Illumina-based identification of arbuscular mycorrhizal fungi from Karachay-Cherkessia soils for development of bio-fertilizers

The aim of the study was to investigate the species diversity of AM fungi in different parts of the North Caucasus, biodiversity hotspot, the center of the world’s biological diversity. Samples were taken from 5 locations (stationary trial plots, STPs) in different ecosystems and at various altitudes. Identification was performed using sequencing for ITS1 and ITS2 regions, amplified with universal primers, Illumina MiSeq was employed. 19 genera of AM fungi were found on all STPs. The work did not reveal a correlation between the altitude and the species composition of AM fungi. At the same time, it should be assumed that a correlation could be found between the biodiversity of AM fungi and the type of ecosystem, which should be done in the future. The study shows it is necessary to use an analysis for both ITS regions, since the data obtained for each ITS region differ and complement each other. Analysis for the ITS2 region revealed 1.3 times more virtual taxa than for the ITS1, while the number of OTUs identified per species was similar for both regions. The highest biodiversity of AM fungi was found in STP #3 (with meadow flora). Only 4 species (Rhizophagus irregularis, R. intraradices, Paraglomus laccatum, and Claroideoglomus claroideum) were found on all five analyzed STPs. We found unexpectedly that with such a high biodiversity among the identified fungi, no different species were found in the Paraglomus genus, all the sequences of Paraglomus belonged to Paraglomus laccatum, whereas at least 9 species are distinguished in the genus by morphology. Further research will allow us to identify new strains of AM fungi, the efficiency of which may be higher than already studied ones. In the future this will make it possible to create more effective microbial biofertilizers for agriculture.

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Identification of arbuscular mycorrhizal fungi in soils of the North Caucasus based on Illumina MiSeq data for ITS1 and ITS2 regions

BIO Web of Conferences ◽

10.1051/bioconf/20202302013 ◽

2020 ◽

Vol 23 ◽

pp. 02013

Author(s):

Andrey P. Yurkov ◽

Alexey A. Kryukov ◽

Anastasia O. Gorbunova ◽

Andrey V. Shcherbakov ◽

Peter M. Zhurbenko

Keyword(s):

Sample Preparation ◽

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Illumina Miseq ◽

North Caucasus ◽

Operational Taxonomic Units ◽

The North ◽

First Time ◽

Its1 And Its2

The objective of our research was to analyze the efficiency of identification of arbuscular mycorrhizal fungi (AMF) for 2 regions: ITS1 and ITS2 regions of AMF DNA isolated from the soils of the North Caucasus (Karachay-Cherkessia). For the first time the necessity of different AMF species identification using both ITS regions was revealed, but not one region. The research demonstrated: 1) the set of taxa is different using ITS1- and ITS2-based identification; 2) analysis of the ITS1 region reveals a greater number of operational taxonomic units; 3) ITS2 allows identification of AMF at the species level more often. Sample preparation for Illumina MiSeq analysis was optimized. Obligatory stages in the sample preparation were the purification of DNA in the agarose gel in Silica after isolation, as well as separate amplification of ITS1 and ITS2 followed by combining and joint sequencing for each sample. The results showed the highest AMF biodiversity for the 176Te sample from the ecosystem of the subalpine meadow of the southeastern slope of Malaya Hatipara mountain (43°25′48.0″N 41°42′31.0″E; 2401 m above sea level), in which 8 species of AMF were identified (Archaeospora spainiae, Claroideoglomus claroideum, Diversispora versiformis, Entrophpora infrequens, Funneliformis mosseae, Glomus indicum, Paraglomus laccatum, Rhizophagus irregularis).

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Biodiversity and distribution of arbuscular mycorrhizal fungi in Araucaria angustifolia forest

Scientia Agricola ◽

10.1590/s0103-90162007000400010 ◽

2007 ◽

Vol 64 (4) ◽

pp. 393-399 ◽

Cited By ~ 24

Author(s):

Milene Moreira ◽

Dilmar Baretta ◽

Siu Mui Tsai ◽

Sandra Maria Gomes-da-Costa ◽

Elke Jurandy Bran Nogueira Cardoso

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Root Colonization ◽

Biological Diversity ◽

Diversity Index ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Araucaria Angustifolia ◽

Forest Sustainability ◽

Shannon’S Diversity Index

Araucaria angustifolia (Bert.) O. Ktze. is an endangered Brazilian coniferous tree that has been almost exterminated in the native areas because of uncontrolled wood exploitation. This tree has been shown to be highly dependent on arbuscular mycorrhizal fungi (AMF) and, therefore, AMF may be essential for forest sustainability and biological diversity. Root colonization, density and diversity of AMF spores were assessed in two Araucaria forest stands at the State Park of Alto Ribeira (PETAR), at two sampling dates: May and October. A comparison was made between a mature native stand composed of Araucaria trees mixed into a variety of tropical trees and shrubs, without any sign of anthropogenic interference (FN) and an Araucaria stand planted in 1987 (R), which has been used as a pasture. Assessments included percent root colonization, AMF spore numbers and species richness, Simpson's dominance index (Is), and Shannon's diversity index (H). Mycorrhizal root colonization did not differ between ecosystems in May. In October, however, the native stand (FN) presented a higher colonization than the planted forest (R), and the root colonization was more intense than in May. When considering both sampling periods and forests, 27 species of AM fungi, with higher numbers of spores in FN than in R were found. Canonical discriminant analysis (CDA) indicated Shannon's diversity index as the ecological attribute that contributed the most to distinguish between forest ecosystems, with higher value of H in FN in relation to R. CDA showed to be a useful tool for the study of ecological attributes.

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Detection of Arbuscular Mycorrhizal Fungi in the Roots of Strawberry Plants Fertilized with Organic Bioproducts

Vegetable Crops Research Bulletin ◽

10.2478/v10032-012-0012-3 ◽

2012 ◽

Vol 77 (1) ◽

pp. 17-27 ◽

Cited By ~ 1

Author(s):

Anna Lisek ◽

Lidia Sas Paszt ◽

Beata Sumorok

Keyword(s):

Plant Growth ◽

Arbuscular Mycorrhizal Fungi ◽

Nested Pcr ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Universal Primers ◽

Mineral Fertilizers ◽

Reaction Products ◽

The Impact

Summary In organic farming, mineral fertilizers are replaced by various preparations to stimulate plant growth and development. Introduction of new biopreparations into horticultural production requires an assessment of their effects on the growth and yielding of plants. Among the important indicators of the impact on plants of beneficial microorganisms contained in bioproducts is determination of their effectiveness in stimulating the growth and yielding of plants. Moreover, confirmation of the presence of arbuscular mycorrhizal (AM) fungi in the roots and plant growth promoting rhizobacteria (PGPR) in the rhizosphere is also necessary. In addition to conventional methods, molecular biology techniques are increasingly used to allow detection and identification of AM fungi in plant roots. The aim of this study was identification and initial taxonomic classification of AM fungi in the roots of ‘Elkat’ strawberry plants fertilized with various biopreparations using the technique of nested PCR. Tests were performed on DNA obtained from the roots of ‘Elkat’ strawberry plants: not fertilized, treated with 10 different biopreparations, or fertilized with NPK. Amplification of the large subunit of ribosomal gene (LSU rDNA) was carried out using universal primers, and then, in the nested PCR reaction, primers specific for the fungi of the genera Glomus, Acaulospora, and Scutellospora were used. Colonization of strawberry roots by arbuscular mycorrhizal fungi was determined on the basis of the presence of DNA fragments of a size corresponding to the types of the fungi tested for. As a result of the analyses, the most reaction products characterizing AM fungi were found in the roots of plants treated with the preparation Florovit Eko. The least fragments characteristic of AM fungi were detected in the roots of plants fertilized with NPK, which confirms the negative impact of mineral fertilizers on the occurrence of mycorrhizal fungi in the roots of strawberry plants. The roots of plants fertilized with Tytanit differed from the control plants by the presence of one of the clusters of fungi of the genus Glomus and by the absence of a cluster of fungi of the genus Scutellospora. In the roots of plants treated with other biopreparations there were reaction products indicating the presence of fungi of the genera Glomus, Scutellospora and Acaulospora, like in the roots of the control plants. The results will be used to assess the suitability of microbiologically enriched biopreparations in horticultural production.

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Molecular-genetic identification of arbuscular mycorrhiza fungi from Teberda natural reserve

Abstract book of the 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology" PLAMIC2020 ◽

10.28983/plamic2020.134 ◽

2020 ◽

Author(s):

А. А. Kryukov ◽

A. O. Gorbunova ◽

Sh. K. Kurbanniyazov ◽

Yu. V. Mikhaylova ◽

A. V. Rodionov ◽

...

Keyword(s):

Arbuscular Mycorrhiza ◽

Molecular Genetic ◽

Its Region ◽

Illumina Miseq ◽

Genetic Identification ◽

Universal Primers ◽

North Caucasus ◽

Arbuscular Mycorrhiza Fungi ◽

Natural Reserve ◽

Molecular Genetic Identification

Arbuscular mycorrhiza fungi of soil samples from North Caucasus were identified via Illumina Miseq and universal primers for ITS region. It was shown, that both ITS1 and ITS2 are necessary for identification.

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Metabarcoding of Soil Fungal Communities from Perturbed Areas Reveal Drive Role of Environmental Factors in Microbial Diversity of Colombian Andosols

10.21203/rs.3.rs-1128776/v1 ◽

2021 ◽

Author(s):

RAUL ALEXANDER ARANGUREN AROCA ◽

Samuele Voyron ◽

Fabrizio Ungaro ◽

Julio Cañón ◽

Erica Lumini

Keyword(s):

Land Use ◽

Fungal Community ◽

Mycorrhizal Fungi ◽

Alpha Diversity ◽

Arbuscular Mycorrhizal ◽

Conservation Agriculture ◽

Illumina Miseq ◽

Fungal Communities ◽

Its2 Region ◽

Fungal Community Composition

Abstract Changes in soil fungal community caused by land use have not been sufficiently studied in South-American Andosols, considered globally as important food production areas. This study analyzed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in the southeastern region of Antioquia, Colombia, to establish differences between fungal communities as indicators of the degree of soil perturbation. The study developed a novel heminested PCR with primers SSUmCf Mix, ITS4 and fITS7 to assess Arbuscular Mycorrhizal Fungi detection in a Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed exploring driver factors of fungal community changes, while fitted Dirichlet-multinomial models and PERMANOVA tests allowed identifying the correlations between alpha diversity indexes and community dissimilarities, as well as the significance of land use effects on fungal community composition. Furthermore, response ratios were determined to assess effect size by land use over relevant taxa. Results suggest a good coverage of fungal diversity with a detection of 10,529 high-quality ITS2 sequences belonged to phylum Glomeromycota. The analysis shows strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities among land uses (r=0.94), related to variations in temperature, air humidity and organic matter contents that lead to significant responses in abundances of relevant orders (such as Wallemiales and Trichosporonales). The study highlights the rich fungal biodiversity of the tropical Andosols, their specific sensitivities to environmental perturbation factors, and the useful range of a metabarcoding approach to characterize soil fungal communities.

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Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats

Microorganisms ◽

10.3390/microorganisms9020229 ◽

2021 ◽

Vol 9 (2) ◽

pp. 229

Author(s):

Martti Vasar ◽

John Davison ◽

Siim-Kaarel Sepp ◽

Maarja Öpik ◽

Mari Moora ◽

...

Keyword(s):

Plant Root ◽

Significant Proportion ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Illumina Miseq ◽

Desert Ecosystems ◽

Fungal Dna ◽

Root Symbionts ◽

Arbuscular Mycorrhizal Fungal

Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.

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

Journal of Lipids ◽

10.1155/2012/236807 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 43

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.

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

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4329946 ◽

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.

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

10.22541/au.160635429.93596387/v1 ◽

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.

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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

Journal of Fungi ◽

10.3390/jof7080671 ◽

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.

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