Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces

@article{Schmidt2018RecognizingPS,
  title={Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces},
  author={Hannes Schmidt and Naoise Nunan and Alexander H{\"o}ck and Thilo Eickhorst and Christina Kaiser and Dagmar Woebken and Xavier Raynaud},
  journal={Frontiers in Environmental Science},
  year={2018}
}
Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on the abundance and diversity of microbial communities at root-soil interfaces is now substantial, information on their spatial distribution at the microscale is still scarce. In this study, a standardized… 

Figures from this paper

Two-way microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging.
TLDR
The results indicate that two-way immigrant bacteria - resident microbiota interactions affect the microscale spatial organization of leaf microbiota, and possibly that of other surface-related microbial communities.
Framework for Quantification of the Dynamics of Root Colonization by Pseudomonas fluorescens Isolate SBW25
TLDR
A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization, which allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally.
Microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging
TLDR
It is indicated that two-way immigrant bacteria – resident microbiota interactions affect the microscale spatial organization of leaf microbial communities; and that preferential attachment – previously suggested as a general strategy that increases fitness under periodic stress – is a common surface colonization strategy.
Rhizosphere size and shape: Temporal dynamics and spatial stationarity
Rhizosphere Spatiotemporal Organization–A Key to Rhizosphere Functions
TLDR
It is proposed that the combination of modern experimental and modeling techniques, with a focus on imaging approaches, allows for understanding the complex feedbacks between plant resource acquisition, microbiome-related plant health, soil carbon sequestration, and soil structure development.
Characterization of Biofilm Formed by Phenanthrene-Degrading Bacteria on Rice Root Surfaces for Reduction of PAH Contamination in Rice
TLDR
The present work provides significant new insights into lowering the environmental risks of polycyclic aromatic hydrocarbons (PAHs) in crop products from contaminated agriculture soils.
Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces
TLDR
The role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization is addressed and a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities is introduced.
Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli
TLDR
This review synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role theirExudation plays in plant nutrient acquisition strategies, and proposes a novel conceptual framework forRoot exudates.
Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota
TLDR
This mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
...
1
2
3
...

References

SHOWING 1-10 OF 59 REFERENCES
Roots shaping their microbiome: global hotspots for microbial activity.
TLDR
A three-step enrichment model for shifts in community structure from bulk soil toward roots, based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, is presented.
Spatial Ecology of Bacteria at the Microscale in Soil
TLDR
This work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.
Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research
TLDR
The findings suggest that a careful evaluation of separation strategies prior to molecular community analysis is indispensable, especially when endophytes are the subject of interest.
Spatial scales of interactions among bacteria and between bacteria and the leaf surface
TLDR
Spatial point-pattern analyses prove a comprehensive tool to determine the different spatial scales of bacterial interactions on plant leaves and will help microbiologists to better understand the interplay between these interactions.
Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH).
TLDR
Efforts to manage rhizosphere bacteria for sustainable agricultural systems should continue to focus on root cap and mucilage chemistry, and remnant roots as sources of beneficial bacteria.
Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescence in situ hybridization.
TLDR
Root tips, elongation zones, and openings at the base of lateral roots represented preferential areas for microbial colonization, which were often covered with iron coatings and densely colonized with potential iron-oxidizing Betaproteobacteria (59% of bacteria).
Spatial Patterns of Rhizoplane Populations of Pseudomonas fluorescens
TLDR
Geostatistical analysis was used to compare rhizoplane colonization patterns of an antibiotic-producing biological control bacterium versus a non-antibiotic-producing mutant strain, indicating that the lack of phenazine production did not influence spatial patterns on the rhizplane.
Using stable isotopes to explore root-microbe-mineral interactions in soil
Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization.
TLDR
A spatial explicit approach was developed and applied that allowed the use of fluorescence in situ hybridization (FISH) to study bacterial phylloplane communities of environmentally grown Arabidopsis thaliana, and spatial aggregation patterns were observed for all probe-targeted populations at distances up to 7 μm.
Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy
TLDR
The scope of this review is to highlight the importance of confocal microscopy in the study of plant-microbe interactions and to be an inspiration for integrating microscopy with molecular techniques in future researches of microbial ecology.
...
1
2
3
4
5
...