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Journal articles on the topic 'FUNGuild database'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Foster, Z. S. L., J. E. Weiland, C. F. Scagel, and N. J. Grünwald. "The Composition of the Fungal and Oomycete Microbiome of Rhododendron Roots Under Varying Growth Conditions, Nurseries, and Cultivars." Phytobiomes Journal 4, no. 2 (2020): 156–64. http://dx.doi.org/10.1094/pbiomes-09-19-0052-r.

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The microbiome of agricultural crops influences processes such as nutrient absorption, drought stress, and susceptibility to pathogens. Interactions between a plant’s genotype and its environment influence the composition of the microbiome, but these interactions are not well understood. We compared how the fungal and oomycete microbiomes of rhododendrons from Oregon nurseries differed among cultivars, growth conditions, and nurseries. Roots were sampled from randomly selected container and field-grown plants of three cultivars of rhododendron at four nurseries. The internal transcribed spacer

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Nelson, Aaron, Roo Vandegrift, George C. Carroll, and Bitty A. Roy. "Double lives: transfer of fungal endophytes from leaves to woody substrates." PeerJ 8 (August 28, 2020): e9341. http://dx.doi.org/10.7717/peerj.9341.

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Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree

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Cheng, Xuefei, Siyuan Jiang, Ali El-Naggar, Yingzhou Tang, Xin Liu, and Jinchi Zhang. "Dynamics of Fine Root Decomposition in Different Vegetation Types: Investigating the Impact of Soil Fungal Communities and Enzyme Activities." Forests 14, no. 7 (2023): 1321. http://dx.doi.org/10.3390/f14071321.

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Fine root decomposition plays a vital role in driving the carbon cycle in terrestrial ecosystems, as it constitutes a substantial part of annual net primary production and, as transient tissues, returns to the soil within relatively short timescales. Soil fungal communities and enzyme activities strongly influence this process. In this study, we used an in situ soil core decomposition method to compare the fine root decomposition rates of Liriodendron chinense (Hemsl.) Sargent, Cunninghamia lanceolata (Lamb.) Hook, and Phyllostachys edulis (Carrière) J.Houz forests over a 1-year period (March

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Moreira, Geisianny, Jefferson Brendon Almeida dos Reis, Elisa Catão Caldeira Pires, Cristine Chaves Barreto, and Helson Mario Martins do Vale. "Fungal Guilds Reveal Ecological Redundancy in a Post-Mining Environment." Mining 5, no. 2 (2025): 28. https://doi.org/10.3390/mining5020028.

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Mining significantly impacts terrestrial ecosystems despite its importance to the global economy. As part of soil ecosystems, fungi are highly responsive to environmental and human-induced drivers, shifting community composition and structure. Indeed, fungi play a key role in maintaining ecosystem resilience. Thus, we aim to address the question of whether soil fungal communities maintain similar ecological functions despite changes in community composition due to the impact of mining across ecosystems. To evaluate the ecological role of fungi across four ecosystems with varying iron mining im

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Deng, Qizhang, Yong Wu, Xiang Zhao, et al. "Influence of different irrigation methods on the alfalfa rhizosphere soil fungal communities in an arid region." PLOS ONE 17, no. 6 (2022): e0268175. http://dx.doi.org/10.1371/journal.pone.0268175.

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Xinjiang is the largest arid and saline agricultural region in China. The common irrigation methods in this area are traditional flood irrigation and drip irrigation. In this study, we investigated the effects of these two irrigation methods on the fungal diversity, community structures, and functions in alfalfa rhizosphere soil as well as the associated environmental factors in northern Tianshan Mountain (Xinjiang, China). Soil enzyme activities (urease and neutral phosphatase) were significantly higher in the drip-irrigated alfalfa rhizosphere soil than in the flood-irrigated alfalfa rhizosp

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Zeng, Xinhua, Haixin Diao, Ziyi Ni, et al. "Temporal Variation in Community Composition of Root Associated Endophytic Fungi and Carbon and Nitrogen Stable Isotope Abundance in Two Bletilla Species (Orchidaceae)." Plants 10, no. 1 (2020): 18. http://dx.doi.org/10.3390/plants10010018.

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Mycorrhizae are an important energy source for orchids that may replace or supplement photosynthesis. Most mature orchids rely on mycorrhizae throughout their life cycles. However, little is known about temporal variation in root endophytic fungal diversity and their trophic functions throughout whole growth periods of the orchids. In this study, the community composition of root endophytic fungi and trophic relationships between root endophytic fungi and orchids were investigated in Bletilla striata and B. ochracea at different phenological stages using stable isotope natural abundance analys

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Gao, Menghan, Bihong Liu, Jianming Li, et al. "Diversity and Distribution of Fungi in the Marine Sediments of Zhanjiang Bay, China." Journal of Fungi 10, no. 12 (2024): 867. https://doi.org/10.3390/jof10120867.

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Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary–coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of

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Zarza, Eugenia, Alejandra López-Pastrana, Anne Damon, Karina Guillén-Navarro, and Luz Verónica García-Fajardo. "Fungal diversity in shade-coffee plantations in Soconusco, Mexico." PeerJ 10 (June 29, 2022): e13610. http://dx.doi.org/10.7717/peerj.13610.

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Background As forested natural habitats disappear in the world, traditional, shade-coffee plantations offer an opportunity to conserve biodiversity and ecosystem services. Traditional coffee plantations maintain a diversity of tree species that provide shade for coffee bushes and, at the same time, are important repositories for plants and animals that inhabited the original cloud forest. However, there is still little information about shade-coffee plantation’s fungal diversity despite their relevance for ecosystem functioning as decomposers, symbionts and pathogens. Specifically, it is unkno

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Shen, Fangyuan, Ning Liu, Yujiao Wang, Huifeng Liu, Haikuan Jia, and Lixue Yang. "The Effects of Korean Pine and Manchurian Walnut Monocultures and Mixed Plantations on Soil Fungal and Bacterial Communities." Forests 14, no. 8 (2023): 1594. http://dx.doi.org/10.3390/f14081594.

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(1) Background: Korean pine (Pinus koraiensis) and Manchurian walnut (Juglans mandshurica) are the main tree species for plantation regeneration in Northeast China, and the mixed plantation of them is one of the typical measures adopted to address the decline in stand productivity in long-term monocultures. However, little is known about the effects of Korean pine and Manchurian walnut monocultures and mixed plantations on soil microbial diversity, composition, and functional groups. (2) Methods: We used ITS and 16S rRNA gene sequencing to detect fungal and bacterial communities and used the F

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Wang, Zhen, Shuang Wang, Ting Bian, Tianqi Wang, Hongdan Fu, and Zhouping Sun. "Revealing the Response of Cucumber Soil Microbial Community Composition and Function to Nitrogen Addition in Northern Chinese Greenhouses." Horticulturae 10, no. 10 (2024): 1090. http://dx.doi.org/10.3390/horticulturae10101090.

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At present, the soil of Chinese greenhouses is experiencing severe nitrogen input in the form of fertilizer, which will cause damage to the soil environment and restrict crop growth in the long run. The response of potential functions of microorganisms as drivers of nutrient cycling and material transformation to nitrogen enrichment has rarely been reported in northern vegetable planting systems. Therefore, we set up four cucumber pot experiments with different nitrogen addition rates (0, 258, 516, and 1032 kg N ha−1 yr−1) in the greenhouse. Bacterial and fungal communities were detected by 16

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Tanunchai, Benjawan, Li Ji, Simon Andreas Schroeter, et al. "FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species." Microbial Ecology, February 5, 2022. http://dx.doi.org/10.1007/s00248-022-01973-2.

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Abstract Recently, a new annotation tool “FungalTraits” was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)–based amplicon

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Peng, Fangfang, Xunlan Li, Zhaoxin Wei, Youjin Luo, Wu Wang, and Guohui Han. "Structure and Ecological Function of Fungal Endophytes from Stems of Different Mulberry Cultivars." Current Microbiology 80, no. 12 (2023). http://dx.doi.org/10.1007/s00284-023-03504-9.

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AbstractTo explore the microbial community structure and ecological function of mulberry and their potential relationship with the resistance of mulberry, the community structure and function of endophytic fungi in 18 mulberry cultivars were analyzed and predicted by using high-throughput sequencing technology and the FUNGuild database. A total of 352 operational taxonomic units of fungi were observed at a 97% similarity level, representing six phyla of fungi, Fungi_unclassified, Ascomycota, Basidiomycota, Zygomycota, Rozellomycota, and Chytridiomycota. Fungi_unclassified was dominant, and Asc

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Chopra, Mayuri, Swarnaprava Behera, Loganathan Jagadeesan, Vivek Rachuri, and Belle Damodara Shenoy. "Exploring fungal diversity and their ecological roles in the coastal waters of Ramakrishna Beach, Visakhapatnam, India." MycoAsia, 2024. http://dx.doi.org/10.59265/mycoasia.2024-01.

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The coastal waters of Ramakrishna Beach, Visakhapatnam, India, present a unique ecosystem for exploring fungal diversity and ecological roles, yet have been underexplored in mycological studies. This study utilizes amplicon sequencing targeting the fungal ITS region from environmental DNA to fill this knowledge gap. Our findings reveal a predominant presence of Ascomycota, with Candida and Aspergillus being the most abundant genera. Notably, Candida tropicalis emerged as the most prevalent species, followed by Candida hyderabadensis and Aspergillus penicillioides. This study not only contribut

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Zhao, Wen, Ya‐li Yin, Shi‐xiong Li, Jiang‐qin Song, Yi‐ling Dong, and Shi‐feng Su. "Establishing Artificial Grassland on Extremely Degraded Alpine Meadow Changes the Soil Fungal Community and Function in the Qilian Mountain Area." Land Degradation & Development, January 12, 2025. https://doi.org/10.1002/ldr.5402.

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ABSTRACTThe establishment of artificial grasslands is a recognized method for restoring severely degraded alpine meadows, yet its impact on soil fungi remains poorly understood. To investigate the impact of artificial grassland establishment on soil fungal communities, we selected a typical 4‐year‐old artificial grassland as the research subject, with non‐degraded and extremely degraded alpine meadows serving as controls. Soil fungal communities and functional groups were analyzed using Illumina sequencing of internal transcribed spacer (ITS) genes, and functional groups were predicted using t

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Guo, Wen, Jian Zhang, Mai-He Li, and Lianghua Qi. "Soil fungal community characteristics vary with bamboo varieties and soil compartments." Frontiers in Microbiology 14 (February 6, 2023). http://dx.doi.org/10.3389/fmicb.2023.1120679.

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Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not af

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Luigi, Orrù, Canfora Loredana, Trinchera Alessandra, et al. "How Tillage and Crop Rotation Change the Distribution Pattern of Fungi." June 17, 2021. https://doi.org/10.3389/fmicb.2021.634325.

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Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotro

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Zhu, Ping, Xinyu Hu, Qiang Zou, et al. "Shifts in fungal community diversity and potential function under natural forest succession and planted forest restoration in the Kunyu Mountains, East China." Ecology and Evolution 14, no. 8 (2024). http://dx.doi.org/10.1002/ece3.70055.

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AbstractSoil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine‐broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural

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18

Geng, Xinze, Jincheng Zuo, Yunhao Meng, et al. "Changes in nitrogen and phosphorus availability driven by secondary succession in temperate forests shape soil fungal communities and function." Ecology and Evolution 13, no. 10 (2023). http://dx.doi.org/10.1002/ece3.10593.

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AbstractThe soil fungal community plays an important role in forest ecosystems and is crucially influenced by forest secondary succession. However, the driving factors of fungal community and function during temperate forest succession and their potential impact on succession processes remain poorly understood. In this study, we investigated the dynamics of the soil fungal community in three temperate forest secondary successional stages (shrublands, coniferous forests, and deciduous broad‐leaved forests) using high‐throughput DNA sequencing coupled with functional prediction via the FUNGuild

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Sun, Xingzhao, Judith Sitters, Joske Ruytinx, Martin J. Wassen, and Harry Olde Venterink. "Microbial community composition in the dung of five sympatric European herbivore species." Ecology and Evolution 14, no. 3 (2024). http://dx.doi.org/10.1002/ece3.11071.

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AbstractThe dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid‐Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non‐ruminants) and diverse dietary preferences on the microbial community comp

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Du, Jianfeng, Qixiong Gao, Chao Ji, et al. "Bacillus licheniformis JF-22 to Control Meloidogyne incognita and Its Effect on Tomato Rhizosphere Microbial Community." Frontiers in Microbiology 13 (April 7, 2022). http://dx.doi.org/10.3389/fmicb.2022.863341.

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Meloidogyne incognita is one of the most destructive soil pests, causing serious economic losses in tomato production. Here, in vitro experiments demonstrated that the Bacillus licheniformis strain JF-22 has the potential to prevent M. incognita infection. A pot experiment confirmed that B. licheniformis strain JF-22 isolated from the tomato rhizosphere soil and planted in the tomato root-knot nematode disease area effectively prevented and controlled M. incognita, reducing its negative effect on tomato growth. Additionally, the composition of volatile substances secreted by B. licheniformis s

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Wan, Qian, Lei Li, Bo Liu, Zhihao Zhang, Yalan Liu, and Mingyu Xie. "Different and unified responses of soil bacterial and fungal community composition and predicted functional potential to 3 years’ drought stress in a semiarid alpine grassland." Frontiers in Microbiology 14 (March 14, 2023). http://dx.doi.org/10.3389/fmicb.2023.1104944.

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IntroductionSoil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear.MethodsHere, a field experiment was conducted under ambient precipitation as a control, −20% and −40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the nor

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Pei, Lixin, Siyuan Ye, Liujuan Xie, et al. "Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China." Frontiers in Microbiology 15 (March 27, 2024). http://dx.doi.org/10.3389/fmicb.2024.1347821.

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The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. a

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Martins, da Cunha Kelmer, Edilene Souza-Leite, García Glen Jasper Yupanqui, et al. "code from "Unveiling the rich and functionally diverse Southern Brazilian Highland Grasslands soil funga for promoting conservation" v1.0." March 6, 2025. https://doi.org/10.5281/zenodo.14982669.

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contact: kelmermartinscunha@gmail.com This is a static version of the same dataset available at https://github.com/LBMCF/SBHG_mycobiota. All necessary code and data for replicating the results presented in the article entitled "Unveiling the rich and functionally diverse Southern Brazilian Highland Grasslands soil funga for promoting conservation" can be found in this repository. R and python scripts are named based on which analyses were perfomed, and throghouly documented for guiding the execution of each step in the analysis pipeline.  Raw shotgun metagenomic data can be found under NC

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Xie, Lele, Yushou Ma, Yanlong Wang, Yuan Ma, and Xiaoli Wang. "Changes in Soil Bacterial and Fungal Community Composition and Functional Groups During the Artificial Restoration of Degraded Grassland of “Black‐Soil Mountain”." Ecology and Evolution 14, no. 10 (2024). http://dx.doi.org/10.1002/ece3.70361.

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ABSTRACTAbout 35% of grassland in Sanjiangyuan area of China has degenerated into black‐soil mountain. Artificial grassland is considered to be an effective measure to alleviate the severely degraded grassland in the alpine region of the three rivers and has been widely used. However, the pattern, potential function, and changes of carbon and nitrogen contents of soil microorganisms in degraded grassland in Heimushan by planting artificial grassland are still unclear. In this study, mixed‐sown artificial alpine grassland (AG) was the focus of our study, whereas degraded black‐soil mountain gra

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Wang, Kai, Mengxia Liu, Changyang Cai, et al. "The impact of genetic modified Ma bamboo on soil microbiome." Frontiers in Microbiology 13 (November 1, 2022). http://dx.doi.org/10.3389/fmicb.2022.1025786.

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Evaluating the potential alteration of microbial communities is a vital step for biosafety of genetic modified plants. Recently, we have produced genetic modified Ma bamboo with increased cold and drought tolerance by anthocyanin accumulation. In this work, we aim to study the potential effects on microbial communities in rhizosphere soils during the cultivation of genetic modified bamboo. Rhizosphere and surrounding soil were collected at 3-month post-transplant. The amplicon (16S rDNA and ITS1) were sequenced for analysis of bacterial and fungal communities. Multiple software and database (P

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Meng, Xiangzheng, Manhong Liu, Zhaojun Meng, et al. "Effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, China." Frontiers in Microbiology 15 (May 14, 2024). http://dx.doi.org/10.3389/fmicb.2024.1403849.

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Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, we employed a “time and space parallel” method. Four restoration stages, namely corn field (Corn), short-term restoration wetland (2 years, ST), long-term restoration wetland (8 years, LT) and natural wetland (&gt;25 years, NW), were selected to represent the restoration time and geographical location in Naolihe Nature Wetland. We investigated the composition and di

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Elkhateeb, Yomna A. M., and Mohamed Fadel. "Bioinformatic Studies, Experimental Validation of Phytase Production and Optimization of Fermentation Conditions for Enhancing Phytase Enzyme Production by Different Microorganisms under Solid-State Fermentation." Open Microbiology Journal 16, no. 1 (2022). http://dx.doi.org/10.2174/18742858-v16-e2202160.

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Background: Phytase is an essential enzyme necessary for the digestive process. It is a natural enzyme found in plant materials. It prevents bad effect of phytic acid on protein and energy utilization. Phytase frees the bound minerals such as phosphorus, calcium, zinc, iron, magnesium and manganese from the phytic acid molecule providing essential minerals available for healthy nutrition. This study depends on converting food processing waste into highly valuable products. Optimizing the fermentation conditions for enhancing high phytase production with low cost was the objective of this resea

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Elkhateeb, Yomna A. M., and Mohamed Fadel. "Bioinformatic Studies, Experimental Validation of Phytase Production and Optimization of Fermentation Conditions for Enhancing Phytase Enzyme Production by Different Microorganisms under Solid-State Fermentation." Open Microbiology Journal 16, no. 1 (2022). http://dx.doi.org/10.2174/18742858-v16-e2202160.

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Background: Phytase is an essential enzyme necessary for the digestive process. It is a natural enzyme found in plant materials. It prevents bad effect of phytic acid on protein and energy utilization. Phytase frees the bound minerals such as phosphorus, calcium, zinc, iron, magnesium and manganese from the phytic acid molecule providing essential minerals available for healthy nutrition. This study depends on converting food processing waste into highly valuable products. Optimizing the fermentation conditions for enhancing high phytase production with low cost was the objective of this resea

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