Keywords

1 Introduction

Soil is a complex ecosystem and is composed of multiple and minute habitats. Soil harbours almost all major groups of fungi. Stotzky (1997) has reported that the number of genera and species existing in soil is more than in any other environment. Soil being exposed to various conditions including extreme situations encases all microorganisms present on this planet. It is a known fact that fungi are the decomposing agents, help in biogeochemical transformations and recycle the stored energy and nutrients of organic matter which has been degraded by other microbes. Therefore, fungi have been considered as major players as recyclers of biosphere. It is established that physico-chemical composition of soil influences its fertility and also plays an important role in the distribution, seasonal variations and activity of fungi inhabiting the soil. However, it is also true that the soil fertility is dependent on the qualitative and quantitative structure and function of microbes and fungi inhabiting it. But for fungi being natural scavengers the planet could have been surrounded by piles of detritus and dead plant matter. Further geo-fungi are involved in the food chain cycle through their interaction with other living biota. Fungi are also known as recyclers of waste products, chemicals, transformers and biodegraders of xenobiotics. Soil is conglomerate of abiotic compounds with diversified microscopic organisms.

2 Soil as an Ecosystem, Fungal Diversity and Their Distribution in Soil

Soil is a natural medium in which diversified plant groups live, multiply and die which in turn becomes a perennial source of organic matter that gets recycled by microbes and fungi for plant growth and nutrition. A variety of fungi occurs in soil which range from lower (Chytrids) to higher fungi (Agarics), saprophytes to pathogens and predaceous to mutualistic mycorrhizal fungi. Fungi belonging to all groups occur in soil as hyphae, rhizomorphs, chlamydospores, sclerotia, asexual spores such as zoospores and conidia and sexual spores such as oospores, zygospores, ascospores and basidiospores.

The fungal diversities in soil have been studied by different workers (Watanabe 2011; Manoharachary et al. 2014) to know the fungi occurring in soil both quantitatively and qualitatively, ecologically, in relation to environmental variables, colonizing habitats and also to domesticate them effectively so as to use them in manufacturing nutritional, fermentative, pharmaceutical, agriculturally important materials, cosmetic materials and others. The diversity data also provides database on the available fungi and also about the invading or imported taxa in various habitats. The fungal diversities in soil can be understood readily by going through the list of the fungi reported in various soils of the world. More accurate, reliable and critical identification of soil fungi by both traditional and modern techniques is required. However, the modern system is still in the embryonic stage; therefore, the available gene data is in poor condition. Many morpho-taxonomists have been lost, some being endemic, and the classical taxonomy has received little attention due to shifting of mycologists towards molecular taxonomy. Many of the herbaria lack type species, which has created the lacunae in the fungal taxonomy. Therefore, confusion exists due to loss of traditional morpho-taxonomists and upcoming modern molecular taxonomists who are in the embryonic stage. Presently, the fungal taxonomy is now surrounded by morpho-taxonomists and gene analysis.

Soil is an ecosystem which comprises many microhabitats and harbours diversified groups of microbes and fungi. Most of the fungi are microscopic and some of them are macroscopic (Agaricales), and these microbiota are the decomposers, agents of mineral cycling, recycles stored energy and components of organic matter. Soil also includes symbiotic rhizobia, actinorhiza and mycorrhizae which serve the purpose of soil fertilization and uptake of nutrients to crops and forest plants. Fungi and other microbes play an important role as recyclers of biosphere. The quantitative and qualitative nature of microbes is of paramount importance in maintaining soil fertility along with chemical composition of soils. Soil fungi are also involved in food web through their interaction with other living biotic communities. Fungi are also involved as transformers and biodegraders of xenobiotics. The microphyte diversity of terrestrial ecosystems is dependent on below ground microbial diversity. Mycota is one of the diverse groups of organisms on the earth, which are the agents that govern carbon cycling, plant nutrition and plant disease production. These are distributed in different soil ecosystems but the distribution of different fungal groups has been less documented. Several edaphic factors, namely, pH, N, P, K, Ca and others, have greater impact on fungal distribution. Many fungal taxa are cosmopolitan in distribution but their endemicity is strong in tropical conditions. They also play an important role in driving carbon cycling in forest soils, mineral nutrition of plants and alleviate carbon utilization by other soil microbes.

Soil inhabits fungi and other microorganisms such as bacteria actinobacteria, cyanobacteria, protozoa and others. There are two groups of soil fungi which include indigenous fungi being isolated only from soil and other arrivals which are frequently isolated from surrounding habitats. Fungi colonizing underground parts considered as soil-borne appear to be typical soil fungi, sometimes fungi from air get contaminated into soil and are considered as casuals. Carris et al. (1989) have isolated 63 fungal species from the cyst Heterodera schachtii that causes disease in soybean and often the fungi associated with roots, decomposing litter fallen seeds and other plant parts and dead animals may get associated with soil. Fungal floras of various soil types have been studied worldwide. Thousands of research publications are available on soil fungi from all over the world, and some researchers might have described the fungi in detail while others might have listed without any descriptions. Therefore, numerous fungi have been described from different parts of the world; hence, it is almost impossible to list out all such soil fungi and also to refer all publications equally. Interestingly, isolation methods, media used, incubation conditions, soil types, soil physical conditions and other factors influence the quantitative and qualitative composition of fungi and microbes. It is possible that various species of Pythium, Saprolegnia , Achlya and others can be detected by means of baiting methods using boiled grass blades, cucumber seeds, hemp seeds, pollen grains, insect parts and others. Some ascomycetous fungi may get isolated including basidiomycetes by Warcup soil plate method but an overgrowth of fast-growing fungi such as Rhizopus and Aspergillus may not allow other fungi to grow. Waksman (1916) dilution plate method may yield a variety of fungi but did not yield perennating fungi. Majority of soil fungi remain unidentified because of non-sporulation. Identification of soil fungi with the adaption of appropriate scientific names is important for the study of soil fungi. In view of the importance attached to soil fungi, research activity on soil fungal floras has increased. Therefore, soil fungal floristics need to be observed more on an individual capacity rather than in en masse. Mother earth though has been explored all over the world, still it harbours new fungi which need to be discovered and classified accurately.

The global fungal estimate is 0.8 million to 5.1 million (Blackwell 2011), of which only 1 lakh fungal species are described. Around 29,000 fungi are reported from India. However, majority of such fungi are from soil. The diversity and distribution of soil fungi is shaped by macro-ecological and community assembly processes. Interestingly, very little is known about patterns of soil fungal diversity and their functional roles over large geographic scales. It is also known that soil fungi may exhibit strong biogeographical patterns. Based on the available data of fungal diversity (Manoharachary et al. 2014), it is indicated that the most dominant fungi are species of Aspergillus followed by Penicillium, hyphomycetes and some members of Ascomycota. This indicates the available techniques are inadequate to find out fungi that are present in different soil ecosystems.

Fungi are distributed worldwide in soils and are versatile. For example, Aspergilli are more common in tropical soils, while Penicilli are abundant in temperate soils. Among zygomycetes, Rhizopus, Mucor, Absidia and Cunninghamella have often been isolated. Zoosporic fungi such as Pythium and Allomyces have been isolated more frequently, and among the ascomycetous fungi, perfect states of Aspergillus and Penicillium besides Chaetomium are the most common ascomycetous fungi; basidiomycetous fungi have not been isolated commonly. Anamorphic fungi are frequently isolated fungi and are richly represented by asexual states of Aspergillus, Penicillium, Alternaria, Drechslera, Curvularia and others. Non-sporulating fungi are usually not identified; therefore, it is difficult to classify them in spite of using molecular tools as the sterile fungi show more than one perfect stage. However, it is hoped that with increasing knowledge and techniques, unidentified fungi on agar culture may get identified more readily together with the molecular studies. The authors have isolated 104 soil fungi from wild soils, cultivated soils, forest soils, pond muds, rhizosphere soils, etc. and are listed in Table 4.1. Similarly, soil fungi that are isolated in pure culture have to be named with right names on the basis of diversified characteristic features. Fungal diversities have to be widely acknowledged on the basis of voucher specimens such as holotype for the record and description of new species. Cultures are always essential for their effective use in biotechnology. The original cultures need to be single source culture.

Table 4.1 List of common soil fungi
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3 Methodology

Soil samples need to be collected from cultivated and uncultivated soils of diversified habitats along with soil passport card. The soil fungi can be isolated by various methods, but soil dilution plate method, soil plate method by direct soil inoculation and baiting methods are the best methods for isolation of various soil fungi. By single hyphal tip from germinating reproductive unit may be placed on full pledged agar mediam and the growth of colony be observed. Czapek’s agar medium, plain water agar medium, PDA medium, soil extract agar medium and others are recommended. The main drawback for dilution plate method is that it neglects slow-growing fungi. The diluted soil suspensions are poured on to appropriate selective isolation media, and single-spore cultures are established later (Davet and Rouxel 2000).

Warcup soil plate method (1950) includes direct soil inoculation on to the sterile agar medium in a sterile Petri dish. The media include Czapek’s agar, tomato agar, soil extract agar and others. The drawback of this method is that it tends to neglect fungi of qualitative nature and overgrowth of the fast-growing fungi. Bating method is often used for Zoosporic fungi. Immersion slide method (Chesters 1948) has also been found useful to isolate soil fungi as this also represents the soil fungi associated with soil profile. Molecular methods such as total fungal community DNA extraction, metagenomics, phylogenetic analysis of 18S, 16S rDNA sequences, understanding of genetic diversity, PCR and several other modern techniques are available to understand and evaluate soil fungal community.

4 Identification of Soil Fungi

Fungal taxa thus isolated have been identified on the basis of morpho-taxonomic criteria by comparing with known species; the morphologies that are observed through a stereomicroscope, compound microscope and electron microscope along with cultural characters have to be noted. Hyphal morphology, spore morphology, ontogeny, cultural characteristics, fruiting structures, etc. have to be noted down.

Experienced mycologists may identify some fungi at a glance; however, the most suitable taxon may be assessed after repeated observations and suitable literature survey. In case of new species, the Melbourne code 2013 has to be adopted and deposition be made at gene bank.

The morphologies of fungi be maintained continuously and molecular techniques may be employed for clarifying ambiguous and vague entities.

The available monographs on geo-fungi are many (Gilman 1957; Domsch et al. 1980; Watanabe 2002); however, different monographs are available for different groups of fungi (Raper and Thom 1949; Raper and Fennel 1965; Barron 1968; Ellis 1971, 1976; Subramanian 1971). Domsch et al. (1980) has listed 450 species, and Nagamani et al. (2006) have described 332 fungal species from India. The inventorization, monitoring and biodiversity status of soil fungi have been discussed by Bills et al. (2004).

5 Ecological Grouping of Soil Fungi

Fungi are known to colonize cultivated crop soils, wild forest soils, soils of highest mountain peaks, deep permafrost soils, geothermal and humid soils of the volcanic horizon, mine soils and highly alkaline soils. Cold-loving fungi are restricted to Polar Regions which can tolerate 0–16 °C, and examples of this group belong to Leptomitus, Penicillium, Cryptococcus, Chrysosporium and others. The fungi occurring in extreme environments may be of biotechnological importance as they have the potential for the production of extremozymes, secondary metabolites, bioremediation properties and others (Nonzom and Sumbali 2015). Desert soils contain a variety of yeasts that have been documented from hot and cold deserts. It seems that man-made contaminations of Antarctica might have added Penicillium, Aspergillus and other common fungi from soil and air. Endolithic conidial fungi are also common (Sterflinger et al. 2012). Halophilic fungi are considered as a major source of diverse and novel metabolites. The salt-loving fungi mainly belonging to Ascomycota do occur in marine soils. A distinctive group of fungi exist in marine waters and marine soils. Terrestrial aquatic hyphomycetes are associated with the litter fallen on to the soil.

Thermophiles are a group of extremophiles which require relatively high temperature (41–122 °C). Successful isolation of soil thermophiles requires incubation of soil on specified media at 45 °C/50 °C. Normally, thermopiles occur in compost, hay, wood chips and also in tropical desert soils. Some of the common soil thermophiles include Aspergillus fumigatus, Scytalidium thermophilum , Chaetomium thermophilum , Thermomyces sp., Humicola sp. and others. Thermophilic fungi possess valuable enzymes such as pectinase, cellulase, xylanase and also secrete a number of secondary metabolites of biotechnological importance (Rajasekaran and Maheshwari 1993). The voluminous literature that has accumulated on soil fungi (Manoharachary et al. 2014; Taylor and Sinsabaugh 2015; Taylor et al. 2000) indicates that a number of fungal species do occur in wild and forest soils consisting of rich diversified flora and medicinal plants. This clearly indicates that mesophiles dominate the soil fungal biotic community. Cultivated soils also support rich fungal flora. Quantitatively and qualitatively, the fungi are more and diversified in species composition with reference to wild and forest soils. However, the cultivated soils no doubt support quantitatively richness of fungi but qualitatively it is represented by few fungal species. The author’s experience indicates that wild and forest soils have shown quantitatively and qualitatively richness of fungi in scrub jungle forest, deciduous forests and also in grassland soils than in cultivated crop soils. However, grassland soils have shown richness of fusarial fungi (Manoharachary and Ramarao 1978; Manoharachary et al. 1989; Madhusudhan Rao and Manoharachary 1981). Submerged mud soils were rich in melanin pigment containing fungi, such as Ascomycetes, dematiaceous hyphomycetes and others. Manoharachary et al. (2014) have isolated 340 fungal species and have also indicated that anamorphic fungi formed the bulk in soil fungal biota. Further, it has also been shown that Aspergillus and Penicillium species are predominantly followed by Chaetomium and anamorphic fungi than other groups. Many soil-borne and root-borne pathogenic fungi were also encountered; 18 species representing the genus Trichoderma, a well-known biocontrol agent, were isolated. In general, it has been shown that forest and wild soils followed by rhizosphere soils and cultivated soils harbour a more number of fungi and richness of fungal species than mud soils, riverbank soils, sea shore soils, herbicide-treated soils, polluted soils and poultry farm soils (Manoharachary et al. 2014).

Temperature, pH, moisture, soil texture, soil organic matter, soil NPK and gaseous composition are known to influence the distribution and composition of soil fungi. Plant communities existing in diversified soils may have a greater impact on the quantitative and qualitative composition of soil fungi.

6 Soil Fungi and Soil Health

Soil health depends on soil quality and fertility. Soil health is the resultant of the interaction between different processes, properties and activities of soil microbiota including soil fungi. Soil fungi are the biological controllers, ecosystem regulators, decomposers and compound transformers. Therefore, soil fungi serve as ecosystem regulators, responsible for soil structure formation and modification of the habitats. Mycorrhizal fungi are known to stabilize the soil structure and serve as biofertilizer for plant growth. Fungi present in the soil also participate in hormone production, biological control, stress management, stabilization of soil organic matter and biodegradation of residues. Thus, soil health maintained by soil fungi is directly connected with the production of healthy food which has an impact on public and animal health (Frac et al. 2018).

Certain soils are not congenial to live for plant pathogens by limiting their survival or growth of the pathogen. The suppressive soils reduce fungal attack and are often effective against only one or two pathogens. Suppressiveness is of two types: (1) long-standing suppression which is a biological condition and appears to survive in the absence of plants and (2) inclusive suppression is initiated and sustained by crop monoculture by the addition of target pathogen. A number of soil-borne pathogens are represented by Fusarium sp., Gaumannomyces sp., Phytophthora sp. and Pythium spp. Few cause diseases in plants growing in conducive soils, and few other pathogens cause no disease in plants. Suppressiveness may be because of soil microflora and abiotic factors and may vary with the type of pathogen. Some studies have indicated that activities of antagonistic soil fungi, bacteria, actinomycetes and others are responsible for the suppression of pathogens. The formation of suppressive soils is due to the mechanisms envisaged by soil fungi and soil microbiota, namely, nutrient competition, amensalism, antagonism, parasitism and systemic-induced resistance. However, understanding of the exact mechanism in suppressive soil is still far from satisfaction and probably the application molecular assessment tools may bring more understanding of such activity (Garbeva et al. 2004).

7 Functions and Biotechnological Aspects of Soil Fungi

Fungi are known to play a role in organic matter production, decomposition, carbon sequestration, carbon mineralization and cycling of elements. Mycorrhizal associations in plants not only boost plant productivity but also the acquisition of water, phosphorus and nutrients. Fungal endophytes offer resistance to biotic and abiotic stress. Filamentous soil fungi promote macro-aggregate formation through soil particle binding with fungal hyphae and the fungal cell wall material as adhesive, while the most common activity of the soil fungi is the nutrient cycling. Most hydrolytic and oxidative capabilities are elaborated by soil fungi as they are principle degraders of plant cell wall material during decomposition. Production of cellulases, pectinases, laccases and others have been elaborated by many soil fungi. The potential use of chitin as a nitrogen source is widespread among fungi because the fungal cell wall includes chitin. Chitinase activity is used as an indicator of fungal biomass and metabolism. Further, the proteins get degraded by many fungi which is the largest source of nitrogen. The inorganic phosphate solubilizing fungi supply phosphorus to the plants. Mineral phosphates get degraded by Penicillium, Aspergillus and other soil fungi into organic soluble phosphate which then get transported to fungal hyphae and to the plants. A number of soil fungi are also known to play an important role in bioremediation. Fungi are linked to many other organisms in a complex soil food web. For example, wood decay fungi and nematodes live together. Fungal hyphae in soil secrete both extracellular and intracellular bacteria. Mycorrhizal helper bacteria help in the formation of ecto- and endo-mycorrhizas. Many insects consume fungal hyphae (Taylor and Sinsabaugh 2015).

Soil fungi are important in everyday affairs of human beings. Soil fungi are well-known degraders of raw or manufactured materials such as foodstuff, timber, textiles, leather, paint, glue, plastics, petroleum products, optical glasses and others. Some of the soil fungi such as Aspergillus are known to produce aflatoxins, ochratoxins and others. Soil yeasts are used in brewery industries, while mushrooms, truffles and morels are edible and some species like Amanita, Clitocybe and Inocybe are poisonous. Species of Psilocybe and Paniolus are hallucinogenic. Soil fungi are also used in food processing. Several antibiotics, growth hormones, organic acids, enzymes, mycoproteins and vitamins are extracted from soil fungi. Soil fungi play an important role in the biosphere by involving in the recycling of nutrients, afforestation programmes, wastewater treatments, detoxification, xenobiotics, biocontrol of diseases and in several other ways. Soil fungi are also involved in metabolic pathways and studying genetic mechanisms. However, some of the soil fungi such as Phytophthora, Pythium, Rhizoctonia, Sclerotium, Macrophomina, Fusarium, Verticillium and few others are also involved in causing soil-borne and root-borne diseases. Soil fungi are very successful organisms due to their great plasticity and physiological versatility. Some of the important soil-borne diseases include damping off seedlings, wilt diseases, root rot and several others.

The intense influence of soil microbes and fungi on human life and global biogeochemical cycles necessitates exploration of microbial and fungal genomes to expand our understanding of most microbial and fungal species on earth, particularly those showing low relative abundance. There is a need to understand the ecology of such rare microbes and fungal population and highlight molecular and computational methods for targeting taxonomic blind spots within the rare biosphere.

Soil fungi play an important role in pharmaceutical industries in the isolation of compounds such as penicillin, cyclosporine, lovastatin, etc. Some of the fungi such as Trichoderma spp. are considered as potential biocontrol agents to control parasites and predators as antagonists. Fungi such as Arthrobotrys have been considered as nematophagous fungi, while species of Metarhizium and Beauveria have been considered as insect pathogens. Soil fungi have gained importance in recent times and have been exploited for bioremediation of anthropogenic pollutants including pesticides, benzene, toluene, xylene, dyes, hydrocarbons and others. The unexplored soil fungi may become rich resource material for new genes and species valuable to biotechnology and medicine. Soil fungal biodiversity plays a pivotal role in sustaining growth and management of the ecosystem. In future, soil fungal diversity seems to be very challenging and advantageous to the biosphere. As on today, the number of species considered to be true soil fungi is around 15,000. It is estimated that a gram of soil may hold several thousand fungal species. The revised species in future will be additional new species which may get revealed under Genealogical Concordance Phylogenetic Species Recognition (GCPSR) programme (Taylor et al. 2000).

8 Rhizosphere Soil Fungi

The rhizosphere soil is the specialized ecological region, which is adjacent to the root system of the plant as influenced by the root exudates. The term rhizosphere was proposed by Hiltner (1904). The root exudates and root debris products attract many fungi and microbes. The interaction of fungi and plant root is essential for the nutrition and growth of the plant. The growth, development, productivity of many crop plants, forest plants, orchids, oilseed crops, horticultural plants, medicinal plants, cash crops and others are largely dependent on soil health, which is maintained by soil microbes, soil fungi and also rhizosphere microflora including fungi. Therefore, rhizosphere studies are of great interest to agriculturists, soil biologists, chemists, mycologists, microbiologists and molecular biologists. The rhizosphere microbes and fungi may influence the availability of nutrients, water and growth promoter and may also change the oxidation cum reduction potential. Mycorrhizae, a symbiotic association, are beneficial in the uptake of phosphorus, zinc and other minerals besides increasing the root surface area of the plant for effective ion absorption. The soil microbial and fungal interactions such as antagonism, competition, synergism occurring in soil and rhizosphere are of great importance in studying the microbial and fungal ecology of rhizosphere (Mukerji et al., 2006). The rhizosphere exudates include a wide range of organic and inorganic compounds that affect the microbial and fungal population. Therefore, the authors have studied the rhizosphere fungal flora employing soil plate, soil dilution and immersion methods. Selective media and enrichment techniques are used, which include CFU, MPN, particle counts, fluorescence microscopy, and biochemical methods such as assay for ATP, immunological and molecular techniques. The fungi isolated from rhizospheres of various plants are listed in Table 4.2.

Table 4.2 Rhizosphere soil fungi
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9 Soil Fungi and Climate Change

Soil fungi play a critical role in the carbon cycle. Carbon which is essential for life on earth moves between air, soil and water. After the death of the plants, the carbon enters the soil, making the soil a reservoir of the carbon. The dead plant material is broken down by microbes and fungi in the soil, thus releasing the carbon into the air. The rate at which the carbon left the soil will have a major impact on the amount of atmospheric carbon, which is the key factor to drive climate change. One of the limiting factors to the growth of these decomposing fungi is the availability of nitrogen in the soil, which get solved by mycorrhizal fungi. The mycorrhizal fungi extract the nitrogen from the soil and make it available to the plants through their roots. Recently, it has been found by scientists that soils supporting ectomycorrhizal fungi contain 70 percent more carbon than the soils dominated by arbuscular mycorrhizal fungi. Thus, fungi have a greater role in the control of the global carbon cycle. Since the plants and mycorrhizae are interconnected, the future carbon cycling cannot be predicted without thinking about plants and mycorrhiza.

10 Conclusions

  1. 1.

    Soil is a dynamic medium for fungi and microbes and maintains balance in spite of constellation of physico-chemical factors.

  2. 2.

    Soil harbours diversified groups of fungi belonging to zoosporic fungi, zygomycota, Ascomycota and Basidiomycota.

  3. 3.

    Soil is a rich nutrient medium for the sustenance of fungi.

  4. 4.

    Diversified soils such as desert soils, temperate soils, tropical soils, forest soils, crop soils sand dunes, submerged soils, saline and mangrove soils, soils of high attitude and low attitude, and others support not only specific fungal taxa but also fungi common to all soils.

  5. 5.

    Soil physico-chemical factors, plant vegetation, altitude, meteorological conditions and other related factors influence the soil fungi both quantitatively and qualitatively.

  6. 6.

    There is a definite seasonal variation among soil fungi. Some fungal species are characteristically associated with one or the other soils. Further fungi like Aspergilli are distributed widely in tropics, while the Penicilli are associated with temperate soils.

  7. 7.

    Soil fungi are the fastest decomposing agents, help in biogeochemical transformations and recycle stored energy and nutrients. Soil fungi also help in carbon sequestration besides serving as natural scavengers, and are useful in industry, medicine, agriculture, waste management, and in biotechnology and other activities.

  8. 8.

    Some fungi exhibit antagonistic activity and plant growth promotion.

There is a need for in-depth studies on soil fungi, their diversity, ecology, conservation and utility for human welfare.