Transcriptome of an entomophthoralean fungus (Pandora formicae) shows molecular machinery adjusted for successful host exploitation and transmission

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Expression of trematode-induced zombie-ant behavior is strongly associated with temperature

Parasite-induced modification of host behavior increasing transmission to a next host is a common phenomenon. However, field-based studies are rare, and the role of environmental factors in eliciting host behavioral modification is often not considered. We examined the effects of temperature, relative humidity (RH), time of day, date, and an irradiation proxy on behavioral modification of the ant Formica polyctena (Förster, 1850) by the brain-encysting lancet liver fluke Dicrocoelium dendriticum (Rudolphi, 1819). This fluke induces ants to climb and bite to vegetation by the mandibles in a state of temporary tetany. A total of 1264 individual ants expressing the modified behavior were observed over 13 non-consecutive days during one year in the Bidstrup Forests, Denmark. A sub-set of those ants (N = 172) was individually marked to track the attachment and release of infected ants in relation to variation in temperature. Infected ants primarily attached to vegetation early and late in the day, corresponding to low temperature and high RH, presumably coinciding with the grazing activity of potential herbivorous definitive hosts. Temperature was the single most important determinant for the induced phenotypic change. On warm days, infected ants altered between the manipulated and non-manipulated state multiple times, while on cool days, many infected ants remained attached to the vegetation all day. Our results suggest that the temperature sensitivity of the infected ants serves the dual purpose of exposing infected ants to the next host at an opportune time, while protecting them from exposure to high temperatures, which might increase host (and parasite) mortality.

The transcriptome of the entomopathogenic fungus Culicinomyces clavisporus contains an ortholog of the insecticidal ribotoxin Hirsutellin

The entomopathogenic fungus Culicinomyces clavisporus is known to infect and kill mosquito larvae and therefore has been seen as a potential biological control agent against disease vector mosquitoes. Whereas most fungal entomopathogens infect hosts by penetrating the external cuticle, C. clavisporus initiates infection through ingestion (per os). This unique infection strategy suggests that the C. clavisporus genome may be mined for novel pathogenicity factors with potential for vector control. To this end, an Isoseq-based transcriptome analysis was initiated, and resulted in a total of 3,512,145 sequences, with an average length of 1,732 bp. Transcripts assembly and annotation suggested that the C. clavisporus transcriptome lacked the cuticle-degrading proteins that have been associated with other entomopathogenic fungi, supporting the per os pathogenicity process. Furthermore, mining of the sequence data unexpectedly revealed C. clavisporus transcripts homologous to the Hirsutellin toxin. Comparative sequence analyses indicated that the C. clavisporus Hirsutellin predicted protein has retained the canonical molecular features that have been associated with the ribotoxic and insecticidal properties of the original toxin isolated from Hirsutella thompsonii. The identification of an Hirsutellin ortholog in C. clavisporus was supported by phylogenetic analyses demonstrating that Culicinomyces and Hirsutella were closely related genera in the Ophiocordycipitaceae family. Validation of the mosquitocidal activity of this novel C. clavisporus protein has yet to be performed but may help position Hirsutellin orthologs as prime candidates for the development of alternative biocontrol approaches complementing the current toolbox of vector mosquito management strategies.

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.

Disentangling the Taxonomy, Systematics, and Life History of the Spider-Parasitic Fungus Gibellula (Cordycipitaceae, Hypocreales)

Gibellula (Cordycipitaceae, Hypocreales) is frequently observed growing on spiders, but little is known about their host range. One of the greatest challenges in describing these interactions is identifying the host, since the fungus often rapidly consumes the parasitised spiders and destroys important diagnostic taxonomic traits. Additionally, the global diversity of Gibellula remains unclear, as does the natural history and phylogenetic relationships of most of the species. Herein, we performed an extensive investigation on the species of Gibellula, reconstructed the most complete molecular phylogeny of the genus in the context of Cordycipitaceae, and performed a systematic review in order to provide the foundations towards a better understanding of the genus. Therefore, we have performed an integrative study to investigate the life history of the genus and to disentangle the questionable number of valid species proposed over time. We provided novel molecular data for published species that had not been sequenced before, such as G. mirabilis and G. mainsii, and evaluated all the original and modern morphological descriptions. In addition, we presented its global known distribution and compiled all available molecular data. We suggested a set of terms and morphological traits that should be considered in future descriptions of the genus and that a total of 31 species should be considered as accepted.

Microbiome Analysis of the Bamboo Aphid Melanaphis bambusae Infected with the Aphid Obligate Pathogen Conidiobolus obscurus (Entomophthoromycotina)

Insect-associated microbes exert diverse effects on host fitness. This study provides insights into the microbiota of the bamboo aphid, Melanaphis bambusae, and their response to Conidiobolus obscurus infection. 16S rRNA and ITS sequencing data were used to analyze the bacterial and fungal samples associated with healthy, infected, and starved aphids. At ≥97% nucleotide similarity, the total reads were clustered into 79 bacteria and 97 fungi operational Taxonomic Units (OTUs). The phyla Proteobacteria and Ascomycota dominated the bacterial and fungal communities, respectively. The significant divergence in OTU distribution presented differential profiles of the microbiota in response to host conditions. Lower α-diversity indices were found in bacterial and fungal diversity when the aphids were experiencing fungal infection and starvation stresses, respectively. The β-diversity analyses of the communities showed significant differences among the three host conditions, demonstrating that aphid-associated microbiota could significantly shift in response to varying host conditions. Moreover, some OTUs increased under fungal infection, which potentially increased aphid susceptibility. Presumably, C. obscurus infection contributed to this increase by causing the disintegration of host tissues other than host starvation. In conclusion, understanding the differentiation of aphid microbiota caused by fungal entomopathogens helped facilitate the development of novel pest management strategies.

Genome-Wide Study of Conidiation-Related Genes in the Aphid-Obligate Fungal Pathogen Conidiobolus obscurus (Entomophthoromycotina)

Fungi in the Entomophthorales order can cause insect disease and epizootics in nature, contributing to biological pest control in agriculture and forestry. Most Entomophthorales have narrow host ranges, limited to the arthropod family level; however, rare genomic information about host-specific fungi has been reported. Conidiation is crucial for entomopathogenic fungi to explore insect resources owing to the important roles of conidia in the infection cycle, such as dispersal, adhesion, germination, and penetration into the host hemocoel. In this study, we analyzed the whole genome sequence of the aphid-obligate pathogen Conidiobolus obscurus strain ARSEF 7217 (Entomophthoromycotina), using Nanopore technology from Biomarker Technologies (Beijing, China). The genome size was 37.6 Mb, and encoded 10,262 predicted genes, wherein 21.3% genes were putatively associated to the pathogen–host interaction. In particular, the serine protease repertoire in C. obscurus exhibited expansions in the trypsin and subtilisin classes, which play vital roles in the fungus’ pathogenicity. Differentially expressed transcriptomic patterns were analyzed in three conidiation stages (pre-conidiation, emerging conidiation, and post-conidiation), and 2915 differentially expressed genes were found to be associated with the conidiation process. Furthermore, a weighted gene co-expression network analysis showed that 772 hub genes in conidiation are mainly involved in insect cuticular component degradation, cell wall/membrane biosynthesis, MAPK signaling pathway, and transcription regulation. Our findings of the genomic and transcriptomic features of C. obscurus help reveal the molecular mechanism of the Entomophthorales pathogenicity, which will contribute to improving fungal applications in pest control.

The genus Entomophthora: bringing the insect destroyers into the twenty-first century

The fungal genus Entomophthora consists of highly host-specific pathogens that cause deadly epizootics in their various insect hosts. The most well-known among these is the "zombie fly" fungus E. muscae, which, like other Entomophthora species, elicits a series of dramatic behaviors in infected hosts to promote optimal spore dispersal. Despite having been first described more than 160 years ago, there are still many open questions about Entomophthora biology, including the molecular underpinnings of host behavior manipulation and host specificity. This review provides a comprehensive overview of our current understanding of the biology of Entomophthora fungi and enumerates the most pressing outstanding questions that should be addressed in the field. We briefly review the discovery of Entomophthora and provide a summary of the 21 recognized Entomophthora species, including their type hosts, methods of transmission (ejection of spores after or before host death), and for which molecular data are available. Further, we argue that this genus is globally distributed, based on a compilation of Entomophthora records in the literature and in online naturalist databases, and likely to contain additional species. Evidence for strain-level specificity of hosts is summarized and directly compared to phylogenies of Entomophthora and the class Insecta. A detailed description of Entomophthora's life-cycle and observed manipulated behaviors is provided and used to summarize a consensus for ideal growth conditions. We discuss evidence for Entomophthora's adaptation to growth exclusively inside insects, such as producing wall-less hyphal bodies and a unique set of subtilisin-like proteases to penetrate the insect cuticle. However, we are only starting to understand the functions of unusual molecular and genomic characteristics, such as having large > 1 Gb genomes full of repetitive elements and potential functional diploidy. We argue that the high host-specificity and obligate life-style of most Entomophthora species provides ample scope for having been shaped by close coevolution with insects despite the current general lack of such evidence. Finally, we propose six major directions for future Entomophthora research and in doing so hope to provide a foundation for future studies of these fungi and their interaction with insects.

Mechanisms behind the Madness: How Do Zombie-Making Fungal Entomopathogens Affect Host Behavior To Increase Transmission?

Transmission is a crucial step in all pathogen life cycles. As such, certain species have evolved complex traits that increase their chances to find and invade new hosts. Fungal species that hijack insect behaviors are evident examples. Many of these "zombie-making" entomopathogens cause their hosts to exhibit heightened activity, seek out elevated positions, and display body postures that promote spore dispersal, all with specific circadian timing. Answering how fungal entomopathogens manipulate their hosts will increase our understanding of molecular aspects underlying fungus-insect interactions, pathogen-host coevolution, and the regulation of animal behavior. It may also lead to the discovery of novel bioactive compounds, given that the fungi involved have traditionally been understudied. This minireview summarizes and discusses recent work on zombie-making fungi of the orders Hypocreales and Entomophthorales that has resulted in hypotheses regarding the mechanisms that drive fungal manipulation of insect behavior. We discuss mechanical processes, host chemical signaling pathways, and fungal secreted effectors proposed to be involved in establishing pathogen-adaptive behaviors. Additionally, we touch on effectors' possible modes of action and how the convergent evolution of host manipulation could have given rise to the many parallels in observed behaviors across fungus-insect systems and beyond. However, the hypothesized mechanisms of behavior manipulation have yet to be proven. We, therefore, also suggest avenues of research that would move the field toward a more quantitative future.

Long noncoding RNAs are potentially involved in the degeneration of virulence in an aphid-obligate pathogen, Conidiobolus obscurus (Entomophthoromycotina)

Virulence attenuation frequently occurs in in vitro culturing of pathogenic microbes. In this study, we investigated the total putative long noncoding RNAs (lncRNAs) in an aphid-obligate pathogen, Conidiobolus obscurus, and screened the differentially expressed (DE) lncRNAs and protein-coding genes involved in the virulence decline. The virulence was significantly attenuated after eight subculturing events, in which the median lethal concentration of the conidia ejected from mycelial mats relative to the bamboo aphid, Takecallis taiwanus, increased from 36.1 to 126.1 conidia mm^–2, four days after inoculation. In total, 1,252 lncRNAs were identified based on the genome-wide transcriptional analysis. By characterizing their molecular structures and expression patterns, we found that the lncRNAs possessed shorter transcripts, lower expression, and fewer exons than did protein-coding genes in C. obscurus. A total of 410 DE genes of 329 protein-coding genes and 81 lncRNAs were identified. The functional enrichment analysis showed the DE genes were enriched in peptidase activity, protein folding, autophagy, and metabolism. Moreover, target prediction analysis of the 81 lncRNAs revealed 3,111 cis-regulated and 23 trans-regulated mRNAs, while 121 DE lncRNA-mRNA pairs were possibly involved in virulence decline. Moreover, the DE lncRNA-regulated target genes mainly encoded small heat shock proteins, secretory proteins, transporters, autophagy proteins, and other stress response-related proteins. This implies that the decline in virulence regulated by lncRNAs was likely associated with the environmental stress response of C. obscurus. Hence, these findings can provide insights into the lncRNA molecules of Entomophthoromycotina, with regards to virulence regulators of entomopathogens.

Insect Behavioral Change and the Potential Contributions of Neuroinflammation-A Call for Future Research

Many organisms are able to elicit behavioral change in other organisms. Examples include different microbes (e.g., viruses and fungi), parasites (e.g., hairworms and trematodes), and parasitoid wasps. In most cases, the mechanisms underlying host behavioral change remain relatively unclear. There is a growing body of literature linking alterations in immune signaling with neuron health, communication, and function; however, there is a paucity of data detailing the effects of altered neuroimmune signaling on insect neuron function and how glial cells may contribute toward neuron dysregulation. It is important to consider the potential impacts of altered neuroimmune communication on host behavior and reflect on its potential role as an important tool in the "neuro-engineer" toolkit. In this review, we examine what is known about the relationships between the insect immune and nervous systems. We highlight organisms that are able to influence insect behavior and discuss possible mechanisms of behavioral manipulation, including potentially dysregulated neuroimmune communication. We close by identifying opportunities for integrating research in insect innate immunity, glial cell physiology, and neurobiology in the investigation of behavioral manipulation.

Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

The fungal genus Massospora (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of Massospora spp. are not well understood. The acquisition of M. diceroproctae from Arizona, M. tettigatis from Chile, and M. platypediae from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate whether these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1-D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (EFL), and beta-tubulin (BTUB), Massospora was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the three-gene concatenated tree (EFL) or a basal polytomy (28S, BTUB). Massospora levispora and M. platypediae isolates formed a single lineage in all analyses and are synonymized here as M. levispora. Massospora diceroproctae was sister to M. cicadina in all three single-gene trees and on an extremely long branch relative to the other Massospora, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxon sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of Massospora, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring coevolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.

Characterization of a cytolytic-like gene from the aphid-obligate fungal pathogen Conidiobolus obscurus

Cytolytic (Cyt)-like genes are known by omics analyses to exist widely in bacterial and fungal pathogens, but their insecticidal activities in fungi remains unknown. A full-length coding sequence of a Cyt-like gene was first amplified from Conidiobolus obscurus (an obligate aphid-pathogenic fungus) through RACE (rapid-amplification of cDNA ends). The deduced protein structure was structurally characterized by a single Cyt-typical α/β domain. The expression level of the Cyt-like gene in conidia correlated well with the fungal virulence against aphids (r² = 0.97). The results demonstrate the Cyt-like gene acts as an important virulence factor of C. obscurus against aphids, and has potential for exploitation in aphid control.

Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens

Entomopathogenic fungi routinely kill their hosts before releasing infectious spores, but a few species keep insects alive while sporulating, which enhances dispersal. Transcriptomics- and metabolomics-based studies of entomopathogens with post-mortem dissemination from their parasitized hosts have unraveled infection processes and host responses. However, the mechanisms underlying active spore transmission by Entomophthoralean fungi in living insects remain elusive. Here we report the discovery, through metabolomics, of the plant-associated amphetamine, cathinone, in four Massospora cicadina-infected periodical cicada populations, and the mushroom-associated tryptamine, psilocybin, in annual cicadas infected with Massospora platypediae or Massospora levispora, which likely represent a single fungal species. The absence of some fungal enzymes necessary for cathinone and psilocybin biosynthesis along with the inability to detect intermediate metabolites or gene orthologs are consistent with possibly novel biosynthesis pathways in Massospora. The neurogenic activities of these compounds suggest the extended phenotype of Massospora that modifies cicada behavior to maximize dissemination is chemically-induced.

Where the baculoviruses lead, the caterpillars follow: baculovirus-induced alterations in caterpillar behaviour

Baculoviruses are well-known for altering the behaviour of their caterpillar hosts by inducing hyperactivity (enhanced locomotion) and/or tree-top disease (climbing to elevated positions before death). These features, along with the genomic small size of baculoviruses compared to non-viral parasites and the at hand techniques for producing mutants, imply that baculoviruses are excellent tools for unravelling the molecular mechanisms underlying parasitic alteration of host behaviour. Baculoviruses can be easily mutated, allowing an optimal experimental setup in comparative studies, where for instance host gene expression can be compared between insects infected with wild-type viruses or with mutant viruses lacking genes involved in behavioural manipulation. Recent studies have revealed the first insight into the underlying molecular pathways that lead to the typical behaviour of baculovirus-infected caterpillars and into the role of light therein. Since host behaviour in general is mediated through the host's central nervous system (CNS), a promising future step will be to study how baculoviruses regulate the neuronal activity of the host.

Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases

Insect-pathogenic fungi use subtilisin-like serine proteases (SLSPs) to degrade chitin-associated proteins in the insect procuticle. Most insect-pathogenic fungi in the order Hypocreales (Ascomycota) are generalist species with a broad host-range, and most species possess a high number of SLSPs. The other major clade of insect-pathogenic fungi is part of the subphylum Entomophthoromycotina (Zoopagomycota, formerly Zygomycota) which consists of high host-specificity insect-pathogenic fungi that naturally only infect a single or very few host species. The extent to which insect-pathogenic fungi in the order Entomophthorales rely on SLSPs is unknown. Here we take advantage of recently available transcriptomic and genomic datasets from four genera within Entomophthoromycotina: the saprobic or opportunistic pathogens Basidiobolus meristosporus, Conidiobolus coronatus, C. thromboides, C. incongruus, and the host-specific insect pathogens Entomophthora muscae and Pandora formicae, specific pathogens of house flies (Muscae domestica) and wood ants (Formica polyctena), respectively. In total 154 SLSP from six fungi in the subphylum Entomophthoromycotina were identified: E. muscae (n = 22), P. formicae (n = 6), B. meristosporus (n = 60), C. thromboides (n = 18), C. coronatus (n = 36), and C. incongruus (n = 12). A unique group of 11 SLSPs was discovered in the genomes of the obligate biotrophic fungi E. muscae, P. formicae and the saprobic human pathogen C. incongruus that loosely resembles bacillopeptidase F-like SLSPs. Phylogenetics and protein domain analysis show this class represents a unique group of SLSPs so far only observed among Bacteria, Oomycetes and early diverging fungi such as Cryptomycota, Microsporidia, and Entomophthoromycotina. This group of SLSPs is missing in the sister fungal lineages of Kickxellomycotina and the fungal phyla Mucoromyocta, Ascomycota and Basidiomycota fungi suggesting interesting gene loss patterns.

Human Pathogenic Entomophthorales

The pathogenic entomophthoralean fungi cause infection in insects and mammalian hosts. Basidiobolus and Conidiobolus species can be found in soil and insect, reptile, and amphibian droppings in tropical and subtropical areas. The life cycles of these fungi occur in these environments where infecting sticky conidia are developed. The infection is acquired by insect bite or contact with contaminated environments through open skin. Conidiobolus coronatus typically causes chronic rhinofacial disease in immunocompetent hosts, whereas some Conidiobolus species can be found in immunocompromised patients. Basidiobolus ranarum infection is restricted to subcutaneous tissues but may be involved in intestinal and disseminated infections. Its early diagnosis remains challenging due to clinical similarities to other intestinal diseases. Infected tissues characteristically display eosinophilic granulomas with the Splendore-Höeppli phenomenon. However, in immunocompromised patients, the above-mentioned inflammatory reaction is absent. Laboratory diagnosis includes wet mount, culture serological assays, and molecular methodologies. The management of entomophthoralean fungi relies on traditional antifungal therapies, such as potassium iodide (KI), amphotericin B, itraconazole, and ketoconazole, and surgery. These species are intrinsically resistant to some antifungals, prompting physicians to experiment with combinations of therapies. Research is needed to investigate the immunology of entomophthoralean fungi in infected hosts. The absence of an animal model and lack of funding severely limit research on these fungi.

Transcriptomic insight into pathogenicity-associated factors of Conidiobolus obscurus, an obligate aphid-pathogenic fungus belonging to Entomopthoromycota

BACKGROUND

Conidiobolus obscurus is a widespread fungal entomopathogen with aphid biocontrol potential. This study focused on a de novo transcriptomic analysis of C. obscurus.

RESULTS

A number of pathogenicity-associated factors were annotated for the first time from the assembled 17 231 fungal unigenes, including those encoding subtilisin-like proteolytic enzymes (Pr1s), trypsin-like proteases, metalloproteases, carboxypeptidases and endochitinases. Many of these genes were transcriptionally up-regulated by at least twofold in mycotized cadavers compared with the in vitro fungal cultures. The resultant transcriptomic database was validated by the transcript levels of three selected pathogenicity-related genes quantified from different in vivo and in vitro material in real-time quantitative polymerase chain reaction (PCR). The involvement of multiple Pr1 proteases in the first stage of fungal infection was also suggested. Interestingly, a unique cytolytic (Cyt)-like δ-endotoxin gene was highly expressed in both mycotized cadavers and fungal cultures, and was more or less distinct from its homologues in bacteria and other fungi.

CONCLUSION

Our findings provide the first global insight into various pathogenicity-related genes in this obligate aphid pathogen and may help to develop novel biocontrol strategy against aphid pests. © 2018 Society of Chemical Industry.

Fungal Genomes and Insights into the Evolution of the Kingdom

The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

Comparative genomic analyses reveal the features for adaptation to nematodes in fungi

Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.

Use of electrical penetration graphs (EPG) and quantitative PCR to evaluate the relationship between feeding behaviour and Pandora neoaphidis infection levels in green peach aphid, Myzus persicae

A real-time qPCR method was developed, validated, and used to quantity the fungal pathogen, P. neoaphidis, within aphids at different times during infection; colonization rate fitted the Gompertz model well (R² = 0.9356). Feeding behaviour of P. neoaphidis-infected and uninfected M. persicae were investigated, for the first time, using DC-electrical penetration graphs (DC-EPG) that characterized the waveforms made during different aphid stylet probing periods corresponding to epidermis penetration, salivation and ingestion. In the 6 h following the 12-h incubation period (to achieve infection), there were significant differences in the number of events of Np (non-probing) and C (stylet pathway) between infected and uninfected aphids. However, the difference between total duration of Np and C were not significantly different between infected and uninfected aphids. There were no significant differences in the number of events or total duration of E1 (phloem salivation) or E2 (phloem ingestion) between infected and uninfected aphids. There were significant differences in mean number of events and total duration of the pd waveform (intracellular punctures) in infected and uninfected aphids. In the 16 h prior to death, the same differences in behaviour were observed but they were even more obvious. Furthermore, the total duration time of E2 was significantly greater in uninfected aphids than infected aphids, a change that had not been observed in the first 6 h observation period. In conclusion, qPCR quantification demonstrated 'molecular' colonization levels throughout infection, and EPG data analysis during the two periods (during early infection and then during late infection just prior to death) demonstrated the actual physical effects of fungal infection on feeding behaviour of M. persicae; this has the potential to decrease the aphid's capacity of transmission and dispersal. These studies increase our understanding of the interaction between P. neoaphidis and its host aphid.

Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants

Some microbes possess the ability to adaptively manipulate host behavior. To better understand how such microbial parasites control animal behavior, we examine the cell-level interactions between the species-specific fungal parasite Ophiocordyceps unilateralis sensu lato and its carpenter ant host (Camponotus castaneus) at a crucial moment in the parasite's lifecycle: when the manipulated host fixes itself permanently to a substrate by its mandibles. The fungus is known to secrete tissue-specific metabolites and cause changes in host gene expression as well as atrophy in the mandible muscles of its ant host, but it is unknown how the fungus coordinates these effects to manipulate its host's behavior. In this study, we combine techniques in serial block-face scanning-electron microscopy and deep-learning-based image segmentation algorithms to visualize the distribution, abundance, and interactions of this fungus inside the body of its manipulated host. Fungal cells were found throughout the host body but not in the brain, implying that behavioral control of the animal body by this microbe occurs peripherally. Additionally, fungal cells invaded host muscle fibers and joined together to form networks that encircled the muscles. These networks may represent a collective foraging behavior of this parasite, which may in turn facilitate host manipulation.

Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins

Much can be gained from revealing the mechanisms fungal entomopathogens employ. Especially intriguing are fungal parasites that manipulate insect behavior because, presumably, they secrete a wealth of bioactive compounds. To gain more insight into their strategies, we compared the genomes of five ant-infecting Ophiocordyceps species from three species complexes. These species were collected across three continents, from five different ant species in which they induce different levels of manipulation. A considerable number of (small) secreted and pathogenicity-related proteins were only found in these ant-manipulating Ophiocordyceps species, and not in other ascomycetes. However, few of those proteins were conserved among them, suggesting that several different methods of behavior modification have evolved. This is further supported by a relatively fast evolution of previously reported candidate manipulation genes associated with biting behavior. Moreover, secondary metabolite clusters, activated during biting behavior, appeared conserved within a species complex, but not beyond. The independent co-evolution between these manipulating parasites and their respective hosts might thus have led to rather diverse strategies to alter behavior. Our data indicate that specialized, secreted enterotoxins may play a major role in one of these strategies.

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

Fusarium wilt is one of the major biotic stresses reducing chickpea productivity. The use of wilt-resistant cultivars is the most appropriate means to combat the disease and secure productivity. As a step towards understanding the molecular basis of wilt resistance in chickpea, we investigated the transcriptomes of wilt-susceptible and wilt-resistant cultivars under both Fusarium oxysporum f.sp. ciceri (Foc) challenged and unchallenged conditions. Transcriptome profiling using LongSAGE provided a valuable insight into the molecular interactions between chickpea and Foc, which revealed several known as well as novel genes with differential or unique expression patterns in chickpea contributing to lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense, etc. Similarly, several Foc genes characteristically required for survival and growth of the pathogen were expressed only in the susceptible cultivar with null expression of most of these genes in the resistant cultivar. This study provides a rich resource for functional characterization of the genes involved in resistance mechanism and their use in breeding for sustainable wilt-resistance. Additionally, it provides pathogen targets facilitating the development of novel control strategies.

The Insect Pathogens

Fungi are the most common disease-causing agents of insects; aside from playing a crucial role in natural ecosystems, insect-killing fungi are being used as alternatives to chemical insecticides and as resources for biotechnology and pharmaceuticals. Some common experimentally tractable genera, such as Metarhizium spp., exemplify genetic diversity and dispersal because they contain numerous intraspecific variants with distinct environmental and insect host ranges. The availability of tools for molecular genetics and multiple sequenced genomes has made these fungi ideal experimental models for answering basic questions on the genetic and genomic processes behind adaptive phenotypes. For example, comparative genomics of entomopathogenic fungi has shown they exhibit diverse reproductive modes that often determine rates and patterns of genome evolution and are linked as cause or effect with pathogenic strategies. Fungal-insect pathogens represent lifestyle adaptations that evolved numerous times, and there are significant differences in host range and pathogenic strategies between the major groups. However, typically, spores landing on the cuticle produce appressoria and infection pegs that breach the cuticle using mechanical pressure and cuticle-degrading enzymes. Once inside the insect body cavity, fungal pathogens face a potent and comprehensively studied immune defense by which the host attempts to eliminate or reduce an infection. The Fungal Kingdom stands alone in the range, extent, and complexity of their manipulation of arthropod behavior. In part, this is because most only sporulate on cadavers, so they must ensure the dying host positions itself to allow efficient transmission.

Pandora formicae, a specialist ant pathogenic fungus: New insights into biology and taxonomy

Among fungi from the order Entomophthorales (Entomophthoromycota), there are many specialized, obligatory insect-killing pathogens. Pandora formicae (Humber & Bałazy) Humber is a rare example of an entomophthoralean fungus adapted to exclusively infect social insects: wood ants from the genus Formica. There is limited information available on P. formicae; many important aspects of this host-pathogen system remain hitherto unknown, and the taxonomical status of the fungus is unclear. Our study fills out some main gaps in the life history of P. formicae, such as seasonal prevalence and overwintering strategy. Field studies of infection prevalence show a disease peak in late summer and early autumn. Typical thick-walled entomophthoralean resting spores of P. formicae are documented and described for the first time. The proportion of cadavers with resting spores increased from late summer throughout autumn, suggesting that these spores are the main overwintering fungal structures. In addition, the phylogenetic status of Pandora formicae is outlined. Finally, we review the available taxonomical literature and conclude that the name P. formicae should be used rather than the name P. myrmecophaga for ant-infecting fungi displaying described morphological features.

Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

Obligate parasites are under strong selection to increase exploitation of their host to survive while evading detection by host immune defences. This has often led to elaborate pathogen adaptations and extreme host specificity. Specialization on one host, however, often incurs a trade-off influencing the capacity to infect alternate hosts. Here, we investigate host adaptation in two morphologically indistinguishable and closely related obligate specialist insect-pathogenic fungi from the phylum Entomophthoromycota, Entomophthora muscae sensu stricto and E. muscae sensu lato, pathogens of houseflies (Musca domestica) and cabbage flies (Delia radicum), respectively. We compared single nucleotide polymorphisms within and between these two E. muscae species using 12 RNA-seq transcriptomes from five biological samples. All five isolates contained intra-isolate polymorphisms that segregate in 50:50 ratios, indicative of genetic duplication events or functional diploidy. Comparative analysis of dN/dS ratios between the multinucleate E. muscae s.str. and E. muscae s.l. revealed molecular signatures of positive selection in transcripts related to utilization of host lipids and the potential secretion of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar utilization was probably important for the evolutionary transition to obligate insect pathogenicity in E. muscae. These results support the hypothesis that genetically based host specialization in specialist pathogens evolves in response to the challenge of using resources and dealing with the immune system of different hosts.

New insights on the phylogeny and biology of the fungal ant pathogen Aegeritella

This paper evaluates the phylogenetic position of the ectoparasitic fungus Aegeritella tuberculata Bałazy & Wiśniewski, and broadly discusses its presence on ants in southern Poland. Field work was conducted in the Silesian Beskid Mountains in 2011-2013. The fungus was found on four species of ants: Lasius niger L., Lasius brunneus Latr., Formica lemani Bondr. and Formica fusca L. The first three species have not been noted previously in the literature as hosts of Aegeritella fungi. The infection rate ranged from 1% for Formica lemani to 21% for L. brunneus. Molecular analysis based on ITS and SSU rDNA sequences revealed close relationships between Aegeritella and Trichosporon isolates. We conclude that the genus Aegeritella-inceratae sedis until now, should be placed within the fungal group Basidiomycota, Tremellomycetes, Tremellomycetidae, Tremellales, Trichosporonaceae.