The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

Background

Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating closely related species, selection of virulent microbial isolates which are amenable to industrial scale production and formulation and through the reduction of phenotypic variability. The genome of Metarhizium isolate ARSEF23 was recently published as a model for M. anisopliae, however phylogenetic analysis has since re-classified this isolate as M. robertsii. We present a new annotated genome sequence of M. anisopliae (isolate Ma69) and whole genome comparison to M. robertsii (ARSEF23) and M. acridum (CQMa 102).

Results

Whole genome analysis of M. anisopliae indicates significant macrosynteny with M. robertsii but with some large genomic inversions. In comparison to M. acridum, the genome of M. anisopliae shares lower sequence homology. While alignments overall are co-linear, the genome of M. acridum is not contiguous enough to conclusively observe macrosynteny. Mating type gene analysis revealed both MAT1-1 and MAT1-2 genes present in M. anisopliae suggesting putative homothallism, despite having no known teleomorph, in contrast with the putatively heterothallic M. acridum isolate CQMa 102 (MAT1-2) and M. robertsii isolate ARSEF23 (altered MAT1-1). Repetitive DNA and RIP analysis revealed M. acridum to have twice the repetitive content of the other two species and M. anisopliae to be five times more RIP affected than M. robertsii. We also present an initial bioinformatic survey of candidate pathogenicity genes in M. anisopliae.

Conclusions

The annotated genome of M. anisopliae is an important resource for the identification of virulence genes specific to M. anisopliae and development of species- and strain- specific assays. New insight into the possibility of homothallism and RIP affectedness has important implications for the development of M. anisopliae as a biopesticide as it may indicate the potential for greater inherent diversity in this species than the other species. This could present opportunities to select isolates with unique combinations of pathogenicity factors, or it may point to instability in the species, a negative attribute in a biopesticide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-660) contains supplementary material, which is available to authorized users.     

Metarhizium anisopliae Pathogenesis of Mosquito Larvae: A Verdict of Accidental Death

Metarhizium anisopliae, a fungal pathogen of terrestrial arthropods, kills the aquatic larvae of Aedes aegypti, the vector of dengue and yellow fever. The fungus kills without adhering to the host cuticle. Ingested conidia also fail to germinate and are expelled in fecal pellets. This study investigates the mechanism by which this fungus adapted to terrestrial hosts kills aquatic mosquito larvae. Genes associated with the M. anisopliae early pathogenic response (proteinases Pr1 and Pr2, and adhesins, Mad1 and Mad2) are upregulated in the presence of larvae, but the established infection process observed in terrestrial hosts does not progress and insecticidal destruxins were not detected. Protease inhibitors reduce larval mortality indicating the importance of proteases in the host interaction. The Ae. aegypti immune response to M. anisopliae appears limited, whilst the oxidative stress response gene encoding for thiol peroxidase is upregulated. Cecropin and Hsp70 genes are downregulated as larval death occurs, and insect mortality appears to be linked to autolysis through caspase activity regulated by Hsp70 and inhibited, in infected larvae, by protease inhibitors. Evidence is presented that a traditional host-pathogen response does not occur as the species have not evolved to interact. M. anisopliae retains pre-formed pathogenic determinants which mediate host mortality, but unlike true aquatic fungal pathogens, does not recognise and colonise the larval host.     

Genome‐assisted development of nuclear intergenic sequence markers for entomopathogenic fungi of the Metarhizium anisopliae species complex

Entomopathogenic fungi in the genus Metarhizium are useful for biological control programmes against economically important arthropod pests worldwide. However, understanding the true diversity and ecology of these organisms is hampered by convergent morphologies between species. The application of molecular techniques has enabled greater resolution of species than allowed by morphology alone. In particular, the commonly used biocontrol agent M. anisopliae was found to be a species complex composed of nine species. This prior work was conducted with commonly used markers in fungal phylogenetics (BTUB, RPB1, RPB2 and TEF), which likely under‐represent diversity in the M. anisopliae complex. Using sequence data from nuclear genomes of M. acridum and M. robertsii we identified regions of conserved gene synteny and developed primers to amplify intergenic regions of seven loci. Using ex‐type and authenticated tissue specimens for species in the M. anisopliae complex, we demonstrate that sequence data derived from intergenic loci is more variable and phylogenetically informative than previously available markers. These new markers will facilitate investigations at or below the species level for the M. anisopliae complex. The method of marker development employed here should be extendable to any group with sufficiently divergent genome data available.     

Genetic diversity of the Metarhizium anisopliae complex in Colima,Mexico, using microsatellites

Metarhizium anisopliae is a complex of cryptic species with wide geographical distribution and versatile lifestyles. In this study, 45 isolates of the Metarhizium genus harbored in the “Colección de Hongos Entomopatógenos” of the “Centro Nacional de Referencia de Control Biológico” from different substrates, insect-host, and localities from Colima, Mexico, were phylogenetically identified using the 5′end of translation elongation factor 1-α (5′TEF) and intergenic nuclear region MzFG543igs. Seven species were recognized, M. acridum (n = 26), M. pemphigi (n = 1), and within the PARB and MGT clades: M. anisopliae (N = 7; sensu stricto: n = 2; sensu lato: n = 5), M. brunneum (n = 2), M. guizhouense (n = 2), M. pingshaense (n = 2), and M. robertsii (n = 5). Twenty-nine SSR markers were developed for M. acridum; according to the analysis of 12 polymorphic SSR loci, M. acridum showed low genetic diversity, revealing five genotypes with a dominant one (n = 21). Based on the analysis of 13 specific SSR loci, 14 genotypes were identified within the PARB and MGT clades. This study contributes to generating valuable information about the community structure and genotypic diversity of Metharhizum species in the state of Colima, Mexico.     

Cloning of the subtilisin Pr1A gene from a strain of locust specific fungus, <Emphasis Type="Italic">Metarhizium anisopliae,</Emphasis> and functional expression of the protein in <Emphasis Type="Italic">Pichia pastoris</Emphasis>

The subtilisin-like protease Pr1A plays a role in insect cuticle breach and has been used in the development of advanced engineered biopesticides. We have identified and cloned the Pr1A gene from a locust specific Metarhizium anisopliae strain, CQMa102. The cDNA of Pr1A and its deduced protein sequence were deposited in GenBank (accession numbers EF627449 and ABR20899, respectively). Sequence analysis reveals that Pr1A belongs to the subtilisin-like serine protease family. Analysis of homologous species shows that the protein exhibits 99% identity with the subtilisin Pr1A from M. anisopliae var. acridum strain FI-985. The CQMa102 Pr1A protein was expressed in Pichia pastoris to verify its protease activity. Our results show that the Pr1A gene cloned from M. anisopliae strain CQMa102 has cuticle-degrading function and is a potential virulence factor for the development of engineered biopesticides.     

The inhibitory effect of the fungal toxin, destruxin A, on behavioural fever in the desert locust

During an infection locusts behaviourally fever by seeking out higher environmental temperatures. This behaviour places the pathogen at sub-optimal growth temperatures while improving the efficiency of the immune system, thereby prolonging the lifespan of the host. It is therefore in the interest of the pathogen to either adapt to fever-like temperatures or to evolve mechanisms to interfere with, or inhibit fever. We investigated the behavioural fever response of desert locusts to two fungal pathogens. A prolonged fever was observed in locusts infected with Metarhizium acridum. However, fever was comparatively short-lived during infection with Metarhizium robertsii. In both cases restriction of thermoregulation reduced lifespan. Destruxin A (dtx A) produced by M. robertsii, but not M. acridum has previously been associated with the inhibition of the insect immune system. Injection of dtx A during infection with the fever-causing M. acridum inhibited fever and was particularly effective when administered early on in infection. Furthermore, locusts injected with dtx A were more susceptible to M. acridum infection. Therefore engineering M. acridum isolates currently used for locust biocontrol, to express dtx A may improve efficiency of control by interfering with fever.     

Susceptibility of Metarhizium spp. and other entomopathogenic fungi to dodine-based selective media

The fungicide dodine has been widely used in selective media to isolate entomopathogenic fungi (EF) from contaminating microorganisms, primarily bacteria and non-entomopathogenic fungi. In order to isolate the fungus Metarhizium acridum from soil for grasshopper and Mormon cricket control in the western USA, the susceptibility of M. acridum was compared with two Metarhizium spp. and other EF species. The isolates were inoculated onto mycological media with concentrations of dodine ranging from 0.0001 to 0.03% active ingredient (A.I.). In addition, susceptibilities of five Metarhizium spp. isolates to two sources of dodine, Syllit® commercial fungicide (65% A.I.) and Sigma® reagent grade (99% A.I.), were compared using Czapek agar medium. Responses to the two dodine sources were virtually identical. Accordingly, subsequent experiments used the less expensive Syllit dodine. Three media [Czapek, potato dextrose agar plus yeast extract (PDAY) and oatmeal agar] were evaluated for appropriateness as the base in selective media. Germination of all three of the M. acridum isolates tested was almost completely inhibited by dodine concentrations of 0.002% A.I. in Czapek or 0.006% A.I. in PDAY. On the other hand, M. robertsii and M. anisopliae isolates were considerably more tolerant, with germination not being inhibited until 0.010% A.I. in Czapek or 0.030% A.I. in PDAY. The higher vulnerability of the isolates to low concentrations of dodine in Czapek medium suggests that this medium would be less effective than PDAY in a selective medium. Oatmeal agar greatly improved fungal growth, but the levels of inhibition were lower. Therefore, PDAY was selected as the best selective basal medium. The lowest concentration that inhibited a common soil-inhabiting fungus, Aspergillus nidulans, was 0.001% A.I. Dodine tolerances were highest with M. robertsii, M. anisopliae, and Beauveria bassiana, followed by Isaria fumosorosea and Lecanicillium spp. The least tolerant EF isolates were M. acridum.     

Species of the Metarhizium anisopliae complex with diverse ecological niches display different susceptibilities to antifungal agents

Species of the Metarhizium anisopliae complex are globally ubiquitous soil-inhabiting and predominantly insect-pathogenic fungi. The Metarhizium genus contains species ranging from specialists, such as Metarhizium acridum that only infects acridids, to generalists, such as M. anisopliae, Metarhizium brunneum, and Metarhizium robertsii that infect a broad range of insects and can also colonize plant roots. There is little information available about the susceptibility of Metarhizium species to clinical and non-clinical antifungal agents. We determined the susceptibility of 16 isolates comprising four Metarhizium species with different ecological niches to seven clinical (amphotericin B, ciclopirox olamine, fluconazole, griseofulvin, itraconazole, tebinafine, and voriconazole) and one non-clinical (benomyl) antifungal agents. All isolates of the specialist M. acridum were clearly more susceptible to most antifungals than the isolates of the generalists M. anisopliae sensu lato, M. brunneum, and M. robertsii. All isolates of M. anisopliae, M. brunneum, and M. robertsii were resistant to fluconazole and some were also resistant to amphotericin B. The marked differences in susceptibility between the specialist M. acridum and the generalist Metarhizium species suggest that this characteristic is associated with their different ecological niches, and may assist in devising rational antifungal treatments for the rare cases of mycoses caused by Metarhizium species.     

Discovery of a North American genetic variant of the entomopathogenic fungus <Emphasis Type="Italic">Metarhizium anisopliae</Emphasis> var. <Emphasis Type="Italic">anisopliae</Emphasis> pathogenic to grasshoppers

A genetic variant of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae, isolated from a soil in Alberta, Canada, from a location with a history of severe grasshopper infestations, was evaluated for pathogenicity in bioassays of living grasshoppers. Mortality in treated individuals drawn from a laboratory colony was 99% (LT₅₀ = 6.7 days, LT₉₀ = 9.6 days) at 12 days post-inoculation compared to 100% (LT₅₀ = 4.1 days, LT₉₀ = 5.8 days) mortality at 8 days in insects exposed to a commercial isolate of M. anisopliae var. acridum (IMI 330189). Experimental infection of field-collected grasshoppers under laboratory conditions with the native isolate of M. anisopliae var. anisopliae resulted in 100% (LT₅₀ = 4.4 days, LT₉₀ = 5.4 days) mortality attained within 7 days compared to 100% (LT₅₀ = 4.7 days, LT₉₀ = 6.3 days) mortality in 9 days in insects treated with M. anisopliae var. acridum. Amplification of fungal genomic DNA from the indigenous isolate with primers for the specific detection of M. anisopliae var. anisopliae produced a product almost 300 bp larger than expected based on previously known isolates. This is the first demonstration of a highly virulent, indigenous non-chemical control agent of grasshoppers in North America. GenBank Accession Nos. DQ342236, DQ342237.     

Mapmi gene contributes to stress tolerance and virulence of the entomopathogenic fungus, Metarhizium acridum

Phosphomannose isomerase (PMI) catalyzes the reversible interconversion of fructose 6-phosphate (Fru-6-P) and mannose 6-phosphate (Man-6-P), providing a link between glycolysis and the mannose metabolic pathway. In this study, we identified pmi gene (Mapmi) from the entomopathogenic fungus, Metarhizium acridum, and analyzed its functions using RNA interference (RNAi). Amending the growth medium with cell stress chemicals significantly reduced growth, conidial production and percent germination in Mapmi-RNAi mutant strain, compared to the wild-type strain. Growth of RNAi mutant was lower than the wild type strain with glucose or fructose as sole carbon source. RNAi mutant exhibited a normal growth phenotype with mannose at low concentrations, while trace or high concentration of mannose was more negatively impacted the growth of RNAi mutant than the wild type strain. Infection with Mapmi-RNAi mutant against Locusta migratoria manilensis (Meyen) led to a significantly reduced virulence compared to infection with the wild-type strain. These results suggest that Mapmi plays essential roles in stress tolerance and pathogenicity of M. acridum.     

Comparative gene expression and genomics reflect geographical divergence in the plant symbiotic and entomopathogenic fungal genus Metarhizium

Several species within the fungal genus Metarhizium can both infect insects and colonize plant roots. In Brazil, a specific subgroup within Metarhizium anisopliae s.str. named “subclade Mani 2” is frequently observed infecting above-ground insects, whereas sympatric M. robertsii and M. brunneum predominantly occur in the soil environment. Genotypic variability within the genus may be linked to adaptations to these different habitats. We present a comparative analysis of the complete genomes and the adhesin genes Mad1 and Mad2 of 14 Metarhizium isolates representing M. anisopliae Mani 2 (n = 6), M. robertsii (n = 5) and M. brunneum (n = 3). In addition, the relative gene expression of six selected target genes was compared in root exudate solution and insect cuticle suspension. We hypothesized that M. anisopliae Mani 2 is adapted to insect-pathogenicity in the above-ground environment, reflected by higher relative expression of pathogenicity-related genes. In contrast, M. robertsii and M. brunneum are adapted to the soil environment, hence hypothesized to have a higher expression of genes related to plant associations. Phylogenomic and adhesin phylogenetic trees revealed species differences but also intraspecific variability associated with the geographic origin of isolates. Differences in relative gene expression were observed, with one pathogenicity-related gene (Pr1) being higher expressed in M. anisopliae. The insect adhesion Mad1 gene was more conserved than the plant adhesion Mad2 and similarly expressed in exudate solution, while Mad2 was highly expressed by all Brazilian isolates in both exudate and cuticle conditions. The variabilities observed correlated with different habitats and lifestyles, demonstrating the importance of selecting a diverse collection of isolates in genomic and gene expression studies.     

Antifungal activity of the termite alkaloid norharmane against the mycelial growth of Metarhizium anisopliae and Aspergillus nomius

Antifungal activity of norharmane, a β-carboline alkaloid found in termites (Isoptera, Rhinotermitidae) was tested against two entomopathogenic fungi, Metarhizium anisopliae and Aspergillus nomius. It was determined that, at physiological concentration (10 μg ml⁻¹), norharmane had no significant effect on A. nomius mycelial growth rate but reduced M. anisopliae growth rate by 11.9%. Contrary to previous findings, we suggest that norharmane has a limited role in disease resistance against fungal pathogens in individual subterranean termites, and we discuss the potential role of this chemical at a colony level.     

Molecular detection of the airborne entomopathogen fungus Metarhizium acridum using specific oligonucleotides

We describe a technique to detect the presence of airborne conidia from the fungus M. acridum (formerly Metarhizium anisopliae var. acridum) (Hypocreales: Clavicipitaceae) with great accuracy. Airborne conidia were collected using Hirst-type spore traps. DNA extractions were optimized to achieve the best possible recovery. DNA was examined using polymerase chain reaction (PCR) with specific oligonucleotides to enable the detection of a single conidium. Experiments using a mini-wind tunnel were conducted to validate the method. Subsequently, this technique was applied to an agricultural region of Mexico, where M. acridum was sprayed to control the grasshopper, Sphenarium purpurascens, population (Orthoptera: Pyrgomorphidae). M. acridum conidia were detected 2 days after spraying in San Mateo Coatepec (Puebla, site of grasshopper study).     

Efficacy of genetically transformed Metarhizium anisopliae against Spodoptera litura and Aphis craccivora

To increase the insecticidal potency of the entomopathogen, Metarhizium anisopliae (Metsch.) Sorok, the fungus was genetically modified with scorpion neuro β-toxin LqqIT1a and two different insect specific heterologous toxic proteins viz., Cry1a and GNA. LqqIT1 is an anti-insect neurotoxin derived from yellow scorpion, Leiurus quinquestriatus quinquestriatus (Ehren.). The present study reports the bio-efficacy of genetically modified fungus, M. anisopliae, in which scorpion neurotoxin gene ‘LqqIT1′ is stacked in its genome, for improved efficacy against the tobacco caterpillar, Spodoptera litura (Fab.) and Aphis craccivora (Koch). All the transformed clones of M. anisopliae were found potent against S. litura and A. craccivora under laboratory conditions. The virulent clones viz., Ma-2(2), Ma-2(7) and MaGKS-14 caused 40 to 90 per cent mortality at fourth day of treatment. Compared to untransformed parent strain, Ma-C, the median lethal time of transformed clones Ma-2(2), Ma-2(7) and MaGKS-14 got reduced by 2, 3 and 3-folds, respectively. No significant differences were noted with respect to percent mortality of transformed clone, MaGKS-13 in comparison to untransformed strain Ma-C. The results indicated that the incorporation of LqqIT1 toxin gene enhanced the potency of strain Ma-C, against immature stages of S. litura and A. craccivora by shortening the median lethal time without affecting conidial development. Therefore, LqqIT1 scorpion toxin gene showed the potential to improve efficacy of M. anisopliae against lepidopteran and hemipteran insects.     

The mitochondrial genome contribution to the phylogeny and identification of Metarhizium species and strains

The genus Metarhizium is composed of entomopathogenic fungal biological control agents (BCAs) used for invertebrate pest control. The phylogenetic relationships of species within this genus are still under scrutiny as several cryptic species can be found. In this work, the mitochondrial (mt) genome of Metarhizium brunneum ARSEF 4556 was fully sequenced and a comparative genome analysis was conducted with 7 other available mt genomes, belonging to 5 Metarhizium species: M. anisopliae, M. brunneum, M. robertsii, M. guizhouense and M. majus. Results showed that Metarhizium demonstrates greater conserved stability than other fungal mt genomes. Furthermore, this analysis located 7 diverse regions in both intergenic domains and gene fragments which were ideal for species/strain discrimination. The sequencing of these regions revealed several SNPs among 38 strains tested, 11 of which were uncharacterized. Single gene phylogenies presented variable results which may be used further for intra-species discrimination. Phylogenetic trees based on the concatenation of mt domains and the nuclear ITS1-5.8S-ITS2 region showed discrimination of the species studied and allowed the identification of uncharacterized strains. These were mostly placed within species M. anisopliae and M. brunneum. Five strains clustered together in a clade related to M. brunneum, suggesting that they comprise a cryptic species.     

Genetic diversity of Metarhizium anisopliae var. anisopliae in southwestern British Columbia

The abundance and genetic diversity of the entomopathogenic fungus, Metarhizium anisopliae var. anisopliae, in southwestern British Columbia (BC) and southern Alberta was examined. The fungus was found to be widespread in soil throughout southwestern BC, and was recovered from 56% of 85 sample sites. In contrast to southwestern BC, no M. anisopliae isolates were recovered in southern Alberta. An automated fluorescent amplified fragment length polymorphism (AFLP) method was used to examine genetic diversity. In excess of 200 isolates were characterized. The method identified 211 polymorphic amplicons, ranging in size from ≈92 to 400 base pairs, and it was found to be reproducible with a resolution limit of 86.2% similarity. The AFLP method distinguished Metarhizium from other entomopathogenic fungal genera, and demonstrated considerable genetic diversity (25 genotypes) among the reference strains of M. anisopliae isolates examined (i.e. recovered from various substrates and geographical locations). Although 13 genotypes of M. anisopliae var. anisopliae were recovered from southwestern BC soils, the vast majority of isolates (91%) belonged to one of two closely-related genotypes. Furthermore, these two genotypes predominated in urban, agricultural and forest soils. The reasons for the limited diversity of M. anisopliae var. anisopliae in southwestern BC are uncertain. However, findings of this study are consistent with island biogeography theory, and have significant implications for the development of this fungus for microbial control of pest insects.     

Field observations of the effects of fenitrothion and Metarhizium anisopliae var. acridum on non-target ground dwelling arthropods in the Sahel

The effect of the chemical insecticide, fenitrothion, and a mycoinsecticide based on Metarhizium anisopliae var. acridum on the activity of non-target epigeal arthropod scavengers was investigated in areas of open savannah in southeast Niger Republic, West Africa. Both insecticides were applied as full cover sprays to unreplicated 800 ha plots to assess their season-long control of Sahelian grasshoppers. Compared with control plots, fenitrothion caused an immediate but temporary reduction in grasshopper numbers, whereas M. anisopliae var. acridum provided delayed but prolonged control. Scavenging rates of pyrethroid-killed grasshoppers placed along transects in unsprayed plots and those treated with fenitrothion and M. anisopliae var. acridum at various intervals after spraying were assessed. In the fenitrothion plot, an immediate reduction in scavenging activity occurred that was still apparent after 40 days at the plot center, although recovery at the plot edges was more rapid. By contrast scavenging rates remained high over equivalent areas in the M. anisopliae var. acridum and two untreated plots. Concurrent to the scavenging study, counts of grasshopper cadavers resulting from the spray treatments were conducted. These counts revealed that the density of grasshopper cadavers remained low throughout the M. anisopliae var. acridum plot and explained <1% of the reduction in live grasshoppers resulting from treatment, compared with >20% in the fenitrothion plot. This shortfall in grasshopper cadavers resulting from the spray treatment in the M. anisopliae var. acridum plot was unexpected because in a monitoring study, fungus-killed (unlike pyrethroid-killed) grasshoppers were unattractive to scavengers and readily persisted in this plot, and thus should have become apparent. Given we did not observe significant grasshopper dispersal, the scarcity of cadavers generated in the M. anisopliae var. acridum plot, together with unquantified visual observations, suggests that predation of infected but living grasshoppers was high. Our data provide circumstantial evidence that the different effects of chemical and biological grasshopper control on grasshopper natural enemies may influence the efficacy of large-scale treatments.