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Plant Ecology Laboratory

Research in our lab focuses on diversity patterns in biological communities, and on the interactions underlying these patterns. The main questions we address are: how do communities vary along natural gradients and gradients of human impact? What are the major assembly rules shaping communities; and are they attributable to biotic interactions or environmental heterogeneity? What are the roles of different biotic interactions - including competition, facilitation, herbivory and symbiosis - in structuring communities? Read more

News archive - August

Increased sequencing depth by Illumina does not increase captured diversity of arbuscular mycorrhizal fungi compared to 454

August 2017

Doctoral student Martti Vasar with co-authors investigated how two sequencing platforms (454 and Illumina) compare with each other. To achive this, MaarjAM database with BLAST+ software was used. 454 sequencing is now discontinued and alternative had to be found. This raised a question how new sequencing platform results are comparable with previous platvorm. Both platforms were sequenced by same 12 samples from Järvselja forest. 454 sequences were at least 500+ base pair long, which filled interested amplicon of the SSU rRNA gene. Illumina have shorter sequences (previous generation 2x250bp, now 2x300bp), which have overlap at the end of sequence. Tagmentation was used for Illumina, which locates sequences at random location on the amplicon, but 454 sequences were starting from fixed position. Illumina produced 100x more raw sequences compared to 454, but catched fewer rare virtual taxon (VT – see MaarjAM database). After quality filtering, large portion of Illumina sequences were discarded, but this did not affect end results as the captured diversity was similar with 454.

Vasar, M.; Andreson, R.; Davison, J.; Jairus, T.; Moora, M.; Remm M.; Young, J. P. W.; Zobel, M. & Öpik, M. 2017. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza doi: 10.1007/s00572-017-0791-y.

9th International Conference on Mycorrhiza

August 2017

ICOM9 was held in August in Prague, Czech Republic, with the overarching theme: „Mycorrhizal functioning: from wilderness to megacities”. Mari, Maarja, Guille, Inga, David, Lena, Maret and Tanel from our team and Leho and Petr from Tedersoo’s lab were presenting either posters or oral talks – indeed numerous participation! Mari gave a plenary talk on „Biogeography of mycorrhizal symbiosis: using plant mycorrhizal traits in space and time” and Maarja organized a workshop together with Tom Bruns and John Taylor and gave a lecture on „Molecular taxon concepts in AM fungi used in community ecology”. Thanks to the organizers for a great conference! See more from the conference Twitter.

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