June 2018
- Newsome, Laura; Lopez Adams, Rebeca; Downie, Helen F.
- FEMS Microbiology Ecology, Vol. 94, Issue 8
Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology
journal, January 2016
- Wu, Fabai; Dekker, Cees
- Chemical Society Reviews, Vol. 45, Issue 2
Quantifying water-stable soil aggregate turnover and its implication for soil organic matter dynamics in a model study
journal, October 2006
- De Gryze, S.; Six, J.; Merckx, R.
- European Journal of Soil Science, Vol. 57, Issue 5
Water flow between soil aggregates
journal, September 2006
- Carminati, A.; Kaestner, A.; Ippisch, O.
- Transport in Porous Media, Vol. 68, Issue 2
Bacterial growth and motility in sub-micron constrictions
journal, August 2009
- Mannik, J.; Driessen, R.; Galajda, P.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 35
The effect of aggregate size on water retention and pore structure of two silt loam soils of different genesis
journal, December 2007
- Lipiec, J.; Walczak, R.; Witkowska-Walczak, B.
- Soil and Tillage Research, Vol. 97, Issue 2
Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System
journal, August 2016
- Ho, Adrian; Angel, Roey; Veraart, Annelies J.
- Frontiers in Microbiology, Vol. 7
Visualization, modelling and prediction in soil microbiology
journal, September 2007
- O'Donnell, Anthony G.; Young, Iain M.; Rushton, Steven P.
- Nature Reviews Microbiology, Vol. 5, Issue 9
Physical fractionation of soil and structural and functional complexity in organic matter turnover
journal, September 2001
- Christensen, B. T.
- European Journal of Soil Science, Vol. 52, Issue 3
Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods
journal, June 2008
- Eickhorst, Thilo; Tippkötter, Rolf
- Soil Biology and Biochemistry, Vol. 40, Issue 6
Soil aggregates as massively concurrent evolutionary incubators
journal, April 2017
- Rillig, Matthias C.; Muller, Ludo AH; Lehmann, Anika
- The ISME Journal, Vol. 11, Issue 9
Spectral soil analysis and inference systems: A powerful combination for solving the soil data crisis
journal, December 2006
- McBratney, Alex B.; Minasny, Budiman; Viscarra Rossel, Raphael
- Geoderma, Vol. 136, Issue 1-2
Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes
journal, November 2018
- Schimel, Joshua P.
- Annual Review of Ecology, Evolution, and Systematics, Vol. 49, Issue 1
Micro-scale determinants of bacterial diversity in soil
journal, November 2013
- Vos, Michiel; Wolf, Alexandra B.; Jennings, Sarah J.
- FEMS Microbiology Reviews, Vol. 37, Issue 6
Alterations in anaerobic ammonium oxidation of paddy soil following organic carbon treatment estimated using 13C-DNA stable isotope probing
journal, December 2017
- Zhang, Qichun; Gu, Chao; Zhou, Huifang
- Applied Microbiology and Biotechnology, Vol. 102, Issue 3
Quantitative and qualitative microscale distribution of bacteria in soil
journal, October 2001
- Ranjard, Lionel; Richaume, Agnès
- Research in Microbiology, Vol. 152, Issue 8
Tomography of insulating biological and geological materials using focused ion beam (FIB) sectioning and low-kV BSE imaging
journal, March 2009
- Winter, D. A. Matthijs De; Schneijdenberg, C. T. W. M.; Lebbink, M. N.
- Journal of Microscopy, Vol. 233, Issue 3
Rates of Root and Organism Growth, Soil Conditions, and Temporal and Spatial Development of the Rhizosphere
journal, March 2006
- Watt, Michelle; Silk, Wendy K.; Passioura, John B.
- Annals of Botany, Vol. 97, Issue 5
Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge
journal, June 2016
- Frossard, Aline; Hammes, Frederik; Gessner, Mark O.
- Frontiers in Microbiology, Vol. 7
Microaggregates in soils
journal, August 2017
- Totsche, Kai Uwe; Amelung, Wulf; Gerzabek, Martin H.
- Journal of Plant Nutrition and Soil Science, Vol. 181, Issue 1
A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics
journal, September 2004
- Six, J.; Bossuyt, H.; Degryze, S.
- Soil and Tillage Research, Vol. 79, Issue 1
A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling
journal, January 1996
- Paerl, H. W.; Pinckney, J. L.
- Microbial Ecology, Vol. 31, Issue 3
Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event: Microbial resuscitation in biological soil crusts
journal, May 2013
- Angel, Roey; Conrad, Ralf
- Environmental Microbiology
Spatial distribution of microbial biomass in microaggregates of a silty-loam soil and the relation with the resistance of microorganisms to soil drying
journal, April 1996
- Van Gestel, M.; Merckx, R.; Vlassak, K.
- Soil Biology and Biochemistry, Vol. 28, Issue 4-5
Rhizosphere Soil Aggregation and Plant Growth Promotion of Sunflowers by an Exopolysaccharide-Producing Rhizobium sp. Strain Isolated from Sunflower Roots
journal, August 2000
- Alami, Y.; Achouak, W.; Marol, C.
- Applied and Environmental Microbiology, Vol. 66, Issue 8
Sorption kinetics of hydrophobic organic compounds to natural sediments and soils
journal, July 1986
- Wu, Shian Chee.; Gschwend, Philip M.
- Environmental Science & Technology, Vol. 20, Issue 7
Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh: Sulfur cycling in pink berries of the Sippewissett Marsh
journal, February 2014
- Wilbanks, Elizabeth G.; Jaekel, Ulrike; Salman, Verena
- Environmental Microbiology, Vol. 16, Issue 11
Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis
journal, July 2001
- Orphan, V. J.
- Science, Vol. 293, Issue 5529
Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils
journal, November 2016
- Yan, Zhifeng; Liu, Chongxuan; Todd-Brown, Katherine E.
- Biogeochemistry, Vol. 131, Issue 1-2
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, August 2015
- Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
- The ISME Journal, Vol. 10, Issue 2
Ocean viruses and their effects on microbial communities and biogeochemical cycles
journal, September 2012
- Weitz, Joshua; Wilhelm, Steven
- F1000 Biology Reports
Spatial Ecology of Bacteria at the Microscale in Soil
journal, January 2014
- Raynaud, Xavier; Nunan, Naoise
- PLoS ONE, Vol. 9, Issue 1
Tuning a Genetic Switch: Experimental Evolution and Natural Variation of Prophage Induction: Tuning the Genetic Switch of Phage λ
journal, October 2009
- Refardt, Dominik; Rainey, Paul B.
- Evolution, Vol. 64, Issue 4
Microbial competition in porous environments can select against rapid biofilm growth
journal, December 2016
- Coyte, Katharine Z.; Tabuteau, Hervé; Gaffney, Eamonn A.
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 2
Non-destructive Analysis of Oil-Contaminated Soil Core Samples by X-ray Computed Tomography and Low-Field Nuclear Magnetic Resonance Relaxometry: a Case Study
journal, May 2010
- Nakashima, Yoshito; Mitsuhata, Yuji; Nishiwaki, Junko
- Water, Air, & Soil Pollution, Vol. 214, Issue 1-4
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
journal, January 2016
- Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren
- PeerJ, Vol. 4
Soil microbes and community coalescence
journal, January 2016
- Rillig, Matthias C.; Lehmann, Anika; Aguilar-Trigueros, Carlos A.
- Pedobiologia, Vol. 59, Issue 1-2
Components and microbial biomass content of size fractions in soils of contrasting aggregation
journal, August 1991
- Jocteur Monrozier, L.; Ladd, J. N.; Fitzpatrick, R. W.
- Geoderma, Vol. 50, Issue 1-2
Denitrifiers and denitrifying activity in size fractions of a mollisol under permanent pasture and continuous cultivation
journal, January 1995
- Lensi, R.; Clays-Josserand, A.; Jocteur Monrozier, L.
- Soil Biology and Biochemistry, Vol. 27, Issue 1
Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition
journal, November 2001
- C., Chenu; J., Hassink; J., Bloem
- Biology and Fertility of Soils, Vol. 34, Issue 5
Co-culture systems and technologies: taking synthetic biology to the next level
journal, July 2014
- Goers, Lisa; Freemont, Paul; Polizzi, Karen M.
- Journal of The Royal Society Interface, Vol. 11, Issue 96
New methodology for soil aggregate fractionation to investigate phosphorus transformations in iron oxide-rich tropical agricultural soil: New fractionation method for tropical soil
journal, November 2016
- Garland, G.; Bünemann, E. K.; Six, J.
- European Journal of Soil Science, Vol. 68, Issue 1
Enhanced microbial degradation of pentachlorophenol from soil in the presence of earthworms: Evidence of functional bacteria using DNA-stable isotope probing
journal, February 2015
- Li, Xiaomin; Lin, Zhong; Luo, Chunling
- Soil Biology and Biochemistry, Vol. 81
Mercury Porosimetry: A General (Practical) Overview
journal, June 2006
- Giesche, Herbert
- Particle & Particle Systems Characterization, Vol. 23, Issue 1
Temperature dependent bacteriophages of a tropical bacterial pathogen
journal, November 2014
- Shan, Jinyu; Korbsrisate, Sunee; Withatanung, Patoo
- Frontiers in Microbiology, Vol. 5
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival
journal, September 2015
- Greening, Chris; Biswas, Ambarish; Carere, Carlo R.
- The ISME Journal, Vol. 10, Issue 3
Three-Dimensional Quantification of Intra-Aggregate Pore-Space Features using Synchrotron-Radiation-Based Microtomography
journal, January 2008
- Peth, S.; Horn, R.; Beckmann, F.
- Soil Science Society of America Journal, Vol. 72, Issue 4
Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions
journal, April 2009
- Li, Tianlun; Mazéas, Laurent; Sghir, Abdelghani
- Environmental Microbiology, Vol. 11, Issue 4
Patterns and ecological drivers of ocean viral communities
journal, May 2015
- Brum, J. R.; Ignacio-Espinoza, J. C.; Roux, S.
- Science, Vol. 348, Issue 6237
Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile
journal, January 2008
- Hansel, C. M.; Fendorf, S.; Jardine, P. M.
- Applied and Environmental Microbiology, Vol. 74, Issue 5
Interactive effects of root endophytes and arbuscular mycorrhizal fungi on an experimental plant community
journal, September 2013
- Rillig, Matthias C.; Wendt, Stefanie; Antonovics, Janis
- Oecologia, Vol. 174, Issue 1
Bacteriophage evolution differs by host, lifestyle and genome
journal, July 2017
- Mavrich, Travis N.; Hatfull, Graham F.
- Nature Microbiology, Vol. 2, Issue 9
Diversity and Ecology of Viruses in Hyperarid Desert Soils
journal, November 2015
- Zablocki, Olivier; Adriaenssens, Evelien M.; Cowan, Don
- Applied and Environmental Microbiology, Vol. 82, Issue 3
Model Demonstrating the Potential for Coupled Nitrification Denitrification in Soil Aggregates
journal, June 2005
- Kremen, Arie; Bear, Jacob; Shavit, Uri
- Environmental Science & Technology, Vol. 39, Issue 11
Direct Measurement of Oxygen Profiles and Denitrification Rates in Soil Aggregates1
journal, January 1985
- Sexstone, Alan J.; Revsbech, Niels Peter; Parkin, Timothy B.
- Soil Science Society of America Journal, Vol. 49, Issue 3
Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review
journal, June 2007
- Or, D.; Smets, B. F.; Wraith, J. M.
- Advances in Water Resources, Vol. 30, Issue 6-7
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
journal, September 2016
- Roux, Simon; Brum, Jennifer R.; Dutilh, Bas E.
- Nature, Vol. 537, Issue 7622
Detection of soil water in macropores of undisturbed soil using microfocus X-ray tube computerized tomography (μCT)
journal, September 2009
- Tippkötter, Rolf; Eickhorst, Thilo; Taubner, Heidi
- Soil and Tillage Research, Vol. 105, Issue 1
On the application of focused ion beam nanotomography in characterizing the 3D pore space geometry of Opalinus clay
journal, January 2011
- Keller, Lukas M.; Holzer, Lorenz; Wepf, Roger
- Physics and Chemistry of the Earth, Parts A/B/C, Vol. 36, Issue 17-18
Microbial diversity affects self-organization of the soil–microbe system with consequences for function
journal, October 2011
- Crawford, John W.; Deacon, Lewis; Grinev, Dmitri
- Journal of The Royal Society Interface, Vol. 9, Issue 71
Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems
journal, February 2013
- Drescher, Knut; Shen, Yi; Bassler, Bonnie L.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content
journal, June 2017
- Trivedi, Pankaj; Delgado‐Baquerizo, Manuel; Jeffries, Thomas C.
- Environmental Microbiology, Vol. 19, Issue 8
New techniques for isolation of single prokaryotic cells
journal, December 2000
- Fröhlich, Jürgen; König, Helmut
- FEMS Microbiology Reviews, Vol. 24, Issue 5
Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture
journal, December 2000
- Six, J.; Elliott, E. T.; Paustian, K.
- Soil Biology and Biochemistry, Vol. 32, Issue 14
Contributions of interacting biological mechanisms to soil aggregate stabilization in restored prairie1The submitted manuscript has been created by the University of Chicago as operator of Argonne National Laboratory under Contract No. W-31-109-ENG-38 with the U.S. Department of Energy.1
journal, July 1998
- Jastrow, J. D.; Miller, R. M.; Lussenhop, J.
- Soil Biology and Biochemistry, Vol. 30, Issue 7
Spatial complexity of soil organic matter forms at nanometre scales
journal, March 2008
- Lehmann, Johannes; Solomon, Dawit; Kinyangi, James
- Nature Geoscience, Vol. 1, Issue 4
Changes in bacterial communities and Azospirillum diversity in soil fractions of a tropical soil under 3 or 19years of natural fallow
journal, August 2002
- Chotte, Jean-Luc; Schwartzmann, Alexia; Bally, René
- Soil Biology and Biochemistry, Vol. 34, Issue 8
Defined spatial structure stabilizes a synthetic multispecies bacterial community
journal, November 2008
- Kim, H. J.; Boedicker, J. Q.; Choi, J. W.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 47
Dynamics of bacterial communities in relation to soil aggregate formation during the decomposition of 13C-labelled rice straw
journal, February 2012
- Blaud, A.; Lerch, T. Z.; Chevallier, T.
- Applied Soil Ecology, Vol. 53
Flow cytometry discrimination between bacteria and clayâhumic acid particles during growth-linked biodegradation of phenanthrene by Pseudomonas aeruginosa 19SJ
journal, February 2003
- Resina-Pelfort, Olga; GarcÃa-Junco, Marta; Ortega-Calvo, José Julio
- FEMS Microbiology Ecology, Vol. 43, Issue 1
Bacterial Synergism in Lignocellulose Biomass Degradation – Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source
journal, October 2017
- Cortes-Tolalpa, Larisa; Salles, Joana F.; van Elsas, Jan Dirk
- Frontiers in Microbiology, Vol. 8
Organic matter and water-stable aggregates in soils
journal, June 1982
- Tisdall, J. M.; Oades, J. M.
- Journal of Soil Science, Vol. 33, Issue 2
Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments: Syntrophic butyrate oxidation facilitated by nanoFe
journal, August 2014
- Li, Huijuan; Chang, Jiali; Liu, Pengfei
- Environmental Microbiology, Vol. 17, Issue 5
Cold-active bacteriophages from the Baltic Sea ice have diverse genomes and virus-host interactions: Comparative genomics of the sea-ice phages
journal, October 2014
- Senčilo, Ana; Luhtanen, Anne-Mari; Saarijärvi, Mikko
- Environmental Microbiology, Vol. 17, Issue 10
Interactions and Self-Organization in the Soil-Microbe Complex
journal, June 2004
- Young, I. M.
- Science, Vol. 304, Issue 5677
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
journal, March 2017
- Howard-Varona, Cristina; Hargreaves, Katherine R.; Abedon, Stephen T.
- The ISME Journal, Vol. 11, Issue 7
Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability
journal, July 2009
- Boedicker, James Q.; Vincent, Meghan E.; Ismagilov, Rustem F.
- Angewandte Chemie International Edition, Vol. 48, Issue 32
Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model
journal, June 2016
- Ebrahimi, Ali; Or, Dani
- Global Change Biology, Vol. 22, Issue 9
In Situ Spatial Patterns of Soil Bacterial Populations, Mapped at Multiple Scales, in an Arable Soil
journal, December 2002
- Nunan, N.; Wu, K.; Young, I. M.
- Microbial Ecology, Vol. 44, Issue 4
Soil aggregate isolation method affects measures of intra-aggregate extracellular enzyme activity
journal, February 2014
- Bach, Elizabeth M.; Hofmockel, Kirsten S.
- Soil Biology and Biochemistry, Vol. 69
Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics
journal, April 2014
- Rinke, Christian; Lee, Janey; Nath, Nandita
- Nature Protocols, Vol. 9, Issue 5
Determining the composition of mineral-organic mixes using UV–vis–NIR diffuse reflectance spectroscopy
journal, December 2006
- Viscarra Rossel, R. A.; McGlynn, R. N.; McBratney, A. B.
- Geoderma, Vol. 137, Issue 1-2
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
journal, July 2015
- Roux, Simon; Hallam, Steven J.; Woyke, Tanja
- eLife, Vol. 4
3D printing of microscopic bacterial communities
journal, October 2013
- Connell, J. L.; Ritschdorff, E. T.; Whiteley, M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 46
Microaggregates in Soils1
journal, March 1967
- Edwards, A. P.; Bremner, J. M.
- Journal of Soil Science, Vol. 18, Issue 1
Pore-scale simulation of gas diffusion in unsaturated soil aggregates: Accuracy of the dusty-gas model and the impact of saturation
journal, October 2017
- Li, Zhongyang; Zhang, Xiaoxian; Liu, Yuan
- Geoderma, Vol. 303
Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O
journal, February 2007
- Schwartz, E.
- Applied and Environmental Microbiology, Vol. 73, Issue 8
Silicon Hyperuniform Disordered Photonic Materials with a Pronounced Gap in the Shortwave Infrared
journal, December 2013
- Muller, Nicolas; Haberko, Jakub; Marichy, Catherine
- Advanced Optical Materials, Vol. 2, Issue 2
Elevated Abundance of Bacteriophage Infecting Bacteria in Soil
journal, January 2003
- Ashelford, K. E.; Day, M. J.; Fry, J. C.
- Applied and Environmental Microbiology, Vol. 69, Issue 1
Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases
journal, January 2018
- Bravo, Andrea G.; Zopfi, Jakob; Buck, Moritz
- The ISME Journal, Vol. 12, Issue 3
Microbial Population Structures in Soil Particle Size Fractions of a Long-Term Fertilizer Field Experiment
journal, September 2001
- Sessitsch, A.; Weilharter, A.; Gerzabek, M. H.
- Applied and Environmental Microbiology, Vol. 67, Issue 9
Works referencing / citing this record:
Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media
journal, October 2019
- Kleyer, Hannah; Tecon, Robin; Or, Dani
- Applied and Environmental Microbiology, Vol. 86, Issue 1
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journal, June 2020
- Berg, Gabriele; Rybakova, Daria; Fischer, Doreen
- Microbiome, Vol. 8, Issue 1
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journal, December 2019
- Baquero, Fernando; Coque, Teresa M.; Martínez, José-Luis
- Frontiers in Microbiology, Vol. 10
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text, January 2020
- Kleyer, Hannah; Tecon, Robin; Or, Dani
- ETH Zurich