Editorial: Rhizosphere Functioning and Structural Development as Complex Interplay Between Plants, Microorganisms and Soil Minerals

Mueller, Carsten W.; Carminati, Andrea; Kaiser, Christina; Subke, Jens‐Arne; Gutjahr, Caroline

doi:10.3389/fenvs.2019.00130

Cited by 25 publications

(20 citation statements)

References 6 publications

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“…Generally, organotrophic bacteria proliferate faster in the soil than actinobacteria as a result of organic matter inflow to the natural environment [13]. Such a response of microorganisms is not always associated with their ecological diversity [48]. In the present study, the highest value of the ecophysiological diversity index (EP) of organotrophic bacteria was determined in the winter wheat rhizosphere (0.877) and that of actinobacteria in the field pea rhizosphere.…”

Section: Counts and Diversity Of Bacteriamentioning

confidence: 52%

“…The k strategists, i.e., the slow-growing bacteria, are more stable in this respect. They are responsible for maintaining soil homeostasis, and are also resistant to the adverse effects of environmental conditions [67], as well as being typical of soil ecosystems [15,48].…”

Section: Counts and Diversity Of Bacteriamentioning

confidence: 99%

“…Under natural conditions, microbiome stability is largely affected by the species of growing plant and, especially, by its root system [41,48]. By providing water-soluble compounds to plants, including organic acids, sugars, or amino acids, the roots of plants stimulate the microbiological activity of soil [68,69], whereas plant growth promoting bacteria (PGPR) colonize roots and increase the root system biomass [40,70].…”

Section: Counts and Diversity Of Bacteriamentioning

confidence: 99%

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Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

et al. 2019

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This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

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Section: Counts and Diversity Of Bacteriamentioning

confidence: 52%

Section: Counts and Diversity Of Bacteriamentioning

confidence: 99%

Section: Counts and Diversity Of Bacteriamentioning

confidence: 99%

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Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

et al. 2019

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“…Particularly, the structural and biochemical complexity and spatial arrangement of microbes of the rhizosphere as the main driver of terrestrial biogeochemical cycles is little understood. To explore such relationships between multiple components (Ganther et al, 2020), it is crucial to characterize all soil components whilst keeping their structural and chemical integrity i.e., chemical composition and spatial organization of minerals, non-living organic matter and microbial counterparts such as bacteria, fungi, and plant roots during the analysis (Nunan et al, 2007;Mueller et al, 2013Mueller et al, , 2019Steffens et al, 2017;Vidal et al, 2018;Juyal et al, 2019Juyal et al, , 2020Fadel et al, 2020). The main reason that confines studies to a single discipline, rather than expanding to combinatorial characterization is associated with sample preparation.…”

Section: Introductionmentioning

confidence: 99%

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context

et al. 2021

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During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro− to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.

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“…Therefore, the recent studies, focused on microbial community networks models (Melke et al, 2010;Barto et al, 2012;Succurro and Ebenhöh, 2018;Mai et al, 2019), have to be adapted to the complexity of the rhizosphere. The dissection of such rhizospheric communication is essential for the improvement of the benefic aspects of such communication (Mueller and Sachs, 2015;Checcucci et al, 2017;Mueller et al, 2019) with a view to agricultural applications.…”

Section: Discussionmentioning

confidence: 99%

The Rhizosphere Talk Show: The Rhizobia on Stage

Checcucci¹,

Marchetti²

2020

Front. Agron.

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From bacterial quorum sensing to the signals of bees, communication is the basis of biotic interactions. Frequently, more than two organisms can take part in the speeches, resulting in a complex network of cross-talks. Recent advances in plant-microbe interactions research have shown that communication, both inter-kingdom and intra-kingdom, is shaped by a broad spectrum of factors. In this context, the rhizosphere (i.e., the soil close to the root surface) provides a specific microhabitat where complex interactions occur. The complex environment that makes up the rhizosphere can select for certain microbial populations, which are adapted to this unique niche. Among them, rhizobia have emerged as an important component of the rhizospheric microbiome. The aim of this review is to explore the components of such a rhizospheric Talk Show in the frame of the rhizobium-legume interactions. This symbiosis is a complex process that involves several signals that can be shaped by plant rhizospheric exudates and microbiome composition. The relationship established by rhizobia with other rhizospheric organisms, together with the influence of the environmental factors, results in their beneficial role on host plant health. Here, we resume research accounting strategies, molecules, and organisms that influence the place of rhizobia in the rhizosphere. The focus is on the most recent approaches for the study and subsequent exploitation of the diversity of the organisms. Indeed, the study of plant-microbes communication and evolution is fundamental to develop highly efficient inoculants able to reduce the use of fertilizers in agriculture.

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Editorial: Rhizosphere Functioning and Structural Development as Complex Interplay Between Plants, Microorganisms and Soil Minerals

Cited by 25 publications

References 6 publications

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context

The Rhizosphere Talk Show: The Rhizobia on Stage

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