Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments

Nematodes and fungi are both ubiquitous in marine environments, yet few studies have investigated relationships between these two groups. Microbial species share many well-documented interactions with both free-living and parasitic nematode species, and limited data from previous studies have suggested ecological associations between fungi and nematodes in benthic marine habitats. This study aimed to further document the taxonomy and distribution of fungal taxa often co-amplified from nematode specimens. A total of 15 fungal 18S rRNA phylotypes were isolated from nematode specimens representing both deep-sea and shallow water habitats; all fungal isolates displayed high pairwise sequence identities with published data in Genbank (99-100%) and unpublished high-throughput 454 environmental datasets (>95%). BLAST matches indicate marine fungal sequences amplified in this study broadly represent taxa within the phyla Ascomycota and Basidiomycota, and several phylotypes showed robust groupings with known taxa in phylogenetic topologies. In addition, some fungal phylotypes appeared to be present in disparate geographic habitats, suggesting cosmopolitan distributions or closely related species complexes in at least some marine fungi. The present study was only able to isolate fungal DNA from a restricted set of nematode taxa; further work is needed to fully investigate the taxonomic scope and function of nematode-fungal interactions.     

Specificity of assemblage,not fungal partner species,explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants

Mycoheterotrophic plants (MHPs) growing on arbuscular mycorrhizal fungi (AMF) usually maintain specialized mycorrhizal associations. The level of specificity varies between MHPs, although it remains largely unknown whether interactions with mycorrhizal fungi differ by plant lineage, species, and/or by population. Here, we investigate the mycorrhizal interactions among Burmannia species (Burmanniaceae) with different trophic modes using high-throughput DNA sequencing. We characterized the inter- and intraspecific dynamics of the fungal communities by assessing the composition and diversity of fungi among sites. We found that fully mycoheterotrophic species are more specialized in their fungal associations than chlorophyllous species, and that this specialization possibly results from the gradual loss of some fungal groups. In particular, although many fungal species were shared by different Burmannia species, fully MHP species typically host species-specific fungal assemblages, suggesting that they have a preference for the selected fungi. Although no apparent cophylogenetic relationship was detected between fungi and plants, we observe that evolutionarily closely related plants tend to have a greater proportion of shared or closely related fungal partners. Our findings suggest a host preference and specialization toward fungal assemblages in Burmannia, improving understanding of interactions between MHPs and fungi.Subject terms: Fungi, Plant sciences, Evolution     

Further advances in orchid mycorrhizal research

Orchid mycorrhizas are mutualistic interactions between fungi and members of the Orchidaceae, the world’s largest plant family. The majority of the world’s orchids are photosynthetic, a small number of species are myco-heterotrophic throughout their lifetime, and recent research indicates a third mode (mixotrophy) whereby green orchids supplement their photosynthetically fixed carbon with carbon derived from their mycorrhizal fungus. Molecular identification studies of orchid-associated fungi indicate a wide range of fungi might be orchid mycobionts, show common fungal taxa across the globe and support the view that some orchids have specific fungal interactions. Confirmation of mycorrhizal status requires isolation of the fungi and restoration of functional mycorrhizas. New methods may now be used to store orchid-associated fungi and store and germinate seed, leading to more efficient culture of orchid species. However, many orchid mycorrhizas must be synthesised before conservation of these associations can be attempted in the field. Further gene expression studies of orchid mycorrhizas are needed to better understand the establishment and maintenance of the interaction. These data will add to efforts to conserve this diverse and valuable association.     

Root-associated community composition and co-occurrence patterns of fungi in wild grapevine

Crops’ wild relatives host a wide range of microorganisms, including some beneficial species that are not found or are under-represented in the domesticated crops. Our goal was to study the underexplored composition of root-associated fungal communities in endangered wild grapevines. We found high taxonomic diversity representing multiple trophic guilds that include beneficial symbiotrophs and endophytes. Soil factors explain a relatively small part of their overall variability. In contrast, the majority of the associated fungal taxa shows a close fit to the neutral model for prediction of their distributions. Only beneficial arbuscular mycorrhizal fungi and the pathogenic Ilyonectria depart from the neutral distribution model and form intimate interactions with the plant host. In addition, pathogenic fungi rarely occurred in samples that included ectomycorrhizal fungi, which suggested potentially applicable inter-microorganism interactions. High abundance and diversity of fungal endophytes on the wild grapevine roots highlight the need for their careful consideration in future studies.     

Spatial patterns and determinants of common root-associated fungi in a subtropical forest of China

Aims Spatial patterns of fungal populations are affected by plant distribution, abiotic factors, fungal dispersal ability and inter-species interactions. While several studies have addressed spatial patterns of some mycorrhizal, saprotrophic and pathogenic fungi, the method based on fruit-body surveys is not efficient and unreliable to study the spatial pattern of root-associated fungal species because most fungi in plant roots do not have sporocarps and cannot be identified based only on morphological traits. Our aims are (i) to determine the spatial pattern of common root-associated fungi; (ii) to evaluate whether the abundance and spatial pattern of root-associated fungi and categories of fungi, reflect their biotic and abiotic niche constraints.     

The effects of arbuscular mycorrhizal (AM) fungal and garlic mustard introductions on native AM fungal diversity

Introduced, non-native organisms are of global concern, because biological invasions can negatively affect local communities. Arbuscular mycorrhizal (AM) fungal communities have not been well studied in this context. AM fungi are abundant in most soils, forming symbiotic root-associations with many plant species. Commercial AM fungal inocula are increasingly spread worldwide, because of potentially beneficial effects on plant growth. In contrast, some invasive plant species, such as the non-mycorrhizal Alliaria petiolata, can negatively influence AM fungi. In a greenhouse study we examined changes in the structure of a local Canadian AM fungal community in response to inoculation by foreign AM fungi and the manipulated presence/absence of A. petiolata. We expected A. petiolata to have a stronger effect on the local AM fungal community than the addition of foreign AM fungal isolates. Molecular analyses indicated that inoculated foreign AM fungi successfully established and decreased molecular diversity of the local AM fungal community in host roots. A. petiolata did not affect molecular diversity, but reduced AM fungal growth in the greenhouse study and in a in vitro assay. Our findings suggest that both introduced plants and exotic AM fungi can have negative impacts on local AM fungi.     

Interactions between arbuscular mycorrhizal fungi and soil bacteria

The soil environment is interesting and complicated. There are so many interactions taking place in the soil, which determine the properties of soil as a medium for the growth and activities of plants and soil microorganisms. The soil fungi, arbuscular mycorrhiza (AM), are in mutual and beneficial symbiosis with most of the terrestrial plants. AM fungi are continuously interactive with a wide range of soil microorganisms including nonbacterial soil microorganisms, plant growth promoting rhizobacteria, mycorrhiza helper bacteria and deleterious bacteria. Their interactions can have important implications in agriculture. There are some interesting interactions between the AM fungi and soil bacteria including the binding of soil bacteria to the fungal spore, the injection of molecules by bacteria into the fungal spore, the production of volatiles by bacteria and the degradation of fungal cellular wall. Such mechanisms can affect the expression of genes in AM fungi and hence their performance and ecosystem productivity. Hence, consideration of such interactive behavior is of significance. In this review, some of the most important findings regarding the interactions between AM fungi and soil bacteria with some new insights for future research are presented.     

Diversity of saprobic microfungi

The data needed to derive an accurate estimate of saprobic microfungi are insufficient, incomplete and contradictory. We therefore address issues that will ultimately reveal whether there are 1.5 million global fungal species, which is the generally accepted working estimate. Our data indicates that large numbers of fungi occur on host families, such as Musaceae, host genera such as Nothofagus and individual host species such as Eucalyptus globulus, and that fungi may be specific or recurrent on different plant groups. Recent studies have shown that fungal numbers on hosts may be larger than originally thought as saprobes are organ-specific/-recurrent and changes in fungal communities occur as substrata decays. Other issues, such as the impact of geography, of methodology and of taxonomy are also addressed. There is evidence that fungi on the same host at different locations also differs; site-specific factors and geographic distance may be more important than host/substrate in shaping fungal assemblages. Methodology impacts on estimates of species diversity with many more taxa observed using indirect isolation protocols as compared to direct isolations from leaves. Our understanding of fungal species numbers in speciose genera is important. In some fungal groups accepted species have been reduced to a few species, while in other groups many cryptic species are being uncovered. While we make a number of generalisations from the studies reported here, this review also highlights some of the limitations mycologists currently have to contend with. A large body of knowledge exists for certain groups of microfungi or for microfungi occurring on certain substrata/hosts. However, it is likely that we are drawing conclusions from data that are somewhat biased toward fungi and host/substrata that are of interest to human endeavours. The discrepancy between the numbers of fungi described from only one economically important genus, Eucalyptus, and all the other members of the Myrtaceae is but one example of this bias. By incorporating the large body of work that is already available and adding appropriate complementary studies, we can accelerate our understanding of microfungal diversity and this will eventually lead us to a realistic estimate of global fungal species numbers.     

Fungal molecular diagnostics: a mini review

Conventional methods to identify fungi have often relied on identification of disease symptoms, isolation and culturing of environmental organisms, and laboratory identification by morphology and biochemical tests. Although these methods are still fundamental there is an increasing move towards molecular diagnostics of fungi in all fields. In this review, some of the molecular approaches to fungal diagnostics based on polymerase chain reaction (PCR) and DNA/RNA probe technology are discussed. This includes several technological advances in PCR-based methods for the detection, identification and quantification of fungi including real-time PCR which has been successfully used to provide rapid, quantitative data on fungal species from environmental samples. PCR and probe based methods have provided new tools for the enumeration of fungal species, but it is still necessary to combine the new technology with more conventional methods to gain a fuller understanding of interactions occurring in the environment. Since its introduction in the mid 1980's PCR has provided many molecular diagnostic tools, some of which are discussed within this review, and with the advances in micro-array technology and real-time PCR methods the future is bright for the development of accurate, quantitative diagnostic tools that can provide information not only on individual fungal species but also on whole communities.     

Allergenicity of airborne basidiospores and ascospores: need for further studies

Many known fungal species are grouped among basidiomycetes and ascomycetes. Active mechanisms of spore release into air currents are among the main features of these fungi. Aerobiological studies have described their presence in many regions worldwide. In some areas, fungi have been described as the predominant outdoor airborne biological particulate with much higher concentrations than pollen. Other studies have determined that among the fungal aerospora, the highest concentrations belong to basidiospores and ascospores. Nevertheless, the allergenic potential of spores from basidiomycetes and meiotic forms of ascomycetes has not been studied to the extent of mitosporic fungi and allergens from other sources. The need to further evaluate the role of basidiomycetes and meiotic ascomycetes in allergies is evidenced by the few genera with characterized allergens and limited studies that had demonstrated levels of sensitization similar or higher to that of mitosporic fungi and other allergens. In this review, based on the existing aerobiological, epidemiological, immunological, and molecular biology studies, we provide evidence that the role of basidiomycetes and ascomycetes deserves more attention with respect to their roles as potential aeroallergens.     

施氮对森林生态系统AM真菌群落组成及多样性的影响

丛枝菌根（AM）真菌能够和绝大多数陆生植物形成互惠共生体,具有重要的生态功能。在氮（N）沉降日益严重的背景下,越来越多的土壤生态学家开始关注N沉降对AM真菌群落的影响,然而已有研究大多数集中在草地生态系统,对森林生态系统的关注相对较少,而在森林生态系统开展的模拟研究又多采用林下施N的方式,忽略了冠层发生的一系列生态过程,可能无法准确反映真实情形。依托鸡公山野外控制试验平台,采用高通量测序技术就不同施N方式（林下vs林冠）及速率对AM真菌alpha多样性和群落组成的影响进行了连续4 a的监测。试验综合考虑植被、坡向和坡度等因素,采用完全随机区组设计,包括4个区组（重复）,每个区组随机设置5个样方,对应5个不同处理：对照（CK）、林冠施N 25 kg hm^-2 a^-1（CN25）和50 kg hm^-2 a^-1（CN50）、林下施N 25 kg hm^-2 a^-1（UN25）和50 kg hm^-2 a^-1（UN50）。结果发现,在目前的N素添加水平和时间尺度上,施N方式和施N速率对AM真菌的alpha多样性都没有显著影响,二者之间也无交互作用。然而,经过一年的试验处理,施N方式对AM真菌群落组成产生了轻微的影响,而施N速率有极显著的影响,且二者之间存在显著交互作用。当施N速率为25 kg hm^-2 a^-1时,林冠施N和对照相比差异不显著,而林下施N处理AM真菌群落组成与对照相比差异极显著,与林冠施N相比,差异也极显著;当施N速率为50 kg hm^-2 a^-1时,林冠施N与对照处理群落组成有略微差异（P=0.080）,林下施N与林冠施N及对照处理相比AM真菌群落组成均没有显著变化。在接下来的三年中,施N方式和施N速率对AM真菌的群落组成都没有显著影响,二者之间也无显著交互作用。这说明在特定的施N速率和处理时间下,林下施N可能会高估自然N沉降对AM真菌群落组成的影响。随着处理时间的延长,不同处理下AM真菌群落有趋同的趋势,可能是因为AM真菌群落对N沉降产生了适应性。本研究评估了施N方式对森林生态系统AM真菌群落组成与结构的影响,在未来的研究中需要设定更多的N素梯度和更长的时间跨度,才能够更全面的认识N沉降的生态效应。     

Fungal diversity living in the root and sporophore of the endemic Korean fern Mankyua chejuense

Ferns represent the basal group of vascular plants and are known to have fungal interactions with arbuscular mycorrhizal fungi, but diversity of endophytic fungi from ferns is rarely studied. Moreover, fungal diversity associated with ferns is likely underestimated as most studies have been performed based on a microscopic or culture-dependent approach. In this study, we investigated the endophytic fungal diversity within roots and sporophore of an endangered Korean fern (Mankyua chejuense), and compared it to fungi in surrounding soil using a metabarcoding approach. A high diversity of endophytic fungi (236 OTUs), mostly belonging to Ascomycota, was detected and fungal richness and composition were significantly different between habitats. Indicator species analysis showed that endophytic fungi have similar ecological characteristics to fungal species found from other land plants. Our results suggest that various fungal species are associated with ferns, thus understanding fern-associated fungal diversity can have a great implication for fern biology and conservation.     

The effects of geographic origin and genotype on fungal diversity of silver birch (Betula pendula)

Soil microbes, especially root symbiotic fungi, often have drastic effects on the successful growth and establishment of plants. While plant intraspecific genetic variation is known to affect many ecosystem processes and functions, the effect it has on root fungal communities has received less attention. To determine the effect plant origin and genotype have on root fungal communities, we used high-throughput amplicon sequencing of ITS-regions to detect fungi from the roots of 64 clonally propagated silver birch (Betula pendula) trees representing four different geographical origins and 16 genotypes, all grown together in a common garden. We found that fungal alpha and beta-diversity but not community composition differ by silver birch genotype. Some birch genotypes are potentially more plastic in terms of their fungal interactions, which could make them more robust against environmental changes and provide a competitive advantage especially in disturbed habitats.     

Modeling mycorrhizal fungi dispersal by the mycophagous swamp wallaby (Wallabia bicolor)

Despite the importance of mammal‐fungal interactions, tools to estimate the mammal‐assisted dispersal distances of fungi are lacking. Many mammals actively consume fungal fruiting bodies, the spores of which remain viable after passage through their digestive tract. Many of these fungi form symbiotic relationships with trees and provide an array of other key ecosystem functions. We present a flexible, general model to predict the distance a mycophagous mammal would disperse fungal spores. We modeled the probability of spore dispersal by combining animal movement data from GPS telemetry with data on spore gut‐retention time. We test this model using an exemplar generalist mycophagist, the swamp wallaby (Wallabia bicolor). We show that swamp wallabies disperse fungal spores hundreds of meters—and occasionally up to 1,265 m—from the point of consumption, distances that are ecologically significant for many mycorrhizal fungi. In addition to highlighting the ecological importance of swamp wallabies as dispersers of mycorrhizal fungi in eastern Australia, our simple modeling approach provides a novel and effective way of empirically describing spore dispersal by a mycophagous animal. This approach is applicable to the study of other animal‐fungi interactions in other ecosystems.     

Pathogenesis of Dermatophytosis

Despite the superficial localization of most dermatophytosis, host-fungus relationship in these infections is complex and still poorly elucidated. Though many efforts have been accomplished to characterize secreted dermatophytic proteases at the molecular level, only punctual insights have been afforded into other aspects of the pathogenesis of dermatophytosis, such as fungal adhesion, regulation of gene expression during the infection process, and immunomodulation by fungal factors. However, new genetic tools were recently developed, allowing a more rapid and high-throughput functional investigation of dermatophyte genes and the identification of new putative virulence factors. In addition, sophisticated in vitro infection models are now used and will open the way to a more comprehensive view of the interactions between these fungi and host epidermal cells, especially keratinocytes.     

Evolutionary histories and mycorrhizal associations of mycoheterotrophic plants dependent on saprotrophic fungi

Mycoheterotrophic plants (MHPs) are leafless, achlorophyllous, and completely dependent on mycorrhizal fungi for their carbon supply. Mycorrhizal symbiosis is a mutualistic association with fungi that is undertaken by the majority of land plants, but mycoheterotrophy represents a breakdown of this mutualism in that plants parasitize fungi. Most MHPs are associated with fungi that are mycorrhizal with autotrophic plants, such as arbuscular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. Although these MHPs gain carbon via the common mycorrhizal network that links the surrounding autotrophic plants, some mycoheterotrophic lineages are associated with saprotrophic (SAP) fungi, which are free-living and decompose leaf litter and wood materials. Such MHPs are dependent on the forest carbon cycle, which involves the decomposition of wood debris and leaf litter, and have a unique biology and evolutionary history. MHPs associated with SAP fungi (SAP-MHPs) have to date been found only in the Orchidaceae and likely evolved independently at least nine times within that family. Phylogenetically divergent SAP Basidiomycota, mostly Agaricales but also Hymenochaetales, Polyporales, and others, are involved in mycoheterotrophy. The fungal specificity of SAP-MHPs varies from a highly specific association with a single fungal species to a broad range of interactions with multiple fungal orders. Establishment of symbiotic culture systems is indispensable for understanding the mechanisms underlying plant–fungus interactions and the conservation of MHPs. Symbiotic culture systems have been established for many SAP-MHP species as a pure culture of free-living SAP fungi is easier than that of biotrophic AM or ECM fungi. Culturable SAP-MHPs are useful research materials and will contribute to the advancement of plant science.

     

Influence of Serum and Albumin on Echinocandin In Vitro Potency and Pharmacodynamics

The echinocandins target fungi by inhibiting the production of (1,3)-β-d-glucan, an essential component of the fungal cell wall. These agents have less toxicity to mammalian cells, as compared to other antifungals; however, they maintain potent activity against many pathogenic fungi, including polyene- and azole-resistant isolates. Members of this class are highly protein-bound, and the addition of serum or albumin to the growth medium has profound effects on their in vitro potency and pharmacodynamics. In addition, studies have demonstrated an association between in vitro activity, in the presence of serum, and outcomes in animal models of invasive fungal infections. Serum and albumin may also be useful to help detect echinocandin-resistant Candida isolates with point mutations in the gene that encodes for glucan synthase. Thus, in vitro studies evaluating echinocandins in the presence of protein can provide valuable insight regarding their potency and pharmacodynamics.     

Causes and consequences of changes to New Zealand?s fungal biota

This paper briefly reviews advances in knowledge of the non-lichenised fungi of New Zealand over the past 25 years. Since 1980, the number of species recorded from New Zealand has doubled, and molecular techniques have revolutionised studies on fungal phylogeny and our understanding of fungal distribution, biology and origins. The origins of New Zealand?s fungi are diverse; a few appear to be ancient, whereas many have arrived in geologically more recent times following trans-oceanic dispersal. Some of these more recent arrivals have evolved subsequently to form local endemic species, while others may be part of larger populations maintained through regular, trans-oceanic gene flow. Although questions remain about which fungi truly are indigenous and which are exotic, about one-third of the fungi recorded from New Zealand are likely to have been introduced since human settlement. While most exotic species are confined to human-modified habitats, there are some exceptions. These include species with potential to have significant impacts at the landscape scale. Examples from saprobic, pathogenic, endophytic and ectomycorrhizal fungi are used to discuss the factors driving the distribution and dispersal of New Zealand?s fungi at both global and local scales, the impact that historical changes to New Zealand?s vascular plant and animal biota have had on indigenous fungi, and the broader ecological impact of some of the exotic fungal species that have become naturalised in native habitats. The kinds of fungi present in New Zealand, and the factors driving the distribution and behaviour of those fungi, are constantly changing. These changes have occurred over a wide scale, in both time and space, which means New Zealand?s indigenous fungi evolved in response to ecological pressures very different from those found in New Zealand today.     

真菌系统学大趋势：越来越多的分类单元

分子生物学技术与真菌系统学的有机融合,为真菌分类和系统发育研究带来了革命性的变化。最近20年来,真菌学家们建立了大量的新目、新科、新属和新种,掀开了真菌多样性及其起源进化研究的新纪元,但很多重要的系统发育问题仍没有解决,特别是大量目间、科间的亲缘关系并不清楚。细分是真菌系统学的主流趋势,野生食用菌和毒蘑菇的分类也是如此,近年涌现了越来越多的新分类单元,如在2010-2019年的10年间,中国发表大型真菌（含地衣）新种1 240余个。本专刊收载的15篇论文是对我国野生食用菌和毒蘑菇研究工作的部分总结,对真菌资源利用、毒蘑菇中毒预防与治疗具有较重要的科学意义和应用价值。     

The effects of grazing history,soil properties and stand structure on the communities of saprotrophic fungi in wood-pastures

Wood-pastures are threatened anthropogenic biotopes that provide habitat for an extensive group of species. Here we studied the effect of management, grazing intensity, time since abandonment, historical land-use intensity, soil properties and stand conditions on communities of saprotrophic fungi in wood-pastures in Central Finland. We found that the proportion of broadleaved trees and soil pH are the major drivers in the communities of saprotrophic fungi in these boreal wood-pastures. In addition, tree species richness, soil moisture, historical land-use intensity and time since abandonment affected the communities of saprotrophic fungi. Current management or grazing intensity did not have a clear effect on saprotrophic fungal species richness, although dung-inhabiting fungal species richness was highest at intermediate to high grazing intensity. Obviously, there were many more dung-inhabiting fungal species on grazed than on abandoned sites. Our study highlights the conservation value of wood-pastures as hotspots of saprotrophic fungi.