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

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.

scholarly journals Changes in Soil-Borne Communities of Arbuscular Mycorrhizal Fungi during Natural Regrowth of Abandoned Cattle Pastures Are Indicative of Ecosystem Restoration

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2468
Author(s):  
Carlos H. Rodríguez-León ◽  
Clara P. Peña-Venegas ◽  
Armando Sterling ◽  
Herminton Muñoz-Ramirez ◽  
Yeny R. Virguez-Díaz
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Small Subunit ◽  
Fungal Communities ◽  
Small Subunit Rrna ◽  
Fungal Community Composition ◽  
Natural Restoration ◽  
Degraded Pastures

Natural restoration of ecosystems includes the restoration of plant-microbial associations; however, few studies had documented those changes in tropical ecosystems. With the aim to contribute to understand soil microbial changes in a natural regrowth succession of degraded pastures that were left for natural restoration, we studied changes in arbuscular mycorrhizal (AM) fungal communities. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, improving plant nutrition. Amplification of the small subunit rRNA with specific primers and subsequent Illumina sequencing were used to search soil-borne AM fungal communities in four successional natural regrowth stages in two landscapes (hill and mountain) with soil differences, located in the Andean-Amazonian transition. Molecular results corroborated the results obtained previously by spores-dependent approaches. More abundance and virtual taxa of AMF exist in the soil of degraded pastures and early natural regrowth stages than in old-growth or mature forest soils. Although changes in AM fungal communities occurred similarly over the natural regrowth chronosequence, differences in soil texture between landscapes was an important soil feature differentiating AM fungal community composition and richness. Changes in soil-borne AM fungal communities reflect some signals of environmental restoration that had not been described before, such as the reduction of Glomus dominance and the increase of Paraglomus representativeness in the AM fungal community during the natural regrowth chronosequence.

scholarly journals Fungal community assembly in soils and roots under plant invasion and nitrogen deposition

2018 ◽  
Author(s):  
Michala L. Phillips ◽  
S□ren E. Weber ◽  
Lela V. Andrews ◽  
Emma L. Aronson ◽  
Michael F. Allen ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Native Species ◽  
Arbuscular Mycorrhizal ◽  
N Deposition ◽  
Fungal Communities ◽  
Atmospheric Nitrogen ◽  
Annual Grass ◽  
Fungal Community Composition ◽  
Rapid Changes

AbstractAbstract Fungal community composition in the Anthropocene is driven by rapid changes in environmental conditions caused by human activities. This study examines the relative importance of two global change drivers – atmospheric nitrogen (N) deposition and annual grass invasion – on structuring fungal communities in a California chaparral ecosystem, with emphasis on arbuscular mycorrhizal fungi. We used molecular markers, functional groupings, generalized linear statistics and joint distribution modeling, to examine how environmental variables structure taxonomic and functional composition of fungal communities. Invasion of a chaparral ecosystem decreased richness and relative abundance of non-AMF symbionts and rhizophilic AMF (e.g. Glomeraceae) as well as the proportion of edaphophilic AMF (e.g. Gigasporaceae). We found increased richness and the proportion of rhizophilic and edaphophilic AMF with increasing soil NO3. Our findings suggest that invasive persistence may decrease the presence of multiple soil symbionts that native species depend on for pathogen protection and increased access to soil resources.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

scholarly journals Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches

MycoKeys ◽  
2018 ◽  
Vol 42 ◽  
pp. 73-88 ◽  
Author(s):  
L. Fernández Bidondo ◽  
R. P. Colombo ◽  
M. Recchi ◽  
V. A. Silvani ◽  
M. Pérgola ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Sequence Similarity ◽  
Arbuscular Mycorrhizal ◽  
Soil Disturbance ◽  
Fungal Species ◽  
Fungal Community Composition ◽  
Molecular Approaches ◽  
Field Samples ◽  
Fungal Specificity

Arbuscular mycorrhizal (AM) fungal community associated with pecan (Caryaillinoinensis) roots and rhizospheric soils was assessed by spore isolation and morphological characterisation and by pyrosequencing of AM molecular markers. The AM fungal community associated with pecan growing in the field, was always more diverse than that associated with pecan growing in containers. This was not observed when AM richness was studied, suggesting that soil disturbance by a reduction in host plant richness leads to a less equitable distribution of AM fungal species, in contrast to natural soils. The chosen primers (AMV4.5F/AMDGR) for pyrosequencing showed high AM fungal specificity. Based on 97% sequence similarity, 49 operational taxonomic units (MOTUs) were obtained and, amongst these, 41 MOTUs corresponded to the Glomeromycotaphylum. The number of obtained AM sequences ranged from 2164, associated with field samples, to 5572 obtained from pecan trap pot culture samples, defining 30 and 29 MOTUs, respectively. Richness estimated by conventional species identification was 6 and 9 AM fungal species in soil and pot samples, respectively. Claroideoglomuslamellosum, Funneliformismosseae and Entrophosporainfrequens were the only taxa detected using both techniques. Predominant sequences in the pecan rhizosphere samples, such as Rhizoglomusirregulare and other less abundant (Dominikiairanica, Dominikiaindica, Sclerocystissinuosa, Paraglomuslaccatum), were detected only by pyrosequencing. Detection of AM fungal species based on spore morphology, in combination with molecular approaches, provides a more comprehensive estimate of fungal community composition.

scholarly journals Long-Term Monoculture Negatively Regulates Fungal Community Composition and Abundance of Tea Orchards

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 466 ◽  
Author(s):  
Yasir Arafat ◽  
Muhammad Tayyab ◽  
Muhammad Umar Khan ◽  
Ting Chen ◽  
Hira Amjad ◽  
...  
Keyword(s):  
Soil Ph ◽  
Fungal Community ◽  
Cropping System ◽  
Alpha Diversity ◽  
Fungal Species ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Fungal Community Composition ◽  
Continuous Cropping System ◽  
Tea Plants

Continuous cropping frequently leads to soil acidification and major soil-borne diseases in tea plants, resulting in low tea yield. We have limited knowledge about the effects of continuous tea monoculture on soil properties and the fungal community. Here, we selected three replanted tea fields with 2, 15, and 30 years of monoculture history to assess the influence of continuous cropping on fungal communities and soil physiochemical attributes. The results showed that continuous tea monoculture significantly reduced soil pH and tea yield. Alpha diversity analysis showed that species richness declined significantly as the tea planting years increased and the results based on diversity indicated inconsistency. Principal coordinate analysis (PCoA) revealed that monoculture duration had the highest loading in structuring fungal communities. The relative abundance of Ascomycota, Glomeromycota, and Chytridiomycota decreased and Zygomycota and Basidiomycota increased with increasing cropping time. Continuous tea cropping not only decreased some beneficial fungal species such as Mortierella alpina and Mortierella elongatula, but also promoted potentially pathogenic fungal species such as Fusarium oxysporum, Fusarium solani, and Microidium phyllanthi over time. Overall, continuous tea cropping decreased soil pH and potentially beneficial microbes and increased soil pathogenic microbes, which could be the reason for reducing tea yield. Thus, developing sustainable tea farming to improve soil pH, microbial activity, and enhanced beneficial soil microbes under a continuous cropping system is vital for tea production.

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

2021 ◽  
Vol 285 ◽  
pp. 03001
Author(s):  
Andrey Yurkov ◽  
Alexey Kryukov ◽  
Yulia Mikhaylova ◽  
Peter Zhurbenko
Keyword(s):  
Mycorrhizal Fungi ◽  
Biological Diversity ◽  
Arbuscular Mycorrhizal ◽  
Its Region ◽  
Am Fungi ◽  
Illumina Miseq ◽  
Universal Primers ◽  
Its2 Region ◽  
North Caucasus ◽  
The Future

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.

scholarly journals The Diversity Analysis and Functional Prediction of Endophytic Fungi Community of Gymnadenia Conopsea from Different Altitudes in Tibet

2021 ◽  
Author(s):  
Xiu Yin ◽  
Erhao Zhang ◽  
Yazhou Lu ◽  
Hong Quan ◽  
Lianqiang Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Endophytic Fungi ◽  
Fungal Community ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Reproduction Rate ◽  
Gymnadenia Conopsea ◽  
Different Altitudes

Abstract Gymnadenia conopsea has high economic value, and can be used as a medicinal and ornamental plant. Due to its low natural reproduction rate and overexploitation, the extinction of this plant is gradually accelerating. Understanding the composition and diversity of endophytic fungi is of great significance in promoting its propagation and the utilization of beneficial fungal strains. In this study, the diversity of fungal communities from roots, stems, leaves, fruits, and soils at four different elevations was studied with Illumina MiSeq sequencing. A total of 3,707,871 sequences were detected from all samples, and the number of clustering OTUs was 14,800. The OTUs were assigned to 4 phyla, 17 classes, 41 orders, 73 families, and 99 genera. The predominant fungal groups included Ascomycota and Basidiomycota, accounting for 33.71%-86.38% and 6.98%-58.30% of the total species, respectively. According to the alpha diversity index analysis, the diversity and richness of endophytic fungal communities in plant tissues at low altitudes were higher than those at high altitudes, while the diversity and richness of soil fungi were the opposite. In addition, principal coordinate analysis (PCoA) not only showed that the fungal community structure was correlated with altitude but also indicated tissue specificity of the community structure. Our study explored the composition of the endophytic fungal community among different tissues from different altitudes and included functional analysis, which might provide new ideas for saving the endangered species G. conopsea.

scholarly journals Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Jake J Grossman ◽  
Allen J Butterfield ◽  
Jeannine Cavender-Bares ◽  
Sarah E Hobbie ◽  
Peter B Reich ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Arbuscular Mycorrhizal ◽  
Tree Diversity ◽  
Fungal Communities ◽  
Juniperus Virginiana ◽  
Lipid Fatty Acid ◽  
Neutral Lipid Fatty Acid ◽  
Fungal Abundance

ABSTRACT While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

scholarly journals Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil

2021 ◽  
Vol 9 (6) ◽  
pp. 1333
Author(s):  
Robin Raveau ◽  
Anissa Lounès-Hadj Sahraoui ◽  
Mohamed Hijri ◽  
Joël Fontaine
Keyword(s):  
Trace Element ◽  
Community Composition ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Rhizospheric Soil ◽  
Lead Smelter ◽  
Amf Communities

Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.

scholarly journals The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingjing Chang ◽  
Yu Sun ◽  
Lei Tian ◽  
Li Ji ◽  
Shasha Luo ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Wild Rice ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogen Invasion ◽  
Rice Rhizosphere ◽  
Soilborne Fungi

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.

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