Special Issue "Diversity of Soil Fungal Communities"

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 9487

Special Issue Editors

Dr. Fabiana Canini
E-Mail Website
Guest Editor
Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
Interests: soil communities; microbial ecology; molecular ecology; mycology; extreme environments; Antarctica; Arctic
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Laura Zucconi
E-Mail Website
Guest Editor
Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
Interests: mycology; microbial ecology; soil communities; extreme environments; antarctica; arctic; cultural heritage

Special Issue Information

Dear Colleagues,

It is well-known that fungi dominate the microbial biomass in all terrestrial environments and play key roles in ecosystem functioning as symbionts (mycorrhizae, endophytes, lichens), pathogens, and decomposers, thus influencing plant primary production, elements mineralization and sequestration, soil structure, and fertility, and acting in the regulation of soil carbon balance. Nevertheless, the processes underpinning fungal community assembly remain largely unknown. Recently, fungal species on Earth were estimated to number around 12 million, the majority of which remain to be discovered. A number of novel taxa have been established in the last decade, and high-throughput sequencing techniques are expected to reveal in the near future this potential enormous diversity. Besides the fungal diversity, the mechanisms governing the microbial community processes and how they influence the ecological communities also remain poorly understood. These gaps make this research field of extreme interest, also in the light of the wide metabolic potential already demonstrated for soil fungi. Additionally, due to the still-limited knowledge of this kingdom, it is difficult to comprehensively assess the influence of environmental changes on terrestrial fungal communities of different biomes in terms of the adaptation, migration, acclimatization, or extinction of their components.

This Special Issue wishes to encourage the submission of original research papers and review manuscripts dealing with the composition, evolution and adaptations of soil fungal communities and the environmental conditions determining their establishment and survival, aiming to gain the widest possible vision of these ecosystems.

Dr. Fabiana Canini
Prof. Dr. Laura Zucconi
Guest Editors

Manuscript Submission Information

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Keywords

  • ecology
  • mycology
  • soil communities
  • adaptation
  • evolution

Published Papers (8 papers)

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Research

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Article
Soil Fungal Diversity of the Aguarongo Andean Forest (Ecuador)
Biology 2021, 10(12), 1289; https://doi.org/10.3390/biology10121289 - 07 Dec 2021
Cited by 1 | Viewed by 1067
Abstract
Fungi represent an essential component of ecosystems, functioning as decomposers and biotrophs, and they are one of the most diverse groups of Eukarya. In the tropics, many species are unknown. In this work, high-throughput DNA sequencing was used to discover the biodiversity of [...] Read more.
Fungi represent an essential component of ecosystems, functioning as decomposers and biotrophs, and they are one of the most diverse groups of Eukarya. In the tropics, many species are unknown. In this work, high-throughput DNA sequencing was used to discover the biodiversity of soil fungi in the Aguarongo forest reserve, one of the richest biodiversity hotspots in Ecuador. The rDNA metabarcoding analysis revealed the presence of seven phyla: Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Glomeromycota, Chytridiomycota, and Monoblepharomycota. A total of 440 identified species were recorded. They mainly belonged to Ascomycota (263) and Basidiomycota (127). In Mortierellomycota, 12 species were recorded, among which Podila verticillata is extremely frequent and represents the dominant species in the entire mycobiota of Aguarongo. The present research provides the first account of the entire soil mycobiota in the Aguarongo forest, where many fungal species exist that have strong application potential in agriculture, bioremediation, chemical, and the food industry. The Aguarongo forest hides a huge number of unknown fungal species that could be assessed, and its protection is of the utmost importance. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
Soil Fungal Community Composition Correlates with Site-Specific Abiotic Factors, Tree Community Structure, and Forest Age in Regenerating Tropical Rainforests
Biology 2021, 10(11), 1120; https://doi.org/10.3390/biology10111120 - 31 Oct 2021
Cited by 2 | Viewed by 1031
Abstract
Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data [...] Read more.
Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data to compare richness and community composition along secondary forest succession in Costa Rica and assessed the potential roles of abiotic factors influencing them. We found a strong coupling of tree and soil fungal community structure in wet tropical primary and regenerating secondary forests. Forest age, edaphic variables, and regional differences in climatic conditions all had significant effects on tree and fungal richness and community composition in all functional groups. Furthermore, we observed larger site-to-site compositional differences and greater influence of edaphic and climatic factors in secondary than in primary forests. The results suggest greater environmental heterogeneity and greater stochasticity in community assembly in the early stages of secondary forest succession and a certain convergence on a set of taxa with a competitive advantage in the more persisting environmental conditions in old-growth forests. Our work provides unprecedented insights into the successional dynamics of fungal communities during secondary tropical forest succession. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
The Mycobiota of High Altitude Pear Orchards Soil in Colombia
Biology 2021, 10(10), 1002; https://doi.org/10.3390/biology10101002 - 05 Oct 2021
Cited by 3 | Viewed by 836
Abstract
In Colombia, the cultivation of deciduous fruit trees such as pear is expanding for socio-economic reasons and is becoming more and more important for the local population. Since organized cultivation is slowly replacing sustenance cultivation, scientific information on the present agro-environment is needed [...] Read more.
In Colombia, the cultivation of deciduous fruit trees such as pear is expanding for socio-economic reasons and is becoming more and more important for the local population. Since organized cultivation is slowly replacing sustenance cultivation, scientific information on the present agro-environment is needed to proceed in this change in an organic and environmentally friendly way. In particular, this study is an accurate description of the mycobiota present in the bulk soil of two different high altitude pear orchards in the Colombian Andes. The metabarcoding of soil samples allowed an in-depth analysis of the whole fungal community. The fungal assemblage was generally dominated by Ascomycota and secondly by Mortierellomycota. As observed in other studies in Colombia, the genus Mortierella was found to be especially abundant. The soil of the different pear orchards appeared to host quite different fungal communities according to the soil physico-chemical properties. The common mycobiota contained 35 fungal species, including several species of Mortierella, Humicola, Solicoccozyma and Exophiala. Moreover, most of the identified fungal species (79%) were recorded for the first time in Colombian soils, thus adding important information on soil biodiversity regarding both Colombia and pear orchards. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
Diversity and Co-Occurrence Patterns of Fungal and Bacterial Communities from Alkaline Sediments and Water of Julong High-Altitude Hot Springs at Tianchi Volcano, Northeast China
Biology 2021, 10(9), 894; https://doi.org/10.3390/biology10090894 - 10 Sep 2021
Cited by 1 | Viewed by 785
Abstract
The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure [...] Read more.
The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure and networks in sediments and water from the Julong hot springs using a combination of culture-based methods and metabarcoding. A total of 65 fungal and 21 bacterial strains were isolated. Fungal genera Trichoderma and Cladosporium were dominant in sediments, while the most abundant fungi in hot spring water were Aspergillus and Alternaria. Bacterial communities in sediments and water were dominated by the genera Chryseobacterium and Pseudomonas, respectively. Metabarcoding analysis revealed significant differences in the microorganism communities from the two hot springs. Results suggested a strong influence of pH on the analyzed microbial diversity, at least when the environmental conditions became clearly alkaline. Our analyses indicated that mutualistic interactions may play an essential role in shaping stable microbial networks in the studied hot springs. The much more complicated bacterial than fungal networks described in our study may suggest that the more flexible trophic strategies of bacteria are beneficial for their survival and fitness under extreme conditions. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
New Species of Talaromyces (Fungi) Isolated from Soil in Southwestern China
Biology 2021, 10(8), 745; https://doi.org/10.3390/biology10080745 - 04 Aug 2021
Cited by 3 | Viewed by 1146
Abstract
Southwestern China belongs among the global biodiversity hotspots and the Daba Mountains are recognized as one of the priority conservation areas. During the exploration of fungal biodiversity from soil samples collected from Mount Daba, two species of Talaromyces were discovered as new to [...] Read more.
Southwestern China belongs among the global biodiversity hotspots and the Daba Mountains are recognized as one of the priority conservation areas. During the exploration of fungal biodiversity from soil samples collected from Mount Daba, two species of Talaromyces were discovered as new to science based on phylogenetic analyses and morphological comparisons. Talaromyces chongqingensis sp. nov. is a sister taxon of T. minioluteus and T. minnesotensis in the section Trachyspermi; and T. wushanicus sp. nov., affiliated to the section Talaromyces, is closely related to T. cnidii and T. siamensis. The new species differ from their sisters in DNA sequences, growth rates, and morphological characteristics. Descriptions and illustrations of them are provided in detail. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
Growth Forms and Functional Guilds Distribution of Soil Fungi in Coastal Versus Inland Sites of Victoria Land, Antarctica
Biology 2021, 10(4), 320; https://doi.org/10.3390/biology10040320 - 11 Apr 2021
Cited by 4 | Viewed by 1331
Abstract
In Victoria Land, Antarctica, ice-free areas are restricted to coastal regions and dominate the landscape of the McMurdo Dry Valleys. These two environments are subjected to different pressures that determine the establishment of highly adapted fungal communities. Within the kingdom of fungi, filamentous, [...] Read more.
In Victoria Land, Antarctica, ice-free areas are restricted to coastal regions and dominate the landscape of the McMurdo Dry Valleys. These two environments are subjected to different pressures that determine the establishment of highly adapted fungal communities. Within the kingdom of fungi, filamentous, yeasts and meristematic/microcolonial growth forms on one side and different lifestyles on the other side may be considered adaptive strategies of particular interest in the frame of Antarctic constraints. In this optic, soil fungal communities from both coastal and Dry Valleys sites, already characterized thorough ITS1 metabarcoding sequencing, have been compared to determine the different distribution of phyla, growth forms, and lifestyles. Though we did not find significant differences in the richness between the two environments, the communities were highly differentiated and Dry Valleys sites had a higher evenness compared to coastal ones. Additionally, the distribution of different growth forms and lifestyles were well differentiated, and their diversity and composition were likely influenced by soil abiotic parameters, among which soil granulometry, pH, P, and C contents were the potential main determinants. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Article
Diversity of Mycobiota Associated with the Cereal Cyst Nematode Heterodera filipjevi Originating from Some Localities of the Pannonian Plain in Serbia
Biology 2021, 10(4), 283; https://doi.org/10.3390/biology10040283 - 01 Apr 2021
Viewed by 873
Abstract
Cereals, particularly wheat, are staple food of the people from the Balkans, dating back to the Neolithic age. In Serbia, cereals are predominantly grown in its northern part between 44° and 45.5° N of the Pannonian Plain. One of the most economically important [...] Read more.
Cereals, particularly wheat, are staple food of the people from the Balkans, dating back to the Neolithic age. In Serbia, cereals are predominantly grown in its northern part between 44° and 45.5° N of the Pannonian Plain. One of the most economically important nematodes on wheat is the cereal cyst nematode, Heterodera filipjevi. Cysts of H. filipjevi survive in soil for years and shelter a large number of microorganisms. The aims of this study were to investigate the diversity of mycobiota associated with the cereal cyst nematode H. filipjevi, to infer phylogenetic relationships of the found mycobiota, and to explore the ecological connection between fungi and the field history, including the potential of fungi in bioremediation and the production of novel bioactive compounds. Cysts were isolated from soil samples with a Spears apparatus and collected on a 150-µm sieve. The cysts were placed on potato dextrose agar, and maintained for two weeks at 27°C. Following fungal isolation and colony growing, the fungal DNA was extracted, the ITS region was amplified, and PCR products were sequenced. The study showed that the isolated fungal species belong to diverse phyla, including Ascomycota, Basidiomycota, and Mucoromycota. Ascomycota is represented by the families Clavicipitaceae, Sarocladiaceae, Nectriaceae, and Phaeosphaeriaceae. Basidiomycota is represented by the families Cerrenaceae, Polyporaceae, Phanerochaetaceae, and Meruliaceae, and the order Cantharellales. The family Mortierellaceae represents Mucoromycota. The members of Ascomycota and Basidiomycota both depict the field history. Ascomycota indicate the fungal infection is of recent origin, while Basidiomycota point toward the preceding host plants, enabling the plant field colonization history to be traced chronologically. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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Review

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Review
Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change
Biology 2021, 10(9), 865; https://doi.org/10.3390/biology10090865 - 03 Sep 2021
Cited by 4 | Viewed by 1199
Abstract
Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to [...] Read more.
Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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