Fungal Community Responses to Past and Future Atmospheric CO2Differ by Soil Type

ABSTRACTSoils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2in the black clay (P< 0.04,R2> 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2in the sandy loam (P= 0.02,R2= 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r= 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r= 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2.

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Fungal Communities Respond to Long-Term CO2Elevation by Community Reassembly

Applied and Environmental Microbiology ◽

10.1128/aem.04040-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2445-2454 ◽

Cited By ~ 32

Author(s):

Qichao Tu ◽

Mengting Yuan ◽

Zhili He ◽

Ye Deng ◽

Kai Xue ◽

...

Keyword(s):

Relative Abundance ◽

Fungal Community ◽

Geodesic Distance ◽

Fungal Species ◽

Fungal Communities ◽

Rrna Gene ◽

28S Rrna ◽

Ecological Network ◽

Community Reassembly

ABSTRACTFungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2(eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO2, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2for 12 years. Long-term eCO2did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO2were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4+availability. This study provided novel insights into how eCO2shapes soil fungal communities in grassland ecosystems.

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Communities of Fungi in Black Cherry Stumps and Effects of Herbicide

Plants ◽

10.3390/plants9091126 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1126

Author(s):

Robert Korzeniewicz ◽

Marlena Baranowska ◽

Hanna Kwaśna ◽

Gniewko Niedbała ◽

Jolanta Behnke-Borowczyk

Keyword(s):

Species Richness ◽

Environmental Dna ◽

Bioinformatic Analysis ◽

Diversity Indices ◽

Fungal Species ◽

Fungal Communities ◽

Reference Sequence ◽

Deciduous Tree ◽

Black Cherry ◽

5.8S Rdna

So far, there have been no studies on fungal communities in Prunus serotina (black cherry) wood. Our objectives were to characterize fungal communities from P. serotina wood and to evaluate effects of glyphosate (Glifocyd 360 SL) used on P. serotina stumps on abundance, species richness and diversity of those communities. In August 2016, in the Podanin Forest District, stumps of black cherry trees left after felling were treated with the herbicide. Control stumps were treated with water. Wood discs were cut from the surface of the stumps in May and July–August 2017. Eight treatment combinations (2 herbicide treatments × 2 disc sizes × 2 sample times) were tested. Sub-samples were pooled and ground in an acryogenic mill. Environmental DNA was extracted with a Plant Genomic DNA Purification Kit. The ITS1, 5.8S rDNA region was used to identify fungal species, using primers ITS1FI2 5′-GAACCWGCGGARGGATCA-3′ and 5.8S 5′-CGCTGCGTT CTTCATCG-3′. The amplicons were sequenced using the Illumina system. The results were subjected to bioinformatic analysis. Sequences were compared with reference sequences from the NCBI database using the BLASTn 2.8.0 algorithm. Abundance of fungi was defined as the number of Operational Taxonomic Units (OTUs), and diversity as the number of species in a sample. Differences between the number of OTUs and taxa were analyzed using the chi-squared test (χ2). Diversity in microbial communities was compared using diversity indices. A total of 54,644 OTUs were obtained. Culturable fungi produced 49,808 OTUs (91.15%), fungi not known from culture had 2571 OTUs (4.70%), non-fungal organisms had 1333 (2.44%) and organisms with no reference sequence in NCBI, 934 OTUs (1.71%). The total number of taxa ranged from 120 to 319. Fungi in stump wood were significantly more abundant in July–August than in May, in stumps >5 cm diameter than in stumps <5 cm diameter, in glyphosate-treated than in untreated stumps when sampled in May, and in untreated than in glyphosate-treated stumps when sampled in July–August. Species richness was significantly greater in July–August than in May, and in stumps >5 cm diameter than in stumps <5 cm diameter, either treated or untreated, depending on size. Herbicides can therefore affect the abundance and diversity of fungal communities in deciduous tree wood. The greater frequency of Ascomycota in herbicide-treated than in untreated stumps indicates their greater tolerance of glyphosate.

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

Agronomy ◽

10.3390/agronomy9080466 ◽

2019 ◽

Vol 9 (8) ◽

pp. 466 ◽

Cited By ~ 4

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.

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Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Scientific Reports ◽

10.1038/s41598-021-04097-8 ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Marie-Thérèse Mofini ◽

Abdala G. Diedhiou ◽

Marie Simonin ◽

Donald Tchouomo Dondjou ◽

Sarah Pignoly ◽

...

Keyword(s):

Community Structure ◽

Pearl Millet ◽

Relative Abundance ◽

Fungal Community ◽

Management Practices ◽

Pennisetum Glaucum ◽

Fungal Communities ◽

Fungal Community Structure ◽

The Core ◽

Factors Influencing

AbstractFungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

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Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities

Botany ◽

10.1139/cjb-2013-0194 ◽

2014 ◽

Vol 92 (4) ◽

pp. 303-311 ◽

Cited By ~ 88

Author(s):

Steven W. Kembel ◽

Rebecca C. Mueller

Keyword(s):

Host Plant ◽

Tropical Forests ◽

Fungal Community ◽

Tree Species ◽

High Throughput Sequencing ◽

Plant Traits ◽

Fungal Species ◽

Fungal Communities ◽

Fungal Community Composition ◽

Individual Tree

The aerial surface of plants, known as the phyllosphere, represents a widespread and diverse habitat for microbes, but the fungal communities colonizing the surface of leaves are not well characterized, and how these communities are assembled on hosts is unknown. We used high-throughput sequencing of fungal communities on the leaves of 51 tree species in a lowland tropical rainforest in Panama to examine the influence of host plant taxonomy and traits on the fungi colonizing the phyllosphere. Fungal communities on leaves were dominated by the phyla Ascomycota (79% of all sequences), Basidiomycota (11%), and Chytridiomycota (5%). Host plant taxonomic identity explained more than half of the variation in fungal community composition across trees, and numerous host functional traits related to leaf morphology, leaf chemistry, and plant growth and mortality were significantly associated with fungal community structure. Differences in fungal biodiversity among hosts suggest that individual tree species support unique fungal communities and that diverse tropical forests also support a large number of fungal species. Similarities between phyllosphere and decomposer communities suggest that fungi inhabiting living leaves may have significant roles in ecosystem functioning in tropical forests.

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Effects of Artificial Defoliation of Pines on the Structure and Physiology of the Soil Fungal Community of a Mixed Pine-Spruce Forest

Applied and Environmental Microbiology ◽

10.1128/aem.71.4.1996-2000.2005 ◽

2005 ◽

Vol 71 (4) ◽

pp. 1996-2000 ◽

Cited By ~ 14

Author(s):

Ken Cullings ◽

Christopher Raleigh ◽

Michael H. New ◽

Joan Henson

Keyword(s):

Species Richness ◽

Filamentous Fungus ◽

Fungal Community ◽

Denaturing Gradient Gel Electrophoresis ◽

Soil Microbial Communities ◽

Soil Fungus ◽

Fungal Species ◽

Ectomycorrhizal Fungus ◽

Spruce Forest ◽

Soil Fungal Community

ABSTRACT Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

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Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

Microorganisms ◽

10.3390/microorganisms8030443 ◽

2020 ◽

Vol 8 (3) ◽

pp. 443 ◽

Cited By ~ 2

Author(s):

Manoj Kaushal ◽

Rony Swennen ◽

George Mahuku

Keyword(s):

Fusarium Oxysporum ◽

Relative Abundance ◽

Fungal Community ◽

Bacterial Communities ◽

Fungal Communities ◽

Fungal Community Composition ◽

Core Microbiome ◽

Fungal Microbiota ◽

Diversity Structure ◽

Plant Components

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa.

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It matters who you know, down below: Different mycorrhizal fungal communities differentially affect plant phenolic defences against herbivory

10.1101/2020.07.06.190710 ◽

2020 ◽

Author(s):

Adam Frew ◽

Bree A. L. Wilson

Keyword(s):

Fungal Community ◽

Community Assembly ◽

Plant Defence ◽

Insect Herbivory ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Fungal Species ◽

Fungal Communities ◽

Insect Herbivore ◽

Terrestrial Plants

ABSTRACTArbuscular mycorrhizal (AM) fungi are ubiquitous symbionts of most terrestrial plants. These fungi not only provide their host plants with access to nutrients and resources but are known to augment plant defences against insect herbivores. Relatively little is known about the role of AM fungal diversity and community assembly on the expression of plant defence traits. Here, we report how plant (Triticum aestivum) phenolic-based resistance to insect herbivory is differentially affected by different AM fungal communities. An inoculant of four AM fungal species and a field-sourced native AM fungal community increased plant phenolics by 47.9% and 50.2%, respectively, compared to plants inoculated with only one fungal species. Correspondingly, the performance (relative growth rate) of the insect herbivore was 36% and 61.3% lower when feeding on plants associated with these AM fungal communities. Furthermore, there was a negative correlation between foliar phenolics and herbivore growth. We propose that AM fungal community assembly can drive insect herbivore performance by affecting phenolic-based defence mechanisms.

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Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China

Forests ◽

10.3390/f13010037 ◽

2021 ◽

Vol 13 (1) ◽

pp. 37

Author(s):

Yubiao Lin ◽

Jiejun Kong ◽

Ling Yang ◽

Qian He ◽

Yan Su ◽

...

Keyword(s):

Community Structure ◽

Relative Abundance ◽

Fungal Community ◽

Southern China ◽

Soil Microbial Communities ◽

Fungal Communities ◽

Eucalyptus Plantation ◽

Soil Microbial ◽

Soil Bacterial ◽

Throughfall Reduction

In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.

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Forest tree species composition and abiotic site conditions drive soil fungal communities and functional groups

10.1101/2021.07.21.453256 ◽

2021 ◽

Author(s):

Likulunga Emmanuel Likulunga ◽

Carmen Alicia Rivera P&eacuterez ◽

Dominik Schneider ◽

Rolf Daniel ◽

Andrea Polle

Keyword(s):

Species Richness ◽

Tree Species ◽

Mycorrhizal Fungi ◽

Fungal Diversity ◽

Fungal Species ◽

Douglas Fir ◽

Fungal Communities ◽

Site Conditions ◽

Saprotrophic Fungi ◽

Tree Species Composition

Soil fungi, especially the functional guilds of saprotrophic and mycorrhizal fungi, play a central role in ecosystem processes by degrading litter, mining for mineral nutrients and linking above- and belowground nutrient fluxes. Fungal community structures are influenced by abiotic habitat filters and management decisions such as tree species selection. Yet, the implications of the enrichment of temperate forests consisting of tree species in their natural range with non-native tree species on soil fungal diversity and their functional groups are unknown. Here, we studied fungal communities in 40 plots located in two regions differing in site conditions (nutrient content and soil moisture) in forests composed of European beech, Norway spruce and Douglas-fir (non-native) and mixtures of beech with either spruce or Douglas-fir. We hypothesized that fungal community structures are driven by soil resources and tree species composition, generally resulting in higher fungal diversity in mixed than in mono-specific forests. We further hypothesized that Douglas-fir has a negative effect on ectomycorrhizal fungal species richness compared to native species, whereas saprotrophic fungal richness is unaffected. We found strong separation of fungal communities between nutrient-rich and nutrient-poor sites and taxonomic divergence between beech and conifer fungal communities and an intermediate pattern in mixed forests. Mycorrhizal species richness did not vary with forest type, but the relative abundance of mycorrhizal species was lower in Douglas-fir and in mixed beech-Douglas-fir forests than in spruce or beech-spruce mixture. Conifer forests contained higher relative abundances of saprotrophic fungi than mono-specific beech forests. Among 16 abundant fungal orders in soil, two containing saprotrophic fungi (Tremellales, Hymenochaetales) were enriched in conifer forests, regardless of site conditions and tree species mixture. The other fungal orders, including those dominated by mycorrhizal fungi (Russulales, Boletales, Atheliales, Cantharellales) showed variable patterns depending on site conditions and tree species. In conclusion, Douglas-fir mono-specific or mixed forests show no loss of fungal species richness, but a shift in functional composition towards saprotrophic fungi.

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