scholarly journals Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens

2020 ◽  
Author(s):  
Erqin Li ◽  
Henan Jiang ◽  
Corné M.J. Pieterse ◽  
Alexandre Jousset ◽  
Peter A.H.M. Bakker ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Reverse Genetics ◽  
Plant Root ◽  
Plant Immunity ◽  
Plant Performance ◽  
Nucleotide Polymorphisms ◽  
Bacterial Adaptation ◽  
Global Regulators ◽  
Rhizosphere Colonization ◽  
Beneficial Microorganisms

AbstractBeneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including the ability to outcompete neighboring microorganisms and suppression of plant immunity. Forward and reverse genetics approaches have led to the identification of diverse mechanisms that are used by beneficial microorganisms to overcome these challenges such as the production of iron-chelating compounds, biofilm formation, or downregulation of plant immunity. However, how such mechanisms have developed from an evolutionary perspective is much less understood. In an attempt to study bacterial adaptation in the rhizosphere, we employed an experimental evolution approach to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens CHA0 in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant, and one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We found that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel in our evolutionary experiment, underlining several different strategies of bacterial adaptation to the rhizosphere. In total we identified 35 mutations, including single-nucleotide polymorphisms, smaller indels and larger deletions, distributed over 28 genes in total. Altogether these results underscore the strength of experimental evolution to identify key genes and pathways for bacterial rhizosphere colonization, as well as highlighting a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future.

scholarly journals Protists as main indicators and determinants of plant performance

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sai Guo ◽  
Wu Xiong ◽  
Xinnan Hang ◽  
Zhilei Gao ◽  
Zixuan Jiao ◽  
...  
Keyword(s):  
Plant Growth ◽  
Organic Fertilizer ◽  
Agricultural Practices ◽  
Plant Performance ◽  
Organic Fertilization ◽  
Plant Yield ◽  
Growing Seasons ◽  
Beneficial Microorganisms ◽  
Plant Growth Promoting ◽  
Plant Growth Promoting Microbes

Abstract Background Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. Results Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. Conclusions We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers.

scholarly journals Plant Root Hair Growth in Response to Hormones

2018 ◽  
Vol 47 (2) ◽  
pp. 278-281 ◽  
Author(s):  
Dejian ZHANG ◽  
Chunyan LIU ◽  
Yujie YANG ◽  
Qiangsheng WU ◽  
Yeyun LI
Keyword(s):  
Jasmonic Acid ◽  
Methyl Jasmonate ◽  
Root Hair ◽  
Hair Growth ◽  
Reverse Genetics ◽  
Current Knowledge ◽  
Plant Root ◽  
Root Surface Area ◽  
Acid Methyl ◽  
Root Hair Growth

Plant root hair is tubular projections from the root epidermis. Its can increase root surface area, which is very important for nutrients and water uptake as well as interaction with soil microorganisms. In this short review, we discussed the effects of hormones (auxin, ethylene, jasmonic acid, methyl jasmonate, strigolactones, and brassinosteroids) on root hair growth. It was highlight the interaction between auxin and ethylene on root hair growth. Furthermore, the mechanisms of jasmonic acid, methyl jasmonate, strigolactone and brassinosteroids on root hair growth may through auxin or ethylene signaling pathway partly. In future, more genes relating to root hair growth needed clone and elucidate their roles, as well as undertaking reverse genetics and mutant complementation studies to add the current knowledge of the signaling networks, which are involved in root hair growth that regulated by hormones.

scholarly journals Root hair specification and its growth in response to nutrients

2021 ◽  
Vol 49 (2) ◽  
pp. 12258
Author(s):  
Xian HUANG ◽  
Tianzhi GONG ◽  
Mei LI ◽  
Cenghong HU ◽  
Dejian ZHANG ◽  
...  
Keyword(s):  
Root Hair ◽  
Reverse Genetics ◽  
Current Knowledge ◽  
Plant Root ◽  
Root Hairs ◽  
Root Surface ◽  
Root Surface Area ◽  
Root Hair Development ◽  
Hair Development ◽  
Calcium Iron

Plant root hairs are cylindrical tubular projections from root epidermal cells. They increase the root surface area, which is important for the acquisition of water and nutrients, microbe interactions, and plant anchorage. The root hair specification, the effect of root hairs on nutrient acquisition and the mechanisms of nutrients (calcium, iron, magnesium, nitrogen, phosphorus, and potassium) that affect root hair development and growth were reviewed. The gene regulatory network on root hair specification in the plant kingdom was highlighted. More work is needed to clone the genes of additional root hair mutants and elucidate their roles, as well as undertaking reverse genetics and mutant complementation studies to add to the current knowledge of the signaling networks, which are involved in root hair development and growth regulated by nutrients.

scholarly journals Effect of inoculation of the plant root system by the endophyte Cylindrocarpon magnusianum on plant performance when exposed to heavy metal salts

2020 ◽  
Author(s):  
I. L. Bukharina ◽  
N. A. Islamova
Keyword(s):  
Heavy Metal ◽  
Root System ◽  
Plant Root ◽  
Metal Salts ◽  
Plant Performance ◽  
Heavy Metal Salts ◽  
Effective Partnership ◽  
Plant Root System

The effect of inoculation of Cylindrocarpon magnusianum on plants under the action of heavy metal salts was studied. Effective partnership of the fungus and plants was revealed in the conditions most extreme for the life of plants.

scholarly journals Shaping Bacterial Symbiosis With Legumes by Experimental Evolution

2014 ◽  
Vol 27 (9) ◽  
pp. 956-964 ◽  
Author(s):  
Marta Marchetti ◽  
Alain Jauneau ◽  
Delphine Capela ◽  
Philippe Remigi ◽  
Carine Gris ◽  
...  
Keyword(s):  
Immune Responses ◽  
Experimental Evolution ◽  
Plant Immunity ◽  
Parallel Evolution ◽  
In Planta ◽  
Plant Selection ◽  
Bacterial Symbiosis ◽  
Symbiotic Plasmid ◽  
Nodulation Competitiveness ◽  
Evolution Experiment

Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta–in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.

scholarly journals The Medical Triazole Voriconazole Can Select for Tandem Repeat Variations in Azole-Resistant Aspergillus Fumigatus Harboring TR34/L98H Via Asexual Reproduction

2020 ◽  
Vol 6 (4) ◽  
pp. 277
Author(s):  
Jianhua Zhang ◽  
Jan Zoll ◽  
Tobias Engel ◽  
Joost van den Heuvel ◽  
Paul E. Verweij ◽  
...  
Keyword(s):  
Aspergillus Fumigatus ◽  
Asexual Reproduction ◽  
Tandem Repeat ◽  
Experimental Evolution ◽  
High Frequency ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Single Nucleotide ◽  
Resistant Phenotype ◽  
Selection Of

Azole-resistant Aspergillus fumigatus isolates recovered at high frequency from patients, harbor mutations that are associated with variation of promoter length in the cyp51A gene. Following the discovery of the TR34/L98H genotype, new variations in tandem repeat (TR) length and number of repeats were identified, as well as additional single nucleotide polymorphisms (SNPs) in the cyp51A gene, indicating that the diversity of resistance mutations in A. fumigatus is likely to continue to increase. Investigating the development routes of TR variants is critical to be able to design preventive interventions. In this study, we tested the potential effects of azole exposure on the selection of TR variations, while allowing haploid A. fumigatus to undergo asexual reproduction. Through experimental evolution involving voriconazole (VOR) exposure, an isolate harboring TR343/L98H evolved from a clinical TR34/L98H ancestor isolate, confirmed by whole genome sequencing. TR343/L98H was associated with increased cyp51A expression and high VOR and posaconazole MICs, although additional acquired SNPs could also have contributed to the highly azole-resistant phenotype. Exposure to medical azoles was found to select for TR343, thus supporting the possibility of in-host selection of TR34 variants.

scholarly journals Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization in the presence of soil microbes

2021 ◽  
Author(s):  
Mathilde Nordgaard ◽  
Christopher Blake ◽  
Gergely Maroti ◽  
Mikael L. Strube ◽  
Akos T. Kovacs
Keyword(s):  
Arabidopsis Thaliana ◽  
Bacillus Subtilis ◽  
Experimental Evolution ◽  
Soil Microbes ◽  
Root Colonization ◽  
Plant Root ◽  
Phenotypic Characterization ◽  
Plant Interactions ◽  
Plant Polysaccharide ◽  
Selective Environment

The soil ubiquitous Bacillus subtilis is known to promote plant growth and protect plants against disease. These characteristics make B. subtilis highly relevant in an agricultural perspective, fueling the interest in studying B. subtilis-plant interactions. Here, we employ an experimental evolution approach to explore adaptation of B. subtilis to Arabidopsis thaliana roots. B. subtilis rapidly adapts to the plant root environment, as evidenced by improved root colonizers observed already after 12 consecutive transfers between seedlings in a hydroponic setup. Further phenotypic characterization of evolved isolates from transfer 30 revealed that increased root colonization was associated with robust biofilm formation in response to the plant polysaccharide xylan. Additionally, several evolved isolates across independent populations were impaired in motility, a redundant trait in the selective environment. Interestingly, two evolved isolates outcompeted the ancestor during competition on the root but suffered a fitness disadvantage in non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by a selected evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings provide novel insights into how a well-known PGPR rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.

scholarly journals Bacterial adaptation to diet is a key evolutionary force shaping Drosophila-Lactobacillus symbiosis

2018 ◽  
Author(s):  
Maria Elena Martino ◽  
Pauline Joncour ◽  
Ryan Leenay ◽  
Hugo Gervais ◽  
Malay Shah ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Lactobacillus Plantarum ◽  
Experimental Evolution ◽  
Driving Force ◽  
Bacterial Adaptation ◽  
Evolutionary Force ◽  
Host Growth ◽  
Growth Promoting ◽  
Facultative Symbiosis

AbstractAnimal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health (1–3). Yet, due to the flexible nature of their association, the selection pressures acting on animals and their facultative symbionts remain elusive (4, 5). Here, by applying experimental evolution to a well-established model of facultative symbiosis: Drosophila melanogaster associated with Lactobacillus plantarum, one of its growth promoting symbiont (6, 7), we show that the diet, instead of the host, is a predominant driving force in the evolution of this symbiosis and identify the mechanism resulting from the bacterial adaptation to the diet, which confers host growth benefits. Our study reveals that adaptation to the diet can be the foremost step in the determination of the evolutionary course of a facultative symbiosis.

scholarly journals OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa)

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yaomin Guo ◽  
Qi Wu ◽  
Zizhao Xie ◽  
Bo Yu ◽  
Rongfeng Zeng ◽  
...  
Keyword(s):  
Flowering Time ◽  
Flower Development ◽  
Reverse Genetics ◽  
Plant Root ◽  
Lateral Roots ◽  
Primary Root ◽  
Auxin Biosynthesis ◽  
Wild Type ◽  
Rice Plants ◽  
Ros Homeostasis

Abstract Background FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood. Results As a homologue of AtFPF1, FPF1-like protein 4 of rice (OsFPFL4) is expressed in various tissues of plants. The functions of OsFPFL4 in rice were investigated by the reverse genetics approaches. Plants overexpressing OsFPFL4 have shorter primary root, more lateral roots and adventitious roots than wild type; however, RNA interference (RNAi) of OsFPFL4 significantly inhibits the growth of root system, and also delays the flowering time in rice. Interestingly, increased or repressed expression of OsFPFL4 leads to shrunken anthers and abnormal pollen grains. It is well recognized that auxin plays important roles in plant root and flower development, and the root elongation is also regulated by reactive oxygen species (ROS) homeostasis. Here, our results show that rice plants overexpressing OsFPFL4 accumulate more auxin in the shoot and root, whereas RNAi lines have less auxin than wild type. As expected, the transcript levels of genes responsible for auxin biosynthesis and polar transport are altered in these OsFPFL4 transgenic plants. As to ROS, slightly higher ROS levels were detected in overexpression root and inflorescence than the counterparts of wild type; however, the ROS levels were significantly increased in the RNAi lines, due to increased expression of ROS-producers and reduced expression of ROS-scavengers. Conclusion Our results reveal that OsFPFL4 is involved in modulating the root and flower development by affecting auxin and ROS homeostasis in rice plants. OsFPFL4 controls auxin accumulation via affecting auxin biosynthesis and transport, and also modulates ROS homeostasis by balancing ROS producing and scavenging. Thus, auxin-mediated ROS production might play a role in regulating redox status, which controls plant root and flower development.

scholarly journals Polygenicity and epistasis underlie fitness-proximal traits in the Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel

2017 ◽  
Author(s):  
Luke M. Noble ◽  
Ivo Chelo ◽  
Thiago Guzella ◽  
Bruno Afonso ◽  
David D. Riccardi ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Experimental Evolution ◽  
Complex Traits ◽  
Genetic Basis ◽  
Natural Populations ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
C Elegans ◽  
Mapping Panel ◽  
Trait Locus

ABSTRACTUnderstanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty is problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here we report a recombinant inbred line (RIL) quantitative trait locus (QTL) mapping panel for the hermaphroditic nematode Caenorhabditis elegans, the C. elegans multiparental experimental evolution (CeMEE) panel. The CeMEE panel, comprising 507 RILs, was created by hybridization of 16 wild isolates, experimental evolution at moderate population sizes and predominant outcrossing for 140-190 generations, and inbreeding by selfing for 13-16 generations. The panel contains 22% of single nucleotide polymorphisms known to segregate in natural populations, and complements existing mapping resources for C. elegans by providing high nucleotide diversity across >95% of the genome. We apply it to study the genetic basis of two fitness components, fertility and hermaphrodite body size at time of reproduction, with high broad sense heritability in the CeMEE. While simulations show we should detect common alleles with additive effects as small as 5%, at gene-level resolution, the genetic architectures of these traits does not feature such alleles. We instead find that a significant fraction of trait variance, particularly for fertility, can be explained by sign epistasis with weak main effects. In congruence, phenotype prediction, while generally poor (r2 < 10%), requires modeling epistasis for optimal accuracy, with most variance attributed to the highly recombinant, rapidly evolving chromosome arms.

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