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I am broadly interested in the evolution and structure of host-associated microbial communities. Of the numerous taxa that compose the Arabidopsis microbiome, fungi make up a substantial portion, but studies to date have tended to focus on the bacterial portion. With the help of my labmate Manon Guilberteau, I have cultured over thirty unique fungal species from natural populations of Arabidopsis. By infecting sterile Arabidopsis with specific microbial taxa under tightly controlled environmental conditions, I will investigate the role of fungi in formation of the non-mycorrhizal plant microbiome.

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I am a phytopathologist in Sichuan Agricultural University, China. My research is mainly focused on the interaction mechanisms between rice fungal pathogens and hosts. I have worked on the cytology, morphology, histologic pathology, genomics and epidemiology of rice sheath blight and kernel smut disease pathogens, and illustrated the effectors and evolution mechanism against hosts. A second line of research deals with defenses against Lepidoptera, Homoptera and nematode pests. We clone plant defensive genes, do functional verification, create transgenic crops but we are also interested in the genomics of Bacillus thuringiensis, a Gram-positive bacteria that often is used as a biological pesticide. In the Bergelson lab, I am investigating the fitness of Pseudomonas syringae among different crops. Pseudomonas syringae is multi host generalist pathogen, it can infect more than 100 families plants. It has a complex life history, including pathogenic, epiphytic and saprophytic phases. The mechanisms of pathogen virulence and host resistance have been well characterized in several model systems. But knowledge about genetic dynamics in ecology is limited. Tn-seq high-throughput parallel sequencing will be used to elucidate the fitness mechanism of Pseudomonas syringae in crops. One can find me in the following website: https://www.researchgate.net/profile/Aiping_Zheng2 http://scholar.google.com/citations?hl=en&user=98cgrigAAAAJ&sortby=pubdate&view_op=list_works and http://wiki.pestinfo.org/wiki/Aiping_Zheng. Selected Publications Lei D, Lin R, Yin C, Li P, Zheng A. Global protein-protein interaction network of rice sheath blight pathogen. J Proteome Res. 2014 Jul 3;13(7):3277-93. doi: 10.1021/pr500069r. Aiping Zheng, Runmao Lin, Danhua Zhang, etc. The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nature Communications. 2013, 4: 1424 doi:10.1038/ncomms2427. Li S, Li W, Huang B, Cao X, Deng Q, Wang S, Zheng A, Zhu J, Liu H, Wang L, Li P. Natural variation in PTB1 regulates rice seed setting rate by controlling pollen tube growth. Nature Communications. 2013, 4:2793. doi: 10.1038/ncomms3793. Guan P, Ai P, Dai X, Zhang J, Xu L, Deng Q, Li S, Wang S, Liu H, Wang L, Li P, Zheng A. Complete genome sequence of Bacillus thuringiensis serovar Sichuansis strain MC28. J Bacteriol. 2012 Dec;194(24):6975. doi: 10.1128/JB.01861-12.

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The evolution of resistance to pathogens

Plant pathogen interactions have been thought to undergo arms race dynamics, where there is consistant, dynamic turnover of resistance alleles – R genes – in the host, and avirulence alleles in the pathogen. If this were the case, resistance alleles segregating in natural populations should be relatively young.

However, over a decade ago we learned that, instead, R genes in plants are frequently maintained as ancient, balanced polymorphisms. Through field trials with transgenic A. thaliana lines, we have demonstrated that large fitness costs are associated with R genes experiencing balancing selection for presence/absence polymorphisms.

Not all R genes experiencing balancing selection are presence/absence polymorphisms. We are interested in how ecological and evolutionary forces combine to shape patterns of variation at RPS2, an R gene under balancing selection for disease resistance and susceptibility which is present in all natural populations of A. thaliana sequenced to date.

We have conducted a field trial with transgenic A. thaliana lines differing in only the native allele of RPS2 that they contain. We found that there was no cost of carrying a resistant allele of RPS2 in the field; instead, having any allele of RPS2 was beneficial in the field relative to a mutant that lacked RPS2.

RPS2
High fitness benefit of RPS2 presence in the absence of pathogen!

Currently we are trying to understand the fitness benefit of RPS2 presence. We are exploring whether RPS2 has some alternative function, aside from the previously known resistance to avrRpt2, which gives plants with RPS2 a fitness benefit relative to plants that don’t. To support our field results, we are also determining if variation in RPS2 is associated with any fitness changes in the Recombinant Inbred Lines phenotyped by Ben Brachi.

To explore the benefit of RPS2 presence, we first asked if there was a difference in metabolome between plants with RPS2 and plants without.  We used mass spectrometry to look at the metabolomes of our transgenic lines with and without RPS2, but we found no convincing differences between these lines. We are now using RNAseq to further characterize differences between these different transgenic lines.

We are also exploring the prevalence of homologs of avrRpt2, the avirulence gene that interacts with RPS2, in the environment. Diffuse interactions with common avirulence genes in other species may help to explain the maintenance of RPS2 in all accessions. Though we did not detect avrRpt2 using PCR for any of our field samples, these PCRs may not have picked up other homologs of avrRpt2. A weak homolog of avrRpt2 seems to be present in dot blots of most P. syringae strains from the Midwestern US; if RPS2 can recognize this homolog, it may explain the consistent presence of RPS2 and the fitness benefit of RPS2 presence.

Though we expected that R genes without presence-absence polymorphisms should not carry high fitness costs of resistance, we were surprised that the presence of RPS2 carried a substantial fitness benefit. We think understanding this benefit may help us understand the difference between R genes are under balancing selection for presence/absence polymorphisms and those that always present.