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Diversity
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Biodiversity and Ecology of Soil Fungal Communities
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Biodiversity and Ecology of Soil Fungal Communities

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 12520

Special Issue Editor

Dr. Xin-Cun Wang

E-Mail Website
Guest Editor
Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Interests: Aspergillaceae; Discinaceae; fungal biodiversity; fungal taxonomy; Ganodermataceae; Helvellaceae; mitochondrial genome; phylogenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil is one of the principal substrata of life on Earth and an important participant in the cycling of carbon and other elements in the planet. It plays vital roles in both global ecosystems and human societies. Soil microorganisms have kinds of ecological functions and shape global element cycles in life and death. They are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter, the Earth’s largest terrestrial carbon pool.

More and more fungal species have been discovered and described from soil, and further studies for different purposes in biology and the other related disciplines are required. Nevertheless, the biodiversity of fungal species in soil is still badly underestimated and the ecological functions of them are not fully recognized.

This Special Issue will focus on biodiversity, new species/taxon of fungal species, and their ecological functions in soil communities. This Special Issue is also an exciting opportunity to combine and synthesize all knowledge that is being generated in these fields. Therefore, Diversity’s team kindly invites you to submit a manuscript on any of the above topics, as well as those addressing broader implications.

Dr. Xin-Cun Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungal diversity
  • new species
  • new taxon
  • ecological function
  • soil community

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Published Papers (6 papers)

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Research

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8 pages, 1173 KiB  
Communication
Nigrospora humicola (Apiosporaceae, Amphisphaeriales), a New Fungus from Soil in China
by Ying-Ying Zhang, Ting Zhang, Hai-Yan Li, Ran Zheng, Jie Ren, Qin Yang and Ning Jiang
Diversity 2024, 16(2), 118; https://doi.org/10.3390/d16020118 - 12 Feb 2024
Cited by 2 | Viewed by 2409
Abstract
The fungal genus Nigrospora is known to be a plant pathogen, endophyte, and saprobe, and it is usually isolated from various substrates like soil and air. During the surveys of soil fungi in Hebei Province of China, two isolates of Nigrospora were obtained. [...] Read more.
The fungal genus Nigrospora is known to be a plant pathogen, endophyte, and saprobe, and it is usually isolated from various substrates like soil and air. During the surveys of soil fungi in Hebei Province of China, two isolates of Nigrospora were obtained. A multi-locus phylogeny of combined loci of the 5.8S nuclear ribosomal gene with the two flanking transcribed spacers (ITS), part of the translation elongation factor 1-alpha (tef1), and the beta-tubulin (tub2) loci, in conjunction with morphological characters were used to identify the newly collected isolates. Nigrospora humicola sp. Nov. is described and proposed herein, which differs from its phylogenetically close species N. chinensis and N. globosa by the sequences of ITS, tef1, and tub2. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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18 pages, 3733 KiB  
Article
Soil Horizons Harbor Differing Fungal Communities
by Enno Mager, Ronja Brockhage, Meike Piepenbring, Francisca Segers, Nourou Soulemane Yorou, Ingo Ebersberger and Ralph Daniel Mangelsdorff
Diversity 2024, 16(2), 97; https://doi.org/10.3390/d16020097 - 1 Feb 2024
Viewed by 1594
Abstract
In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. [...] Read more.
In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. For each soil depth and horizon, fungal diversity and community composition were analyzed as well as the potential impact of site characteristics, like vegetation, on these traits. The retrieved sequences revealed in all their replicates high similarities between fungal communities of samples from the same site and soil horizon, but differed within one site in their horizons. It was possible to assign a saprotrophic, symbiotrophic, or parasitic lifestyle to 24% of the recorded fungal mOTUs. Plant parasites were found in all samples in similar proportions. The presence of ectomycorrhizal fungi in one site could be linked to the presence of ectomycorrhizal trees. Overall, it was observed that fungal diversity decreased with increasing depth if only one horizon was present, whereas a deeper horizon present at one site contained communities with a distinct composition regarding the taxonomical affiliations and lifestyles of the fungi found compared to the upper layer. Hence, soil horizonation seems to drive differences in the composition of fungal communities, and should be regarded with more attention when analyzing soil mycobiomes. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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14 pages, 2504 KiB  
Article
The Addition of a High Concentration of Phosphorus Reduces the Diversity of Arbuscular Mycorrhizal Fungi in Temperate Agroecosystems
by Feng Miao, Senlin Wang, Yuxiang Yuan, Yun Chen, Erhui Guo and Yuan Li
Diversity 2023, 15(10), 1045; https://doi.org/10.3390/d15101045 - 28 Sep 2023
Cited by 2 | Viewed by 1476
Abstract
Phosphorus (P) is an essential macronutrient crucial for both plant growth and crop production, playing a pivotal role in agriculture since the early 20th century. The symbiotic relationship between AMF and plants serves as a classic illustration. These fungi play a regulatory role [...] Read more.
Phosphorus (P) is an essential macronutrient crucial for both plant growth and crop production, playing a pivotal role in agriculture since the early 20th century. The symbiotic relationship between AMF and plants serves as a classic illustration. These fungi play a regulatory role in the growth and development of plants, especially in facilitating the absorption of P and carbon molecules by plants. While there has been a growing body of research on the community assembly of arbuscular mycorrhizal fungi (AMF) in recent decades, our knowledge of the processes governing the coexistence of these AMF communities influenced by P in agroecosystems remains limited. To investigate the impact of various P fertilizers on AMF communities in temperate agroecosystems, this study was conducted using soils sourced from wheat–maize rotation farmland at Henan Agricultural University Yuanyang Base. With the Illumina MiSeq high-throughput sequencing technique, we systematically examined the taxonomic composition of soil AMF at the Yuanyang Base of Henan Agricultural University in a wheat–maize rotation agricultural field. Our primary objective was to unravel the mechanisms behind AMF community assembly and stability under varying P gradient fertilization conditions. Nonmetric Multidimensional Scaling (NMDS) analysis revealed significant differences among AMF communities in field soil subjected to various treatments (p < 0.05). A torus translations test demonstrated positive associations with the three treatments in 36 out of the 51 examined AMF operational taxonomic units (OTUs), making up 70.59% (p < 0.05) of the results. Furthermore, 37.84% (14/37) of the OTUs displayed preferences for the low P concentration treatment, while 34.29% (12/35) and 32.26% (10/31) favored medium and high P concentrations, respectively. An analysis of the Normalized Stochasticity Ratio (NST) and Checkerboard Score (C-score) indicated that in temperate agroecosystems, deterministic processes predominantly governed AMF in all treatment groups, with high P conditions exerting a stronger influence than low or medium P conditions. This study underscores the profound impact of long-term P fertilizer application on AMF community structures within temperate agricultural systems employing wheat–maize rotation. Additionally, it highlights the dominant role played by deterministic processes in shaping the assembly of AMF communities in these temperate agricultural systems that use P fertilizers. These findings emphasize the need for balanced nutrient management, particularly concerning P, to ensure the stability of AMF communities. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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16 pages, 2749 KiB  
Article
Phenotypic and Molecular Characterization of Yeast Diversity Associated to Postharvest Fermentation Process of Coffee Fruits in Southern Ecuador
by David Apolo, José Miguel Fernández, Ángel Benítez, Jorge G. Figueroa, Karla Estrada and Darío Cruz
Diversity 2023, 15(9), 984; https://doi.org/10.3390/d15090984 - 31 Aug 2023
Cited by 3 | Viewed by 1676
Abstract
Coffee (Coffea arabica), produced and marketed in Ecuador and worldwide, can be organoleptically improved by means of microorganisms such as well-characterized yeasts. This study aimed to isolate and characterize yeasts from three postharvest fermentation processes (i.e., Natural aerobic at room temperature; Carbonic [...] Read more.
Coffee (Coffea arabica), produced and marketed in Ecuador and worldwide, can be organoleptically improved by means of microorganisms such as well-characterized yeasts. This study aimed to isolate and characterize yeasts from three postharvest fermentation processes (i.e., Natural aerobic at room temperature; Carbonic maceration with a CO2 atmosphere at room temperature; and Carbonic refrigerated maceration with a CO2 atmosphere to 10 °C) of coffee fruits in Ecuador. Phenotypic and molecular analyses were conducted on 329 yeast isolates obtained from coffee farms in Loja, Olmedo, and Gonzanamá. Three universal media were used for yeast isolation diversity, and phenotypic characterization included morphology, sugar fermentation, salt tolerance, and ethanol resistance. Molecular characterization involved DNA analysis. The isolated diversity was classified into 12 morphotypes, nine distinct biochemical groups and nine genetic species. Only six species (i.e., Kurtzmaniella quercitrusa, Hanseniaspora opuntiae, Pichia. kluyveri, Torulaspora delbrueckii, T. quercuum, and Wickerhamomyces anomalus) identified phylogenetically corresponded to the designated morphotypes. But surprisingly, nine genetic species matched with the nine biochemical groups determined phenotypically analyzed using principal component analysis (PCA). Most of this diversity was found in the coffee plantation located in Gonzanamá, in contrast to Olmedo and Loja, without statistical significance (p value: 0.08295). On the other hand, the richness is not similar statistically (p value: 0.02991) between postharvest fermentation treatments. The findings suggest that the application of biochemical tests is useful for species determination, although morphological data may be ambiguous. Notably, Pichia kluyveri, detected in this study, holds potential for biotechnological evaluation in coffee fermentation processes. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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Review

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18 pages, 2510 KiB  
Review
Responses of Natural Microorganisms to Land Reclamation and Applications of Functional Microorganisms in Biorestoration of Coal Mining Area
by Zhen Mao, Jim Harris and Zheyu Zhang
Diversity 2024, 16(2), 86; https://doi.org/10.3390/d16020086 - 28 Jan 2024
Cited by 2 | Viewed by 2421
Abstract
Extensive coal mining causes significant ecological and environmental impacts on the local ecosystem, especially on the terrestrial ecosystem. Mining activities induce the degradation of topsoil physico–chemical characteristics and the succession of soil microbial communities. The soil microbial community is sensitive to soil disturbance [...] Read more.
Extensive coal mining causes significant ecological and environmental impacts on the local ecosystem, especially on the terrestrial ecosystem. Mining activities induce the degradation of topsoil physico–chemical characteristics and the succession of soil microbial communities. The soil microbial community is sensitive to soil disturbance and restoration practices, being significant in soil reconstruction and land restoration. Microbes could be effective instruments to restore or reclaim disturbed terrestrial ecosystems and indispensable, unambiguous, indicators to assess reclaimed soils. In the present review, we aimed to provide insight into the effects of mining and subsequent land reclamation on soil microorganisms and the importance and application of microorganisms in the reclamation process. We address changes in the diversity and structure of the soil microbial community after reclamation and discuss the main driving factors of the community. We hypothesize that there is a discernible pattern or regularity in the variation of microbial community composition during the process of restoration succession. By employing the life strategy concept, the study attempts to identify and understand how microbial communities evolve during land reclamation. Land reclamation could improve the nutrients in the soil while increasing the proportion of saprotrophic microorganisms. In community succession, vegetation, soil properties, and reclamation time are key determining factors. Whereas bacteria, fungi, and archaea showed different responses to these factors, as they responded differently to varied soil environments, nutrition, and plants, and occupied different biological niches. Finally, we describe the applications of microorganisms as land reclamation monitors or promoters. This knowledge and understanding can provide comprehensive insight into the soil health condition and strong support for forecasting and decision-making in mine land restoration. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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26 pages, 4873 KiB  
Review
Trichoderma Diversity in Mexico: A Systematic Review and Meta-Analysis
by Hector Osvaldo Ahedo-Quero, Teodulfo Aquino-Bolaños, Yolanda Donají Ortiz-Hernández and Edgar García-Sánchez
Diversity 2024, 16(1), 68; https://doi.org/10.3390/d16010068 - 20 Jan 2024
Viewed by 2248
Abstract
Trichoderma is a genus of cosmopolitan fungi with more than 375 species described today. Despite its global significance in agriculture, ecosystems, and industry, few studies have focused on studying the diversity and distribution of this genus in Mexico. In this systematic review and [...] Read more.
Trichoderma is a genus of cosmopolitan fungi with more than 375 species described today. Despite its global significance in agriculture, ecosystems, and industry, few studies have focused on studying the diversity and distribution of this genus in Mexico. In this systematic review and meta-analysis, we aimed to understand the diversity and distribution of Trichoderma species in Mexico, both in ecosystems and agroecosystems. For this systematic review, we used the PRISMA methodology. We reviewed forty-one scientific articles, two book chapters, and the GBIF database. We recorded a total of 1082 isolates, revealing the presence of 57 species of the genus Trichoderma in 29 states of Mexico. We found that species from the genus Trichoderma were reported in 20 agroecosystems and 6 ecosystems. T. harzianum was the predominant species in both agricultural and undisturbed soil. Tabasco and Veracruz were the states with the highest species diversity, with 20 and 14 species reported, respectively. Chiapas had the highest diversity indices (Menhinick had 3.20, Simpson had 0.89, and Margalef had 4.16). The coffee crop was the agroecosystem with the highest diversity, with 12 species reported. In the undisturbed ecosystems, tropical rainforests featured 12 different species. This study highlights the distribution of the genus Trichoderma as a cosmopolitan genus. We argue for the importance of the species that comprise the genus and its applications for social benefits. Full article
(This article belongs to the Special Issue Biodiversity and Ecology of Soil Fungal Communities)
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