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A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Environmental and Ecological Interactions of Fungi".

Deadline for manuscript submissions: 31 January 2025 | Viewed by 7699

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Special Issue Editors

Dr. Ke Dong

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Guest Editor

Major of Life Science, Kyonggi University, Suwon-si 16227, Republic of Korea
Interests: soil microbiome; microbial ecology; environmental microbiology; biogeography; biogeochemical cycles

Prof. Dr. Nan Li

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Guest Editor

College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China
Interests: mangrove microbiome; microbial ecology; marine functional microbes; regional ecological security, biogeography, biogeochemical cycles

Special Issue Information

Dear Colleagues,

Fungi, as key components of ecosystems, play pivotal roles in the decomposition of biomass and nutrient cycling, forming complex interactions with plants, animals, and other microorganisms, influencing ecological balance and the maintenance of biodiversity. In diverse environments, the composition and function of fungal communities display significant variations. These differences not only reflect the fungi’s adaptability to specific environmental disturbance, but also indicate the impact of environmental changes on ecosystem health. In this Special Issue, we look for studies that delve into the diversity and composition of fungal communities within a variety of environments—ranging from terrestrial to aquatic and from urban to extreme habitats. Additionally, we seek research that illuminates the vital ecological roles and functions that fungi perform, including, but not limited to, nutrient cycling, soil formation, plant symbiosis, and the decomposition of organic matter. We are also interested in studies examining how fungal communities adapt to environmental stresses, such as climate change, pollution, and habitat fragmentation. Furthermore, contributions that investigate the complex interactions between fungi and other organisms including plants, bacteria, and animals, showcasing the range of mutualistic, commensal, and parasitic relationships, are also welcomed.

Dr. Ke Dong
Prof. Dr. Nan Li
Guest Editors

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Keywords

fungi
ecosystems
environmental stresses
community assembly
diversity and composition
ecological interactions
ecological functions

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Published Papers (8 papers)

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Research

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 585

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 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 682

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 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 937

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 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 1 | Viewed by 948

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, 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

Viewed by 609

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, 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

Viewed by 1103

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 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

Viewed by 1048

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 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

Viewed by 1059

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, 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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