scholarly journals Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis

2021 ◽  
Author(s):  
Philipp Wendering ◽  
Zoran Nikoloski
Keyword(s):  
Mycorrhizal Fungi ◽  
Molecular Mechanisms ◽  
Arbuscular Mycorrhizal ◽  
Dry Weight ◽  
Metabolic Model ◽  
Rhizophagus Irregularis ◽  
Plant Performance ◽  
System Level ◽  
Cofactor Biosynthesis ◽  
Genome Scale

Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here we used all published genomics, transcriptomics, and metabolomics resources to gain insights in the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to: (1) accurately predict increased growth of R. irregularis on myristate with minimal medium; (2) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (= 0.74) to measured hyphal dry weight; and (3) simulated growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance.

scholarly journals Effects of Arbuscular Mycorrhizal Fungi on Gazania rigens Pot Plant Cultivation in a Mediterranean Environment

2018 ◽  
Vol 47 (1) ◽  
pp. 221-226 ◽  
Author(s):  
Leo SABATINO ◽  
Fabio D’ANNA ◽  
Livio TORTA ◽  
Giorgio FERRARA ◽  
Giovanni IAPICHINO
Keyword(s):  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Dry Weight ◽  
Rhizophagus Irregularis ◽  
High Performing ◽  
Beneficial Effects ◽  
Bedding Plants ◽  
Plant Cultivation ◽  
Bedding Plant

Herbaceous plants used in island beds and borders need to be rapid growing, high performing and maintaining good visual quality during the growing season. Arbuscular mycorrhizal (AM) fungi application is acquiring interest for its beneficial effects on ornamental bedding plants. Gazania rigens is a herbaceous ornamental plant grown for its large daisy-like flowers. The species thrives in the coastal areas of the Mediterranean region, particularly in the mild climate of southern Italy and Sicily, where performs well in summer bedding schemes in sea side gardens even in dry and windy conditions. The aim of this study was to evaluate the effect of inoculation with Rhizophagus irregularis on several ornamental parameters of Gazania rigens. Prior to transplanting, three-months-old plants received a mycorrhizal inoculum carrying 40 spores g-1 of Rhizophagus irregularis. Inoculum was applied at a rate of 10 g plant-1. The AM application significantly increased number of flowers per clump by 100% and number of flowers per plant by 124.0%. Rhizophagus irregularis also positively influenced number of leaves per plant, plant height, and roots dry weight. Our findings indicated that mycorrhizal inoculation with R. irregularis may be beneficial to nursery growers wishing to produce high quality gazania for spring-summer bedding plant schemes.

scholarly journals Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Jingru Zhou ◽  
Yingping Zhuang ◽  
Jianye Xia
Keyword(s):  
Aspergillus Niger ◽  
Large Scale ◽  
Measurement Techniques ◽  
Metabolic Model ◽  
System Level ◽  
Metabolic Phenotype ◽  
Omics Data ◽  
Prediction Ability ◽  
Phenotype Prediction ◽  
Genome Scale

Abstract Background Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level. Results Based on the basic GSMM model iHL1210 of Aspergillus niger, we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of A. niger by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale $$k_{{cat}}$$ k cat values, predicting the differential expression of enzymes under different growth conditions. Conclusions This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with A. niger. Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of A. niger by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for A. niger, the enzyme-constrained GSMM model will show greater application space on the system level.

scholarly journals The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anurag Chaturvedi ◽  
Joaquim Cruz Corella ◽  
Chanz Robbins ◽  
Anita Loha ◽  
Laure Menin ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Plant Species ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal Fungus ◽  
Mycorrhizal Fungus ◽  
Arbuscular Mycorrhizal ◽  
Rhizophagus Irregularis ◽  
Functional Differences ◽  
Phosphate Regulation ◽  
Very High

AbstractEarly-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis.

scholarly journals A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression

Metabolites ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 456
Author(s):  
Pejman Salahshouri ◽  
Modjtaba Emadi-Baygi ◽  
Mahdi Jalili ◽  
Faiz M. Khan ◽  
Olaf Wolkenhauer ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Progression ◽  
Gut Microbiome ◽  
Metabolic Model ◽  
System Level ◽  
Mathematical Framework ◽  
Bacterial Populations ◽  
Colorectal Cancer Progression ◽  
Genome Scale ◽  
High Throughput Data Analysis

The human gut microbiota plays a dual key role in maintaining human health or inducing disorders, for example, obesity, type 2 diabetes, and cancers such as colorectal cancer (CRC). High-throughput data analysis, such as metagenomics and metabolomics, have shown the diverse effects of alterations in dynamic bacterial populations on the initiation and progression of colorectal cancer. However, it is well established that microbiome and human cells constantly influence each other, so it is not appropriate to study them independently. Genome-scale metabolic modeling is a well-established mathematical framework that describes the dynamic behavior of these two axes at the system level. In this study, we created community microbiome models of three conditions during colorectal cancer progression, including carcinoma, adenoma and health status, and showed how changes in the microbial population influence intestinal secretions. Conclusively, our findings showed that alterations in the gut microbiome might provoke mutations and transform adenomas into carcinomas. These alterations include the secretion of mutagenic metabolites such as H2S, NO compounds, spermidine and TMA, as well as the reduction of butyrate. Furthermore, we found that the colorectal cancer microbiome can promote inflammation, cancer progression (e.g., angiogenesis) and cancer prevention (e.g., apoptosis) by increasing and decreasing certain metabolites such as histamine, glutamine and pyruvate. Thus, modulating the gut microbiome could be a promising strategy for the prevention and treatment of CRC.

Response of Taxus times media var. densiformis to inoculation with arbuscular mycorrhizal fungi

1998 ◽  
Vol 28 (1) ◽  
pp. 150-153
Author(s):  
J N Gemma ◽  
R E Koske ◽  
E M Roberts ◽  
S Hester
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Glomus Intraradices ◽  
Arbuscular Mycorrhizal ◽  
Dry Weight ◽  
Root Systems ◽  
Stem Diameter ◽  
Rooted Cuttings ◽  
Shoot Dry Weight ◽  
Mycorrhizal Plants

Rooted cuttings of Taxus times media var. densiformis Rehd. were inoculated with the arbuscular mycorrhizal fungi Gigaspora gigantea (Nicol. & Gerd.) Gerd. & Trappe or Glomus intraradices Schenck and Smith and grown for 9-15 months in a greenhouse. At the completion of the experiments, leaves of inoculated plants contained significantly more chlorophyll (1.3-4.1 times as much) than did noninoculated plants. In addition, mycorrhizal plants had root systems that were significantly larger (1.3-1.4 times) and longer (1.7-2.1 times) than nonmycorrhizal plants, and they possessed significantly more branch roots (1.3-2.9 times). No differences in stem diameter and height or shoot dry weight were evident at the end of the experiments, although the number of buds was significantly greater in the cuttings inoculated with G. intraradices after 15 months.

scholarly journals Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

2018 ◽  
Author(s):  
Ivan D. Mateus ◽  
Frédéric G. Masclaux ◽  
Consolée Aletti ◽  
Edward C. Rojas ◽  
Romain Savary ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Arbuscular Mycorrhizal ◽  
Mycorrhizal Symbiosis ◽  
Rna Seq ◽  
Plant Host ◽  
Transcriptional Responses ◽  
Plant Genes ◽  
Fungal Genetic

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

scholarly journals Divergence in bidirectional plant-soil feedbacks between montane annual and coastal perennial ecotypes of yellow monkeyflower (Mimulus guttatus)

2020 ◽  
Author(s):  
Mariah M. McIntosh ◽  
Lorinda Bullington ◽  
Ylva Lekberg ◽  
Lila Fishman
Keyword(s):  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Plant Performance ◽  
Fungal Communities ◽  
Mechanistic Study ◽  
List Type ◽  
Mimulus Guttatus ◽  
Plant Variation ◽  
Plant Soil ◽  
Soil Origin

SUMMARYUnderstanding the physiological and genetic mechanisms underlying plant variation in interactions with root-associated biota (RAB) requires a micro-evolutionary approach. We use locally adapted montane annual and coastal perennial ecotypes of Mimulus guttatus (yellow monkeyflower) to examine population-scale differences in plant-RAB-soil feedbacks.We characterized fungal communities for the two ecotypes in-situ and used a full-factorial greenhouse experiment to investigate the effects of plant ecotype, RAB source, and soil origin on plant performance and endophytic root fungal communities.The two ecotypes harbored different fungal communities and responsiveness to soil biota was highly context-dependent. Soil origin, RAB source, and plant ecotype all affected the intensity of biotic feedbacks on plant performance. Feedbacks were primarily negative, and we saw little evidence of local adaptation to either soils or RAB. Both RAB source and soil origin significantly shaped fungal communities in roots of experimental plants. Further, the perennial ecotype was more colonized by arbuscular mycorrhizal fungi (AMF) than the montane ecotype, and preferentially recruited home AMF taxa.Our results suggest life history divergence and distinct edaphic habitats shape plant responsiveness to RAB and influence specific associations with potentially mutualistic root endophytic fungi. Our results advance the mechanistic study of intraspecific variation in plant–soil–RAB interactions.

Improvement of plant performance under water deficit with the employment of biological and chemical priming agents

2018 ◽  
Vol 156 (5) ◽  
pp. 680-688 ◽  
Author(s):  
R. Balestrini ◽  
W. Chitarra ◽  
C. Antoniou ◽  
M. Ruocco ◽  
V. Fotopoulos
Keyword(s):  
Mycorrhizal Fungi ◽  
Crop Production ◽  
Current Knowledge ◽  
Arbuscular Mycorrhizal ◽  
Plant Performance ◽  
Plant Tolerance ◽  
Climate Change Research ◽  
Chemical Agents ◽  
Chemical Priming

AbstractDrought represents one of the major constraints on agricultural productivity and food security and in future is destined to spread widely as a consequence of climate change. Research efforts are focused on developing strategies to make crops more resilient and to mitigate the effects of stress on crop production. In this context, the use of root-associated microbial communities and chemical priming strategies able to improve plant tolerance to abiotic stresses, including drought, have attracted increasing attention in recent years. The current review offers an overview of recent research aimed at verifying the role of arbuscular mycorrhizal fungi and chemical agents to improve plant tolerance to drought and to highlight the mechanisms involved in this improvement. Attention will be devoted mainly to current knowledge on the mechanisms involved in water transport.

scholarly journals Enhancement of Drought Tolerance in Trifoliate Orange by Mycorrhiza: Changes in Root Sucrose and Proline Metabolisms

2018 ◽  
Vol 46 (1) ◽  
pp. 270-276 ◽  
Author(s):  
Fei ZHANG ◽  
Jia-Dong HE ◽  
Qiu-Dan NI ◽  
Qiang-Sheng WU ◽  
Ying-Ning ZOU
Keyword(s):  
Drought Tolerance ◽  
Mycorrhizal Fungi ◽  
Water Status ◽  
Lateral Roots ◽  
Arbuscular Mycorrhizal ◽  
Dry Weight ◽  
Sucrose Phosphate Synthase ◽  
Poncirus Trifoliata ◽  
Trifoliate Orange ◽  
Am Symbiosis

Sucrose and proline metabolisms are often associated with drought tolerance of plants. This study was conducted to investigate the effects of two arbuscular mycorrhizal fungi (AMF) species (Funneliformis mosseae and Paraglomus occultum) on root biomass, lateral root number, root sucrose and proline metabolisms in trifoliate orange (Poncirus trifoliata) seedlings under well-watered (WW) or drought stress (DS). All the AMF treatments significantly increased root dry weight, taproot length, and the number of lateral roots in 1st, 2nd, and 3rd class under WW and DS. Mycorrhizal seedlings conferred considerably higher fructose and glucose concentrations but lower sucrose accumulation, regardless of soil water status. Under DS, F. mosseae treatment significantly increased root sucrose synthase (SS, degradative direction) and sucrose phosphate synthase (SPS) activity but deceased root acid invertase (AI) and neutral invertase (NI) activity, and P. occultum inoculation markedly increased root AI, NI, SS, and SPS activities. AMF treatments led to a lower proline accumulation in roots, in company with lower activities of Δ1-pyrroline-5-carboxylate synthetase (P5CS), δ-ornithine aminotransferase (OAT), Δ1-pyrroline-5-carboxylate reductase (P5CR), and proline dehydrogenase (ProDH) in roots. It appears that the AM symbiosis induced greater root development and sucrose and proline metabolisms to adapt DS.

scholarly journals Monosporic Inoculation of Economically Important Horticultural Species with Native Endomycorrhizae under Greenhouse Conditions

Agronomy ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 130
Author(s):  
Flor Hernandez ◽  
Rosalinda Villarreal ◽  
Valentin Torres ◽  
Adrien Gallou
Keyword(s):  
Mycorrhizal Fungi ◽  
Agricultural Intensification ◽  
Arbuscular Mycorrhizal ◽  
Dry Weight ◽  
Phosphorus Concentration ◽  
Root Weight ◽  
Fresh Weight ◽  
Flower Number ◽  
Total Dry Weight ◽  
Total Fresh Weight

Research into the symbiotic relationship between plants and arbuscular mycorrhizal fungi (AMF) is key for sustainable agricultural intensification. The objective of the present study is to evaluate native AMF at the monosporic level in greenhouse-grown, economically important crops. Agricultural soil samples from three locations (Saltillo, Zaragoza, and Parras) were obtained by combining portions resulting from a zigzag sampling pattern. From these samples, 15 morphotypes were extracted according to a modified Gerdemann’s technique and monosporically inoculated on melon, cucumber, tomato, and onion, 30 days after their sowing. Under a completely random experimental design, 16 treatments with three repetitions were defined. Plant height, root length, stem diameter, total fresh weight, fresh root weight, dry root weight, bulb weight, fresh leaf weight, total dry weight, flower number, leaf number, fruit number, spore number, and percentage of colonization were all evaluated. The results were subjected to the analysis of variance (ANOVA) and the Tukey comparison test (p ≤ 0.05), which showed that the monosporic inoculation favors significantly the AMF and the host, while the T6 (Saltillo spore + Steiner modified with 20% of the normal phosphorus concentration) showed a greater response uniformity on onion and melon, which indicates its great potential as an inoculum.

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