scholarly journals Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Christine Jade Dilla-Ermita ◽  
Ricky W. Lewis ◽  
Tarah S. Sullivan ◽  
Scot H. Hulbert
Keyword(s):  
Abiotic Stress Tolerance ◽  
Root Disease ◽  
Disease Suppression ◽  
Growth Chamber ◽  
Wheat Genotypes ◽  
Microbiome Composition ◽  
Rhizoctonia Root Rot ◽  
Bacterial Microbiota ◽  
Controlled Environments ◽  
Viable Approach

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

Organic matter input influences incidence of root rot caused by Rhizoctonia solani AG8 and microorganisms associated with plant root disease suppression in three Australian agricultural soils

Soil Research ◽  
2019 ◽  
Vol 57 (4) ◽  
pp. 321 ◽  
Author(s):  
Rowena S. Davey ◽  
Ann M. McNeill ◽  
Stephen J. Barnett ◽  
Vadakattu V. S. R. Gupta
Keyword(s):  
Rhizoctonia Solani ◽  
Root Rot ◽  
Microbial Biomass Carbon ◽  
Plant Root ◽  
Abiotic Factors ◽  
Root Disease ◽  
Disease Suppression ◽  
Gaeumannomyces Graminis ◽  
Wheat Seedlings ◽  
Rhizoctonia Root Rot

Soil-borne plant root disease caused by Rhizoctonia solani AG8 is prevalent in cereal farming systems worldwide, particularly in semiarid agricultural regions. A controlled environment study was undertaken using three Australian soils to test the hypothesis that OM input from crop roots and residues decreases infection by Rhizoctonia root rot via biologically mediated disease suppression. The specific aim was to determine the relative effect of two different OM inputs (wheat stubble or roots) on (a) abundance (DNA) of the pathogen R. solani AG8 and soil organisms putatively associated with disease suppression, and (b) incidence of Rhizoctonia root rot infection of wheat seedlings (% root infected). An increase in microbial biomass carbon (C) following OM amendment indicated a potential for enhanced general biological disease suppression in all soils. OM inputs also increased the population size (DNA) of certain bacteria and fungi putatively associated with specific suppression for Rhizoctonia root rot, suggesting a C resource-mediated change in microbial functions related to disease suppression. There were no significant changes to measured pathogens with stubble addition. However, OM inputs via root residues and rhizodeposits from living roots increased the populations of R. solani AG8 and Gaeumannomyces graminis var. tritici so that in subsequently planted wheat there was greater incidence of root disease infection and reduced plant shoot and root DM compared with that following OM input as stubble. Differences between soils in terms of plant and soil organism responses to each OM input suggest that abiotic factors modify the development of biological disease suppression and the expression of the disease.

Plant-Microbiome Interactions for Bacterial Wilt Suppression in Modern Tobacco Production

2020 ◽  
Author(s):  
Raymond O. García-Rodríguez ◽  
Lindsey D. Thiessen
Keyword(s):  
Management Strategies ◽  
Soil Health ◽  
Disease Suppression ◽  
Current Management ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Sequencing Technologies ◽  
Bacterial Microbiota ◽  
Culture Independent ◽  
Functional Capacities

The soil-borne bacterium Ralstonia solanacearum continues to represent a major threat to flue-cured tobacco (Nicotiana tabacum) production in the southeastern United States and other major producing regions throughout the world. Beneficial microorganisms naturally found in the soil represent an alternative solution for R. solanacearum’s suppression that may reduce soil health impacts of current management strategies. Biological controls and microbiota manipulation together represent a unique opportunity to reduce disease caused by R. solanacearum. Current high-throughput DNA sequencing technologies and advances in bioinformatic analyses enable culture-independent approaches to study root-associated microorganisms and their interactions. The structure and dynamics of tobacco root-associated microbiota, as well as functional capacities of certain taxa, may improve how we apply disease management strategies in the field. Through this review we summarize our current understanding on (i) the role of bacterial microbiota on R. solanacearum survival, (ii) the impacts of current management strategies on the soil bacterial communities, (iii) the rhizospheric and core microbiome composition and inheritance, (iv) the manipulation of the microbiota for enhanced disease suppression, and (v) the shortcomings of the application of plant-associated bacteria for disease suppression.

A new approach to the search for indicators of root disease suppression

1999 ◽  
Vol 28 (1) ◽  
pp. 4 ◽  
Author(s):  
A.H.C. van Bruggen ◽  
A.M. Semenov
Keyword(s):  
Root Disease ◽  
Disease Suppression ◽  
New Approach

Effectiveness of 3 antagonistic bacterial isolates to control Rhizoctonia solani Kühn on lettuce and potato

2005 ◽  
Vol 51 (4) ◽  
pp. 345-353 ◽  
Author(s):  
Rita Grosch ◽  
Franziska Faltin ◽  
Jana Lottmann ◽  
A Kofoet ◽  
Gabriele Berg
Keyword(s):  
Rhizoctonia Solani ◽  
Pseudomonas Fluorescens ◽  
Biological Control Agent ◽  
Dry Mass ◽  
Control Agent ◽  
Disease Suppression ◽  
Growth Chamber ◽  
Bacterial Strains ◽  
Serratia Plymuthica ◽  
Suppression Effect

Rhizoctonia solani causes yield losses in numerous economically important European crops. To develop a biocontrol strategy, 3 potato-associated ecto- and endophytically living bacterial strains Pseudomonas fluorescens B1, Pseudomonas fluorescens B2, and Serratia plymuthica B4 were evaluated against R. solani in potato and in lettuce. The disease-suppression effect of the 3 biocontrol agents (BCAs) was tested in a growth chamber and in the field. In growth chamber experiments, all 3 BCAs completely or significantly limited the dry mass (DM) losses on lettuce and the disease severity (DS) caused by R. solani on potato sprouts. Strain B1 showed the highest suppression effect (52% on average) on potato. Under field conditions, the DS on both crops, which were bacterized, decreased significantly, and the biomass losses on lettuce decreased significantly as well. The greatest disease-suppression effect on potato was achieved by strain B1 (37%), followed by B2 (33%) and then B4 (31%), whereas the marketable tuber yield increased up to 12% (B1), 6% (B2), and 17% (B4) compared with the pathogen control at higher disease pressure. Furthermore, in all experiments, B1 proved to be the most effective BCA against R. solani. Therefore, this BCA could be a candidate for developing a commercial product against Rhizoctonia diseases. To our knowledge, this is the first report on the high potential of endophytes to be used as a biological control agent against R. solani under field conditions.Key words: biocontrol, Rhizoctonia solani, field grown lettuce and potato, antagonistic bacteria, endophytes.

Relationships between the responses of spring wheat genotypes to temperature and photoperiodic treatments and their performance in the field

1981 ◽  
Vol 96 (3) ◽  
pp. 623-634 ◽  
Author(s):  
Margaret A. Ford ◽  
R. B. Austin ◽  
W. J. Angus ◽  
G. C. M. Sage
Keyword(s):  
Spring Wheat ◽  
Field Experiments ◽  
Sowing Date ◽  
Photoperiodic Response ◽  
Low Latitude ◽  
Wheat Varieties ◽  
Wheat Genotypes ◽  
The North ◽  
Controlled Environments ◽  
Late Sowing

SUMMARYThirty-eight spring wheat genotypes of north temperate or low latitude origin, all reasonably well adapted to the English environment, were grown in controlled environments providing the four combinations of 10 and 14 h photoperiods and temperatures of 8 and 16 °C for 6 weeks. They were then transferred to a glasshouse to assess their responses to these treatments. In separate experiments the responses of the genotypes to vernalization for 2 and 4 weeks at 2 and 8 °C were compared with unvernalized controls. The genotypes were also compared in field experiments from early, intermediate or late sowing over 3 years.Both high temperatures and long days hastened ear emergence. At the higher temperature more leaves and spikelets were produced on the main stem while in long days the plants had fewer leaves and spikelets.Most genotypes of north temperate and low latitude origin were responsive to photoperiod but not to the vernalization treatments. As a group, the low latitude ones were as responsive as the north temperate group. Five genotypes of north temperate origin were responsive to vernalization but not to photoperiod and were designated as ‘winter’ ones. Pitic 62 and Hork, from low latitudes, were responsive to vernalization and Hork was unique in also being responsive to photoperiod. The main difference between the north temperate and low latitude genotypes was in time to ear emergence and it is suggested that these differences were due to the effects of earliness genes as distinct from those determining photoperiodic response.Taking all genotypes individually there were no correlations between yield or its sensitivity to sowing date and any of the attributes measured in controlled environments. However, considering class means, the winter genotypes were the latest to reach ear emergence in the field, and their yields, while greatest from the earliest sowings, were proportionally more depressed by late sowing than the others of the north temperate origin. Thus, it may be unwise for plant breeders to incorporate a vernalization response in spring wheat varieties unless genes for ‘earliness’ are also included. The low latitude class gave only slightly lower yields than the north temperate class.It is concluded that genes other than those controlling responses to photoperiod, temperature and vernalization were more important determinants of the differences in yield among this set of genotypes.

scholarly journals Mango Endophyte and Epiphyte Microbiome Composition during Fruit Development and Post-Harvest Stages

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 495
Author(s):  
Malick Bill ◽  
Lizyben Chidamba ◽  
Jarishma Keriuscia Gokul ◽  
Lise Korsten
Keyword(s):  
Fruit Development ◽  
Management Strategies ◽  
Development Stage ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
Post Harvest ◽  
Bacterial Microbiota ◽  
Target Effect ◽  
Generation Sequencing

The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.

scholarly journals Glyphosate and its formulations Roundup Bioflow and RangerPro alter bacterial and fungal community composition in the rat caecum microbiome

2021 ◽  
Author(s):  
Robin Mesnage ◽  
Simona Panzacchi ◽  
Emma Bourne ◽  
Charles A Mein ◽  
Melissa Perry ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Dependent Manner ◽  
Fungal Community Composition ◽  
Potential Health ◽  
Opportunistic Fungi ◽  
Microbiome Composition ◽  
Bacterial Microbiota ◽  
Multigenerational Effects

The potential health consequences of glyphosate-induced gut microbiome alterations have become a matter of intense debate. As part of a multifaceted study investigating toxicity, carcinogenicity and multigenerational effects of glyphosate and its commercial herbicide formulations, we assessed changes in bacterial and fungal populations in the caecum microbiota of rats exposed prenatally until adulthood (13 weeks after weaning) to three doses of glyphosate (0.5, 5, 50 mg/kg body weight/day), or to the formulated herbicide products Roundup Bioflow and RangerPro at the same glyphosate-equivalent doses. Caecum bacterial microbiota were evaluated by 16S rRNA sequencing whilst the fungal population was determined by ITS2 amplicon sequencing. Results showed that both fungal and bacterial diversity were affected by the Roundup formulations in a dose-dependent manner, whilst glyphosate alone significantly altered only bacterial diversity. At taxa level, a reduction in Bacteroidota abundance, marked by alterations in the levels of Alloprevotella, Prevotella and Prevotellaceae UCG-003, was concomitant to increased levels of Firmicutes (e.g., Romboutsia, Dubosiella, Eubacterium brachy group or Christensenellaceae) and Actinobacteria (e.g., Enterorhabdus, Adlercreutzia, or Asaccharobacter). Treponema and Mycoplasma also had their levels reduced by the pesticide treatments. Analysis of fungal composition indicated that the abundance of the rat gut commensal Ascomycota Kazachstania was reduced while the abundance of Gibberella, Penicillium, Claviceps, Cornuvesica, Candida, Trichoderma and Sarocladium were increased by exposure to the Roundup formulations, but not to glyphosate. Altogether, our data suggest that glyphosate and its Roundup RangerPro and Bioflow caused profound changes in caecum microbiome composition by affecting the fitness of major commensals, which in turn reduced competition and allowed opportunistic fungi to grow in the gut, in particular in animals exposed to the herbicide formulations. This further indicates that changes in gut microbiome composition might influence the long-term toxicity, carcinogenicity and multigenerational effects of glyphosate-based herbicides.

scholarly journals Understanding the Interactions between Biomass, Grain Production and Grain Protein Content in High and Low Protein Wheat Genotypes under Controlled Environments

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 706 ◽  
Author(s):  
Vahid Rahimi Eichi ◽  
Mamoru Okamato ◽  
Stephan M. Haefele ◽  
Nathaniel Jewell ◽  
Chris Brien ◽  
...  
Keyword(s):  
Protein Content ◽  
Growth Analysis ◽  
Cropping Systems ◽  
Fertilizer Application ◽  
Grain Protein Content ◽  
Grain Protein ◽  
Biomass Growth ◽  
Wheat Genotypes ◽  
Absolute Growth ◽  
Controlled Environments

Grain protein content (GPC) is a key quality attribute and an important marketing trait in wheat. In the current cropping systems worldwide, GPC is mostly determined by nitrogen (N) fertilizer application. The objectives of this study were to understand the differences in N response between high and low GPC wheat genotypes, and to assess the value of biomass growth analysis to assess the differences in N response. Six wheat genotypes from a range of high to low GPC were grown in low, medium and high N, under glasshouse conditions. This experiment was designed around non-destructive estimation of biomass using a high throughput image-based phenotyping system. Results showed that Spitfire and Mace had higher grain N% than Gazelle and QAL2000, and appeared to demand more N to grow their biomass. Moreover, at low N, Spitfire grew faster and achieved the maximum absolute growth rate earlier than high N-treated plants. High grain N% genotypes seem able to manage grain N reserves by compromising biomass production at low N. This study also indicated the importance of biomass growth analysis to show the differences in the N responsiveness of high and low GPC wheat.

scholarly journals Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths

2020 ◽  
Vol 8 (4) ◽  
pp. 483 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Esaki M. Shankar ◽  
Marcello Chieppa ◽  
Rajaraman Eri ◽  
Kylie Kavanagh
Keyword(s):  
Significant Proportion ◽  
Genetic Material ◽  
Clinical Applications ◽  
Health It ◽  
Human Gut ◽  
Marked Influence ◽  
Microbiome Composition ◽  
Bacterial Microbiota ◽  
Potential Impact

Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.

scholarly journals Structure, variation, and assembly of the root-associated microbiomes of rice

2015 ◽  
Vol 112 (8) ◽  
pp. E911-E920 ◽  
Author(s):  
Joseph Edwards ◽  
Cameron Johnson ◽  
Christian Santos-Medellín ◽  
Eugene Lurie ◽  
Natraj Kumar Podishetty ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Growth Promotion ◽  
Geographical Location ◽  
Methanogenic Archaea ◽  
Root Surface ◽  
Disease Suppression ◽  
Microbial Consortia ◽  
Structure Variation ◽  
Microbiome Composition ◽  
Multistep Model

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.

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