An exciting preprint paper about solving problematic bacterial genome assemblies with the fabulous PI Dr. Christian Ahrens and Michal Schmid at Agroscope, CH, is now available at BioRxiv

We had a great time in Auckland at the NZMEC 5. First of all the Mexican restaurant we found served plenty of wonderful vegetarian food and gluten free food to satisfy everyone in the group. Secondly, the ~100 participant symposium was wonderful (!), a great platform to network and to show off our own science. Erica, Rudolf, Simi and Michal presented their posters and I was invited to present some of the new stuff that we are currently working on.

We cleaned our little lab empire - good reason to finally take a picture of our group. Also, afterwards we binge ate Indian food... hmmm Indian...

Emmanuel just received his grades for MSc thesis. He did a tremendous job working 50 hours + and producing data galore. We wish him all the best in his future endeavours.

​Great job Emmanuel!

We had a class of high school students visiting UC the other day. Hopefully they had as much fun as I did. Also, hopefully the learned something new.

Rudolf and I got a Tansley Insight review out in New Phytologist - Stay tuned for more in the future

​http://onlinelibrary.wiley.com/doi/10.1111/nph.15054/full/

PhD Scholarship – Molecular Plant-Microbe Interactions, Transcriptomics
Transcriptional responses of Arabidopsis thaliana to leaf colonisation by non-pathogenic bacteria.
We seek a PhD candidate for a fully-funded 3-year PhD scholarship in the School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.

The successful candidate will be part of the Remus-Emsermann Lab. The Remus-Emsermann lab is a young and agile team interested in the microbiology of leaf surfaces and plant-microbe interactions using multidisciplinary approaches. The lab is based in the School of Biological Sciences, with close interactions with other PhD students from the School of Biological Sciences.

The project will be supervised by Dr Mitja Remus-Emsermann and Prof. Paula Jameson.

More information about the current research in the Remus-Emsermann Lab can be found here: www.remus-emsermann-lab.org.

Project description
Plant leaves host diverse non-pathogenic bacterial communities. However, we simply don’t know how important these communities are to to plant life, as the impact of non-pathogenic bacteria on plants is barely understood. It is critical that we understand the potential impact of leaf-inhabiting bacteria on plant physiology and health considering the importance of plants as Earth's primary producers. This project will investigate the transcriptional response of Arabidopsis thaliana to their non-pathogenic leaf colonisers.

The University
The University of Canterbury is located in Christchurch, the largest city in New Zealand’s South Island. There are approximately 13,000 students enrolled, and 2,000 postgraduate students. The University’s modern and well-equipped facilities are spread across a spacious suburban campus, with easy access to the city and the cultural and recreational facilities it provides. There are several ski-fields within an hour and a half’s drive, the Pacific Ocean is a 20 minutes drive from campus, and there is good access to the scenic and recreational resources of the Southern Alps and Banks Peninsula.

Funding Notes
The stipend will be for three years at NZ$21,000 p.a. (tax free) plus payment of tuition fees and associated service charges (approx. $9,000 p.a.).

Eligibility
We seek a PhD candidate with a demonstrated high level of academic achievement at the undergraduate and postgraduate level. They will be required to have a BSc (Hons) or a Masters degree in order to enrol as a PhD candidate at the University of Canterbury. The ideal candidate will have a Masters degree in Molecular Plant Biology/ Molecular Plant Pathology or Microbiology and experience in working with RNA, and transcriptomics or genomics.
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As the project will involve extended periods in the lab as well as bioinformatics work, candidates who can demonstrate experience in both analysis of transcriptomic data and hands-on experiments are especially welcome to apply. Previous experience in techniques such as plant RNA extraction, qPCR, next generation sequencing and transcriptome analysis, and bacterial cultivation will be particularly useful.

Applications should include a curriculum vitae, and a cover letter with a brief outline of envisioned experiments, and the addresses of two scientific referees, addressed  to Dr Mitja Remus-Emsermann. The positions remains open until filled. Starting date is up for discussion but we envision the successful candidate to us in June/ July 2018.

Applications + Contact
For more information please contact by email:
Dr Mitja Remus-Emsermann
School of Biological Sciences
University of Canterbury
Christchurch
New Zealand
Email: mitja.remus-emsermann@canterbury.ac.nz
Tel: +64 (3) 36 95351, Ext 95351

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Cosima Pelludat and team just got a paper accepted in Frontiers in Microbiology

PSEUDOMONAS ORIENTALIS F9: A POTENT ANTAGONIST AGAINST PHYTOPATHOGENS WITH PHYTOTOXIC EFFECT IN THE APPLE FLOWER
Veronika Zengerer,   Michael Schmid,   Marco Bieri, Denise C. Muller,   Mitja N. Remus-Emsermann,   Christian H. Ahrens and   Cosima Pelludat

PDMS microfluidic channel network inspired by a circuit board colonised by three E. coli strains that each express a different autofluorescent protein.
Rudolf Schlechter, Rebecca Soffe, Blair Bonnett, Volker Nock, and Mitja Remus-Emsermann
Electronics in form of semiconductor engineering/ thick film/ and printed circuit board (PCB) technology has directly enabled the advent of microfluidics, which has revolutionised microbiology via the Lab-on-a-Chip. Here, we choose to employ such a “synthetic environment” inspired by a PCB board and inoculated with a “synthetic community” to signify the advent of “synthetic ecology”. While the design of the shown PCB inspired chip as a tool for microbial ecology is negligible, the technological advances it embodies are not. Electronics, and semiconductor device manufacturing in particular, have given rise to microfluidic devices and related analytical techniques. The channels incorporated in the latter are used to contain and study microbiological processes, and, in their function, are symbolically equivalent to the traces on a PCB. The particular example shows the possible interactions that can be observed by the mixing of different strains and the avoidance of bacteria to colonise niches on the PDMS chip.
The picture is also a symbol for novel approaches in microbial ecology that are only possible due to close collaborations of engineers with microbiologists. Such collaborations draw from each others knowledge, facilitate each other and push the current boundaries of technology and science.

Dear ISME members - if you can spare the minute, please help us out by voting for our cover picture for the ISME journal 2018. It will look like a circuit board that is colonised by fluorescent bacteria.

Use your personal surveymonkey email link to vote.

Many thanks