scholarly journals Fungal Communities Respond to Long-Term CO2Elevation by Community Reassembly

2015 ◽  
Vol 81 (7) ◽  
pp. 2445-2454 ◽  
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.

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

2014 ◽  
Vol 80 (23) ◽  
pp. 7364-7377 ◽  
Author(s):  
Andrew C. Procter ◽  
J. Christopher Ellis ◽  
Philip A. Fay ◽  
H. Wayne Polley ◽  
Robert B. Jackson
Keyword(s):  
Species Richness ◽  
Relative Abundance ◽  
Fungal Community ◽  
Decomposition Rate ◽  
Soil Type ◽  
Clay Soil ◽  
Sandy Loam ◽  
Fungal Species ◽  
Fungal Communities ◽  
Black Clay

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.

scholarly journals Long-term Effects of Mixed Planting on Arbuscular Mycorrhizal Fungal Communities in the Roots and Soils of Juglans mandshurica Plantations

2020 ◽  
Author(s):  
Li Ji ◽  
Yan Zhang ◽  
Yuchun Yang ◽  
Lixue Yang ◽  
Na Yang ◽  
...  
Keyword(s):  
Fungal Community ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Soil Samples ◽  
Fungal Communities ◽  
Juglans Mandshurica ◽  
Mixed Plantations ◽  
Mixed Plantation ◽  
Unique Otus

Abstract Background: Establishing mixed plantations is an effective way to improve soil fertility and increase forest productivity. Arbuscular mycorrhizal (AM) fungi are obligate symbiotic fungi that can promote mineral nutrient absorption and regulate intraspecific and interspecific competition in plants. However, the effects of mixed plantations on the community structure and abundance of AM fungi are still unclear. Illumina MiSeq sequencing was used to investigate the AM fungal community in the roots and soils of pure and mixed plantations (Juglans mandshurica × Larix gmelinii). The objective of this study is to compare the differential responses of the root and rhizosphere soil AM fungal communities of Juglans mandshurica to long-term mixed plantation management.Results: Glomus and Paraglomus were the dominant genera in the root samples, accounting for more than 80% of the sequences. Compared with that in the pure plantation, the relative abundance of Glomus was higher in the mixed plantation. Glomus, Diversispora and Paraglomus accounted for more than 85% of the sequences in the soil samples. The relative abundances of Diversispora and an unidentified genus of Glomeromycetes were higher and lower in the pure plantation, respectively. The Root_P samples (the roots in the pure plantation) had the highest number of unique OTUs (operational taxonomic units), which belonged mainly to an unidentified genus of Glomeromycetes, Paraglomus, Glomus and Acaulospora. The number of unique OTUs detected in the soil was lower than that in the roots. In both the root and soil samples, the forest type did not have a significant effect on AM fungal diversity, but the Sobs value and the Shannon, Chao1 and Ace indices of AM fungi in the roots were significantly higher than those in the soil.Conclusions: Mixed forest management had little effect on the AM fungal community of Juglans mandshurica roots and significantly changed the community composition of the soil AM fungi, but not the diversity.

Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Dixi Modi ◽  
Suzanne Simard ◽  
Jean Bérubé ◽  
Les Lavkulich ◽  
Richard Hamelin ◽  
...  
Keyword(s):  
Species Composition ◽  
Fungal Community ◽  
Tree Species ◽  
Management Practice ◽  
Tree Regeneration ◽  
Root Disease ◽  
Fungal Communities ◽  
Tree Species Composition ◽  
The Impact

ABSTRACT Stump removal is a common forest management practice used to reduce the mortality of trees affected by the fungal pathogen-mediated root disease, Armillaria root rot, but the impact of stumping on soil fungal community structure is not well understood. This study analyzed the long-term impact of stumping and tree species composition on the abundance, diversity and taxonomic composition of soil fungal communities using internal transcribed spacer (ITS) marker-based DNA metabarcoding in a 48-year-old trial at Skimikin, British Columbia. A total of 108 samples were collected from FH (fermented and humus layers), and soil mineral horizons (A and B) from stumped and unstumped plots of six tree species treatments (pure stands and admixtures of Douglas-fir, western red-cedar and paper birch). Fungal α-diversity in the A horizon significantly increased with stumping regardless of tree species composition, while β-diversity was significantly affected by stumping in all the horizons. We also observed that the relative abundance of the saprotrophic fungal community declined while that of the ectomycorrhizal fungal community increased with stumping. In conclusion, increase in ectomycorrhizal fungal associations, which are positively associated with tree productivity, suggests that stumping can be considered a good management practice for mitigating root disease and promoting tree regeneration.

scholarly journals Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil

Plant Disease ◽  
2008 ◽  
Vol 92 (11) ◽  
pp. 1480-1487 ◽  
Author(s):  
Guiping Yan ◽  
Richard W. Smiley ◽  
Patricia A. Okubara ◽  
Andrea Skantar ◽  
Sandra A. Easley ◽  
...  
Keyword(s):  
Nematode Species ◽  
Wheat Root ◽  
Fungal Species ◽  
Parasitic Nematodes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Pratylenchus Neglectus ◽  
Pcr Products ◽  
Species Specific ◽  
Plant Parasitic

A species-specific polymerase chain reaction (PCR) method was developed to detect and identify the root-lesion nematodes Pratylenchus neglectus and P. thornei from soil. A primer set was designed from Pratylenchus 28S rRNA gene sequences of the D3 expansion domain. Primer specificity was confirmed with 23 isolates of 15 nematode species and other plant-parasitic and non-plant-parasitic nematodes typically present in the soil communities, and with six fungal species commonly associated with wheat root rot. DNA obtained using a commercially available kit and a method developed in our laboratory gave comparable amplification. PCR conditions were optimized and the two species were differentiated by PCR products of 144 bp for P. neglectus and 288 bp for P. thornei. With this assay, we detected a single juvenile in 1 g of sterile, inoculated soil. Examination of 30 field soil samples revealed that this method was applicable to a range of soils naturally infested with these two pathogens in Oregon. This PCR-based method is rapid, efficient, and reliable, does not require expertise in nematode taxonomy and morphology, and could be used as a rapid diagnostic tool for commercial and research applications for disease forecasting and management.

scholarly journals Only a Few Fungal Species Dominate Highly Diverse Mycofloras Associated with the Common Reed

2006 ◽  
Vol 72 (2) ◽  
pp. 1118-1128 ◽  
Author(s):  
Karin Neubert ◽  
Kurt Mendgen ◽  
Henner Brinkmann ◽  
Stefan G. R. Wirsel
Keyword(s):  
Niche Differentiation ◽  
Common Reed ◽  
Fungal Species ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Nonparametric Estimators ◽  
Single Host ◽  
Host Habitat ◽  
Nested Pcr Assays ◽  
Log Normal

ABSTRACT Plants are naturally colonized by many fungal species that produce effects ranging from beneficial to pathogenic. However, how many of these fungi are linked with a single host plant has not been determined. Furthermore, the composition of plant-associated fungal communities has not been rigorously determined. We investigated these essential issues by employing the perennial wetland reed Phragmites australis as a model. DNA extracted from roots, rhizomes, stems, and leaves was used for amplification and cloning of internal transcribed spacer rRNA gene fragments originating from reed-associated fungi. A total of 1,991 clones from 15 clone libraries were differentiated by restriction fragment length polymorphism analyses into 345 operational taxonomical units (OTUs). Nonparametric estimators for total richness (Chao1 and ACE) and also a parametric log normal model predicted a total of about 750 OTUs if the libraries were infinite. Sixty-two percent of the OTUs sequenced were novel at a threshold of 3%. Several of these OTUs represented undocumented fungal species, which also included higher taxonomic levels. In spite of the high diversity of the OTUs, the mycofloras of vegetative organs were dominated by just a few typical fungi, which suggested that competition and niche differentiation influence the composition of plant-associated fungal communities. This suggestion was independently supported by the results of nested PCR assays specifically monitoring two OTUs over 3 years, which revealed significant preferences for host habitat and host organ.

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 Weaning age and its effect on the development of the swine gut microbiome and resistome

2021 ◽  
Author(s):  
Devin B Holman ◽  
Katherine E Gzyl ◽  
Kathy T Mou ◽  
Heather K Allen
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Carbohydrate Active Enzymes ◽  
Fecal Microbiome ◽  
Shotgun Metagenomic Sequencing ◽  
Swine Operations ◽  
Weaning Age

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. In this study, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 21 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that pigs tend to have a more similar microbiome as they age and that weaning age has only a temporary effect on the gut microbiome.

scholarly journals Tundra Type Drives Distinct Trajectories of Functional and Taxonomic Composition of Arctic Fungal Communities in Response to Climate Change – Results From Long-Term Experimental Summer Warming and Increased Snow Depth

2021 ◽  
Vol 12 ◽  
Author(s):  
József Geml ◽  
Luis N. Morgado ◽  
Tatiana A. Semenova-Nelsen
Keyword(s):  
Climate Change ◽  
Community Composition ◽  
Fungal Community ◽  
Snow Depth ◽  
Fungal Communities ◽  
The Arctic ◽  
Fungal Community Composition ◽  
Summer Warming ◽  
Edaphic Variables

The arctic tundra is undergoing climate-driven changes and there are serious concerns related to the future of arctic biodiversity and altered ecological processes under possible climate change scenarios. Arctic land surface temperatures and precipitation are predicted to increase further, likely causing major transformation in terrestrial ecosystems. As a response to increasing temperatures, shifts in vegetation and soil fungal communities have already been observed. Little is known, however, how long-term experimental warming coupled with increased snow depth influence the trajectories of soil fungal communities in different tundra types. We compared edaphic variables and fungal community composition in experimental plots simulating the expected increase in summer warming and winter snow depth, based on DNA metabarcoding data. Fungal communities in the sampled dry and moist acidic tundra communities differed greatly, with tundra type explaining ca. one-third of compositional variation. Furthermore, dry and moist tundra appear to have different trajectories in response to climate change. Specifically, while both warming and increased snow depth had significant effects on fungal community composition and edaphic variables in dry tundra, the effect of increased snow was greater. However, in moist tundra, fungal communities mainly were affected by summer warming, while increased snow depth had a smaller effect and only on some functional groups. In dry tundra, microorganisms generally are limited by moisture in the summer and extremely low temperatures in winter, which is in agreement with the stronger effect of increased snow depth relative to warming. On the contrary, moist tundra soils generally are saturated with water, remain cold year-round and show relatively small seasonal fluctuations in temperature. The greater observed effect of warming on fungi in moist tundra may be explained by the narrower temperature optimum compared to those in dry tundra.

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

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.

scholarly journals Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Lin Tan ◽  
Wei-ai Zeng ◽  
Yansong Xiao ◽  
Pengfei Li ◽  
Songsong Gu ◽  
...  
Keyword(s):  
Bacterial Wilt ◽  
Bacterial Species ◽  
Fungal Species ◽  
Wilt Disease ◽  
Community Diversity ◽  
Fungal Communities ◽  
Ecological Network ◽  
Ecological Network Analysis ◽  
Pathogen Invasion ◽  
Diversity Structure

In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.

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