Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections

Transcriptome studies of Illumina RNA-Seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two-segmented genome characteristics of a comovirus. This comovirus did not induce any visible symptoms in infected A. thaliana plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in A. thaliana plants was confirmed by quantitative reverse transcription polymerase chain reaction, transmission electron microscopy and mechanical inoculation. Arabidopsis latent virus 1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms. A bioinformatics investigation of A. thaliana RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural A. thaliana accessions and in 8.5% of all analyzed SRAs. Arabidopsis latent virus 1 could also be detected in A. thaliana plants collected from the wild. Arabidopsis latent virus 1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected A. thaliana plants. This has probably led to a worldwide distribution in the model plant A. thaliana with as yet unknown effects on plant performance in a substantial number of studies

Using genome diversity to decipher nematode virulence and host susceptibility

The sedentary root-knot nematode Meloidogyne incognita is a widely distributed and highly polyphagous phytopathogen, which causes annual losses in the order of millions of dollars in damage to crops. M. incognita juveniles initiate the development of a permanent feeding site consisting of so-called giant cells. These giant cells nourish the nematodes during their life, while cells surrounding the giant cells are also hypertrophic and hyperplastic and form a large protective gall. The elaborate changes in plant roots leading to the formation of feeding sites are orchestrated by effectors in secretions of M. incognita. To introduce the current concepts of this close interaction at a molecular level in Chapter 1, the latest progress with regard to identification and functional characterization of M. incognita effectors is summarized. Furthermore, it is explained how effectors can play a role in the adaptive evolution of nematodes and hosts.Chapter 2 describes the identification of the effector MiMSP32 based on specific patterns of genetic variation in the M. incognita genome. As a consequence of adaptive evolution, an ancestral gene of MiMSP32 gene has duplicated and diversified into a gene family with at least thirty identified variants, all taxonomically restricted to root-knot nematodes. These gene variants can be subdivided into six clusters based on their similarities. As a pioneer gene, MiMSP32 shows no similarity to any other functionally characterized genes or proteins However, we used the predicted secondary structure to identify a remote homology with several proteins adopting three-layer beta-alpha-beta (βαβ)-sandwich architecture. Based on the positive selection and gene expansion, we hypothesize that MiMSP32 has undergone functional diversification.In Chapter 3, we study the biological relevance of MiMSP32 for infectivity of M. incognita on tomato plants. We functionally characterized MiMSP32 in planta and show that it is indeed an important effector with a role in nematode virulence and host plant susceptibility. Moreover, MiMSP32 proved to be a promiscuous effector, as we identified six host targets by screening a tomato cDNA library in yeast. We confirmed these interactions by multiple protein-protein interaction assays, such as co-immunoprecipitation, co-localization, and FRET-FLIM after transient expression in Nicotiana benthamiana leaves. From these results, a model emerges wherein the effector MiMSP32 promotes the virulence of M. incognita by interacting with multiple unrelated host proteins in tomato.Next, we tested the susceptibility of existing T-DNA knock-out mutants of homologs of the six MiMSP32 host targets in Arabidopsis thaliana, which is a host of M. incognita. We show in Chapter 4 that the Arabidopsis knock-out opr2-1 mutant is significantly more susceptible to M. incognita than wild-type plants. AtOPR2 is thought to take part in an alternative jasmonic acid (JA) biosynthesis pathway downstream of 12-oxo-phytodienoate (OPDA) in the conversion of 4,5-didehydrojasmonate (4,5-ddh-JA) to JA, thereby suggesting that AtOPR2 may function in JA-dependent plant defense. However, our bioassays and transcriptional data provide evidence that AtOPR2 regulates susceptibility of Arabidopsis to M. incognita independent from basal plant immune responses by conversion of the signaling molecule 4,5-ddh-JA.In Chapter 5, we describe an alternative approach to identify sources of tomato resistance to M. incognita. To this purpose, we used a collection of 178 domesticated tomato lines without known major R-genes to gauge the quantitative variation in tomato susceptibility to M. incognita. Next, we linked this trait to genomic regions of 156 of these tomato lines using a genome-wide association study (GWAS), resulting in a catalogue of 380 genes associated with tomato susceptibility to M. incognita. By using additional RNA-Seq of isolated nematode-induced galls on a representative subset of ten tomato accessions, we identified 37 differential regulated genes within the 380 gene candidates from the GWAS. These susceptibility-associated genes likely contain new sources of resistance for use in future studies and breeding applications.In the final chapter of this thesis (Chapter 6), it is argued that genome diversity can help to identify key factors involved in the diversity of nematode virulence and host susceptibility. MiMSP32 was selected for further analyses based on positive, diversifying selection in the M. incognita genome. Likewise, the variation in the S. lycopersicum genome was used to identify genes significantly associated with quantitative variation in plant susceptibility. Host targets of positively selected nematode effectors are likely to generate a detectable genetic signal in studies of host susceptibility. To test this hypothesis, the 380 tomato susceptibility-associated genes (GWA) were compared with the 51 putative host target genes of MiMSP32 (Y2H). With this comparison, the hypothesis could not yet be confirmed, as the overlapping susceptibility-associated gene needs additional confirmation as a host target. However, confirmation of the hypothesis was possible based on the host target AtOPR2, as it regulates susceptibility of Arabidopsis to M. incognita. Therefore, a suggestion for future studies would be to integrate genome diversity of both nematode and host and use the obtained information of this thesis to formulate more efficient plant protection strategie

Data from: The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses of bacterial and fungal communities at a high taxonomic level were optimized, and it was investigated whether changes in the primary decomposer community were translated in alterations in bacterivorous and fungivorous nematode communities. In contrast to J. vulgaris, small but significant reductions were observed for Actinobacteria and Bacteroidetes (both p < 0.05) in case of the invasive S. inaequidens. More pronounced changes were detected for the overall nematode community density, and, more specifically, for the bacterivorous genus Anaplectus and the family Monhysteridae (both p < 0.05), as well as the necromenic Pristionchus (p < 0.001). At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent. The overall bacterial and fungal biomasses, as well as a remarkably consistent set of constituents (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were negatively affected by plant stage for both ragwort species. Although later developmental stages of plants generally coincided with lower levels for individual nematode taxa, densities of the fungivorous genera Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high taxonomic level, differential effects of native and non-native ragwort could be pinpointed. However, plant developmental stage has a more prominent impact and this impact was similar in nature for both native and non-native ragwort species

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses of bacterial and fungal communities at a high taxonomic level were optimized, and it was investigated whether changes in the primary decomposer community were translated in alterations in bacterivorous and fungivorous nematode communities. In contrast to J. vulgaris, small but significant reductions were observed for Actinobacteria and Bacteroidetes (both p < 0.05) in case of the invasive S. inaequidens. More pronounced changes were detected for the overall nematode community density, and, more specifically, for the bacterivorous genus Anaplectus and the family Monhysteridae (both p < 0.05), as well as the necromenic Pristionchus (p < 0.001). At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent. The overall bacterial and fungal biomasses, as well as a remarkably consistent set of constituents (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were negatively affected by plant stage for both ragwort species. Although later developmental stages of plants generally coincided with lower levels for individual nematode taxa, densities of the fungivorous genera Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high taxonomic level, differential effects of native and non-native ragwort could be pinpointed. However, plant developmental stage has a more prominent impact and this impact was similar in nature for both native and non-native ragwort species

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses of bacterial and fungal communities at a high taxonomic level were optimized, and it was investigated whether changes in the primary decomposer community were translated in alterations in bacterivorous and fungivorous nematode communities. In contrast to J. vulgaris, small but significant reductions were observed for Actinobacteria and Bacteroidetes (both p < 0.05) in case of the invasive S. inaequidens. More pronounced changes were detected for the overall nematode community density, and, more specifically, for the bacterivorous genus Anaplectus and the family Monhysteridae (both p < 0.05), as well as the necromenic Pristionchus (p < 0.001). At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent. The overall bacterial and fungal biomasses, as well as a remarkably consistent set of constituents (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were negatively affected by plant stage for both ragwort species. Although later developmental stages of plants generally coincided with lower levels for individual nematode taxa, densities of the fungivorous genera Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high taxonomic level, differential effects of native and non-native ragwort could be pinpointed. However, plant developmental stage has a more prominent impact and this impact was similar in nature for both native and non-native ragwort species

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

© 2017 Nordic Society Oikos. Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses of bacterial and fungal communities at a high taxonomic level were optimized, and it was investigated whether changes in the primary decomposer community were translated in alterations in bacterivorous and fungivorous nematode communities. In contrast to J. vulgaris, small but significant reductions were observed for Actinobacteria and Bacteroidetes (both p < 0.05) in case of the invasive S. inaequidens. More pronounced changes were detected for the overall nematode community density, and, more specifically, for the bacterivorous genus Anaplectus and the family Monhysteridae (both p < 0.05), as well as the necromenic Pristionchus (p < 0.001). At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent. The overall bacterial and fungal biomasses, as well as a remarkably consistent set of constituents (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were negatively affected by plant stage for both ragwort species. Although later developmental stages of plants generally coincided with lower levels for individual nematode taxa, densities of the fungivorous genera Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high taxonomic level, differential effects of native and non-native ragwort could be pinpointed. However, plant developmental stage has a more prominent impact and this impact was similar in nature for both native and non-native ragwort species

Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections

Transcriptome studies of Illumina RNA-Seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two-segmented genome characteristics of a comovirus. This comovirus did not induce any visible symptoms in infected A. thaliana plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in A. thaliana plants was confirmed by quantitative reverse transcription polymerase chain reaction, transmission electron microscopy and mechanical inoculation. Arabidopsis latent virus 1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms. A bioinformatics investigation of A. thaliana RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural A. thaliana accessions and in 8.5% of all analyzed SRAs. Arabidopsis latent virus 1 could also be detected in A. thaliana plants collected from the wild. Arabidopsis latent virus 1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected A. thaliana plants. This has probably led to a worldwide distribution in the model plant A. thaliana with as yet unknown effects on plant performance in a substantial number of studies

Data from: The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses of bacterial and fungal communities at a high taxonomic level were optimized, and it was investigated whether changes in the primary decomposer community were translated in alterations in bacterivorous and fungivorous nematode communities. In contrast to J. vulgaris, small but significant reductions were observed for Actinobacteria and Bacteroidetes (both p < 0.05) in case of the invasive S. inaequidens. More pronounced changes were detected for the overall nematode community density, and, more specifically, for the bacterivorous genus Anaplectus and the family Monhysteridae (both p < 0.05), as well as the necromenic Pristionchus (p < 0.001). At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent. The overall bacterial and fungal biomasses, as well as a remarkably consistent set of constituents (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were negatively affected by plant stage for both ragwort species. Although later developmental stages of plants generally coincided with lower levels for individual nematode taxa, densities of the fungivorous genera Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high taxonomic level, differential effects of native and non-native ragwort could be pinpointed. However, plant developmental stage has a more prominent impact and this impact was similar in nature for both native and non-native ragwort species

Converted-qPCR-Data_nematodes_bacteria_fungi

In this data file you can find the data we used to execute our statistical tests. Converted Ct values are shown and the transformed data is shown in purple. (Making use of linear relationship between primary qPCR output, Ct values, and the number of individuals, nematode concentrations expressed as individuals per 100 g of soil were calculated. As both the resulting nematode densities and the concentrations of bacterial and fungal DNA (ng per 0.25 g soil) didn’t show a normal distribution, data were transformed. Primary counts were log transformed (ln(y+0.1)). A constant (0.1) was added to push data away from the lower bound zero.) A legend is added to explain the meaning of the first six rows