Identification of group-I introns in the 28s rDNA of the entomopathogenic fungus Beauveria brongniartii

Metarhizium caribense sp. nov., a Novel Species of Entomopathogenic Metarhizium Fungi Associated with Weevils Impairing Coffee, Sugar Cane and Sweet Potato Cultivation

(1) Background: Insect pathogenic fungi of the genus Metarhizium are under study and in application as highly solicited, more eco-system friendly substitutes for chemical insecticides in many countries and in different agricultural contexts. In Cuba and Florida, Metarhizium strains have previously been isolated from economically important coffee and sugar cane pests. (2) Methods: Unambiguous species delineation within the Metarhizium anisopliae species complex is methodologically challenging. Recently, a species-discriminating PCR approach has been developed based on ribosomal intergenic spacer (rIGS) sequences that covered the prominent four "PARB" species within the complex. This approach is combined here with further genetic markers and is extended to a further species. (3) Results: Metarhizium isolates from Cuba, found to be more naturally associated with the coffee berry borer, Hypothenemus hampei, were morphologically, microscopically and molecular taxonomically characterized. Multilocus sequence analysis based on 5TEF, MzIGS3 and rIGS markers delineated these weevil-associated strains from all previously established Metarhizium species. (4) Conclusions: The isolates under study represent a new fungal taxon proposed to be designated Metarhizium caribense. The rIGS-based species-discriminating diagnostic PCR is a suitable tool for the identification of new Metarhizium species and can be productively combined to approaches using further genetic markers.

High Virulence of Mexican Entomopathogenic Fungi Against Fall Armyworm, (Lepidoptera: Noctuidae)

Fourteen fungal entomopathogenic strains were isolated from soil samples and infected field-collected fall armyworm larvae, in Guanajuato, Mexico. Isolates were identified by morphology and internal transcribed spacers sequencing. Isolates Ma22, Ma41, and Mr8 showed 99% identity with reference strains (RS) of Metarhizium anisopliae. Isolates Bb9, Bb19, Bb21, Bb40, Bb27, Bb23, and Bb39 showed identity between 99 and 100% with RS of Beauveria bassiana. Isolates Nr1, Nr2, Nr3, and Nr4 showed identity between 98 and 100% with RS of Nomuraea rileyi. Qualitative selection used one concentration (1 × 108 conidia/ml) on fall armyworm eggs and neonate larvae. Strains Ma22, Ma41, and Mr8 showed 100%, and strains Bb39, Bb23, Bb9, Bb40, Bb19, and Bb21 showed 92, 89.2, 87.6, 82.8, 58, and 38% egg mortality, respectively. Bioassays on neonate larvae showed 100% mortality with strains Ma22, Ma41, Mr8, and Bb9. Strains Bb39, Bb19, Bb27, Bb23, Bb21, and Bb40 showed 74, 60, 54, 53, 28, and 19% mortality, respectively. Bioassay estimated LC50s for strains Ma41 at 7.4 × 104, Mr8 at 8.9 × 104, and Ma22 at 10 × 104 conidia/ml, on fall armyworm eggs. LC50s on neonate larvae were estimated at 2.8 × 105, 16 × 105, 26 × 105, and 36 × 105 conidia/ml for strains Ma41, Bb9, Ma22, and Mr8, respectively. Virulence genes mad1 and mad2 were found in Mr8, Ma22, and Ma41, whereas the gen gmact was found only in the strain Ma22. Genes hyd1 and hyd2 were identified in Bb9, Bb19, Bb21, and Bb27. No correlation was observed between the virulence gene detection and the estimated LC50s. Strain Ma41 showed the highest potential to be developed as a bioinsecticide.

Rapid discrimination of Isaria javanica and Isaria poprawskii from Isaria spp. using high resolution DNA melting assays

The current study evaluates the potential of using high resolution DNA melting assays to discriminate species in the genus Isaria. The study utilizes a previously identified 103 base pair PCR amplicon, which was reported to be selective for Isaria fumosorosea. Our study finds the amplicon selective for Isaria javanica and Isaria poprawskii when assayed against all members of the genus. In addition, the high resolution melting profile of this amplicon can be used to discriminate between I. javanica, I. poprawskii and a 1:1 mixture of the two species. The practical application of this technique was confirmed using a bioassay on whitefly nymphs (Bemisia tabaci biotype B) inoculated with I. javanica, I. poprawskii or a 1:1 mixture of the two species. This assay provides a simple assay to identify these two species of entomopathogenic fungi.

Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution

Background

The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana.

Results

Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found.

Conclusion

Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled.

The molecular diversity of different isolates of Beauveria bassiana (Bals.) Vuill. as assessed using intermicrosatellites (ISSRs)

Inter-microsatellite PCR (ISSR-PCR) markers were used to identify and to examine the genetic diversity of eleven Beauveria bassiana isolates with different geographic origins. The variability and the phylogenetic relationships between the eleven strains were analyzed using 172 ISSR-PCR markers. A high level of polymorphism (near 80%) was found using these molecular markers. Seven different isolates showed exclusive bands, and ISSR primer 873 was able to distinguish between all the strains. The dendrogram obtained with these markers is robust and in agreement with the geographical origins of the strains. All the isolates from the Caribbean region were grouped together in a cluster, while the other isolates grouped in the other cluster. The similarity exhibited between the two clusters was less than 50%. This value of homology shows the high genetic variability detected between the isolates from the Caribbean region and the other isolates. ISSR-PCR markers provide a quick, reliable and highly informative system for DNA fingerprinting, and allowed the identification of the different B. bassiana isolates studied.

Detection of potentially valuable polymorphisms in four group I intron insertion sites at the 3'-end of the LSU rDNA genes in biocontrol isolates of Metarhizium anisopliae

Background

The entomopathogenic anamorphic fungus Metarhizum anisopliae is currently used as a biocontrol agent (BCA) of insects. In the present work, we analyzed the sequence data obtained from group I introns in the large subunit (LSU) of rDNA genes with a view to determining the genetic diversity present in an autochthonous collection of twenty-six M. anisopliae isolates selected as BCAs.

Results

DNA fragments corresponding to the 3'-end of the nuclear LSU rDNA genes of 26 M. anisopliae isolates were amplified by PCR. The amplicon sizes ranged from 0.8 to 3.4-kb. Four intron insertion sites, according to Escherichia coli J01695 numbering, were detected- Ec1921, Ec2066, Ec2449 and Ec2563- after sequencing and analysis of the PCR products. The presence/absence of introns allowed the 26 isolates to be distributed into seven genotypes. Nine of the isolates tested showed no introns, 4 had only one, 3 two, and 10 displayed three introns. The most frequent insertion sites were Ec1921 and Ec2449. Of the 26 isolates, 11 showed insertions at Ec2563 and a 1754-bp sequence was observed in ten of them. The most-parsimonious (MP) tree obtained from parsimony analysis of the introns revealed a main set containing four-groups that corresponded to the four insertion sites.

Conclusion

Four insertion sites of group I introns in the LSU rDNA genes allowed the establishment of seven genotypes among the twenty-six biocontrol isolates of M. anisopliae. Intron insertions at the Ec2563 site were observed for first time in this species.

Molecular investigation on strain genetic relatedness and population structure of Beauveria bassiana

Triplicate molecular methods, i.e. polymerase chain reaction-restriction fragment length polymorphism of the pr1 gene, microsatellite markers and 28S rDNA haplotyping by detecting the presence or absence of group I introns, were used for population study of the entomopathogenic fungus, Beauveria bassiana. The findings showed that the average genetic diversity index of geographical populations was significantly smaller than that of populations derived from insect host orders, indicating that the genetic relatedness of B. bassiana strains was highly associated with geographical locality rather than insect host species. The reproductive style of all the B. bassiana populations was found to be non-clonal. Population structure analysis revealed that the average divergent coefficient among populations of B. bassiana was far below 1 (0.1112), which indicated that there was no significant genetic differentiation between populations, and that the overall genetic diversity mainly resulted from the genetic variations within geographical populations. Statistically, genetic distances between populations were positively correlated with geographical distances, suggesting that geographical separation poses an obstacle to the possibility and frequency of genetic exchanges between populations. On the other hand, gene flow was indirectly established to occur between B. bassiana populations.

Nuclear large subunit rDNA group I intron distribution in a population of Beauveria bassiana strains: phylogenetic implications

Four group I introns, designated Bb1, Bb2, Bb3 and Bb4, were identified in the entomopathogenic hyphomycete Beauveria bassiana. Sequence analyses of these introns verified that they were invariably inserted at specific target sequences after conserved positions Ec2563, Ec2449, Ec2066 and Ec1921 of the large nuclear subunit (LSU) rDNA 3'-end. Secondary structure modelling confirmed that Bb1 and Bb3 belonged to subgroup IE while Bb2 and Bb4 belonged to subgroup IC1. Intron presence, distribution and size-variation were studied in a population of 125 B. bassiana strains using site-specific primers. Nucleotide sequences and secondary structures were compared and showed considerable variations usually at P1, P6 and P9 helices, but concomitantly, high homology between members of the same site-specific group. Intron distribution studies revealed that few (7.2%) strains were intron-less, most contained one (28%), two (48%) or three (16%) introns, while only one strain contained all four introns. Bb4-like introns (Ec1921) were the most abundant (86.4%), whereas the other three introns were evenly represented (ca 30%) in the B. bassiana population. Analysis of intron genotype distribution indicated a tenuous dependence upon geographic origin or insect host species. Phylogenetic analysis of all B. bassiana LSU introns and their close relatives from other entomopathogenic fungi showed a strong correlation between specific insertion sites and intron subgroups, fully supported by corresponding clades, suggesting common ancestry of the site specific LSU introns.

IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: excellent tools for isolate detection and phylogenetic analysis

The complete nuclear rDNA gene complex of Metarhizium anisopliae var. anisopliae isolate ME1 is 8118bp long and contains the 18S, 5.8S, and 28S rRNA genes as well as the ITS and IGS regions. Variation in the ITS of isolates of M. anisopliae var. anisopliae and one each of Metarhizium anisopliae var. acridum, Metarhizium flavoviride var. flavoviride, and Metarhizium flavoviride var. minus, clustered 39 out of 40 of M. anisopliae var. anisopliae isolates in one clade. Nucleotide sequence variation in the IGS among 21 of M. anisopliae var. anisopliae isolates showing IGS length variation sorted them into three strongly supported clades, which were weakly correlated with insect hosts and were not correlated with geographic location. Two group-I introns, Ma-int4 and Ma-int5, were discovered in the 18S and the 3(') end of the 28S, in M. anisopliae var. anisopliae isolates ITALY-12 and IMBST 9601. The insertion sites and sub-group of these introns correlated with their closest relatives, as judged by phylogenetic analysis of intron nucleotide sequence.

Molecular studies of co-formulated strains of the entomopathogenic fungus, Beauveria bassiana

A 28S rDNA intron was used as a molecular marker to distinguish between two single spore strains of Beauveria bassiana, Bb123 and Bb151. When co-formulated and assayed against larvae of Galleria mellonella these strains exhibited no synergistic increase in virulence, rather Bb123 usually dominated. This study shows that the success of any strain to infect Galleria is dependent on the dose and method of inoculation (injection versus immersion). The result of co-formulated strains grown on solid culture also showed that usually one strain dominated, i.e., strain displacement could happen both in vivo and in vitro. The speed by which one strain was displaced following successive sub-culturing on PDA partly depended on the ratio of Bb151 and Bb123. The co-formulated inoculum could widen the window over which parent strains would be active on different water activity media. Co-infection did result in heterokaryosis within the Galleria host. Molecular studies also showed that the heterokaryon was not stable and could revert back to the parent strain.

Identification of group-I introns at three different positions within the 28S rDNA gene of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae

Using a set of heterologous primers designed from the 3'-end of the 28S rRNA gene of Verticillium dahliae the corresponding gene region of 30 isolates of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae was amplified. The polymerase chain reaction products obtained could be classified into four groups varying in size from 1.0 to 2.2 kb. Sequence analyses of representative PCR products revealed the presence of five distinct introns, positioned in three different insertion sites. Fungal isolates 316 and 11 both harbored one intron each (374 and 337 bp in size, respectively), whereas isolate 33 harbored three introns (436, 334, and 412 bp) within the relevant 28S rRNA region. All five introns shared the conserved P, Q, R, S elements and all the other characteristic features of group-I introns in their deduced secondary structure; three (316-int, 33-int1, and 33-int3) belong to subgroup IC1 and two (33-int2 and 11-int) belong to subgroup IE. Further, reverse transcription polymerase chain reactions indicated that all these introns were absent from the mature RNA molecules. The appearance of the five introns at identical positions with those from other organisms belonging to various phyla is discussed.

Molecular analysis of hypervirulent somatic hybrids of the entomopathogenic fungi Beauveria bassiana and Beauveria sulfurescens

Protoplast fusion of diauxotrophic mutants of a Beauveria bassiana entomopathogenic strain (Bb28) and a Beauveria sulfurescens toxinogenic strain (Bs2) produced hybrids which were significantly different from the parents in pathogenicity. Some of the hybrids were hypervirulent and killed insects more quickly than the Bb28 strain, probably because these hybrids had acquired the toxic activity of the Bs2 strain. By using six nuclear genes and a telomeric fingerprint probe, the molecular structures of the hybrids were studied. The results demonstrated the occurrence of parasexual events. Hybrids appeared to be diploid or aneuploid, with portions of the genome being heterozygous. A mitochondrial molecular marker indicated homoplasmy of the hybrids and inheritance of mitochondria from strain Bs2 or Bb28. The pathogenicities and the ploidies of the hybrids remained stable after passage through the host insect, showing that somatic hybridization provides an attractive method for the genetic improvement of biocontrol efficiency in the genus Beauveria.

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

BACKGROUND

Group I introns self-splice via two consecutive trans-esterification reactions in the presence of guanosine cofactor and magnesium ions. Comparative sequence analysis has established that a catalytic core of about 120 nucleotides is conserved in all known group I introns. This core is generally not sufficient for activity, however, and most self-splicing group I introns require non-conserved peripheral elements to stabilize the complete three-dimensional (3D) structure. The physico-chemical properties of group I introns make them excellent systems for unraveling the structural basis of the RNA-RNA interactions responsible for promoting the self-assembly of complex RNAs.

RESULTS

We present phylogenetic and experimental evidence for the existence of three additional tertiary base pairings between hairpin loops within peripheral components of subgroup IC1 and ID introns. Each of these new long range interactions, called P13, P14 and P16, involves a terminal loop located in domain 2. Although domains 2 of IC and ID introns share very strong sequence similarity, their terminal loops interact with domains 5 and 9 (subgroup IC1) and domain 6 (subgroup ID). Based on these tertiary contacts, comparative sequence analysis, and published experimental results such as Fe(II)-EDTA protection patterns, we propose 3D models for two entire group I introns, the subgroup IC1 intron in the large ribosomal precursor RNA of Tetrahymena thermophila and the SdCob.1 subgroup ID intron found in the cytochrome b gene of Saccharomyces douglasii.

CONCLUSIONS

Three-dimensional models of group I introns belonging to four different subgroups are now available. They all emphasize the modular and hierarchical organization of the architecture of group I introns and the widespread use of base-pairings between terminal hairpin loops for stabilizing the folded and active structures of large and complex RNA molecules.

A novel group I intron in Candida dubliniensis is homologous to a Candida albicans intron

In the present study, we determined the sequence of group I self-splicing introns found in the large ribosomal RNA subunit of Candida albicans, Candida stellatoidea and the recently-described species Candida dubliniensis. It was found that both the intron and ribosomal RNA nucleotide sequences are almost perfectly identical between different C. albicans strains as well as between C. albicans and C. stellatoidea strains. Comparisons of ribosomal RNA sequences suggest that local isolates of atypical C. albicans from individuals infected with human immunodeficiency virus can be assigned to the C. dubliniensis species. C. dubliniensis strains also harbor a group I intron in their ribosomal RNA, as observed in about 40% of C. albicans strains and all C. stellatoidea strains. This novel C. dubliniensis group I intron is identical to the C. albicans and C. stellatoidea intron, except for two widely divergent stem-loop regions. Despite these differences, the C. dubliniensis intron possesses self-splicing ability in an in vitro assay. Taken together, these data support the idea that C. albicans and C. stellatoidea should be joined together as variants of the same species while C. dubliniensis is a distinct but closely related microorganism. To our knowledge, the C. albicans and C. dubliniensis introns are the first example of a pair of homologous group I introns differing only by the presence of apparently facultative sequences in some stem-loops suspected to be involved in stabilization of tertiary structure.

Rapid mitochondrial probes for analysis of polymorphisms in Fusarium oxysporum special forms

A method is described for the production of simple mitochondrial DNA probes from filamentous fungi for the partial characterization of mitochondrial DNA without the need for cloning, gradient centrifugation or PCR amplification. A probe (P449) consisting of a 3.38 kb mitochondrial fragment from an isolate of Fusarium oxysporum special form cubense was used to determine RFLPs in restriction digests of total DNA from 28 isolates of F. oxysporum from a variety of hosts and locations. The probe showed mtDNA polymorphisms within and between different special forms.