scholarly journals In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

2021 ◽  
Vol 2 ◽  
Author(s):  
Merce Montoliu-Nerin ◽  
Marisol Sánchez-García ◽  
Claudia Bergin ◽  
Verena Esther Kutschera ◽  
Hanna Johannesson ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
De Novo ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Sister Group ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Phylogenomic Analysis ◽  
Wide Range ◽  
Genome Assemblies

Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.

scholarly journals In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

2021 ◽  
Author(s):  
Merce Montoliu-Nerin ◽  
Marisol Sánchez-García ◽  
Claudia Bergin ◽  
Verena Esther Kutschera ◽  
Hanna Johannesson ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
De Novo ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Sister Group ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Phylogenomic Analysis ◽  
Wide Range ◽  
Genome Assemblies

Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the phylogeny and evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates high-quality genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. Based on analyses of sets of orthologous genes, we highlight three alternative topologies among families of AM fungi. In the main topology, Glomerales is polyphyletic and Claroideoglomeraceae, is the basal sister group to Glomeraceae and Diversisporales. Our results support family level classification from previous phylogenetic studies. New evolutionary relationships among families where highlighted with phylogenomic analysis using the hitherto most extensive taxon sampling for AM fungi.

scholarly journals Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Merce Montoliu-Nerin ◽  
Marisol Sánchez-García ◽  
Claudia Bergin ◽  
Manfred Grabherr ◽  
Barbara Ellis ◽  
...  
Keyword(s):  
Large Scale ◽  
Method Development ◽  
De Novo ◽  
Sequence Data ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Life Cycles ◽  
Suitable Model ◽  
Eukaryotic Microorganisms ◽  
Genome Assemblies

AbstractThe advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.

scholarly journals Phosphorus is a critical factor of the in vitro monoxenic culture method for a wide range of arbuscular mycorrhizal fungi culture collections

2021 ◽  
Author(s):  
Takumi Sato ◽  
Kenta Suzuki ◽  
Erika Usui ◽  
Yasunori Ichihashi
Keyword(s):  
Hairy Root ◽  
Mycorrhizal Fungi ◽  
Critical Factor ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Monoxenic Culture ◽  
Culture Collections ◽  
P Concentration ◽  
Wide Range

AbstractEstablishing an effective way to propagate a wide range of arbuscular mycorrhizal (AM) fungi species is desirable for mycorrhizal research and agricultural applications. Although the success of mycorrhizal formation is required for spore production of AM fungi, the critical factors for its construction in the in vitro monoxenic culture protocol remain to be identified. In this study, we evaluated the growth of hairy roots from carrot, flax, and chicory, and investigated the effects of the phosphorus (P) concentration in the mother plate, as well as the levels of P, sucrose, and macronutrients in a cocultivation plate with a hairy root, amount of medium of the cocultivation plate, and location of spore inoculation, by utilizing the Bayesian information criterion model selection with greater than 800 units of data. We found that the flax hairy root was suitable for in vitro monoxenic culture, and that the concentration of P in the cocultivation plate was a critical factor for mycorrhizal formation. We showed that an extremely low concentration of P (3 μM) significantly improved mycorrhizal formation for AM fungi belonging to the Glomerales order, while a high concentration of P (30 μM) was suitable for Diversisporales fungi. Therefore, we anticipate that the refining the P concentration will contribute to future culture collections of a wide range of AM fungi.

scholarly journals Glomus intraradices and Funneliformis mosseae am Strains Influence on Soil Physical, Biological and Chemical Characteristics in Tea Plantations in Kenya

2021 ◽  
pp. 13-18
Author(s):  
Awa Chelangat ◽  
Joseph P Gweyi-Onyango ◽  
Nicholas K Korir ◽  
Maina Mwangi
Keyword(s):  
Mycorrhizal Fungi ◽  
Glomus Intraradices ◽  
Block Design ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Climatic Conditions ◽  
Soil Microbiology ◽  
Funneliformis Mosseae ◽  
Wide Range ◽  
Tea Production

Arbuscular mycorrhizal (AM) fungi occur over a wide range of agro climatic conditions and are geographically ubiquitous. Arbuscular mycorrhizal fungi are the medium of soil structure, they determine the flow of water, nutrients, and air, directs the pathways of root growth, and opens channels for the movement of soil animals. As the moderator of the microbial community, they also determine the metabolic processes of the soil. In other words, the mycorrhizal network is practically synonymous with ecosystem function. The tremendous advances in research on mycorrhizal physiology and ecology over the past 40 years have led to a greater understanding of the multiple roles of AMF in the ecosystem. The current study was informed due to the depletion of nutrients and poor soil microbiology in tea production whose production has declined in the recent years. The trial was conducted in the research and development greenhouse at the James Finlays Farm in Kericho County, Kenya. The experiment was laid out in a Randomized Complete Block Design (RCBD) with factorial arrangements of tea clones and mycorrhizae levels. The phosphorus treatments consisted of a standard rate of 107.66kg ha -1, two clones of the tea (S15/10 and SC 12/28) and two mycorrhizal strains (Funneliformis mosseae and Glomus intraradices) at two rates (50 kg ha-1 and 70 kg ha-1) and an untreated control without mycorrhizae. The soil pH was positively influenced by reducing the acidity content significantly where mycorrhizae strains were introduced with the highest unit change (1.3) was recorded on clone SC 12/28 at the 50 kg Mycorrhizae ha-1 rate. The same treatment also significantly increased the soil total phosphorus level (2.3 g/kg) compared to all other treatments with the least change observed on the control. Application of AMF strains Glomus intraradices and Funneliformis mosseae is recommended in tea production at the rate of 50 kg ha-1 which improves and enhances the general positive characteristics of soil health.

scholarly journals Use of the Signature Fatty Acid 16:1ω5 as a Tool to Determine the Distribution of Arbuscular Mycorrhizal Fungi in Soil

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Christopher Ngosong ◽  
Elke Gabriel ◽  
Liliane Ruess
Keyword(s):  
Fatty Acid ◽  
Mycorrhizal Fungi ◽  
Plant Root ◽  
Background Level ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Biomass Estimation ◽  
Lipid Fatty Acid ◽  
Neutral Lipid Fatty Acid ◽  
Root Symbionts

Biomass estimation of arbuscular mycorrhiza (AM) fungi, widespread plant root symbionts, commonly employs lipid biomarkers, predominantly the fatty acid 16:1ω5. We briefly reviewed the application of this signature fatty acid, followed by a case study comparing biochemical markers with microscopic techniques in an arable soil following a change to AM non-host plants after 27 years of continuous host crops, that is, two successive cropping seasons with wheat followed by amaranth. After switching to the non-host amaranth, spore biomass estimated by the neutral lipid fatty acid (NLFA) 16:1ω5 decreased to almost nil, whereas microscopic spore counts decreased by about 50% only. In contrast, AM hyphal biomass assessed by the phospholipid (PLFA) 16:1ω5 was greater under amaranth than wheat. The application of PLFA 16:1ω5 as biomarker was hampered by background level derived from bacteria, and further enhanced by its incorporation from degrading spores used as microbial resource. Meanwhile, biochemical and morphological assessments showed negative correlation for spores and none for hyphal biomass. In conclusion, the NLFA 16:1ω5 appears to be a feasible indicator for AM fungi of the Glomales group in the complex field soils, whereas the use of PLFA 16:1ω5 for hyphae is unsuitable and should be restricted to controlled laboratory studies.

scholarly journals Response of Arbuscular Mycorrhizal Fungi to Simulated Climate Changes by Reciprocal Translocation in Tibetan Plateau

2015 ◽  
Vol 43 (2) ◽  
pp. 488-493
Author(s):  
Zhaoyong SHI ◽  
Xubin YIN ◽  
Bede MICKAN ◽  
Fayuan WANG ◽  
Ying ZHANG ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Arbuscular Mycorrhizal Fungi ◽  
Reciprocal Translocation ◽  
Mycorrhizal Fungi ◽  
Climate Changes ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Spore Density ◽  
The Tibetan Plateau ◽  
Colonization Frequency

Arbuscular mycorrhiza (AM) fungi are considered as an important factor in predicting plants and ecosystem responses to climate changes on a global scale. The Tibetan Plateau is the highest region on Earth with abundant natural resources and one of the most sensitive region to climate changes. To evaluate the complex response of arbuscular mycorrhizal fungi colonization and spore density to climate changes, a reciprocal translocation experiment was employed in Tibetan Plateau. The reciprocal translocation of quadrats to AM colonization and spore density were dynamic. Mycorrhizal colonization frequency presented contrary changed trend with elevations of quadrat translocation. Colonization frequency reduced or increased in majority quadrats translocated from low to high or from high to low elevation. Responses of colonization intensity to translocation of quadrats were more sensitive than colonization frequency. Arbuscular colonization showed inconsistent trend in increased or decreased quadrat. Vesicle colonization decreased with changed of quadrat from low to high elevations. However, no significant trend was observed. Although spore density was dynamic with signs of decreasing or increasing in translocated quadrats, the majority enhanced and declined respectively in descent and ascent quadrat treatments. It is crucial to understand the interactions between AM fungi and prairie grasses to accurately predict effects of climate change on these diverse and sensitive ecosystems. This study provided an opportunity for understanding the effect of climate changes on AM fungi.

scholarly journals Synergistic community responses of plants and arbuscular mycorrhizal fungi to extreme droughts in a cold-temperate grassland

2020 ◽  
Author(s):  
Wei Fu ◽  
Baodong Chen ◽  
Matthias Rillig ◽  
Wang Ma ◽  
Chong Xu ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Environmental Filtering ◽  
Climate Extremes ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Temperate Grassland ◽  
Community Responses

Mutualistic associations between plants and arbuscular mycorrhizal (AM) fungi may have profound influences on their response to climate changes. Existing theories evaluate the effects of interdependency and environmental filtering on plant-AM fungal community dynamics separately; however, abrupt environmental changes such as climate extremes can provoke duo-impacts on the metacommunity simultaneously. Here, we experimentally tested the relevance of plant and AM fungal community responses to extreme drought (chronic or intense) in a cold temperate grassland. Irrespective of drought intensities, plant species richness and productivity responses were significantly and positively correlated with AM fungal richness and also served as best predictors of AM fungal community shifts. Notably, the robustness of this community synergism increased with drought intensity, likely reflecting increased community interdependence. Network analysis showed a key role of Glomerales in AM fungal interaction with plants, suggesting specific plant-AM fungal pairing. Thus, community interdependence may underpin climate change impact on plant-AM fungal diversity patterns in grasslands.

scholarly journals The Synergy of Arbuscular Mycorrhizal Fungi and Exogenous Abscisic Acid Benefits Robinia pseudoacacia L. Growth through Altering the Distribution of Zn and Endogenous Abscisic Acid

2021 ◽  
Vol 7 (8) ◽  
pp. 671
Author(s):  
Xiao Lou ◽  
Xiangyu Zhang ◽  
Yu Zhang ◽  
Ming Tang
Keyword(s):  
Abscisic Acid ◽  
Mycorrhizal Fungi ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Am Symbiosis ◽  
Antioxidant Defense Systems ◽  
Robinia Pseudoacacia L ◽  
Zn Stress

The simultaneous effects of arbuscular mycorrhizal (AM) fungi and abscisic acid (ABA) on the tolerance of plants to heavy metal (HM) remain unclear. A pot experiment was carried out to clarify the effects of simultaneous applications of AM fungi and ABA on plant growth, Zn accumulation, endogenous ABA contents, proline metabolism, and the oxidative injury of black locust (Robinia pseudoacacia L.) exposed to excess Zn stress. The results suggested that exogenously applied ABA positively enhanced AM colonization, and that the growth of plants only with AM fungi was improved by ABA application. Under Zn stress, AM inoculation and ABA application increased the ABA content in the root/leaf (increased by 48–172% and 92%, respectively) and Zn content in the root/shoot (increased by 63–152% and 61%, respectively) in AM plants, but no similar trends were observed in NM plants. Additionally, exogenous ABA addition increased the proline contents of NM roots concomitantly with the activities of the related synthases, whereas it reduced the proline contents and the activity of Δ1-pyrroline-5-carboxylate synthetase in AM roots. Under Zn stress, AM inoculation and ABA application decreased H2O2 contents and the production rate of O2, to varying degrees. Furthermore, in the roots exposed to Zn stress, AM inoculation augmented the activities of SOD, CAT, POD and APX, and exogenously applied ABA increased the activities of SOD and POD. Overall, AM inoculation combined with ABA application might be beneficial to the survival of black locust under Zn stress by improving AM symbiosis, inhibiting the transport of Zn from the roots to the shoots, increasing the distribution of ABA in roots, and stimulating antioxidant defense systems.

scholarly journals Biocontrol of Sclerotium rolfsii in Groundnut by Using Microbial Inoculants

2017 ◽  
Vol 9 (1) ◽  
pp. 124-130 ◽  
Author(s):  
Khirood DOLEY ◽  
Mayura DUDHANE ◽  
Mahesh BORDE
Keyword(s):  
Mycorrhizal Fungi ◽  
Antioxidant Activities ◽  
Sclerotium Rolfsii ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Stem Rot ◽  
Mycorrhizal Dependency ◽  
Trichoderma Species ◽  
Arachis Hypogaea L ◽  
Microbial Strains

Sclerotium rolfsii (Sacc.) is the causal agent of stem-rot in groundnut (Arachis hypogaea L.)crop. With the increase in demand for the groundnut, control of stem-rot efficiently by microbial strains is fast becoming inevitable as the conventional system of chemicals is degrading our ecosystem. This investigation here emphasizes on inoculation of arbuscular mycorrhizal fungi (AMF) and Trichoderma species for growth achievement and disease control. The present investigation showed that these microbial strains were found to be worth applying as they stimulated growth and decreased harmful effects of S. rolfsii (cv. ‘Western-51’). The increased biochemical parameters and antioxidant activities also indicated their defence related activities in groundnut plants. In spite of positive attributes meted out by these microbial strains towards groundnut crop, the interaction among AM fungi and Trichoderma species seemed to be less co-operative between each other which were noted when mycorrhizal dependency and percent root colonization were observed. However, in summary more practical application of low-input AM fungi along with Trichoderma species may be needed for the advancement of modern agricultural systems.

scholarly journals Haustorium Formation in Medicago truncatula Roots Infected by Phytophthora palmivora Does Not Involve the Common Endosymbiotic Program Shared by Arbuscular Mycorrhizal Fungi and Rhizobia

2015 ◽  
Vol 28 (12) ◽  
pp. 1271-1280 ◽  
Author(s):  
Rik Huisman ◽  
Klaas Bouwmeester ◽  
Marijke Brattinga ◽  
Francine Govers ◽  
Ton Bisseling ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Phytophthora Palmivora ◽  
Living Plant ◽  
Mutualistic Symbiosis ◽  
Membrane Compartment ◽  
Microbe Interactions ◽  
Host Genes

In biotrophic plant-microbe interactions, microbes infect living plant cells, in which they are hosted in a novel membrane compartment, the host-microbe interface. To create a host-microbe interface, arbuscular mycorrhizal (AM) fungi and rhizobia make use of the same endosymbiotic program. It is a long-standing hypothesis that pathogens make use of plant proteins that are dedicated to mutualistic symbiosis to infect plants and form haustoria. In this report, we developed a Phytophthora palmivora pathosystem to study haustorium formation in Medicago truncatula roots. We show that P. palmivora does not require host genes that are essential for symbiotic infection and host-microbe interface formation to infect Medicago roots and form haustoria. Based on these findings, we conclude that P. palmivora does not hijack the ancient intracellular accommodation program used by symbiotic microbes to form a biotrophic host-microbe interface.

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