Principles from community and metapopulation ecology: application to fungal entomopathogens

Fungal entomopathogens are often studied within the context of their use for biological control, yet these natural enemies are also excellent subjects for studies of ecological interactions. Here, we present selected principles from community ecology and discuss these in relation to fungal entomopathogens. We discuss the relevance of apparent competition, food web construction, intraguild predation and density-mediated and trait-mediated indirect effects. Although current knowledge of community interactions involving fungal entomopathogens are limited, fungal entomopathogens can be important, interactive members of communities and the activities of fungal entomopathogens should be evaluated in the context of ecological principles. We also discuss aspects of metapopulation ecology and the application of these principles to fungal entomopathogens. Knowledge of ecological interactions is crucial if we are to understand and predict the effects of fungal entomopathogens on host populations and understand the interactions among fungal entomopathogens and other organisms in the communities in which they occur.     

Arbuscular mycorrhizal fungi assemblages in Chernozem great groups revealed by massively parallel pyrosequencing

The arbuscular mycorrhizal (AM) fungal resources present in wheat fields of the Canadian Prairie were explored using 454 pyrosequencing. Of the 33 dominant AM fungal operational taxonomic units (OTUs) found in the 76 wheat fields surveyed at anthesis in 2009, 14 clustered as Funneliformis - Rhizophagus, 16 as Claroideoglomus, and 3 as Diversisporales. An OTU of Funneliformis mosseae and one OTU of Diversisporales each accounted for approximately 16% of all AM fungal OTUs. The former was ubiquitous, and the latter was mainly restricted to the Black and Dark Brown Chernozems. AM fungal OTU community composition was better explained by the Chernozem great groups (P = 0.044) than by measured soil properties. Fifty-two percent of the AM fungal OTUs were unrelated to measured soil properties. Black Chernozems hosted the largest AM fungal OTU diversity and almost twice the number of AM fungal sequences seen in Dark Brown Chernozems, the great group ranking second for AM fungal sequence abundance. Brown Chernozems hosted the lowest AM fungal abundance and an AM fungal diversity as low as that seen in Gray soils. We concluded that Black Chernozems are most conducive to AM fungal proliferation. AM fungi are generally distributed according to Chernozem great groups in the Canadian Prairie, although some taxa are evenly distributed in all soil groups.     

Soil fungal community changes in response to long-term fire cessation and N fertilization in tallgrass prairie

In grasslands, fire management and fertilization are established drivers of plant community change, but associated soil fungal responses are less well defined. We predicted that soil fungal communities would change seasonally, that decades of fire cessation and nitrogen (N) fertilization would alter fungal distributions, and that plant and fungal community change would be correlated. Surface soils were sampled monthly for 1 y from a 30-y fire by fertilization experiment to evaluate fungal community dynamics and assess correlation with plant community heterogeneity. ITS gene community composition was seasonally stable, excepting increased arbuscular mycorrhizal fungal summer abundance in the burned, fertilized treatment. Long-term treatments affected soil fungal and plant communities, with correlated heterogeneity patterns. Despite woody encroachment in the fire cessation treatment, soil fungal communities did not resemble those of forests. This study provides evidence supporting the strength of feedbacks between fungal and plant community change in response to long-term grassland fire and N management changes.     

Fungal diversity in sheep (Ovis aries) and cattle (Bos taurus) feces assessed by comparison of 18S, 28S and ITS ribosomal regions

To explore the fungal diversity in ruminant feces for bioenergy, libraries based on internal transcribed spacer (ITS), 18S rRNA, and 28S rRNA regions were constructed, respectively. Although the libraries were constructed from the same DNA extracts, the fungal taxa analyses based on these libraries are different. The ITS and 28S libraries comprised higher proportions of fungal clones than 18S libraries, and the ITS libraries converged into the lower diversities. The ITS libraries could be used to analyze the fungal community. The 18S libraries were suitable for the fungi and protozoa community. However, the 28S are suitable for analysis of Ascomycota fungi. The major fungal taxa in cattle feces analyzed by ITS, 18S, and 28S libraries are similar to those of sheep feces, respectively. The fungal taxa detected by the ITS library comprised only 20 % fungal taxa detected by the three libraries. The 18S library comprised 30 % fungal taxa; the 28S library comprised about 50 % fungal taxa. The results indicated that primer sets toward different DNA regions lead to the difference in structures of fungal community. So the selection of primer sets may influence the fungal communities, and libraries based on single primer sets may underestimate the fungal diversity. The comparison of ITS, 18S, and 28S libraries could fid more diverse fungi than that based on only one library.     

Alteration in sphingolipid metabolism: bioassays for fumonisin- and ISP-I-like activity in tissues, cells and other matrices

The first discovered naturally occurring inhibitor of de novo sphingolipid biosynthesis was fumonisin B1. There are now 11 identified fungal inhibitors of ceramide synthase or 'fumonisin B1-like' compounds. With the exception of the australifungins, all other fungal ceramide synthase inhibitors are structurally sphingoid-like. There are several recently discovered fungal inhibitors of another enzyme in the de novo sphingolipid biosynthesis pathway: serine palmitoyltransferase (SPT). One of the SPT inhibitors is named ISP-I. While ceramide synthase inhibitors are toxic to animals, plants and fungi, the SPT inhibitors are not known to cause animal or plant disease, but are potent inhibitors of fungal growth. Very little is known about their toxicity in animals. There are at least 24 fungal SPT inhibitors produced by a variety of fungi. Given that the fungal inhibitors of sphingolipid biosynthesis are chemically and biologically diverse, two bioassays have been developed to screen for fumonisin-like or ISP-I-like activity in naturally contaminated products or fungal culture materials. These bioassays are based on the changes in free sphingoid base concentration that occur when the ceramide synthase or SPT are inhibited. The bioassays have the advantage that they are functionally rather than chemically specific and thus will detect ceramide synthase and SPT inhibitors regardless of their chemical structure.     

Molecular-genetic evaluation of fungal molecules for roles in pathogenesis to plants

Fungus-plant interactions involve complex developmental processes in which a variety of fungal and plant molecules are required to determine whether the outcome is a susceptible reaction (successful fungal colonization of plant tissues) or a resistant reaction (the plant mounts a defence that aborts fungal invasion). To understand the molecular basis of fungal disease, it is necessary to identify the fungal molecules that areessential for pathogenic processes, and to distinguish them from molecules that may be present during infection but not critical to its outcome. Molecular-genetic technology has been developed for fungal pathogens and used to evaluate the roles of fungal molecules in fungal infection processes. Although the field is in its infancy, several molecules have already been proven as essential components of fungal pathogenesis. Some are clearly involved in the adhesion and penetration phases of infection, i.e. hydrophobins, melanin, glycerol, cutinase, and components of signal transduction pathways (which mediate colonization as well), whereas others are required for colonization of plant tissues after penetration, i.e. toxins that induce susceptibility, toxins that induce resistance, and enzymes that inactivate plant defence mechanisms. Molecular-genetic manipulation has also been used to show that certain candidates for roles in pathogenesis are in fact not involved in any detectable way.     

A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe

The fungal transamidase complex that executes glycosylphosphatidylinositol (GPI) lipid anchoring of precursor proteins has overlapping but distinct sequence specificity compared with the animal system. Therefore, a taxon-specific prediction tool for the recognition of the C-terminal signal in fungal sequences is necessary. We have collected a learning set of fungal precursor protein sequences from the literature and fungal proteomes. Although the general four segment scheme of the recognition signal is maintained also in fungal precursors, there are taxon specificities in details. A fungal big-Pi predictor has been developed for the assessment of query sequence concordance with fungi-specific recognition signal requirements. The sensitivity of this predictor is close to 90%. The rate of false positive prediction is in the range of 0.1%. The fungal big-Pi tool successfully predicts the Gas1 mutation series described by C. Nuoffer and co-workers, and recognizes that the human PLAP C terminus is not a target for the fungal transamidase complex. Lists of potentially GPI lipid anchored proteins for five fungal proteomes have been generated and the hits have been functionally classified. The fungal big-Pi prediction WWW server as well as precursor lists are available at     

Insect pathology and fungal endophytes

Fungi that occur inside asymptomatic plant tissues are known as fungal endophytes. Different genera of fungal entomopathogens have been reported as naturally occurring fungal endophytes, and it has been shown that it is possible to inoculate plants with fungal entomopathogens, making them endophytic. Their mode of action against insects appears to be due to antibiosis or feeding deterrence. Research aimed at understanding the fungal ecology of entomopathogenic fungi, and their role as fungal endophytes, could lead to a new paradigm on how to successfully use these organisms in biological control programs.     

丝状真菌次级代谢产物生物合成的表观遗传调控

丝状真菌产生的次级代谢产物是新药的重要来源之一,其生物合成过程受到众多因素的调控。最近的研究表明,表观遗传对多种丝状真菌次级代谢产物的生物合成具有调控作用。DNA和组蛋白的甲基化与乙酰化修饰是目前所知的丝状真菌主要的表观遗传调控形式。通过过表达或缺失相关表观修饰基因和利用小分子表观遗传试剂改变丝状真菌染色体的修饰形式,不仅可以提高多种已知次级代谢产物产量,而且可以通过激活沉默的生物合成基因簇诱导丝状真菌产生新的未知代谢产物。丝状真菌表观遗传学正逐渐成为真菌菌株改良的新策略以及挖掘真菌次级代谢产物合成潜力的强有力手段。     

Arbuscular mycorrhizal communities in tropical forests are affected by host tree species and environment

Arbuscular mycorrhizal (AM) fungi are mutualists with plant roots that are proposed to enhance plant community diversity. Models indicate that AM fungal communities could maintain plant diversity in forests if functionally different communities are spatially separated. In this study we assess the spatial and temporal distribution of the AM fungal community in a wet tropical rainforest in Costa Rica. We test whether distinct fungal communities correlate with variation in tree life history characteristics, with host tree species, and the relative importance of soil type, seasonality and rainfall. Host tree species differ in their associated AM fungal communities, but differences in the AM community between hosts could not be generalized over life history groupings of hosts. Changes in the relative abundance of a few common AM fungal species were the cause of differences in AM fungal communities for different host tree species instead of differences in the presence and absence of AM fungal species. Thus, AM fungal communities are spatially distinguishable in the forest, even though all species are widespread. Soil fertility ranging between 5 and 9 Mg/ha phosphorus did not affect composition of AM fungal communities, although sporulation was more abundant in lower fertility soils. Sampling soils over seasons revealed that some AM fungal species sporulate profusely in the dry season compared to the rainy season. On one host tree species sampled at two sites with vastly different rainfall, relative abundance of spores from Acaulospora was lower and that of Glomus was relatively higher at the site with lower and more seasonal rainfall.     

Fungi associated with beetles dispersing from dead wood – Let's take the beetle bus!

Spore characteristics of wood-inhabiting fungi suggest that wind is their predominant dispersal vector. However, since they are restricted to ephemeral habitats, colonizing new patches should benefit from dispersal by animals with similar habitat preferences because the directed, resource-searching movement of animals increases the likelihood of reaching suitable habitats. Here we determine which fungal guilds are carried by wood-inhabiting beetles and what influences beetle-associated fungal communities. High-throughput sequencing identified >1800 fungal taxa from beetle communities that emerged from 64 experimental logs. Beetle-associated fungi included mutualistic, decomposing, pathogenic and mycorrhizal fungi; decomposers were the most diverse. Partial-procrustes analysis revealed that the total beetle-associated community and mutualists were correlated (p ≤ 0.05) with beetle community composition and decomposers were marginally correlated (p ≤ 0.10) with beetle community composition. All three groups were marginally correlated with the total fungal communities that inhabit the dead wood. Our results show that beetles carry a broad range of wood-inhabiting fungi and beetle-associated fungal communities are determined by environmental factors and the vectoring beetle community and to some degree by the fungal source community. This suggests that wood-inhabiting beetles contribute to fungal dispersal, including directed dispersal, which could affect fungal community assembly and ecosystem processes like wood decomposition.     

New insights on the development of fungal vaccines: from immunity to recent challenges

Fungal infections are emerging as a major problem in part due to high mortality associated with systemic infections, especially in the case of immunocompromised patients. With the development of new treatments for diseases such as cancer and the acquired immune deficiency syndrome pandemic, the number of immunosuppressed patients has increased and, as a consequence, also the number of invasive fungal infections has increased. Several studies have proposed new strategies for the development of effective fungal vaccines. In addition, better understanding of how the immune system works against fungal pathogens has improved the further development of these new vaccination strategies. As a result, some fungal vaccines have advanced through clinical trials. However, there are still many challenges that prevent the clinical development of fungal vaccines that can efficiently immunise subjects at risk of developing invasive fungal infections. In this review, we will discuss these new vaccination strategies and the challenges that they present. In the future with proper investments, fungal vaccines may soon become a reality.     

Fungal pretreatment of lignocellulosic biomass

Pretreatment is a crucial step in the conversion of lignocellulosic biomass to fermentable sugars and biofuels. Compared to thermal/chemical pretreatment, fungal pretreatment reduces the recalcitrance of lignocellulosic biomass by lignin-degrading microorganisms and thus potentially provides an environmentally-friendly and energy-efficient pretreatment technology for biofuel production. This paper provides an overview of the current state of fungal pretreatment by white rot fungi for biofuel production. The specific topics discussed are: 1) enzymes involved in biodegradation during the fungal pretreatment; 2) operating parameters governing performance of the fungal pretreatment; 3) the effect of fungal pretreatment on enzymatic hydrolysis and ethanol production; 4) efforts for improving enzymatic hydrolysis and ethanol production through combinations of fungal pretreatment and physical/chemical pretreatment; 5) the treatment of lignocellulosic biomass with lignin-degrading enzymes isolated from fungal pretreatment, with a comparison to fungal pretreatment; 6) modeling, reactor design, and scale-up of solid state fungal pretreatment; and 7) the limitations and future perspective of this technology.     

Microbial Pathogens in the Fungal Kingdom

The fungal kingdom is vast, spanning ~1.5 to as many as 5 million species diverse as unicellular yeasts, filamentous fungi, mushrooms, lichens, and both plant and animal pathogens. The fungi are closely aligned with animals in one of the six to eight supergroups of eukaryotes, the opisthokonts. The animal and fungal kingdoms last shared a common ancestor ~1 billion years ago, more recently than other groups of eukaryotes. As a consequence of their close evolutionary history and shared cellular machinery with metazoans, fungi are exceptional models for mammalian biology, but prove more difficult to treat in infected animals. The last common ancestor to the fungal/metazoan lineages is thought to have been unicellular, aquatic, and motile with a posterior flagellum, and certain extant species closely resemble this hypothesized ancestor. Species within the fungal kingdom were traditionally assigned to four phyla, including the basal fungi (Chytridiomycota, Zygomycota) and the more recently derived monophyletic lineage, the dikarya (Ascomycota, Basidiomycota). The fungal tree of life project has revealed that the basal lineages are polyphyletic, and thus there are as many as eight to ten fungal phyla. Fungi that infect vertebrates are found in all of the major lineages, and virulence arose multiple times independently. A sobering recent development involves the species Batrachochytrium dendrobatidis from the basal fungal phylum, the Chytridiomycota, which has emerged to cause global amphibian declines and extinctions. Genomics is revolutionizing our view of the fungal kingdom, and genome sequences for zygomycete pathogens (Rhizopus, Mucor), skin-associated fungi (dermatophytes, Malassezia), and the Candida pathogenic species clade promise to provide insights into the origins of virulence. Here we survey the diversity of fungal pathogens and illustrate key principles revealed by genomics involving sexual reproduction and sex determination, loss of conserved pathways in derived fungal lineages that are retained in basal fungi, and shared and divergent virulence strategies of successful human pathogens, including dimorphic and trimorphic transitions in form. The overarching conclusion is that fungal pathogens of animals have arisen repeatedly and independently throughout the fungal tree of life, and while they share general properties, there are also unique features to the virulence strategies of each successful microbial pathogen.     

Diversity and Antimicrobial Activity of Culturable Fungi Isolated from Six Species of the South China Sea Gorgonians

Fungi in gorgonians are now known to cause gorgonian diseases, but little attention has been paid to the nature of fungal communities associated with gorgonians. The diversity of culturable fungi associated with six species of healthy South China Sea gorgonians were investigated using a culture-dependent method followed by analysis of fungal internal transcribed spacer sequences. A total of 121 fungal isolates were recovered and identified using the Basic Local Alignment Search Tool search program. These belonged to 41 fungal species from 20 genera. Of these, 30 species and 12 genera are new reports for gorgonians, and the genera Aspergillus and Penicillium were the most diverse and common in the six gorgonian species. Comparison of the fungal communities in the six gorgonian species, together with results from previous relevant studies, indicated that different gorgonian species and the same gorgonian species living in different geographic locations had different fungal communities. The gorgonian Dichotella gemmacea harbored the most fungal species and isolates, while Echinogorgia aurantiaca had the least fungal diversity. Among the six media used for fungal isolation, potato glucose agar yielded the highest isolates (27 isolates), while glucose peptone starch agar had the best recoverability of fungal species (15 species). The antimicrobial activity of the 121 fungal isolates was tested against three marine bacteria and two marine gorgonian pathogenic fungi. A relatively high proportion (38?%) of fungal isolates displayed distinct antibacterial and antifungal activity, suggesting that the gorgonian-associated fungi may aid their hosts in protection against pathogens. This is the first report comparing the diversity of fungal communities among the South China Sea gorgonians. It contributes to our knowledge of gorgonian-associated fungi and further increases the pool of fungi available for natural bioactive product screening.     

Interactions of antifungal plant defensins with fungal membrane components

Plant defensins are small, basic, cysteine-rich peptides that are generally active against a broad spectrum of fungal and yeast species at micromolar concentrations. Some of these defensins interact with fungal-specific lipid components in the plasmamembrane. Structural differences of these membrane components between fungal and plant cells probably account for the selective activity of plant defensins against fungal pathogens and their nonphytotoxic properties. This review will focus on different classes of complex lipids in fungal membranes and on the selective interaction of plant defensins with these complex lipids.     

Flowering‐mediated root‐fungus symbiosis loss is related to jasmonate‐dependent root soluble sugar deprivation

The role of flowering in root‐fungal symbiosis is not well understood. Because flowering and fungal symbionts are supported by carbohydrates, we hypothesized that flowering modulates root‐beneficial fungal associations through alterations in carbohydrate metabolism and transport. We monitored fungal colonization and soluble sugars in the roots of Arabidopsis thaliana following inoculation with a mutualistic fungus Phomopsis liquidambari across different plant developmental stages. Jasmonate signalling of wild‐type plants, sugar transport, and root invertase of wild‐type and jasmonate‐insensitive plants were exploited to assess whether and how jasmonate‐dependent sugar dynamics are involved in flowering‐mediated fungal colonization alterations. We found that flowering restricts root‐fungal colonization and activates root jasmonate signalling upon fungal inoculation. Jasmonates reduce the constitutive and fungus‐induced accumulation of root glucose and fructose at the flowering stage. Further experiments with sugar transport and metabolism mutant lines revealed that root glucose and fructose positively influence fungal colonization. Diurnal, jasmonate‐dependent inhibitions of sugar transport and soluble invertase activity were identified as likely mechanisms for flowering‐mediated root sugar depletion upon fungal inoculation. Collectively, our results reveal that flowering drives root‐fungus cooperation loss, which is related to jasmonate‐dependent root soluble sugar depletion. Limiting the spread of root‐fungal colonization may direct more resources to flower development.     

Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’

Attempts to assess fungal global species richness are confounded by several problems: uncertainty about the number of described species, incomplete fungal inventories even at a high taxonomic level, high diversity of unknown, often small and elusive taxa, high levels of morphological conservation, and incomplete knowledge of their ecological and biogeographical distributions. The two main bases for estimating total fungal diversity are (1) the number of described species and their taxonomic structure, and (2) extrapolating species-area relationships. We argue that knowledge of fungal taxonomy and environmental sampling of fungi are both too incomplete for either approach to be reliable. However, it is likely that the true number of fungal species on the planet is a seven-digit number, and may even be an order of magnitude higher.