Online citations, reference lists, and bibliographies.
← Back to Search

Microbial Diversity Affects Self-organization Of The Soil–microbe System With Consequences For Function

J. Crawford, L. Deacon, D. Grinev, J. A. Harris, K. Ritz, B. K. Singh, I. Young
Published 2011 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.
This paper references
10.1016/J.SEDGEO.2005.12.012
Translation of energy into morphology : Simulation of stromatolite morphospace using a stochastic model
C. Dupraz (2006)
10.1016/J.SOILBIO.2010.10.010
Microbial biogeography at the soil pore scale
L. Ruamps (2011)
10.1016/S0065-2113(08)00604-4
Microbial distribution in soils: physics and scaling
I. Young (2008)
10.1007/s00253-008-1565-4
Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities
Ursel M. E. Schütte (2008)
10.1007/s00248-006-9062-8
Three-dimensional Microorganization of the Soil–Root–Microbe System
Debbie S. Feeney (2006)
10.1111/J.1365-2389.1997.TB00564.X
The origin and loss of fractal scaling in simulated soil aggregates
J. Crawford (1997)
10.1051/agro:2008052
Integration of soil structure variations with time and space into models for crop management. A review
J. Roger-Estrade (2011)
10.1128/AEM.63.11.4516-4522.1997
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
W. T. Liu (1997)
10.1016/J.PHYSA.2004.01.065
A case for biotic morphogenesis of coniform stromatolites
M. Batchelor (2004)
Soil as a paradigm of a complex system
K. Ritz (2008)
10.1111/J.1365-2389.1982.TB01755.X
Organic matter and water‐stable aggregates in soils
J. Tisdall (1982)
Microbial distribution in soils: physics
A. Spiers (2008)
10.1016/0038-0717(78)90099-8
A physiological method for the quantitative measurement of microbial biomass in soils
J. Anderson (1978)
10.1016/J.ADVWATRES.2006.05.025
Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review
D. Or (2007)
Inte - gration of soil structure variations with time and space into models for crop management
D. L. Sparks (2009)
10.1111/J.2006.0030-1299.14337.X
Antagonism between bacteria and fungi: substrate competition and a possible tradeoff between fungal growth and tolerance towards bacteria
C. Mille-Lindblom (2006)
10.1073/pnas.0800244105
Environmental regulation in a network of simulated microbial ecosystems
H. T. Williams (2008)
10.1038/nprot.2006.392
Multiplex-terminal restriction fragment length polymorphism
B. Singh (2006)
Pesticide mobility: lysimeter study
C. J. Fryer (1997)
10.1126/science.1172975
Soil Microbial Communities and Restoration Ecology: Facilitators or Followers?
J. Harris (2009)
10.1016/b978-0-12-179726-3.x5000-x
Fundamentals of Soil Ecology
J. Lussenhop (1996)
10.1016/J.JAS.2008.04.018
X-ray microtomographic imaging of charcoal
M. Bird (2008)
10.1016/0038-0717(78)90098-6
Mineralization of bacteria and fungi in chloroform-fumigated soils
J. Anderson (1978)
10.1128/AEM.00510-06
Use of Multiplex Terminal Restriction Fragment Length Polymorphism for Rapid and Simultaneous Analysis of Different Components of the Soil Microbial Community▿
B. Singh (2006)
10.1016/0016-7061(93)90002-3
Soils as biotic constructs favouring net primary productivity
N. Breemen (1993)
Physical constraints affecting
S. P. Friedman (2007)
Soils as biotic constructs favouring
N. van Breeman (1993)
Soil microbial communities and restoration ecology: facilitators or followers? Science
J. Harris (2009)
10.1016/S0065-2113(08)00604-4
Chapter 4 Microbial Distribution in Soils
I. Young (2008)
10.1038/nrmicro1714
Visualization, modelling and prediction in soil microbiology
A. O'donnell (2007)
10.1016/J.GEODERMA.2008.11.028
Soils as extended composite phenotypes
J. Phillips (2009)
10.1029/2004WR003818
A mass balance based numerical method for the fractional advection‐dispersion equation: Theory and application
Xiaoxian Zhang (2005)
10.1126/SCIENCE.1097394
Interactions and Self-Organization in the Soil-Microbe Complex
I. Young (2004)
10.1016/S1002-0160(08)60018-1
Simultaneous Preservation of Soil Structural Properties and Phospholipid Proflles: A Comparison ofThree Drying Techniques
L. J. Deacon (2008)
10.1111/J.1365-2389.2004.00670.X
Structural differences between bulk and rhizosphere soil
W. R. Whalley (2005)
10.1016/J.JHYDROL.2004.08.039
Determination of soil hydraulic conductivity with the lattice Boltzmann method and soil thin-section technique
Xiaoxian Zhang (2005)
10.1139/O59-099
A rapid method of total lipid extraction and purification.
E. Bligh (1959)
10.1016/0167-7012(91)90018-L
Microbial biomass measured as total lipid phosphate in soils of different organic content
Å. Frostegård (1991)
10.1007/s11104-008-9717-y
Disentangling the impact of AM fungi versus roots on soil structure and water transport
P. Hallett (2008)



This paper is referenced by
10.1038/s41598-017-14904-w
The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface
J. Helliwell (2017)
10.1111/oik.07213
Resilience trinity: safeguarding ecosystem functioning and services across three different time horizons and decision contexts
H. Weise (2020)
10.1007/s10533-017-0409-7
The Millennial model: in search of measurable pools and transformations for modeling soil carbon in the new century
R. Abramoff (2017)
Discrete-continuum continuum multiscale model for transport, biofilm development and solid restructuring in porous media
Von (2016)
10.1186/s13007-017-0220-4
Quantification of seed–soil contact of sugar beet (Beta vulgaris) using X-ray Computed Tomography
S. Blunk (2017)
10.1007/s11104-013-1621-4
Impact of two root systems, earthworms and mycorrhizae on the physical properties of an unstable silt loam Luvisol and plant production
Roxane Kohler-Milleret (2013)
10.7287/peerj.preprints.1398v1
Microbial interactions and implications for oil biodegradation 2 process in mangrove sediments 3
A. D. Grativol (2015)
10.1111/EJSS.12028
Applications of X‐ray computed tomography for examining biophysical interactions and structural development in soil systems: a review
J. R. Helliwell (2013)
10.1007/978-3-030-10777-2_1
Carbon Cycle Implications of Soil Microbial Interactions
Kelly I. Ramin (2019)
10.1016/J.GEODERMA.2015.02.010
Establishing microbial diversity and functions in weathered and neutral Cu–Pb–Zn tailings with native soil addition☆
Xiaofang Li (2015)
10.1016/j.scitotenv.2019.07.154
Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes.
L. Huang (2019)
10.1038/s41598-020-67631-0
Soil as an extended composite phenotype of the microbial metagenome
A. Neal (2020)
10.1016/J.ADVWATRES.2017.04.001
Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media
N. Ray (2017)
10.1097/SS.0000000000000155
Ecosystem Engineers in a Self-organized Soil: A Review of Concepts and Future Research Questions
P. Lavelle (2016)
10.1007/s11104-020-04592-3
Change in hydraulic properties of the rhizosphere of maize under different abiotic stresses
Di Wang (2020)
10.1038/ismej.2013.87
Linking microbial community structure to β-glucosidic function in soil aggregates
V. Bailey (2013)
10.1016/J.CLAY.2020.105845
Microaggregation of goethite and illite evaluated by mechanistic modeling
Simon Zech (2020)
10.1038/srep16261
Protection of soil carbon within macro-aggregates depends on intra-aggregate pore characteristics
A. Kravchenko (2015)
10.1016/J.SOILBIO.2014.03.009
Quantifying the impact of microbes on soil structural development and behaviour in wet soils
J.R.. Helliwell (2014)
10.1016/J.GEODERMA.2020.114738
High water availability in drought tolerant crops is driven by root engineering of the soil micro-habitat
S. M. F. Rabbi (2021)
10.2136/VZJ2015.09.0131
Modeling Soil Processes: Review, Key Challenges, and New Perspectives
H. Vereecken (2016)
10.1038/s41598-019-43937-6
Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype
A. Bacq-Labreuil (2019)
Interactions between microbial community structure and pathogen survival in soil
E. Moynihan (2012)
10.1002/JPLN.201600451
Microaggregates in soils
K. U. Totsche (2018)
10.14264/UQL.2015.940
Rehabilitation of organic carbon and microbial community structure and functions in Cu-Pb-Zn mine tailings for in situ engineering technosols
Fang You (2015)
10.1016/j.envpol.2020.115933
Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates.
Jiuwei Song (2020)
10.1016/J.AGEE.2014.03.022
Oil mallee biochar improves soil structural properties—A study with x-ray micro-CT
P. Quin (2014)
10.3389/fenvs.2018.00140
Root Exudates Induce Soil Macroaggregation Facilitated by Fungi in Subsoil
V. Baumert (2018)
10.1186/s13007-017-0162-x
Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (µCT)
Saoirse R. Tracy (2017)
Application of ecological theory to explain microbial regulation of soil function
C. Trivedi (2017)
10.1007/698_2020_568
Bioavailability as a Microbial System Property: Lessons Learned from Biodegradation in the Mycosphere
L. Wick (2020)
10.3390/computation3010058
Visual Simulation of Soil-Microbial System Using GPGPU Technology
R. Falconer (2015)
See more
Semantic Scholar Logo Some data provided by SemanticScholar