Journal of Fungi

Research

13 pages, 3488 KiB

Open AccessArticle

Interactions Between Morel Cultivation, Soil Microbes, and Mineral Nutrients: Impacts and Mechanisms

by Yiwen Fu, Muxin Fan, Haiyan Qin, Zeyu Zhang, Shijun Liu, Shuwen Wu, Yun Wang and Xia Yuan

J. Fungi 2025, 11(6), 405; https://doi.org/10.3390/jof11060405 (registering DOI) - 24 May 2025

Abstract

Morel mushrooms (Morchella spp.) are prized for their nutritional and medicinal value. Despite extensive research on their cultivation, the species’ impacts on the soil microbiota and minerals remain unclear. This study systematically evaluated six Morchella species, analyzing their effects on soil physicochemical [...] Read more.

Morel mushrooms (Morchella spp.) are prized for their nutritional and medicinal value. Despite extensive research on their cultivation, the species’ impacts on the soil microbiota and minerals remain unclear. This study systematically evaluated six Morchella species, analyzing their effects on soil physicochemical properties, microbial communities, and mineral nutrients levels. The results showed that yield varied significantly among the species, with an order of M. sextelata > M. exuberans > M. eximia > M. importuna > Mel-13 > Mel-21. Cultivation led to a consistent reduction in soil NO₃⁻-N levels, particularly in M. eximia and Mel-13 (40–50% decrease), while NH₄⁺-N levels did not change significantly, indicating mycelial nitrate preference. Mineral nutrient alterations exhibited distinct species-dependent patterns, with M. eximia showing the greatest increase in exchangeable Ca, while M. importuna and M. sextelata caused the most obvious decreases in available B. Morchella species exerted more pronounced impacts on fungal than bacterial communities, evidenced by significant reductions in alpha diversity—particularly in high-yield M. sextelata—suggesting species-specific fungal inhibition. At the phylum level, consistent depletion of Ascomycota but enrichment of Mortierellomycota were noted. Moreover, correlation analyses identified significant positive associations between morel yield and both fungal community diversity and exchangeable Ca content. This implies that Morchella species restructures soil fungal communities through nutrient competition and mineral-mediated regulation, with calcium acting as a key modulator. Overall, by elucidating the interconnected ‘Morchella species–microbe–mineral’ relationships, this study highlights Morchella species’ distinct regulation of soil microecology, providing valuable insights for the selection of optimized species like M. eximia and targeted soil management in morel cultivation. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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17 pages, 2985 KiB

Open AccessArticle

Distribution Patterns of Wood-Decay Macrofungi (Agaricomycetes) in Floodplain Forest Islands of the Eastern Amazon

by Vitória Pinto Farias, Maria do Perpétuo Socorro Progene Vilhena, Antonio Walison Gondim-Vieira, Richard Bruno Mendes-Freire, Renan Domingues Pacheco, Braian Saimon Frota da Silva and Adriene Mayra da Silva Soares

J. Fungi 2025, 11(4), 288; https://doi.org/10.3390/jof11040288 - 7 Apr 2025

Viewed by 449

Abstract

Macrofungi are key decomposers of organic matter and play an active role in biogeochemical cycles, thereby contributing to carbon sequestration in forest ecosystems. Floodplain forests (várzeas) are characterized by the dynamics of rising and receding waters, which are rich in suspended material and [...] Read more.

Macrofungi are key decomposers of organic matter and play an active role in biogeochemical cycles, thereby contributing to carbon sequestration in forest ecosystems. Floodplain forests (várzeas) are characterized by the dynamics of rising and receding waters, which are rich in suspended material and influence species variation and adaptation. The knowledge about the distribution of macrofungi in várzea environments in the Brazilian Amazon is limited. This study aims to evaluate the diversity and composition of macrofungi on three várzea forest islands, while also examining differences in species richness and abundance between seasonal periods. A total of 88 macrofungal species that belong to the phylum Basidiomycota were identified. The findings revealed significant variations in species composition, yet no notable differences in species richness or abundance were observed between the seasonal periods. The environmental conditions and resources available to macrofungi appear to be consistent among the islands, which leads to a balanced diversity. However, additional research is essential to uncover the true distribution patterns of macrofungi in the várzeas of the Brazilian Amazon, an area under significant threat to its biodiversity. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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15 pages, 6910 KiB

Open AccessArticle

Fungal Community Complexity and Stability in Clay Loam and Sandy Soils in Mangrove Ecosystems

by Shengyao Zhou, Xiaojie Deng, Rajapakshalage Thashikala Nethmini, Huaxian Zhao, Qing He, Gonglingxia Jiang, Qinghua Hou, Qingxiang Chen, Xiaolei Li, Ke Dong and Nan Li

J. Fungi 2025, 11(4), 262; https://doi.org/10.3390/jof11040262 - 28 Mar 2025

Viewed by 368

Abstract

Soil fungi in mangroves are diverse and crucial for organic matter decomposition and element cycling. However, the drivers influencing network complexity and the stability of fungal communities across different mangrove soil habitats remain unclear. This study investigated the main factors driving the composition, [...] Read more.

Soil fungi in mangroves are diverse and crucial for organic matter decomposition and element cycling. However, the drivers influencing network complexity and the stability of fungal communities across different mangrove soil habitats remain unclear. This study investigated the main factors driving the composition, diversity, complexity, and stability of fungal communities in clay loam and sandy soils in mangrove ecosystems. Results showed that Dothideomycetes and Sordariomycetes dominated in clay loam and sandy soils, respectively. Sandy soils exhibited higher alpha diversity than clay loam. Beta diversity analysis revealed significant differences in the fungal community structure between the two soil types. Network analysis demonstrated higher complexity and stability of fungal communities in clay loam than in sandy soil. Spearman’s correlation analysis revealed that NH₄⁺-N and total nitrogen were the main factors affecting complexity and stability in clay loam, respectively. Partial least squares path modeling demonstrated that alpha diversity and soil properties were closely linked to the complexity and stability of fungal communities in clay loam, whereas beta diversity was the primary driver in sandy soil. Our study enhances the understanding of the mechanisms that maintain fungal diversity and community stability in mangrove ecosystems, with important implications for restoring vegetation in degraded areas. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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19 pages, 9560 KiB

Open AccessArticle

Pomegranate Woody Mycobiota Associated with Wood Decay

by Valentino Bergamaschi, Maria Teresa Valente and Rosario Muleo

J. Fungi 2025, 11(4), 254; https://doi.org/10.3390/jof11040254 - 26 Mar 2025

Viewed by 294

Abstract

The rapid expansion of pomegranate (Punica granatum L.) cultivation in central and southern Italy has revealed emerging phytosanitary challenges, including “pomegranate wood decay syndrome”, characterised by cortical cankers, wood browning, and progressive plant decline. This study investigates the fungal microbiota associated with [...] Read more.

The rapid expansion of pomegranate (Punica granatum L.) cultivation in central and southern Italy has revealed emerging phytosanitary challenges, including “pomegranate wood decay syndrome”, characterised by cortical cankers, wood browning, and progressive plant decline. This study investigates the fungal microbiota associated with symptomatic pomegranate wood using a combined approach of traditional fungal isolation and ITS2 metabarcoding analysis. Samples from two orchards in Lazio were examined, revealing a complex fungal community with a high prevalence of Neofusicoccum parvum (putative) and species belonging to the genus Diaporthe. Pathogenicity tests confirmed the role of N. parvum in causing significant wood browning, while other isolates showed variable virulence. Statistical analyses validated the pathogenicity of select isolates, with the putative Diaporthe eres (Nitschke) consistently demonstrating potential pathogenic activity across all trials. Metabarcoding identified 289 taxa, highlighting a richer fungal diversity in the symptomatic wood compared to the asymptomatic sections. Notably, Coniella granati, previously implicated in pomegranate decline, was absent in the studied orchards. The findings reveal that pomegranate wood decay is a complex syndrome driven by fungal pathogens and environmental stressors, such as low temperatures. This study highlights the value of integrative approaches for understanding and managing fungal-associated wood diseases in pomegranate orchards. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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18 pages, 15921 KiB

Open AccessArticle

Variation of Arbuscular Mycorrhizal Fungi Communities Between Root and Rhizosphere Soil of Endangered Plant Heptacodium miconioides Along Elevation Gradient

by Yueling Li, Guangyu Luo, Shijie Wu, Dang Yang, Pengpeng Lv, Zexin Jin and Junmin Li

J. Fungi 2025, 11(3), 222; https://doi.org/10.3390/jof11030222 - 14 Mar 2025

Viewed by 528

Abstract

Arbuscular mycorrhizal fungi (AMF) are considered crucial for the survival of many endangered plant species. However, the dynamics of AMF communities in the roots and rhizosphere soil of Heptacodium miconioides, particularly along elevation gradients, remain underexplored. This study investigates AMF colonization, spore [...] Read more.

Arbuscular mycorrhizal fungi (AMF) are considered crucial for the survival of many endangered plant species. However, the dynamics of AMF communities in the roots and rhizosphere soil of Heptacodium miconioides, particularly along elevation gradients, remain underexplored. This study investigates AMF colonization, spore density, and community structure in the root and rhizosphere soil of H. miconioides across an elevation range from 306 to 1028 m a.s.l., employing high-throughput sequencing. Our results show that AMF colonization and spore density in H. miconioides increased with elevation. Glomus was the dominant genus in both root and rhizosphere samples. Elevation significantly influenced the AMF community structure and diversity in the root, with alpha diversity decreasing linearly with elevation. In contrast, no significant elevation-related changes were observed in the rhizosphere soil alpha diversity. The difference in AMF beta diversity between the root and rhizosphere soil was lowest at the highest elevation. Compared to the rhizosphere soil, the degree and degree centralization of AMF community co-occurrence networks in the root showed a significant increase at higher elevations. Variations in soil properties, particularly soil pH, available phosphorus, and total nitrogen levels strongly influenced AMF communities in rhizosphere soil, while nitrate nitrogen, available potassium, and acid phosphatase were correlated with AMF communities in the root. These findings highlight the impact of elevation on AMF communities in both root and rhizosphere soil, providing valuable insights for the habitat restoration and conservation efforts for this species. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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19 pages, 6313 KiB

Open AccessArticle

Distribution Pattern and Assembly Process of Fungal Communities Along Altitude Gradient in Sediments of the Yellow River Basin

by Kang Fang, Guoce Xu, Xin Chen, Jing Li, Yuting Cheng and Yifan Cheng

J. Fungi 2025, 11(3), 214; https://doi.org/10.3390/jof11030214 - 11 Mar 2025

Viewed by 536

Abstract

Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective [...] Read more.

Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective conservation and management of river ecosystems. However, the distribution patterns and assembly process of fungal communities along elevation gradients in river sediments remain poorly understood. In this study, ITS amplicon sequencing, a neutral community model, and a null model were employed to analyze the distribution patterns and assembly processes of fungal communities in sediments along the altitudinal gradient of the Yellow River. The results indicated that Ascomycota (47.79%) and Basidiomycota (15.68%) were identified as the dominant phyla in the sediments, collectively accounting for 63.47% of the total relative abundance of the community. In the three different altitudinal gradients, the fungal community diversity (Shannon) showed a gradually decreasing trend with increasing altitude. The co-line networks of fungal communities exhibited positive interactions and had more complex and compact networks in the sediments of the Tibetan Plateau area (YRA). Environmental factors in the sediments played an important role in shaping the structure of fungal communities, with lead (Pb), total nitrogen (TN), silt, and total organic carbon (TOC) being the main factors driving changes in community structure, contributing 15.5%, 12.3%, 10.7%, and 10.2%, respectively. In the community assembly process, deterministic processes were found to dominate, with homogenizing selection contributing the most (69.66%). These research results help us understand the distribution patterns of fungal communities along altitudinal gradients and the mechanisms of community assembly, and also provide a scientific basis for biodiversity conservation and the rational use of biological resources. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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18 pages, 4271 KiB

Open AccessArticle

Comparison of Rhizosphere Microbiomes Between Domesticated and Wild Wheat in a Typical Agricultural Field: Insights into Microbial Community Structure and Functional Shifts

by Jie Fang, Mihal Blaschkauer, Assaf Distelfeld, Zihao Liu, Bin Song, Shimon Rachmilevitch and Jonathan M. Adams

J. Fungi 2025, 11(3), 168; https://doi.org/10.3390/jof11030168 - 20 Feb 2025

Viewed by 690

Abstract

While the differences between domesticated crops and their wild relatives have been extensively studied, less is known about their rhizosphere microbiomes, which hold potential for breeding stress-resistant traits. We compared the rhizosphere microbiomes of domesticated wheat (Triticum aestivum L.) and its wild [...] Read more.

While the differences between domesticated crops and their wild relatives have been extensively studied, less is known about their rhizosphere microbiomes, which hold potential for breeding stress-resistant traits. We compared the rhizosphere microbiomes of domesticated wheat (Triticum aestivum L.) and its wild ancestor (Triticum turgidum ssp. dicoccoides) in a typical agricultural field using 16S rRNA and ITS gene sequencing. Our results revealed a high level of conservation in the rhizosphere microbiomes between wild and domesticated wheat, with minimal divergence in community composition and microbial network structure. However, domesticated wheat exhibited a higher prevalence of fungal pathogens and increased functional redundancy, with significant enrichment of genes involved in carbon and nitrogen cycling. The microbial community assemblies in both wheats were predominantly governed by deterministic processes. This suggests that long-term conventional agricultural practices have imposed minor effects on the compositional differences between the microbiomes of wild and domesticated wheat. Nonetheless, the lower abundance of apparent pathogens in the rhizosphere of the wild wheat suggests greater natural biota or innate host plant resistance against pathogenic fungi. This study may provide valuable insights into the host selection, assembly patterns, and functional potential of microbial communities in wild versus domesticated wheat, with implications for manipulating microbial communities in future crop breeding. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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16 pages, 3030 KiB

Open AccessArticle

Shifts in Soil Fungal Community and Trophic Modes During Mangrove Ecosystem Restoration

by Xiaofang Shi, Shengyao Zhou, Lanzi Xu, Rajapakshalage Thashikala Nethmini, Yu Zhang, Liangliang Huang, Ke Dong, Huaxian Zhao and Lianghao Pan

J. Fungi 2025, 11(2), 146; https://doi.org/10.3390/jof11020146 - 14 Feb 2025

Viewed by 684

Abstract

Mangrove ecosystems are valuable coastal ecosystems; however, studies on the diversity and functional features of their soil fungal communities during restoration are limited. In this study, we examined fungal diversity and trophic modes across mudflat, young mangrove, and mature mangrove stages. We found [...] Read more.

Mangrove ecosystems are valuable coastal ecosystems; however, studies on the diversity and functional features of their soil fungal communities during restoration are limited. In this study, we examined fungal diversity and trophic modes across mudflat, young mangrove, and mature mangrove stages. We found that Ascomycota and Basidiomycota were the dominant phyla, with saprotrophs as the most abundant trophic mode. The abundance of the major phyla and trophic modes significantly varied across restoration stages. Although fungal alpha (α)-diversity remained stable among the stages, beta (β)-diversity showed significant differentiation. Spearman’s analysis and partial Mantel tests revealed that total nitrogen and inorganic phosphorus significantly influenced the fungal α-diversity, whereas temperature and pH primarily shaped the fungal β-diversity. Total nitrogen and carbon were key factors affecting the trophic mode α-diversity, whereas total phosphorus and inorganic phosphorus were the main drivers of the trophic mode β-diversity. Variation partitioning analysis confirmed that nutrients, rather than soil properties, were the primary factors shaping fungal communities and trophic modes. Random forest analysis identified key bioindicators, including species such as Paraphyton cookei, and trophic modes such as saprotrophs, both of which were strongly influenced by soil carbon. These findings advance our understanding of fungal ecology in mangrove restoration. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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22 pages, 6301 KiB

Open AccessArticle

Phytophthora Species and Their Associations with Chaparral and Oak Woodland Vegetation in Southern California

by Sebastian N. Fajardo, Tyler B. Bourret, Susan J. Frankel and David M. Rizzo

J. Fungi 2025, 11(1), 33; https://doi.org/10.3390/jof11010033 - 4 Jan 2025

Viewed by 1358

Abstract

Evidence of unintended introductions of Phytophthora species into native habitats has become increasingly prevalent in California. If not managed adequately, Phytophthora species can become devastating agricultural and forest plant pathogens. Additionally, California’s natural areas, characterized by a Mediterranean climate and dominated by chaparral [...] Read more.

Evidence of unintended introductions of Phytophthora species into native habitats has become increasingly prevalent in California. If not managed adequately, Phytophthora species can become devastating agricultural and forest plant pathogens. Additionally, California’s natural areas, characterized by a Mediterranean climate and dominated by chaparral (evergreen, drought-tolerant shrubs) and oak woodlands, lack sufficient baseline knowledge on Phytophthora biology and ecology, hindering effective management efforts. From 2018 to 2021, soil samples were collected from Angeles National Forest lands (Los Angeles County) with the objective of better understanding the diversity and distribution of Phytophthora species in Southern California. Forty sites were surveyed, and soil samples were taken from plant rhizospheres, riverbeds, and off-road vehicle tracks in chaparral and oak woodland areas. From these surveys, fourteen species of Phytophthora were detected, including P. cactorum (subclade 1a), P. multivora (subclade 2c), P. sp. cadmea (subclade 7a), P. taxon ‘oakpath’ (subclade 8e, first reported in this study), and several clade-6 species, including P. crassamura. Phytophthora species detected in rhizosphere soil were found underneath both symptomatic and asymptomatic plants and were most frequently associated with Salvia mellifera, Quercus agrifolia, and Salix sp. Phytophthora species were present in both chaparral and oak woodland areas and primarily in riparian areas, including detections in off-road tracks, trails, and riverbeds. Although these Mediterranean ecosystems are among the driest and most fire-prone areas in the United States, they harbor a large diversity of Phytophthora species, indicating a potential risk for disease for native Californian vegetation. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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23 pages, 8896 KiB

Open AccessArticle

New Species and Records Expand the Checklist of Cellular Slime Molds (Dictyostelids) in Jilin Province, China

by Zhaojuan Zhang, Liang He, Yuqing Sun, Zhuang Li, Yingkun Yang, Chao Zhai, Steven L. Stephenson, Xiangrui Xie, Yu Li and Pu Liu

J. Fungi 2024, 10(12), 834; https://doi.org/10.3390/jof10120834 - 2 Dec 2024

Viewed by 977

Abstract

Dictyostelids represent a crucial element in the protist community, and their abundant presence in Jilin Province underscores their indispensable role in biodiversity conservation. In the present study, a resource survey of dictyostelids used random sampling to collect 28 soil samples from five localities [...] Read more.

Dictyostelids represent a crucial element in the protist community, and their abundant presence in Jilin Province underscores their indispensable role in biodiversity conservation. In the present study, a resource survey of dictyostelids used random sampling to collect 28 soil samples from five localities in Changbai Korean Autonomous County, Jilin Province. In addition, a compilation of dictyostelid species reported from Jilin Province was developed, based on a thorough review of the literature. The survey yielded fifteen isolates of dictyostelids, comprising six species from four genera. Notably, two new species (Dictyostelium longigracilis sp. nov. and Dictyostelium macrosoriobrevipes sp. nov.) were described using morphological characteristics and SSU gene-based phylogenetic analyses. One other species (Polysphondylium patagonicum) was recorded as new for China, while another (Cavenderia aureostipes) was recorded as a new record for Jilin Province. The dictyostelid assemblage in Jilin Province is dominated by the genus Dictyostelium (51.4%), with a total of 35 species, which represent 59.3% of the current total known for all of China. These findings provide a scientific basis for the protection of species diversity and resource utilization of dictyostelids in Jilin Province. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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18 pages, 1768 KiB

Open AccessArticle

The Fungal Community Structure Regulates Elevational Variations in Soil Organic Carbon Fractions in a Wugong Mountain Meadow

by Jinping Wang, Jihong Yuan, Qiong Ren, Liyin Zhou, Huanhuan Zeng, Lujun Miao, Zhiyong Sun, Fang Wan and Yuanying Yan

J. Fungi 2024, 10(11), 772; https://doi.org/10.3390/jof10110772 - 6 Nov 2024

Viewed by 1347

Abstract

Soil organic carbon (SOC) fractions are vital intrinsic indicators of SOC stability, and soil fungi are the key drivers of soil carbon cycling. However, variations in SOC fractions along an elevational gradient in mountain meadows and the role of the fungal community in [...] Read more.

Soil organic carbon (SOC) fractions are vital intrinsic indicators of SOC stability, and soil fungi are the key drivers of soil carbon cycling. However, variations in SOC fractions along an elevational gradient in mountain meadows and the role of the fungal community in regulating these variations are largely unknown, especially in subtropical areas. In this study, an elevation gradient experiment (with experimental sites at 1500, 1700, and 1900 m) was set up in a Miscanthus sinensis community in a meadow on Wugong Mountain, Southeast China, to clarify the effects of elevation on soil fungal community composition, microbial residue carbon, and SOC fractions. The results showed that the contribution of soil microbial residue carbon to SOC was only 16.1%, and the contribution of soil fungal residue carbon to SOC (15.3%) was far greater than that of bacterial residue carbon (0.3%). An increase in elevation changed the fungal community structure and diversity, especially in the topsoil (0–20 cm depth) compared with that in the subsoil (20–40 cm depth), but did not affect fungal residue carbon in the two soil layers. When separating SOC into the fractions mineral-associated organic carbon (MAOC) and particulate organic carbon (POC), we found that the contribution of MAOC (66.6%) to SOC was significantly higher than that of POC (20.6%). Although an increased elevation did not affect the SOC concentration, it significantly changed the SOC fractions in the topsoil and subsoil. The soil POC concentration and its contribution to SOC increased with an increasing elevation, whereas soil MAOC showed the opposite response. The elevational variations in SOC fractions and the POC/MAOC ratio were co-regulated by the fungal community structure and total nitrogen. Our results suggested that SOC stabilization in mountain meadows decreases with an increasing elevation and is driven by the fungal community structure, providing scientific guidance for SOC sequestration and stability in mountain meadows in subtropical areas. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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19 pages, 7301 KiB

Open AccessArticle

A Treasure Trove of Urban Microbial Diversity: Community and Diversity Characteristics of Urban Ancient Ginkgo biloba Rhizosphere Microorganisms in Shanghai

by Jieying Mao, Qiong Wang, Yaying Yang, Feng Pan, Ziwei Zou, Xiaona Su, Yi Wang, Wei Liu and Yaohua Tang

J. Fungi 2024, 10(10), 720; https://doi.org/10.3390/jof10100720 - 16 Oct 2024

Viewed by 1540

Abstract

Rapid urbanization has exerted immense pressure on urban environments, severely constraining the growth of ancient trees. The growth of ancient trees is closely linked to the microbial communities in their rhizospheres, and studying their community characteristics may provide new insights into promoting the [...] Read more.

Rapid urbanization has exerted immense pressure on urban environments, severely constraining the growth of ancient trees. The growth of ancient trees is closely linked to the microbial communities in their rhizospheres, and studying their community characteristics may provide new insights into promoting the growth and rejuvenation of ancient trees. In this study, the rhizosphere soil and root systems of ancient Ginkgo biloba trees (approximately 200 years old) and adult G. biloba trees (approximately 50 years old) in Shanghai were selected as research subjects. Phospholipid fatty acid (PLFA) analysis and high-throughput sequencing were employed to investigate the diversity of microbial communities in the G. biloba rhizosphere. The results indicated that the 19 PLFA species selected to characterize the soil microbial community structure and biomass were present in the rhizosphere soil of both ancient and adult G. biloba trees. However, the total microbial biomass and the microbial biomass in the rhizosphere soil of ancient G. biloba were lower than the microbial biomass in the rhizosphere soil of adult G. biloba. The biomasses of Gram-negative bacteria (G⁻), arbuscular mycorrhizal fungi (AMF), and protozoans (P) were significantly different. Total phosphorus, organic matter, and pH may be the key factors influencing the soil microbial community in the rhizosphere zone of ancient G. biloba. An in-depth study of AMF showed that the roots and rhizosphere soil of G. biloba contained abundant AMF resources, which were assigned to 224 virtual taxa using the MaarjAM reference database, belonging to four orders, ten families, and nineteen genera. The first and second most dominant genera were Glomus and Paraglomus, respectively. Archaeospora and Ambispora were more dominant in the rhizosphere than the roots. Furthermore, the abundance of live AMF was significantly higher in ancient G. biloba than in adult G. biloba. Therefore, future research should focus on the improvement of soil environmental characteristics and the identification and cultivation of indigenous dominant AMF in the rhizosphere of ancient G. biloba, aiming for their effective application in the rejuvenation of ancient trees. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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23 pages, 3046 KiB

Open AccessArticle

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study

by Glen Dierickx, Lowie Tondeleir, Pieter Asselman, Kris Vandekerkhove and Annemieke Verbeken

J. Fungi 2024, 10(10), 708; https://doi.org/10.3390/jof10100708 - 10 Oct 2024

Viewed by 1710

Abstract

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context [...] Read more.

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE’s species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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22 pages, 6193 KiB

Open AccessArticle

Discovery of Gibellula floridensis from Infected Spiders and Analysis of the Surrounding Fungal Entomopathogen Community

by Ross A. Joseph, Abolfazl Masoudi, Mateo J. Valdiviezo and Nemat O. Keyhani

J. Fungi 2024, 10(10), 694; https://doi.org/10.3390/jof10100694 - 4 Oct 2024

Cited by 4 | Viewed by 1969

Abstract

Characterization of fungal spider pathogens lags far behind their insect counterparts. In addition, little to nothing is known concerning the ecological reservoir and/or fungal entomopathogen community surrounding infection sites. Five infected spider cadavers were identified in the neo-tropical climate of north-central Florida, USA, [...] Read more.

Characterization of fungal spider pathogens lags far behind their insect counterparts. In addition, little to nothing is known concerning the ecological reservoir and/or fungal entomopathogen community surrounding infection sites. Five infected spider cadavers were identified in the neo-tropical climate of north-central Florida, USA, from three of which viable cultures were obtained. Multi-locus molecular phylogenetic and morphological characterization identified one isolate as a new Gibellula species, here named, Gibellula floridensis, and the other isolates highly similar to Parengyodontium album. The fungal entomopathogen community surrounding infected spiders was sampled at different habitats/trophic levels, including soil, leaf litter, leaf, and twig, and analyzed using ITS amplicon sequencing. These data revealed broad but differential distribution of insect-pathogenic fungi between habitats and variation between sites, with members of genera belonging to Metarhizium and Metacordyceps from Clavicipitaceae, Purpureocillium and Polycephalomyces from Ophiocordyceps, and Akanthomyces and Simplicillium from Cordycipitaceae predominating. However, no sequences corresponding to Gibellula or Parengyodontium, even at the genera levels, could be detected. Potential explanations for these findings are discussed. These data highlight novel discovery of fungal spider pathogens and open the broader question regarding the environmental distribution and ecological niches of such host-specific pathogens. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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24 pages, 7153 KiB

Open AccessArticle

Dominant Tree Species and Litter Quality Govern Fungal Community Dynamics during Litter Decomposition

by Wenjing Meng, Lin Chang, Zhaolei Qu, Bing Liu, Kang Liu, Yuemei Zhang, Lin Huang and Hui Sun

J. Fungi 2024, 10(10), 690; https://doi.org/10.3390/jof10100690 - 3 Oct 2024

Cited by 2 | Viewed by 1361

Abstract

Litter decomposition is a crucial biochemical process regulated by microbial activities in the forest ecosystem. However, the dynamic response of the fungal community during litter decomposition to vegetation changes is not well understood. Here, we investigated the litter decomposition rate, extracellular enzyme activities, [...] Read more.

Litter decomposition is a crucial biochemical process regulated by microbial activities in the forest ecosystem. However, the dynamic response of the fungal community during litter decomposition to vegetation changes is not well understood. Here, we investigated the litter decomposition rate, extracellular enzyme activities, fungal community, and nutrient cycling-related genes in leaf and twig litters over a three-year decomposition period in a pure Liquidamabar formosana forest and a mixed L. formosana/Pinus thunbergii forest. The result showed that during the three-year decomposition, twig litter in the mixed forest decomposed faster than that in the pure forest. In both leaf litter and twig litter, β-cellobiosidase and N-acetyl-glucosamidase exhibited higher activities in the mixed forest, whereas phosphatase, β-glucosidase, and β-xylosidase were higher in the pure forest. The fungal α-diversity were higher in both litters in the pure forest compared to the mixed forest, with leaf litter showing higher α-diversity than twig litter. Fungal species richness and α-diversity within leaf litter increased as decomposition progressed. Within leaf litter, Basidiomycota dominated in the mixed forest, while Ascomycota dominated in the pure forest. Funguild analysis revealed that Symbiotroph and ectomycorrhizal fungi were more abundant in the mixed forest compared to the pure forest. In the third-year decomposition, genes related to phosphorus cycling were most abundant in both forests, with the pure forest having a higher abundance of cex and gcd genes. Fungal community structure, predicted functional structure, and gene composition differed between the two forest types and between the two litter types. Notably, the fungal functional community structure during the first-year decomposition was distinct from that in the subsequent two years. These findings suggest that dominant tree species, litter quality, and decomposition time all significantly influence litter decomposition by attracting different fungal communities, thereby affecting the entire decomposition process. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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14 pages, 3869 KiB

Open AccessArticle

Elevational Variation in and Environmental Determinants of Fungal Diversity in Forest Ecosystems of Korean Peninsula

by Lei Chen, Zhi Yu, Mengchen Zhao, Dorsaf Kerfahi, Nan Li, Lingling Shi, Xiwu Qi, Chang-Bae Lee, Ke Dong, Hae-In Lee and Sang-Seob Lee

J. Fungi 2024, 10(8), 556; https://doi.org/10.3390/jof10080556 - 7 Aug 2024

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Abstract

Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated [...] Read more.

Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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19 pages, 3010 KiB

Open AccessArticle

Contrasting Patterns of Fungal and Bacterial Endophytes Inhabiting Temperate Tree Leaves in Response to Thinning

by Beiping Liu, Chunhuan Li, Xiuhai Zhao, Chunyu Zhang, Xinyi He, Laiye Qu and Naili Zhang

J. Fungi 2024, 10(7), 470; https://doi.org/10.3390/jof10070470 - 5 Jul 2024

Cited by 1 | Viewed by 1509

Abstract

The phyllosphere is an important but underestimated habitat for a variety of microorganisms, with limited knowledge about leaf endophytes as a crucial component of the phyllosphere microbiome. In this study, we investigated the mechanisms of communities and co-occurrence networks of leaf endophytes in [...] Read more.

The phyllosphere is an important but underestimated habitat for a variety of microorganisms, with limited knowledge about leaf endophytes as a crucial component of the phyllosphere microbiome. In this study, we investigated the mechanisms of communities and co-occurrence networks of leaf endophytes in response to forest thinning in a temperate forest. As we expected, contrasting responses of fungal and bacterial endophytes were observed. Specifically, the diversity of leaf endophytic fungi and the complexity of their co-occurrence networks increased significantly with thinning intensity, whereas the complexity of endophytic bacterial co-occurrence networks decreased. In particular, microbiota inhabiting damaged leaves seem to be more intensively interacting, showing an evident fungi–bacteria trade-off under forest thinning. In damaged leaves, besides the direct effects of thinning, thinning-induced changes in neighbor tree diversity indirectly altered the diversity of leaf fungal and bacterial endophytes via modifying leaf functional traits such as leaf dry matter content and specific leaf area. These findings provide new experimental evidence for the trade-offs between leaf endophytic fungi and bacteria under the different magnitudes of deforestation, highlighting their dependence on the presence or absence of leaf damage. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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14 pages, 7912 KiB

Open AccessArticle

Changes in the Arbuscular Mycorrhizal Fungal Community in the Roots of Eucalyptus grandis Plantations at Different Ages in Southern Jiangxi, China

by Yao Jiang, Xiao-Yong Mo, Li-Ting Liu, Guo-Zhen Lai and Guo-Wei Qiu

J. Fungi 2024, 10(6), 404; https://doi.org/10.3390/jof10060404 - 4 Jun 2024

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Abstract

Eucalyptus roots form symbiotic relationships with arbuscular mycorrhizal (AM) fungi in soil to enhance adaptation in challenging environments. However, the evolution of the AM fungal community along a chronosequence of eucalypt plantations and its relationship with soil properties remain unclear. In this study, [...] Read more.

Eucalyptus roots form symbiotic relationships with arbuscular mycorrhizal (AM) fungi in soil to enhance adaptation in challenging environments. However, the evolution of the AM fungal community along a chronosequence of eucalypt plantations and its relationship with soil properties remain unclear. In this study, we evaluated the tree growth, soil properties, and root AM fungal colonization of Eucalyptus grandis W. Hill ex Maiden plantations at different ages, identified the AM fungal community composition by high-throughput sequencing, and developed a structural equation model among trees, soil, and AM fungi. Key findings include the following: (1) The total phosphorus (P) and total potassium (K) in the soil underwent an initial reduction followed by a rise with different stand ages. (2) The rate of AM colonization decreased first and then increased. (3) The composition of the AM fungal community changed significantly with different stand ages, but there was no significant change in diversity. (4) Paraglomus and Glomus were the dominant genera, accounting for 70.1% and 21.8% of the relative abundance, respectively. (5) The dominant genera were mainly influenced by soil P, the N content, and bulk density, but the main factors were different with stand ages. The results can provide a reference for fertilizer management and microbial formulation manufacture for eucalyptus plantations. Full article

(This article belongs to the Special Issue Fungal Communities in Various Environments)

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