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

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.

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

Agronomy ◽

10.3390/agronomy11122468 ◽

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.

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

10.32942/osf.io/t82ug ◽

2019 ◽

Cited By ~ 1

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.

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

MycoKeys ◽

10.3897/mycokeys.42.26118 ◽

2018 ◽

Vol 42 ◽

pp. 73-88 ◽

Cited By ~ 1

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.

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

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz134 ◽

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.

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Two threatened coexisting indigenous conifer species in the dry Afromontane forests of Ethiopia are associated with distinct arbuscular mycorrhizal fungal communities

Canadian Journal of Botany ◽

10.1139/b06-121 ◽

2006 ◽

Vol 84 (10) ◽

pp. 1617-1627 ◽

Cited By ~ 20

Author(s):

Tesfaye Wubet ◽

Michael Weiß ◽

Ingrid Kottke ◽

Franz Oberwinkler

Keyword(s):

Tree Species ◽

Mycorrhizal Fungi ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Arbuscular Mycorrhizal ◽

Small Subunit ◽

Fungal Communities ◽

Fungal Community Composition ◽

Afromontane Forests ◽

Sequence Types

The molecular diversity of arbuscular mycorrhizal (AM) fungi colonizing roots of Podocarpus falcatus (Thunb.) R.Br. (Podocarpaceae) in the dry Afromontane forests of Ethiopia was investigated. The nuclear gene coding for small subunit ribosomal RNA (nucSSU rDNA) was amplified from colonized roots of P. falcatus, cloned, and sequenced using AM fungal specific primers. Phylogenetic analyses revealed that the glomeromycetous sequences from mycorrhizae of P. falcatus belong to the Glomeraceae, Diversisporaceae, and Archaeosporaceae. Overall, 16 Glomus , three Diversispora , and one Archaeospora sequence types were identified. These sequence types were distinct and only distantly related to sequences from the available defined species. The composition of the AM fungal communities differed significantly between the two study sites. Comparison of the AM fungal community composition of P. falcatus with that of previously investigated Juniperus procera Hochst. ex Endl. (Cupressaceae), the only coexisting indigenous conifer tree species in the dry Afromontane forest ecosystem, yields that the two tree species are colonized by distinct AM fungal communities. This suggests that fungal communities are host plant specific in the natural stand conditions. Therefore, in the conservation of these endangered species and restoration of the degraded ecosystem, the use of appropriate mycorrhizal fungi should be taken into account in future projects.

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Arbuscular Mycorrhization in Colombian and Introduced Rubber (Hevea brasiliensis) Genotypes Cultivated on Degraded Soils of the Amazon Region

Agriculture ◽

10.3390/agriculture11040361 ◽

2021 ◽

Vol 11 (4) ◽

pp. 361

Author(s):

Clara P. Peña-Venegas ◽

Armando Sterling ◽

Tatiana K. Andrade-Ramírez

Keyword(s):

Fungal Community ◽

Hevea Brasiliensis ◽

Plant Nutrition ◽

Root Colonization ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Molecular Techniques ◽

Fungal Communities ◽

Fungal Community Composition ◽

Am Symbiosis

Rubber (Hevea brasiliensis, (Willd. Ex Adr. de Juss) Muell. Arg, Euphorbiaceae) is an important commercial latex-producing plant. Commercially, rubber is reproduced from a limited number of grifting genotypes. New promising genotypes have been selected to replace traditional genotypes. In addition, rubber has been promoted to recuperate Amazon soils degraded by extensive cattle ranching. Arbuscular mycorrhizal (AM) symbiosis is an important alternative for improving plant nutrition in rubber trees and recuperating degraded soils, but AM fungal communities on different plantations and in rubber genotypes are unknown. Spore abundance, root colonization and AM fungal community composition were evaluated in rubber roots of Colombian and introduced genotypes cultivated in degraded soils with different plantation types. Traditional (spore isolation and description; clearing and staining roots) and molecular techniques (Illumina sequencing) were used to assess AM fungi. Rubber roots hosted a diverse AM fungal community of 135 virtual taxa (VT) in 13 genera. The genus Glomus represented 66% of the total AM fungal community. Rubber genotype did not affect the arbuscular mycorrhization, hosting similar AM fungal communities. The composition of the AM fungal community on old and young rubber plantations was different. Diversity in AM fungi in rubber roots is an important characteristic for restoring degraded soils.

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Local Adaptation to Soil Hypoxia Determines the Structure of an Arbuscular Mycorrhizal Fungal Community in Roots from Natural CO2Springs

Applied and Environmental Microbiology ◽

10.1128/aem.00139-11 ◽

2011 ◽

Vol 77 (14) ◽

pp. 4770-4777 ◽

Cited By ~ 38

Author(s):

Irena Maček ◽

Alex J. Dumbrell ◽

Michaela Nelson ◽

Alastair H. Fitter ◽

Dominik Vodnik ◽

...

Keyword(s):

Fungal Community ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Small Subunit ◽

Fungal Communities ◽

Rrna Genes ◽

Soil Conditions ◽

Small Subunit Rrna ◽

Fungal Community Composition ◽

Environmental Selection

ABSTRACTThe processes responsible for producing and maintaining the diversity of natural arbuscular mycorrhizal (AM) fungal communities remain largely unknown. We used natural CO2springs (mofettes), which create hypoxic soil environments, to determine whether a long-term, directional, abiotic selection pressure could change AM fungal community structure and drive the selection of particular AM fungal phylotypes. We explored whether those phylotypes that appear exclusively in hypoxic soils are local specialists or widespread generalists able to tolerate a range of soil conditions. AM fungal community composition was characterized by cloning, restriction fragment length polymorphism typing, and the sequencing of small subunit rRNA genes from roots of four plant species growing at high (hypoxic) and low (control) geological CO2exposure. We found significant levels of AM fungal community turnover (β diversity) between soil types and the numerical dominance of two AM fungal phylotypes in hypoxic soils. Our results strongly suggest that direct environmental selection acting on AM fungi is a major factor regulating AM fungal communities and their phylogeographic patterns. Consequently, some AM fungi are more strongly associated with local variations in the soil environment than with their host plant's distribution.

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Experimentally altered rainfall regimes and host root traits affect grassland arbuscular mycorrhizal fungal communities

10.32942/osf.io/cu4jh ◽

2019 ◽

Author(s):

Coline Deveautour ◽

Suzanne Donn ◽

Sally Power ◽

Kirk Barnett ◽

Jeff Powell

Keyword(s):

Fungal Community ◽

Community Assembly ◽

Root Length ◽

Specific Root Length ◽

Root Traits ◽

Arbuscular Mycorrhizal ◽

Fungal Communities ◽

Rainfall Regime ◽

Precipitation Regimes ◽

Rainfall Regimes

Future climate scenarios predict changes in rainfall regimes. These changes are expected to affect plants via effects on the expression of root traits associated with water and nutrient uptake. Associated microorganisms may also respond to these new precipitation regimes, either directly in response to changes in the soil environment or indirectly in response to altered root trait expression. We characterised arbuscular mycorrhizal (AM) fungal communities in an Australian grassland exposed to experimentally altered rainfall regimes. We used Illumina sequencing to assess the responses of AM fungal communities associated with four plant species sampled in different watering treatments and evaluated the extent to which shifts were associated with changes in root traits. We observed that altered rainfall regimes affected the composition but not the richness of the AM fungal communities, and we found distinctive communities in the increased rainfall treatment. We found no evidence of altered rainfall regime effects via changes in host physiology because none of the studied traits were affected by changes in rainfall. However, specific root length was observed to correlate with AM fungal richness, while concentrations of phosphorus and calcium in root tissue and the proportion of root length allocated to fine roots were correlated to community composition. Our study provides evidence that climate change and its effects on rainfall may influence AM fungal community assembly, as do plant traits related to plant nutrition and water uptake. We did not find evidence that host responses to altered rainfall drive AM fungal community assembly in this grassland ecosystem.

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