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

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 (in chronological order) and a summary of the information I noted down. Based on past conference dates I’ve guessed some conference timings (I’ve noted them as predicted). 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!

*last updated 15 April 2020

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2020

ASPB Plant Biology 2020
July 25-29, 2020 – Washington DC, USA
(Contingency planning underway to potentially move the meeting online)

Plant Health, Agriculture & Bioscience conference (PHAB 2020)
September 9-11, 2020 – The Hague, Netherlands
(Monitoring the situation with COVID-19)

International Plant Health Conference
October 5-8, 2020 – Helsinki, Finland
‘Protecting Plant Health in a Changing World’ – one of the key events of the International Year of Plant Health

Harnessing the Plant Microbiome
October 23-25, 2020 – University of California, Davis, USA
(Monitoring the situation with COVID-19, proceeding as planned at this time)

13th Arab Conference of Plant Protection
November 1-6, 2020 – Hammamat, Tunisia

16th Congress of the Mediterranean Phytopathological Union
November 17-20, 2020 – Limassol, Cyprus
(Rescheduled from March 2020 due to COVID-19)

11th Australasian Soilborne Disease Symposium
November 24-27, 2020 – Cairns, Queensland, Australia

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2021

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

11th symposium of the International Society of Root Research
May 24-28, 2021 – Missouri, USA

16th Meeting of the IOBC-WPRS Working Groups “Biological and Integrated Control of Plant Pathogens”
June, 2021 (dates TBA) – Gdansk, Poland
Meeting theme: Challenges in biocontrol single strains versus synthetic consortia
(Postponed from 2020 due to COVID-19)

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

14th International Conference on Plant Pathogenic Bacteria (ICPPB)
June 6-11, 2021 – Assisi, Umbria, Italy
(Postponed from 2020 due to COVID-19)

PAG Asia 2021
Affiliated with the Plant and Animal Genome Conference (PAG) held in January
June 9-11, 2021 – Shenzhen, China

12th International IOBC-WPRS Workshop on Pome Fruit Diseases
IOBC-WPRS Working Groups “Integrated Plant Protection in Fruit Crops”, Sub Group “Pome Fruit Diseases”
June 14-17, 2021 (tentative) – Plovdiv, Bulgaria
(Postponed from 2020 due to COVID-19)

XIX Congress of International Society of Molecular Plant-Microbe Interactions
June 25-29, 2021 – Jeju, Korea

Plant Biology Europe 2020
(bi-annual event jointly organised by EPSO and FESPB)
June 28-July 1, 2021 – Turin, Italy
(Postponed from 2020 due to COVID-19)

ASPB Plant Biology 2021
July 17-21, 2021 – Pittsburgh, USA

IOBC-WPRS Working Groups “Integrated Control in Protected Crops, Temperate and Mediterranean Climate”
Date TBA (tentative late August-early September 2021) – Brest, France
(Postponed from 2020 due to COVID-19)

13th International Congress on Plant Molecular Biology (IPMB2021)
October 24-28, 2021 – Cairns, Queensland, Australia
Triennial conference (last one held in 2018)

25th International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops
Date TBA – Amersfoort, The Netherlands
(Postponed from 2020 due to COVID-19)

Predicted: AusME – Australian Microbial Ecology conference
(held every 2 years – last one 2019)

Predicted: Biennial conference of Australasian Plant Pathology Society
Hobart, Tasmania
(held every 2 years – last one 2019)

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

Predicted: MiCROPe2021
(Held every 2 years – last one 2019)

Predicted: 7th Asian PGPR Conference
(Held every 2 years – last one 2019)

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2022

ASM Microbe 2022
June 9-13, 2022 – Washington D.C., USA

ASPB Plant Biology 2022
July 9-13, 2022 – Portland, Oregon, USA

Combio 2022
September 28-30, 2020 – Melbourne, Australia
Incorporates annual meetings of five Australian and New Zealand biological societies
(Postponed from 2020 due to COVID-19)

Predicted: 5th International Symposium on Biological Control of Bacterial Plant Diseases
(Held every 3 years – last one 2019)

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2023

ASM Microbe 2023
June 15-19, 2023 – Houston, Texas

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

ASPB Plant Biology 2023
Dates and location TBA

ICPP2023: 12th International Plant Protection Congress
“ONE HEALTH for all plants, crops and trees”
(Held every 5 years)
August 20-25, 2023 – Lyon, France

Predicted: Rhizosphere6
(Held every 4 years? last one 2019, one before 2015)

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Past conferences: 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

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Past conferences: 2019

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

8th International Conference on Polar and Alpine Microbiology
February 4-8, 2019 – Hamilton, New Zealand

AusME – Australian Microbial Ecology conference
February 11-13, 2019 – University of Western Australia

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

Biopesticide Summit 2019
July 2-3, 2019 – Swansea University, Swansea, UK

Rhizosphere5
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

Canadian Soil Science annual meeting
July 9-13, 2019 – Saskatoon, Saskatchewan, Canada

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

17th International Conference on Pseudomonas
July 22-26, 2019 – Malaysia

2019 International Congress on Invertebrate Pathology and Microbial Control
(52nd Annual Meeting of the Society for Invertebrate Pathology)
(17th Meeting of the IOBC-WPRS Working Group “Microbial and Nematode Control of Invertebrate Pests”)
July 28-August 1, 2019 – Valencia, Spain

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

Plant Health 2019
American Phytopathological Society annual meeting
August 3-7, 2019 Cleveland, Ohio, USA

6th International Conference on Bacterial Blight and Bacterial Leaf Streak of Rice
August 18-22, 2019 – Cantho City, Vietnam

Arms Race: The Evolution of Plant Pathogens and Their Hosts
September 2-3, 2019 – Bristol, UK

3rd Wild Plant Pathosystems Conference
September 16-19, 2019 – close to Frankfurt, Germany

Biocontrol Asia
September 25-27, 2019 – Chengdu, Sichuan Province, China

9th meeting of the IOBC-WPRS Working Group “Integrated Protection in Oak Forests”
October 7-11, 2019 – Oeiras, Portugal

2nd Biopesticides North America Conference
October 9-10, 2019 – Orlando, Florida, USA

Meeting of the IOBC-WPRS Working Group “Integrated Protection of Field Vegetables”
October 13-16, 2019 – Stratford-upon-Avon, UK

ABIM 2019, Annual Biocontrol Industry Meeting (ABIM)
October 21-23, 2019 – Basel, Switzerland

Meeting of the IOBC-WPRS Working Group “Integrated Protection in Viticulture”
November 5-8, 2019 – Vila Real, Portugal

XIX International Plant Protection Congress (IPPC2019)
November 10-14, 2019 – Hyderabad, India

Plant BioProTech 2019: 2nd International Symposium on Plant Bioprotection Sciences and Technologies
November 19-22, 2019 – Marrakesh, Morocco

Advances in Biocontrol and IPM 2019: Addressing the Innovation Crisis
November 20-21, 2019 – Lincolnshire, UK

22nd Biennial Australasian Plant Pathology Society conference
November 25-28, 2019 – Melbourne, Australia

4th Australian Pathogen Bioinformatic Symposium (APBS)
Additional ‘workshop’ for Australasian Plant Pathology Society conference
November 25, 2019 – Melbourne Australia

Australian Society of Plant Scientists (ASPS) conference
November 24-29, 2019 – Melbourne, Australia

Ecological Society of Australia conference
November 24-29, 2019 – Hobart, Australia

New Zealand Microbiological Society (NZMS) annual conference
November 25-28, 2019 – Palmerston North, New Zealand

VIII Congress on Plant Protection: “Integrated Plant Protection for Sustainable Crop Production and Forestry
November 25-29, 2019 – Zlatibor, Serbia

MiCROPe2019 International Symposium: Microbe-Assisted Crop Production – Opportunities, Challenges and Needs
December 2-5, 2019 – Vienna, Austria

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Past/cancelled conferences: 2020

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

Microbiology Society Annual Conference
March 31-April 3, 2020 – Edinburgh, Scotland, UK
(Cancelled due to COVID-19)

14th International Conference on Plant Pathogenic Bacteria (ICPPB)
June 7-12, 2020 – Assisi, Umbria, Italy
(Postponed to 2021 due to COVID-19)

12th International IOBC-WPRS Workshop on Pome Fruit Diseases
IOBC-WPRS Working Groups “Integrated Plant Protection in Fruit Crops”, Sub Group “Pome Fruit Diseases”
June 15-18, 2020 – Plovdiv, Bulgaria
(Postponed to 2021 due to COVID-19)

PAG Asia 2020
June 17-19, 2020 – Shenzhen China
(Cancelled due to COVID-19)

ASM Microbe 2020
June 18-22, 2020 – Chicago, Illinois, USA
(Cancelled due to COVID-19, next meeting June 2021)

25th International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops
June 22-26, 2020 – Amersfoort, The Netherlands
(Postponed to 2021 due to COVID-19)

Plant Biology Europe 2020
(bi-annual event jointly organised by EPSO and FESPB)
June 29-July 2, 2020 – Turin, Italy
(Postponed to 2021 due to COVID-19)

8th Conference on Beneficial Microbes
July 12-16, 2020 – Madison, Wisconsin, USA
(Cancelled due to COVID-19)

IOBC-WPRS Working Groups “Integrated Control in Protected Crops, Temperate and Mediterranean Climate”
August 31–September 3, 2020 – Brest, France
(Postponed to 2021 due to COVID-19)

16th Meeting of the IOBC-WPRS Working Groups “Biological and Integrated Control of Plant Pathogens”
September 14-17, 2020 – Gdansk, Poland
(Postponed to June 2021 due to COVID-19)

5th Korea-Japan Joint Symposium on Plant Pathology
September 14, 2020Tsukuba Science City, Ibaraki, Japan
Adjunct symposium with ACPP 2020 – joint meeting of The Phytopathological Society of Japan (PSJ) and The Korean Society of Plant Pathology (KSPP)
(Cancelled due to COVID-19)

Asian Conference on Plant Pathology 2020 (ACPP 2020) 
September 15-18, 2020 – Tsukuba Science City, Ibaraki, Japan
(Cancelled due to COVID-19)

Combio 2020
September 29 – October 2, 2020 – Melbourne, Australia
Incorporates annual meetings of five Australian and New Zealand biological societies
(Postponed to 2022 due to COVID-19)

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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).