scholarly journals Spike Formation Is a Turning Point Determining Wheat Root Microbiome Abundance, Structures and Functions

2021 ◽  
Vol 22 (21) ◽  
pp. 11948
Author(s):  
Alla Usyskin-Tonne ◽  
Yitzhak Hadar ◽  
Dror Minz
Keyword(s):  
Developmental Stage ◽  
Vegetative Growth ◽  
Root Zone ◽  
Antibiotic Production ◽  
Wheat Root ◽  
Root Surface ◽  
Resistance Mechanisms ◽  
Wheat Growth ◽  
Microbiome Composition ◽  
Microbe Interactions

Root selection of their associated microbiome composition and activities is determined by the plant’s developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor’s antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant–microbe and microbe–microbe interactions in the developing root zone.

scholarly journals Wheat Root and Rhizosphere Microbiome Structures and Functions Along Plant Growth

2021 ◽  
Author(s):  
Alla Usyskin-Tonne ◽  
Dror Minz ◽  
Yitzhak Hadar
Keyword(s):  
Developmental Stage ◽  
Root Zone ◽  
Antibiotic Production ◽  
Root Exudation ◽  
Wheat Root ◽  
Root Surface ◽  
Beta Lactam ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Structure And Functions

Abstract Background Roots select their associated microbiome and affect its composition and activities through exudates that provide a nutrient-rich environment based on distance from the root. Root-exudation patterns depend on the plant's developmental stage. We followed field-grown wheat from emergence to spike maturation and compared the structure and functions of the microbiomes in two niches: adjacent, root-associated bacteria and the rhizosphere. The effects of growth stage on root-associated and rhizospheric communities structure and functions were investigated to enhance our understanding of plant–microbe interactions. Results A significant impact of wheat developmental stage during the transition from vegetative growth to spike formation was observed on structure and functions of both root-associated and rhizosphere microbiomes. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Three microbiome functional clusters were specifically associated with root proximity: (1) biofilm and sensorial movement; (2) antibiotic production and resistance; and (3) carbon biosynthesis, degradation and transporters, and amino acid biosynthesis and transporters. Interestingly, in the root-associated microbiome, genes related to all of these functions were influenced by spike formation. Abundance of genes related to nine other functions (lipopolysaccharide transporter and biosynthesis, beta-lactam resistance, metabolism of methane, alanine-aspartate-glutamate and arginine-proline, and biosynthesis of peptidoglycan, lysine and enediyne antibiotics) was significantly influenced by spike formation in both roots and rhizosphere. All of these genes were abundant in the rhizosphere, more so before spike formation when root exudation is high, supporting the notion that some of the root exudates are not fully utilized by the root-associated bacteria and subsequently diffuse into the surrounding soil, creating the rhizosphere. Conclusions We demonstrated functional division in the microbiome of the wheat root zone in both time and space: pre- and post-spike formation and root-associated vs. rhizospheric niches. The responses of the root microbiome were driven by both the plant and the microbial physiology and activities, both of which respond to environmental cues. These findings shed light on the dynamics of plant–microbe and microbe–microbe interactions in the root zone.

Effectiveness of complex inoculation of spring wheat with N[2] -fi xing bacteria Azospirillum brasilense and mold-antagonist Chaetomium cochliodes

2014 ◽  
Vol 1 (3) ◽  
pp. 57-61
Author(s):  
E. Kopylov
Keyword(s):  
Spring Wheat ◽  
Root Zone ◽  
Wheat Root ◽  
Root Surface ◽  
Atmospheric Nitrogen ◽  
Rhizospheric Soil ◽  
Chain Reaction ◽  
Wheat Roots ◽  
Chlorophyll A And B ◽  
Polymerase Chain

Aim. To study the specifi cities of complex inoculation of spring wheat roots with the bacteria of Azospirillum genus and Chaetomium cochliodes Palliser 3250, and the isolation of bacteria of Azospirillum genus, capable of fi xing atmospheric nitrogen, from the rhizospheric soil, washed-off roots and histoshere. Materials and meth- ods. The phenotypic features of the selected bacteria were identifi ed according to Bergi key. The molecular the polymerase chain reaction and genetic analysis was used for the identifi cation the bacteria. Results. It has been demonstrated that during the introduction into the root system of spring wheat the strain of A. brasilensе 102 actively colonizes rhizospheric soil, root surface and is capable of penetrating into the inner plant tissues. Conclusions. The soil ascomucete of C. cochliodes 3250 promotes better settling down of Azospirillum cells in spring wheat root zone, especially in plant histosphere which induces the increase in the content of chlorophyll a and b in the leaves and yield of the crop.

scholarly journals The Rhizosphere Talk Show: The Rhizobia on Stage

2020 ◽  
Vol 2 ◽  
Author(s):  
Alice Checcucci ◽  
Marta Marchetti
Keyword(s):  
Biotic Interactions ◽  
Root Surface ◽  
Talk Show ◽  
Microbiome Composition ◽  
Complex Interactions ◽  
Complex Process ◽  
Bacterial Quorum Sensing ◽  
Microbe Interactions ◽  
Bacterial Quorum ◽  
The Relationship

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.

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

2022 ◽  
Vol 12 ◽  
Author(s):  
Cécile Gruet ◽  
Daniel Muller ◽  
Yvan Moënne-Loccoz
Keyword(s):  
Mycorrhizal Fungi ◽  
Evolutionary History ◽  
Large Body ◽  
Taxonomic Diversity ◽  
Wheat Root ◽  
Wheat Species ◽  
Sequencing Technologies ◽  
The World ◽  
Baseline Information ◽  
Microbe Interactions

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

scholarly journals Health and disease markers correlate with gut microbiome composition across thousands of people

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ohad Manor ◽  
Chengzhen L. Dai ◽  
Sergey A. Kornilov ◽  
Brett Smith ◽  
Nathan D. Price ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Lifestyle Factors ◽  
Clinical Markers ◽  
Human Gut ◽  
Microbiome Composition ◽  
Targeted Interventions ◽  
Human Gut Microbiome ◽  
Host Diet ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Abstract Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.

Rhythmic patterns of nutrient acquisition by wheat roots

2002 ◽  
Vol 29 (5) ◽  
pp. 595 ◽  
Author(s):  
Sergey Shabala ◽  
Andrew Knowles
Keyword(s):  
Root Zone ◽  
Root Hairs ◽  
Rhythmic Activity ◽  
Root Apex ◽  
Root Surface ◽  
Ion Flux ◽  
Nutrient Acquisition ◽  
Wheat Roots ◽  
Non Invasive ◽  
Functional Zone

Oscillatory patterns in H+, K+, Ca2+ and Cl- uptake were observed at different regions of the root surface, including root hairs, using a non-invasive ion flux measuring technique (the MIFE™ technique). To our knowledge, this is the first report of ultradian oscillations in nutrient acquisition in the mature root zone. Oscillations of the largest magnitude were usually measured in the elongation region, 2–4 mm from the root apex. There were usually at least two oscillatory components present for each ion measured: fast, with periods of several minutes; and slow, with periods of 50–80 min. Even within the same functional zone, the periods of ion flux oscillations were significantly different, suggesting that they are driven by some internal mechanisms located in each cell rather than originating from one ‘central clock pacemaker’. There were also significant changes in the oscillatory characteristics (both periods and amplitudes) of fluxes from a single small cluster of cells over time. Analysis of phase shifts between oscillations in different ions suggested that rhythmic activity of a plasma membrane H+-pump may be central to observed rhythmic nutrient acquisition by plant roots. We discuss the possible adaptive significance of such an oscillatory strategy for root nutrient acquisition.

Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Qihui Hou ◽  
Ilana Kolodkin-Gal
Keyword(s):  
Plant Growth ◽  
Antibiotic Production ◽  
Resistance Mechanisms ◽  
Plant Growth Promoting Bacteria ◽  
Plant Defences ◽  
Wide Range ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Rhizosphere Environment ◽  
Plant Microbiome

ABSTRACT A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.

scholarly journals Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function

2020 ◽  
Author(s):  
Alla Usyskin-Tonne ◽  
Yitzhak Hadar ◽  
Uri Yermiyahu ◽  
Dror Minz
Keyword(s):  
Bacterial Abundance ◽  
Root Exudation ◽  
Microbial Community Composition ◽  
Wheat Root ◽  
Root Surface ◽  
Structure And Function ◽  
Secretion Systems ◽  
Functional Changes ◽  
And Function ◽  
Mannose Metabolism

AbstractElevated CO2 stimulates plant growth and affects quantity and composition of root exudates, followed by response of its microbiome. Three scenarios representing nitrate fertilization regimes: limited (30 ppm), moderate (70 ppm) and excess nitrate (100 ppm) were compared under ambient and elevated CO2 (eCO2, 850 ppm) to elucidate their combined effects on root-surface-associated bacterial community abundance, structure and function. Wheat root-surface-associated microbiome structure and function, as well as soil and plant properties, were highly influenced by interactions between CO2 and nitrate levels. Relative abundance of total bacteria per plant increased at eCO2 under excess nitrate. Elevated CO2 significantly influenced the abundance of genes encoding enzymes, transporters and secretion systems. Proteobacteria, the largest taxonomic group in wheat roots (~ 75%), is the most influenced group by eCO2 under all nitrate levels. Rhizobiales, Burkholderiales and Pseudomonadales are responsible for most of these functional changes. A correlation was observed among the five gene-groups whose abundance was significantly changed (secretion systems, particularly type VI secretion system, biofilm formation, pyruvate, fructose and mannose metabolism). These changes in bacterial abundance and gene functions may be the result of alteration in root exudation at eCO2, leading to changes in bacteria colonization patterns and influencing their fitness and proliferation.

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