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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 genetics of local adaptation in Swedish Arabidopsis thaliana populations: a dual ecological-genomic approach

Understanding how organisms adapt to their environment has been a long standing question in evolutionary biology. While demonstrating local adaptation with reciprocal transplants is an old idea (KAWECKI and EBERT 2004), the recent technological advances in genomics present us with an opportunity to better understand the genetics and the process of adaptive evolution.

This is particularly true for the model plant Arabidopsis thaliana. A. thaliana is a small, mostly selfing, winter-annual brassica that was introduced as a model species for its short life cycle and small genome size (THE ARABIDOPSIS GENOME INITIATIVE 2000). Naturally occurring inbred lines (accessions) also have the advantage that once they have been genotyped or sequenced, seeds generated through selfing can be used for multiple experiments with high levels of replication. In addition to being a convenient model, A. thaliana is also a wild plant, found across the world in a great diversity of natural environments and displays great phenotypic variation between and within populations (see for example STINCHCOMBE et al. 2004; KRONHOLM et al. 2012; ZÜST et al. 2012). The recent genomic resources developed for this plant opens an unprecedented opportunity to investigate the genetics underlying adaptive variation
(HORTON et al. 2012; LONG et al. 2013) while the great effort that went into understanding the function of many, if not most, of its genes provides us with a new window into the functions, traits and environmental factors driving in local adaptation.

In this project we investigate local adaptation in natural populations of this small winter annual plant in Sweden. Prior work showed strong population structure (NORDBORG et al. 2005) and isolation by distance (PLATT et al. 2010) throughout the species range, suggesting that populations are stable and have had the opportunity to adapt to local environments. Local adaptation to climate variation was also found to be ubiquitous across Europe (FOURNIER-LEVEL et al. 2011; HANCOCK et al. 2011).
In Sweden we focus on two regions: the High Coast, about 4h drive North of Stockholm, and Skåne, in the South (Figure 1).

Maps of Sweden showing the regions where experiments are located in Sweden (red dots) and the location of origin of each of the 200 accessions used in this study.
Figure 1: Maps of Sweden showing the regions where experiments are located in Sweden (red dots) and the location of origin of each of the 200 accessions used in this study.

These two regions display contrasting climates, with the Northern region of the High Coast displaying colder temperatures, longer snow cover, and a broader range of photoperiod. The High Coast is close to the Northern limit of the species range and in this region Arabidopsis populations are only found on South facing slopes where they can capture the low incidence sun’s rays. In Skåne, in the South, A. thaliana is found in agricultural meadows, fields and on beaches along the Baltic sea.

Building on the old idea of reciprocal transplants (KAWECKI and EBERT 2004), and combining it with cutting edge genomics, we set up experiments designed to test for local adaptation, identify important phenotypes and selective pressures, and detect the molecular bases of local adaptation among natural populations of A. thaliana.
We use a set of 200 accessions all re-sequenced (LONG et al. 2013) in a dual experimental strategy. The first part our experimental design consists of experimental natural selection experiments. In both the High Coast (North) and Skåne (South), we selected 5 locations where the environment seemed suitable for an Arabidopsis population to establish. In each location we set up five-1 m2 plots in which we dispersed a mixture of seeds from the 200 re-sequenced accessions (LONG et al. 2013). Populations were allowed to establish without further intervention and we collected samples three times a year for the last 2 years. After low depth sequencing of the samples, we will be able to track changes in the frequency of individual genotypes, but also changes in allele frequency across the genome.
The second experimental strategy builds more directly on the idea of reciprocal transplants and consists of 4 large common garden type experiments (two in each region). Experiments were installed to coincide with local germination flushes among local natural populations and consisted of three complete randomized blocks, each block included 8 replicates per accessions. These experiments were used to gather data on flowering time, herbivore damage, rosette size, shape and growth, pathogen infections and microbial community composition (see Microbial community paragraph). We also directly measured over-winter survival and estimated seed production, two major fitness components for any annual plant. These experiments will allow us to directly test for local adaptation, investigate the contribution of various significant traits, and to identify the underlying molecular bases of adaptive variation using Genome-Wide Association mapping (ATWELL et al. 2010). While estimating fitness component in the common garden experiment is likely biased because it doesn’t include all components of fitness, the results will help us understand and validate results from the selection experiments.

Preliminary results show evidence for local adaptation. In the Southern Sweden common garden experiments, Southern accessions grew bigger and produced more seeds than Northern accessions (Figure 2).

Relationship between the latitude of origin of accessions and lifetime fecundity, in the four common garden experiments (North: top panels, South: bottom panels). Significant, negative relationships were found in the two Southern experiments Rathckegården and Ullstorp. “cor” indicates the Spearman rank correlation coefficient and p-value, the associated p-value.
Figure 2: Relationship between the latitude of origin of accessions and lifetime fecundity, in the four common garden experiments (North: top panels, South: bottom panels). Significant, negative relationships were found in the two Southern experiments Rathckegården and Ullstorp. “cor” indicates the Spearman rank correlation coefficient and p-value, the associated p-value.

Interestingly, genome-wide association mapping clearly identifies a disease resistance gene explaining a significant fraction of seed production in one of the Southern experiments (Figure 3).

Manhattan plot for lifetime fecundity in Ullstorp, Southern Sweden. The y-axis gives the associations score between an estimate of lifetime fecundity and approximately 2 millions SNPs with allele frequencies over 5%. The x-axis gives the location of the SNPs along the 5 chromosome of Arabidopsis thaliana. The peak annotated as one on Chromosome 1 is located in the vicinity of RLM1.
Figure 3: Manhattan plot for lifetime fecundity in Ullstorp, Southern Sweden. The y-axis gives the associations score between an estimate of lifetime fecundity and approximately 2 millions SNPs with allele frequencies over 5%. The x-axis gives the location of the SNPs along the 5 chromosome of Arabidopsis thaliana. The peak annotated as one on Chromosome 1 is located in the vicinity of RLM1.

In the other Southern experiment, herbivore attacks in the fall are associated with SNP polymorphisms located near the known glucosinolate genes AOP2 and AOP3. The amount of herbivore damage also significantly decreases the probability of overwinter survival. Overall, preliminary results seem to indicate a large contribution of biotic interaction to fitness components. This prompted us to further investigate the leaf microbial community variation among accessions in our four common garden experiments.

Microbial community variation.

In a prior study from our lab, M. Horton and N. Bodenhausen performed a common garden experiment in Michigan in which they grew a set of 196 worldwide accessions in natural conditions (BODENHAUSEN et al. 2013, HORTON et al. In Press). They characterized the bacterial and fungal communities in leaves and roots for each accession by sequencing the taxonomically informative genes 16S rRNA in bacteria and ITS in fungi. One of the major results of these studies is the effect of the plant’s genotype on the composition and diversity of the plant microbiota. Using methods developed in these studies, we aim at better understanding adaptive variation in Sweden by characterizing the leaf microbial communities of the plants in the common garden installed in Sweden. The specific questions here are:

1) Are there differences in the bacterial community among the four study sites? Observing different communities of microbes among our study sites would suggest that plants experience a different biotic environment depending on the location and climate.

2) Can we see differences in the leaf bacterial community among accessions of Arabidopsis thaliana, and if so then what are the genetics driving those differences? Differences in leaf microbial community among accessions grown in the same location would suggest that plants shape the microbial community they host. Because all accessions used in this study have been genome sequenced, we will have the opportunity to study the genetics shaping the leaf microbial community with GWA mapping.

3) Are natural populations of Arabidopsis thaliana locally adapted to the pathogens they encounter in their natural habitat?
Fitness estimates based on seed production will be generated via high throughput analysis of mature plants images. We will investigate if polymorphisms at genes shaping the bacterial community in the different experiments have effects on plant fitness and determine their importance relative to genes underlying other adaptive traits.

Main contributors:

Benjamin Brachi
Daniele Filiault (Gregor Mendel Institute, Vienna)
Svante Holms (Mid-Sweden University)

Principal investigators:

Joy Bergelson
Magnus Nordborg
Caroline Dean

Other contributors:

Envel Kerdaffrec (Gregor Mendel Institute, Austria)
Fernando Rabanal (Gregor Mendel Institute, Austria)
Polina Novikova (Gregor Mendel Institute, Austria)
Takashi Tsuchimatsu (Gregor Mendel Institute, Austria)
Susan Duncan (John Innes Centre, UK)
Timothy Morton (University of Chicago, USA)
Roderick Wooley (University of Chicago)
Matthew Box (John Innes Centre, UK)
Alison Anastasio (University of Chicago, USA)
Arthur Korte (Gregor Mendel Institute, Austria)
Pamela Korte (Gregor Mendel Institute, Austria)
Viktoria Nizhynska (Gregor Mendel Institute, Austria)
Stéphanie Arnoux (Gregor Mendel Institute, Austria)

References:

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Bodenhausen N., Horton M. W., Bergelson J., 2013   Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana (AM Ibekwe, Ed.). PLoS ONE 8: e56329.

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