scholarly journals Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Marta Kinnunen-Grubb ◽  
Rumakanta Sapkota ◽  
Marta Vignola ◽  
Inês Marques Nunes ◽  
Mogens Nicolaisen
Keyword(s):  
Bacterial Communities ◽  
Fungal Pathogens ◽  
Triticum Turgidum ◽  
Wheat Root ◽  
Plant Evolution ◽  
Assembly Model ◽  
Wheat Evolution ◽  
Modern Wheat ◽  
Breeding Selection ◽  
Native Soils

ABSTRACT Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

scholarly journals Wheat domestication has dramatically affected the root-associated microbiome

2020 ◽  
Author(s):  
Marta Kinnunen-Grubb ◽  
Rumakanta Sapkota ◽  
Marta Vignola ◽  
Ines Marques Nunes ◽  
Mogens Nicolaisen
Keyword(s):  
Fungal Pathogens ◽  
Selective Pressure ◽  
Wheat Root ◽  
Plant Evolution ◽  
Wheat Cultivars ◽  
Assembly Model ◽  
Growth Phases ◽  
Wheat Evolution ◽  
Modern Wheat ◽  
Native Soils

Abstract Background: Plants-microbiome associations are the results of millions of years of co-evolution. Due to the accelerated plant evolution during domestication of crops and aided by cultivation in non-native highly managed soils, plant-microbe links created through co-evolution could have been lost. Therefore, we hypothesize that dramatic effects on the root-associated microbiome occurred during domestication of wheat.Results: To uncover domestication effects we analyzed root associated fungal and bacterial communities in a transect of wheat evolution including modern wheat cultivars, landraces, Triticum aestivum ssp. spelta and ancestors of wheat including T. turgidum ssp. dicoccum , T. monococcum ssp. monococcum and T. monococcum ssp. aegilopoides at three growth phases shortly after emergence of seedlings. We found that numbers of observed microbial taxa were highest in the landraces, which had been domesticated in low-input agricultural systems, and lowest in wheat ancestors that evolved in native soils. The root-associated microbial community of modern cultivars was significantly different from that of landraces and ancestors of wheat. Old wheat accessions enriched Acidobacteria and Actinobacteria , while modern cultivars enriched OTUs from Candidatus Saccharibacteria , Verrucomicrobia and Firmicutes . The fungal pathogens Fusarium , Neoascochyta and Microdochium were enriched in modern cultivars. The composition of root-associated microbial communities of modern wheat cultivars significantly followed patterns predicted by the neutral community assembly model. Our observations allowed us to suggest that a stronger selective pressure drives the root-associated microbiome of ancient wheat accessions than that of modern wheat cultivars.Conclusions: Here we demonstrate that the wheat root-associated microbiome has dramatically changed through a transect of evolution from wheat ancestors over landraces to modern cultivars. Colonization of roots of ancient accessions was slower than in modern cultivars, and the root-associated microbiome of ancient wheat accessions was driven by stronger selective pressure than that of the modern wheat cultivars. We identified several taxa including Acidobacteria and Actinobacteria enriched in old cultivars and fungal wheat pathogens that were enriched in modern cultivars.

scholarly journals Role of ptsP, orfT, and sss Recombinase Genes in Root Colonization by Pseudomonas fluorescens Q8r1-96

2006 ◽  
Vol 72 (11) ◽  
pp. 7111-7122 ◽  
Author(s):  
Olga V. Mavrodi ◽  
Dmitri V. Mavrodi ◽  
David M. Weller ◽  
Linda S. Thomashow
Keyword(s):  
Pseudomonas Fluorescens ◽  
Fungal Pathogens ◽  
Root Colonization ◽  
Genomic Library ◽  
Wheat Root ◽  
Gene Replacement ◽  
Nitrogen Utilization ◽  
Gaeumannomyces Graminis ◽  
Natural Soil ◽  
Recombinase Gene

ABSTRACT Pseudomonas fluorescens Q8r1-96 produces 2,4-diacetylphloroglucinol (2,4-DAPG), a polyketide antibiotic that suppresses a wide variety of soilborne fungal pathogens, including Gaeumannomyces graminis var. tritici, which causes take-all disease of wheat. Strain Q8r1-96 is representative of the D-genotype of 2,4-DAPG producers, which are exceptional because of their ability to aggressively colonize and maintain large populations on the roots of host plants, including wheat, pea, and sugar beet. In this study, three genes, an sss recombinase gene, ptsP, and orfT, which are important in the interaction of Pseudomonas spp. with various hosts, were investigated to determine their contributions to the unusual colonization properties of strain Q8r1-96. The sss recombinase and ptsP genes influence global processes, including phenotypic plasticity and organic nitrogen utilization, respectively. The orfT gene contributes to the pathogenicity of Pseudomonas aeruginosa in plants and animals and is conserved among saprophytic rhizosphere pseudomonads, but its function is unknown. Clones containing these genes were identified in a Q8r1-96 genomic library, sequenced, and used to construct gene replacement mutants of Q8r1-96. Mutants were characterized to determine their 2,4-DAPG production, motility, fluorescence, colony morphology, exoprotease and hydrogen cyanide (HCN) production, carbon and nitrogen utilization, and ability to colonize the rhizosphere of wheat grown in natural soil. The ptsP mutant was impaired in wheat root colonization, whereas mutants with mutations in the sss recombinase gene and orfT were not. However, all three mutants were less competitive than wild-type P. fluorescens Q8r1-96 in the wheat rhizosphere when they were introduced into the soil by paired inoculation with the parental strain.

scholarly journals Rhizosphere Community Selection Reveals Bacteria Associated With Reduced Root Disease

2020 ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

Development and discrimination of 12 double ditelosomics in tetraploid wheat cultivar DR147

Genome ◽  
2014 ◽  
Vol 57 (2) ◽  
pp. 89-95 ◽  
Author(s):  
Hao Li ◽  
Changyou Wang ◽  
Shulan Fu ◽  
Xiang Guo ◽  
Baoju Yang ◽  
...  
Keyword(s):  
Triticum Turgidum ◽  
Wheat Cultivar ◽  
Aegilops Tauschii ◽  
Tetraploid Wheat ◽  
Chromosome Complement ◽  
Phenotypic Characteristics ◽  
Wheat Evolution ◽  
Important Group ◽  
Entire Chromosome

As an important group in Triticum, tetraploid wheat plays a significant role in the research of wheat evolution. Several complete aneuploid sets of common wheat have provided valuable tools for genetic and breeding studies, while similar aneuploids of tetraploid wheat are still not well developed. Here, 12 double ditelosomics developed in Triticum turgidum L. var. durum cultivar DR147 (excluding dDT2B and dDT3A) were reported. Hybrids between DR147 and the original double-ditelosomic dDT2B of Langdon lost vigor and died prematurely after the three-leaf stage; therefore, the dDT2B line was not obtained. The cytogenetic behaviors and phenotypic characteristics of each line were detailedly described. To distinguish the entire chromosome complement of tetraploid wheat, the DR147 karyotype was established by fluorescence in situ hybridization (FISH), using the Aegilops tauschii clone pAsl and the barley clone pHvG38 as probes. FISH using a cereal-specific centromere repeat (6C6) probe suggested that all the lines possessed four telosomes, except for 4AS of double-ditelosomic dDT4A, which carried a small segment of the long arm. On the basis of the idiogram of DR147, these lines were successfully discriminated by FISH using the probes pAsl and pHvG38 and were then accurately designated.

scholarly journals Evaluation of Equisetum arvense (Horsetail Macerate) as a Copper Substitute for Pathogen Management in Field-Grown Organic Tomato and Durum Wheat Cultivations

Agriculture ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 5
Author(s):  
Grazia Trebbi ◽  
Lorenzo Negri ◽  
Sara Bosi ◽  
Giovanni Dinelli ◽  
Riccardo Cozzo ◽  
...  
Keyword(s):  
Late Blight ◽  
Durum Wheat ◽  
Fungal Pathogens ◽  
Large Scale ◽  
Triticum Turgidum ◽  
Crop Protection ◽  
Puccinia Triticina ◽  
Equisetum Arvense ◽  
Zymoseptoria Tritici ◽  
Commercial Farms

Effective pathogen management, as an aspect of agroecological crop protection (ACP) necessitates the replacement of copper (Cu) fungicides, but there is little knowledge relating to the performance of potentially suitable alternatives in large-scale, open-field agricultural settings. The present study was aimed at investigating the potential of Equisetum arvense (horsetail macerate) compared to Cu-based treatments for the control of Solanum lycopersicum. and Triticum turgidum ssp. durum fungal pathogens in established organic commercial farms located in Emilia Romagna (Italy) over a three-year period (2017–2019). Both the Cu-based and horsetail foliar sprays were routinely applied as preventative treatments and in the event of pathogen establishment as curative treatments. The Cu-based and horsetail macerate treatments were both equally effective at significantly reducing Phytophthora infestans (late blight) and increasing yield in tomato compared to the untreated control. For durum wheat, the horsetail macerate and Cu-based treatments were successful at significantly reducing Puccinia triticina (brown rust) infection and increasing yield under moderate infection, but unsuccessful under unfavorable meteorological conditions resulting in the combined and severe spread of Puccinia triticina, Fusarium graminearum, and Zymoseptoria tritici. From the present results, horsetail macerate is a promising and suitable Cu-free ACP alternative for late blight management of tomato.

scholarly journals Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

2015 ◽  
Vol 81 (19) ◽  
pp. 6915-6925 ◽  
Author(s):  
Liam Lowrey ◽  
Douglas C. Woodhams ◽  
Luca Tacchi ◽  
Irene Salinas
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Bacterial Communities ◽  
Fungal Pathogens ◽  
Strong Predictor ◽  
Content Type ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Mucosal Surfaces ◽  
16S Rrna Pyrosequencing

ABSTRACTThe mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut.Flectobacilluswas highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Usingin vitroassays, we demonstrated that twoArthrobactersp. skin isolates, aPsychrobactersp. strain, and a combined skin aerobic bacterial sample inhibit the growth ofSaprolegnia australisandMucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases.

scholarly journals Rhizosphere community selection reveals bacteria associated with reduced root disease

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

scholarly journals Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

2019 ◽  
Author(s):  
Inbar Bariah ◽  
Danielle Keidar-Friedman ◽  
Khalil Kashkush
Keyword(s):  
Transposable Element ◽  
Bread Wheat ◽  
Large Scale ◽  
Triticum Turgidum ◽  
Wheat Genome ◽  
Wild Emmer ◽  
Genomic Rearrangements ◽  
Computer Assisted ◽  
Wheat Evolution ◽  
Underlying Mechanisms

Abstract Background: Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. Results: In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they occurred via unequal intra-strand recombination or double-strand break (DSB) events. In most cases, indels breakpoints were located within transposable element sequences. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Conclusions: Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.

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