The association of endophytic fungi with the host plant is called a symbiotic relationship. Studies of the endophytic fungi from tea have been reported in numerous documents, but researchers still largely focus on tea endophytic fungi as they have ability to produce bioactive compounds which have numerous applications. The present work characterizes the fungal endophytic communities associated with healthy tea leaves in Yunnan Province, China. A total of 287 fungal strains were isolated from healthy leaf tissues of tea plants using a culture-dependent approach. Based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequence analyses taken from the fungal cultures, strains were classified into 28 fungal genera with high similarity matches to known sequences in GenBank. The majority of genera (98.25%) belong to the phylum Ascomycota and most of the dominating fungal endophytes are from the genera Colletotrichum and Clonostachys.
Tag: fungal communities
Conversion of rainforest to rubber plantations impacts rhizosphere soil mycobiome and alters soil biological activity
In Asia, large swathes of rainforest have been converted to rubber plantations, with major consequences for biodiversity and ecosystem services. However, the impact of this land use conversion on rhizosphere soil mycobiome has not yet been addressed. This study aims to investigate how rhizosphere soil fungal communities and their associated biological activity (soil respiration, soil methane (CH4) and potential soil enzyme production) are impacted by the conversion of rainforest to rubber plantations. Fungal richness and community composition in rhizosphere soils collected from natural rainforests, immature rubber, and mature rubber plantations were analyzed using paired-end Illumina sequencing. The conversion of natural rainforest to rubber plantations significantly altered fungal community composition of specific functional groups (saprotrophs, pathogens and mycorrhiza). We observed significant loss of saprotrophic and ectomycorrhizal fungi in natural rainforests, but enrichment of plant pathogenic fungi in immature rubber plantations. The mechanism underlying the effects of forest conversion on changes of fungal communities is related to reductions in soil pH, total nitrogen (N) and ammonium (NH4) in rubber plantations. Conversion to rubber plantation also resulted in decline of soil respiration rates and less potential for cellulase and chitinase productions. The significant negative correlations between fungal richness and soil respiration in mature rubber plantations indicated high competition among fungi and low nutrient availability in this system. We demonstrate the negative consequences of the conversion of rainforest to rubber plantations on soil biological activity and significant changes in fungal community composition that could threaten long-term ecosystem functions.
Ectomycorrhizal Mushrooms as a Natural Bio-Indicator for Assessment of Heavy Metal Pollution
Environmental changes and heavy metal pollution are some of the consequences of anthropogenic activities. Many ecosystems, including edaphic ecosystems, suffer from the effects of pollution. The accurate assessment of soil heavy metal contamination leads to better approaches for remediating soils. The exploration of different ways, including biological methods, to conduct environmental monitoring is still ongoing. Here, we focus on reviewing the potential of ectomycorrhizal fungi as a natural indicator of soil heavy metal pollution. Mycorrhizal fungi fulfill basic criteria required as natural bio-indicators for heavy metal contamination. These fungi use different mechanisms such as avoidance and tolerance to survive in metalliferous soils. Thus, we promote ectomycorrhizal fungi as natural indicators. This review also synthesizes existing research on ectomycorrhizal mushrooms as natural bio-indicators for heavy metal pollution and the elaboration of mechanisms, by which ectomycorrhizal fungi meet the criteria required for a successful bio-indicator.
Comprehensive Review of Fungi on Coffee
Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.
Fungal Interactions Matter: Tricholoma matsutake Domination Affect Fungal Diversity and Function in Mountain Forest Soils
Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called ‘shiro’, which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.
Editorial: Emerging Fungal Plant Pathogens
The occurrence of new and emerging phytopathogenic fungal pathogens is on the rise but has largely been overlooked because of inadequate detection methods (Fisher et al., 2012). Factors associated with such a phenomenon can be attributed to plant pathogens expanding beyond their normal geographic ranges due to globalization and international commerce, adaptive potential, climate and ecological changes as well as modern agricultural practices such as modified land uses and the profuse use of antifungal agents in agricultural practices (El-Sayed and Kamel, 2020). Emerging fungal pathogens are an increasing threat to ecosystems, global health, food security and global economy but remain neglected and understudied despite their potential devastating impact on economically important crops (Fones et al., 2020). These emerging pathogens can act as “true reservoirs” for future disease epidemics, but there are still numerous scientific challenges and research gaps to be resolved as to how these fungal pathogens are transmitted, evolving, adopting novel ecological strategies, switching hosts and causing infections. There is published evidence that common saprophytic fungi belonging to Cryptococcus, Aspergillus and Penicillium species are now emergent as potential plant pathogens. The latter can represent a major threat to staple crops such as rice, wheat, maize and potatoes either during cultural practices or during the post-harvest/storage stages (Alshannaq and Yu, 2017). If these pathogens are not detected and accurately identified in a timely matter and targeted disease-management strategies are not implemented, global food security could potentially be dramatically affected (Fones et al., 2020). To generate and promulgate better scientific insights into this new area of research, we proposed the Research Topic “Emerging Fungal Plant Pathogens”. In this Research Topic, we accepted 10 articles, including 5 reviews and 5 original articles that focus on fungal characterization of emerging plant pathogenic fungi based on polyphasic approaches, their functional roles in diseases, their control methods, taxonomy, phylogeny, and evolution. It is anticipated that this Research Topic will enable plant pathologists to gain better insights into the phytopathogenic lifestyles, identification, phylogeny, host associations and evolution of emerging fungal pathogens. Several authors have contributed papers to this Research Topic and an overview of the scientific content is summarized below.
Effects of vegetation type and soil horizon on soil bacterial and fungal communities in a dry–hot valley
Soil horizon and vegetation cover significantly impact the spatial patterns of soil fungal and bacterial communities. However, such impacts and their interactions are poorly characterized in dry–hot environments. Soil samples were collected from two soil horizons (humus and mineral) along a vegetation gradient (shrubland, grassland, and shrub–grass ecotone) in a dry-hot valley of Southwestern China to assess the effects of vegetation versus soil horizons on shaping soil microbial communities. We used denaturing gradient gel electrophoresis to estimate the microbial spatial pattern change across the vegetation gradients and clone libraries targeting small subunit rRNA genes to characterize the microbial community structures between distinct vegetation types and soil horizons. Bacterial DNA profile patterns were not significantly different across vegetation types but strongly correlated with soil horizons, with significant interaction effects. By contrast, fungi were remarkably different across vegetation types and soil horizons, without significant interactions effect. Distinct vegetation types did not necessarily harbor distinct bacterial or fungal community compositions. Rather, both community compositions were most strongly affected by the soil horizons. Together with these results, the soil vertical heterogeneity rather than vegetation changes is suggested to best predict shifts in soil microbial communities in this dry-hot valley area.
Fungal Pathogens in Grasslands
Grasslands are major primary producers and function as major components of important watersheds. Although a concise definition of grasslands cannot be given using a physiognomic or structural approach, grasslands can be described as vegetation communities experiencing periodical droughts and with canopies dominated by grasses and grass-like plants. Grasslands have a cosmopolitan distribution except for the Antarctic region. Fungal interactions with grasses can be pathogenic or symbiotic. Herbivorous mammals, insects, other grassland animals, and fungal pathogens are known to play important roles in maintaining the biomass and biodiversity of grasslands. Although most pathogenicity studies on the members of Poaceae have been focused on economically important crops, the plant-fungal pathogenic interactions involved can extend to the full range of ecological circumstances that exist in nature. Hence, it is important to delineate the fungal pathogen communities and their interactions in man-made monoculture systems and highly diverse natural ecosystems. A better understanding of the key fungal players can be achieved by combining modern techniques such as next-generation sequencing (NGS) together with studies involving classic phytopathology, taxonomy, and phylogeny. It is of utmost importance to develop experimental designs that account for the ecological complexity of the relationships between grasses and fungi, both above and below ground. In grasslands, loss in species diversity increases interactions such as herbivory, mutualism, predation or infectious disease transmission. Host species density and the presence of heterospecific host species, also affect the disease dynamics in grasslands. Many studies have shown that lower species diversity increases the severity as well as the transmission rate of fungal diseases. Moreover, communities that were once highly diverse but have experienced decreased species richness and dominancy have also shown higher pathogenicity load due to the relaxed competition, although this effect is lower in natural communities. This review addresses the taxonomy, phylogeny, and ecology of grassland fungal pathogens and their interactions in grassland ecosystems.
Integrative approaches for species delimitation in Ascomycota
Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta (Dothideomycetes, Botryosphaeriales). Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.
Appressorial interactions with host and their evolution
Fungi have evolved diverse strategies to acquire nutrients as endophytes, saprobes, symbionts, or pathogens. Appressoria have been intensively studied due to their importance in attaching and breaching the host surface. These specialized infection structures have evolved into various morpho-types: proto-appressoria, hyaline appressoria, melanized (dark) appressoria, and compound appressoria. In this review, we discuss the differences in the formation, differentiation, and function of appressoria among fungi with diverse life strategies. Using DNA sequence information, LSU, 5.8S, SSU and rpb2 gene fragments, we reconstructed the ancestral states for appressorial types in the main phyla of fungi and fungus-like organisms and found that the hyaline appressoria was the most ancestral form. Our analysis estimated proto-appressoria diversification during the Mesozoic period (92–239 million years ago), however, its origin remains inconclusive. Our data suggest that these hyaline appressoria diversified into melanized or compound appressoria, with evidence of adaptive radiation.