JAMS symposium = microbiomes, antimicrobial resistance, halotolerant bacteria and picoplankton

On the 20th of March, microbiologists from all over Australia attended the 8th annual symposium of JAMS, the Joint Academic Microbiology Seminars, at the Australian Museum.  JAMS was very popular on Twitter, with many people live tweeting the talks (check out the #JAMS2019 hashtag).

New to JAMS this year was the live-stream of the talks. People all around Australia and the world (or just down the road) had the opportunity to be part of the event, even though they weren’t there in person. What a great way to increase access to microbiology and spread the word far and wide!

Microbiomes were a major topic of the day with talks on:

  • using microbial communities in conjunction with geochemistry to reduce iron in duricrust formation (by Emma Gagen from University of Queensland);
  • moving beyond data generation in microbial ecology and relating the large amount of data back to biological and ecological principles so we can successfully derive biological meaning from these datasets (by Andrew Holmes from Sydney University);
  • the importance and forecasted direction of microbial ecology (by James Tiedje from Michigan State University); and
  • the valuable work the Australian Microbiome Initiative is doing to create a resource of Australian microbial data for use in management, monitoring and R&D (presented by Sophie Mazard).

During the afternoon break we headed to the top floor of the Australian Museum for a poster and networking session. What a wonderful view and so many excellent posters and conversations!

Continuing the environmental microbiology theme there were also talks taking us through:

  • the history of oceanic picoplankton (by Daniel Vaulot from CNRS);
  • the role of wastewater in the transmission of antimicrobial resistance (by Erica Donner from Uni SA’s Future Industries Institute); and
  • identifying novel halotolerant bacteria that can help extract metals from ores (by Liz Watkin from Curtin University).

On top of all of that, it was great to hear about how microbes are related to the sustainable development goals and how JAMS is doing their bit to help with these goals by only partnering with sustainable organisations.

After all the fascinating talks we strolled down to Harpoon Harry for networking, awarding of the student prizes, dinner and a wonderful choice of JAMS-original cocktails from Four Pillars Gin with Stroh sustainable straws (two of the sponsors this year).

Three students from the Paulsen and Mabbut groups at Macquarie University presented posters and Belinda Fabian won the student poster prize with Ben Ford as runner up. Our posters will feature in the corridors of our department to show off the exciting microbiology work happening at Macquarie University.

JAMS_2019_posters

Ben Ford and Belinda Fabian presenting their posters at the JAMS Symposium 2019. Photo of Ben: Geraldine Sullivan; Photo of Belinda: Varsha Naidu

Thanks to the JAMS organising committee for another excellent microbiology meeting – we’re all looking forward to the next monthly JAMS meeting. For more information visit jams.org.au

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Day in the life of a PhD candidate

7:30am Read through notes prepared by my project team to make sure I’m up to speed for this morning’s meeting. Contemplate the lack of suitable clothes in my cupboard and make a mental note to do clothes washing on the weekend.

8:30am Drive to campus. Realise there’s not enough time to get breakfast before my first meeting. Scrounge around in the car to see if there’s anything to eat. Come up with nothing.

9:10am Print notes so I can refer to them during the meeting. Print one-sided even though it’s using more paper, but I want to stick them in my lab book later as a record of what we discussed.

9:15am Pre-meeting with the team on campus to prepare for the Skype meeting with our collaborators. Spend most of the meeting trying to work out if my really busy supervisor is going to attend the meeting (spoiler alert: he didn’t make it).

9:30am  Skype for 2 hours with international and Australian collaborators. First 10 minutes is spent with everyone around the world trying to figure out the updated Skype program that isn’t intuitive. Discuss upcoming experiments with collaborators who have been working in the field for 30 years, make sure there’s nothing silly in our plans. Share the data I’ve generated and talk about the approach we’re taking for the next steps in the project. Collaborators express interest in our results, lament their lack of time to work through it and pronounce that they love doing science vicariously through us.

11:30am Debrief about Skype meeting and the next steps for experimental work and data analysis. Agree with co-supervisor that we’ll still go ahead with what we planned despite some potential problems. We won’t know if those things are problems until we’ve done the experiment and we’ve got a plan for how to identify them if they do occur, so we feel okay about it.

11:45am Get supervisor’s signature on reimbursement paperwork for conference attendance costs and discuss what funding should I use when purchasing a DNA extraction kit for my project.

11:54am Contemplate skipping the upcoming seminar to get lunch seeing I didn’t manage to have breakfast.

11:56am Colleague asks me if I want to walk to the seminar with her and that decides for me that I’m going to the seminar.

 

 

IMG_3760

Notes from the departmental seminar.

12:00pm Seminar hosted by my department – Nature Communications editor discussing his career path from PhD to Post Doc to journal editor, what his job looks like on a daily basis and the editing process for manuscripts submitted in his area. Interesting to hear about what happens at an editorial desk and leaves me feeling like being a journal editor involves too much reading of the scientific literature.

1:00pm Finally get to have some food! Lunch at the campus hub and catch up on a TV show I didn’t get to watch last week. Friends turn up unexpectedly, so stop watching the show and discuss the pros and cons of the latest figure he created in R for a manuscript he’s writing.

2:30pm Pick up purchases from the science store on campus, attach their inventory barcodes and put them away in the fridge/freezer/cupboard in the lab. Update the lab whiteboard to show what is still to be delivered.

2:55pm Remember that I’ve hardly drunk any water today and fill up water bottle on my way to my next meeting.

3:00pm Attend R Users Group meeting on campus and learn about using base R functions instead of downloading an R package (this makes the code more accessible for anyone to use and future-proof as packages can change without your knowledge). Code along with the presenter and feel proud that I can keep up and understand what he’s doing. A knowledgeable guy in the front of the room is asking questions that make me feel out of my depth. Correct the balance by asking the presenter about base R resources for learners.

RStudio screenshot

R code from code-along session in R Users Group meeting.

4:15pm Take reimbursement paperwork to departmental admin staff for checking and processing before the end of year deadline. Answer emails and make sure I’ve dealt with all the budget/invoice emails before the end of year deadline tomorrow.

4:45pm Read some more of the super complicated paper I’ve been working my way through. Highlight some relevant passages. Get frustrated and give up.

5:00pm Discuss experimental plans for next week with a colleague and agree on a date that he’ll have some materials ready for me to preserve some cells for microscopy.  Clarify what I’ll need to do. Lament the fact that even though I’ve been doing useful/necessary things all day I don’t feel like I’ve achieved anything.

5:30pm Order DNA extraction kit using the university’s online ordering system. Marvel at how much better this is than the old paper-based system.

5:45pm Stick notes from this morning’s Skype meeting into my lab book so I can refer to them when planning my next experiments.

6:00pm Check Twitter notifications for my personal account and the lab account that I run. Re-tweet some interesting things from both accounts. Get lost in an internet rabbit hole. Realising I’m hungry makes me stop and pack up.

7:00pm Head out for the night and make my way to the local shopping centre for some Christmas shopping and dinner. Thank goodness that I have a shopping plan and realise that I could finish all my shopping before it’s even December. Yay for those transferrable PhD skills!

Spending time waiting …

IMG_3276

The first step in DNA extraction is to lyse the cells so the DNA is released. These samples are ready to go into the water bath to kick-start this process.

I’ve been doing a lot of DNA extractions this year and with that comes a lot of time waiting for the water bath to heat my samples and the centrifuge to spin. A normal DNA extraction protocol means I’ll spend over an hour just waiting for things to happen. This time really adds up over multiple experiments. These waits can come in timeframes as short as 1 minute, so there’s not enough time to get really invested in anything.

I could spend this time checking social media, but there are some things I do to make myself more productive and feel like I’m being efficient. In a short wait (up to 5 minutes) these tasks can include:

  • Reading through the next steps in the protocol
  • Preparing the materials I’ll need next – getting out the right tubes, labeling them, aliquotting a reagent and changing the pipettes to the right setting can all save time
  • Popping out of the lab for a drink of water – spending hours in the lab can mean I’m dehydrated by the end of the day, so I use these short breaks as a reminder to have a drink
  • Sticking protocols and other printed materials in my lab book – I keep a roll of sticky tape in the lab so I don’t have to spend time updating my lab book once I’m done in the lab
  • IMG_2041

    Benchtop autoclave ready to be loaded with materials to be sterilised under high temperature and pressure.

    Checking through my chemical solutions and see if there is anything that needs to be discarded or needs a GHS compliant label

  • Starting an autoclave cycle – hopefully it’ll be done by the time I’ve finished my DNA extraction and I won’t have to stay late to unload it
  • Emptying my benchtop rubbish bin – working in a PC2 lab means overflowing rubbish bins are a hazard so I do this multiple times a day

Some steps in DNA extraction have a slightly longer wait time, but still not enough to dig deep into a paper or data analysis. During a longer wait of 15-30 minutes I:

  • Load the dishwasher – clean-up is the lab duty that always needs to be done, your lab mates will thank you for it
  • Make a plan or write a protocol for an upcoming experiment – doing this in my lab book makes it much easier when I have to write up my methods for my thesis or publication later
  • IMG_2938

    Bacteria are grown on plates that contain essential nutrients. These plates have just been poured and the molten agar is cooling and drying.

    Collect the materials needed for the next day – from the storage area in the lab or the on-campus scientific materials store

  • Prepare a chemical solution I’ll need in the next few days – this could be a single reagent or a complex media with multiple components
  • Pour agar plates – the molten agar needs to cool after pouring, so it’s good to line up this waiting time with finishing off a DNA extraction
  • Complete a chemical risk assessment for a new experiment and/or make a GHS compliant label I’ll need when I make up the chemical solution
  • Edit the photos I’ve taken of experiments – that way they’re ready to print out and stick in my lab book or put into a presentation

So as you can see there are always a lot of little tasks that need to be done for a successful project and to make the lab run smoothly. Using the snippets of time that would otherwise be wasted means I have larger blocks of time to use for more intensive work that requires lots of concentration. And it makes me feel more productive.

What do you do with your 1-minute spins? Got any good productivity hacks for me?

Finding plant-microbe conferences

For my PhD I’m looking at genes involved in the colonisation of biocontrol (beneficial) bacteria on plant surfaces. Along with the challenge of filtering out predatory conferences, it was really frustrating trying to find meetings that would be relevant for my research area. So I thought I’d share my search strategy and the events I found so you can save time and get a head start.

There’s so many different synonyms for conference –> meeting, symposium, congress, conference, forum, seminar, event, and so on… I wanted to broaden my search without having to do every combination of words to find relevant events, so I devised a shortcut. Keywords that identified for my area of study are: plant, soil, rhizosphere, plant-microbe, microbiology, beneficial bacteria and biocontrol. I googled each keyword along with the year I was looking for. Still a lot of searches, but waaaay less than if I had to include every synonym for conference.

This is the list of conferences I came up with (listed in chronological order) and a summary of the information I noted down. Based on past conference dates I’ve guessing some conference timings (I’ve noted them as predicted). Please let me know if you have more information on any conferences listed here or other conferences that fit in my list. As I find more conferences or more details I’ll update the list.

Enjoy!

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 2018

2nd Plant Microbiome Symposium
February 19-21, 2018 – Amsterdam, The Netherlands

Microbiology Society Annual Conference 2018
April 10-13 – Birmingham, UK

XV Meeting of the IOBC-WPRS Working Group “Biological and integrated control of plant pathogens” – Biocontrol products: from lab testing to product development
International Organisation for Biological and Integrated Control (IOBC)
April 23-26, 2018 Lleida, Catalonia, Spain

1st International Congress of Biological Control
May 14-16, 2018 – Beijing, China

ASM Microbe 2018
June 7-11, 2018 – Atlanta, Georgia, USA

11th International Plant Growth-Promoting Rhizobacteria Workshop
(Held every 3 years)
June 17-21, 2018 – Victoria, British Columbia, Canada

Plant Biology Europe 2018
June 18-21, 2018 – Copenhagen, Denmark

Plant Biotic Stresses & Resistance Mechanisms III
July 2-3, 2018 – Vienna, Austria

SEB Masters of Biology
July 3-6, 2018

7th Conference on Beneficial Microbes
July 8-11, 2018 – Madison Wisconsin

ISRR-10 Exposing the Hidden Half: Root Research at the Forefront of Science
July 8-12, 2018 – Israel

ASPB Plant Biology 2018
July 14-18 – Montreal, Canada

11th International Congress of Plant Pathology (ICPP): Plant Health in a Global Economy
(Held every 5 years)
July 29-August 3, 2018 – Boston, USA

ICOBM-2018 International Conference on Beneficial Microbes: Microbes for the Benefit of Mankind
August 1-3, 2018 – Kuching, Malaysia

10th Australasian Soilborne Diseases Symposium
September 4-7, 2018 – Adelaide, Australia

ComBio 2018
September 23-26, 2018 – Sydney, Australia

1st International Conference on Biological Control: Approaches and Applications
September 27-29, 2018 – Bengaluru, India

Microbes Underpinning Agriculture: Focused Meeting 2018
October 1-2, 2018 – Cork, Ireland

AusBiotech 2018
October 31-November 2, 2018 – Brisbane, Australia

International Symposium of the Plant Microbiome: Exploration of Plant-Microbe Interactions for Improving Agricultural Productivity
November 18-22, 2018 – Hurghada Egypt
************

2019

Plant and Animal Genome XXVII
January 12-16, 2019 – San Diego, California, USA

19th International Meeting on Visualising Biological Data
13-15 March, 2019 – EMBL Heidelberg, Germany

Microbiology Society Annual Conference 2019
April 8-11, 2019 – Belfast Waterfront, UK

ASM Microbe 2019
June 20-24, 2019 – San Francisco, California, USA

Rhizosphere5
(Held every 2 years)
July 7-11, 2019 – Saskatoon, Saskatchewan, Canada

8th Congress of European Microbiologists (FEMS)
July 7-11, 2019 – Glasgow Scotland

4th International Symposium on Biological Control of Bacterial Plant Diseases
July 9-11, 2019 – Viterbo, Italy

New Approaches and Concepts in Microbiology (Symposium)
9-12 July, 2019 – EMBL Heidelberg, Germany

Applied and Environmental Microbiology
Gordon Research Conference & Seminar
July 13-19, 2019 – Mount Holyoke College, South Hadley, MA, USA

XVIII International Society for Molecular Plant-Microbe Interactions (ISMPMI)
July 14-18, 2019 – Glasgow, Scotland

ASPB Plant Biology 2019
August 3-7, 2019 – San Jose, California, USA

Australian Society of Plant Scientists (ASPS) conference
Predicted: September, 2019

17th International Conference on Pseudomonas
Predicted: September, 2019

Micrope2019 International Symposium: Microbe-Assisted Crop Production – Opportunities, Challenges and Needs
Predicted: December, 2019

************

2020

Plant and Animal Genome XXVIII
January 11-15, 2020 – San Diego, California, USA

Plant Biology Europe 2020
(bi-annual event jointly organised by EPSO and FESPB)

ASM Microbe 2020
June 18-22, 2020 – Chicago, Illinois, USA

ASPB Plant Biology 2020
July 25-29, 2020 – Washington DC, USA

Combio 2020
29 September – 2 October 2020
Melbourne, Australia

Predicted: International Conference on Beneficial Microbes

Predicted: 10th meeting of the IOBC-WPRS Working Group “Biological and Integrated Control of Plant Pathogens”

************

2021

Plant and Animal Genome XXIX
January 9-13, 2021 – San Diego, California, USA

ASM Microbe 2021
3-7 June, 2021 – Anaheim, California

ISRR 11th International Symposium
Predicted: Missouri, USA (provisional)

Predicted: 12th International Plant Growth-Promoting Rhizobacteria Workshop
(Held every 3 years – last one 2018)

************

2022

Nothing found yet

************

2023

12th International Congress of Plant Pathology
(Held every 5 years)
August 20-25, 2023 – Lyon, France

XX IBC 2023
July 1-7, 2023 – Rio de Janeiro, Brazil

************

Tiny life sticking to growing green things

Communicating science to non-scientists is important, but often the jargon scientists use makes their work impenetrable, even to other scientists. So how can scientific writing become less obscure and more approachable? Randall Monroe, the creator of xkcd webcomics, gave it a go with his annotation of a Saturn V rocket blueprint. The annotation used only the 1000 most commonly used words, so instead of Saturn V the name of the rocket became Up Goer Five.

So can scientific communication in my field (microbiology and genetics) be effective using only the 1000 most commonly used words? In the interests of simplifying my writing, I wrote a summary of my PhD project using only the 1000 most commonly used words (using this text editor):

This study wants to find the ‘small pieces’ which are important for tiny life (the helping ones) to stick to growing green things. Pseudomonas tiny life are some of the best helping tiny life and one of the most well-known ones, Pseudomonas protegens Pf-5, can control problems in growing green things used for food. But in the field, helping tiny life show does not stick to growing green things very often or very well. This study will look at the whole set of ‘small pieces’ important for P. protegens Pf-5 to stick to growing green things. Making tiny life stick better to growing green things will help lower problems with growing green things and better the return from growing green things used for food, which are important both here and around the world.

This is hilarious and obviously oversimplified (to the point of not making sense in a lot of places). For comparison, this is the ‘normal’ version of my project summary:

The project aims to identify the essential genes for colonisation of plant surfaces by biocontrol bacteria. Pseudomonas bacteria are some of the most successful biocontrol bacteria and one of the most well-known strains, Pseudomonas protegens Pf-5, has the ability to control diseases that affect cotton, wheat, pea, maize, tomatoes and potatoes. Despite this, field trials of biocontrol bacteria show a lack of reliability and persistence on plant surfaces. This project will conduct a genome-wide study of genes essential for P. protegens Pf-5 colonisation of plant surfaces. Enabling reliable colonisation of crop roots by biocontrol bacteria will contribute to lowering plant disease and increasing crop yields, which are important both in Australia and internationally.

From this exercise I learned that some level of complicated language is important to communicate a precise meaning (important in science), but not every complicated word is necessary. Sometimes the language I choose can be off-putting to the reader, make my work harder to understand and appear pretentious even when I don’t mean it to.

So overall, science writing in my field using the 1000 most used words is not practical and makes it harder, not easier to understand (even nonsensical in places). But it’s an interesting exercise to see just how much jargon you’ve used or if a simpler word will do in place of a complicated one. And wouldn’t we all like simpler rather than complex!

JAMS symposium = ECRs, viruses, bacteria, biocontrol, mining, big data and whale snot

On the 21st of March, over 30 Macquarie University staff and students attended the 7th annual symposium of JAMS, the Joint Academic Microbiology Seminars, at the Australian Museum. JAMS was very popular on Twitter, with the #JAMS7 hashtag trending on the day.

Six students from the Paulsen and Tetu groups presented posters and Vanessa Pirotta won the student poster prize. Congratulations Vanessa!

Our new posters will feature in the corridors of our department to show off the exciting microbiology work happening in our group.

A major topic of the day was remediation of contaminated sites with talks on amending microbial communities to assist with remediation, microbes using atmospheric hydrogen to survive in nutrient depleted environments, and stochastic vs directed assembly of microbial communities in mine tailings.

Continuing the environmental microbiology theme there were also talks on marine viruses in contrasting environments, and the physiology and metagenomics of plant-fungi associations.

On top of all of that it was great to hear about the valuable work the EMCR Forum is doing on behalf of early- and mid-career STEM researchers, and to everyone’s relief it’s free to join.

Thanks to the JAMS organising committee for another excellent microbiology meeting – we’re all looking forward to the next monthly JAMS meeting (for more information visit jams.org.au).

A minefield of data issues?

Even creating a small amount of data for my Masters project has brought home to me some of the issues around data – how to store it, where to store it, in what format to store it, how to ensure the appropriate people have access to it, how to stop people accessing it if they shouldn’t have access to it, how to future proof the storage, how to ensure the data and method used to collect it remain linked, who gets to keep it.

And that’s just for a few small plant biology experiments for my Masters. I’m sure there are many more levels of complexity for confidential data and big data. Some of these issue were discussed briefly with my Masters cohort, but it seems like that short conversation was only scratching the surface. I’m sure that as a (very) early career researcher there are a lot of things I don’t know and even more things I’m not even aware that I need to know.

 

Brightfield microscope image of Australian wild cotton (G. australe) leaf cross-section – one of the types of data from my Masters project (Photo: Belinda Fabian)

During my research break between my Masters and my PhD I’m working on up-skilling in a variety of areas; some directly related to my potential research topic(s), some which are generally related to study and/or my career (e.g. learning to code and using R) and others that just broaden my horizons (both scientifically and personally). One of the general study/career areas I’m learning about is data management through the 23 [research data] things program (see below for more information).

I see the 23 [research data] things program as helping me with generic study/career knowledge and skills and ideally it will will form part of a firm footing for me as a researcher. Awareness of the issues related to data management is important for researchers (and keeping digital data adds more concerns), but from my experience an understanding of it comes in a very piecemeal fashion during research training (as with many other things). So hopefully participating in this program will help me get out in front of the curve and make me aware of issues, solutions and strategies for managing data and where to find information down the track when the need becomes pressing.

Things you need to know:

The 23 [research data] things is a program run through ANDS (Australian National Data Service). More information can be found here. There’s an introductory webinar on tomorrow 1 March, 12.30-1.30 AEDT.

The program is free and runs from March to November 2016 (I know that sounds like a lot, but the FAQs suggest that it will only take about an hour a week and there will be breaks and catch-up opportunities during the year).

The program is advertised as being of interest to lots of different types of people – from the 23 [research data] things website: “If you are a person who cares for, and about, research data and want to fill in some gaps, learn more, find out what others are thinking… then this may be for you!” I’m getting involved as a research who will deal with data in my career, but if you’re a person who creates or cares for data then the program may be of interest to you too.

There’s a Meetup group for discussing the activities and other thoughts about the program and search #23RDThings on Twitter for all the buzz.