Musings on a meeting of Australasian plant pathologists

In November 2019 I was excited to attend the Australasian Plant Pathology Society’s biennial conference in Melbourne. A big drawcard for me were the fantastic plenaries and keynotes spread across all three days of the conference. To start off Brett Summerell, the APPS President, showed us how we can effectively communicate scientific findings in a ‘post-truth, post-trust, post-expert world’ where facts are outweighed by opinion. Sophien Kamoun gave the EMBO Keynote lecture where he stressed the importance of sequencing and releasing the genomes of emerging plant pathogens, the new modes we have for releasing information and the impact that worldwide collaboration and free flow of information can have on a disease outbreak. There were also amazing plenaries by Carolee Bull on translational taxonomy, George Sundin on the fire blight pathogen, Thierry Candresse on viral detection with high throughput sequencing, Hailing Jin on small RNAs in plant-pathogen interactions and Neena Mitter on the development of an RNA spray for crop protection. I could go on and on!

There were so many interesting sounding talks across the five parallel sessions – I really wanted to have a Hogwarts time-turner so I could manage to be in multiple places at once! In the end I decided to concentrate my attention on the Biocontrol, Plant-Microbe Interactions and Pathogenomics sessions. These topics complement my PhD work where I’m using a genome-wide methodology to identify plant colonisation genes of a biocontrol bacteria. There were so many fascinating talks – some of the highlights that pushed me to the edge of my knowledge were on fungal genome sequencing, small RNAs and fungal effectors.

The three poster sessions were really busy! I enjoyed seeing a broad cross-section of plant science and meeting so many great scientists. The poster sessions gave me a peek into research areas where I didn’t get to see presentations and gave me lots of fantastic ideas for poster designs and the ways people use posters to communicate their science. It was wonderful to see both early career researchers and more senior members of the community presenting posters. I haven’t seen this broad range of career stages presenting posters at other conferences. This was a really great way to approach more senior scientists.

As well as attending the main conference I really enjoyed participating in two of the satellite sessions. The 4th Australian Pathogen Bioinformatic Symposium (APBS) was held at Agribio, La Trobe University the day before the main conference. I presented my work on transposon insertion sequencing in a plant-associated bacteria and had some great interactions with the researchers in the audience. It was a low-key, collegial start to the conference which meant I already knew a few people when I got to the much bigger main conference. Afterwards I enjoyed the Molecular Plant-Microbe Interactions joint session with the Australian Society of Plant Scientists, again at AgriBio. There were some really engaging presentations on topics as diverse as engineering the root microbiome with plant root exudates, detecting compounds on the surface of pathogenic fungi, and the transport of iron in Rhizobia-legume symbiosis.

To round out a wonderful conference experience there were two fabulous social events. The welcome reception was held the evening before the first full day of the conference and was a superb way to meet new people (plus the food was amazing!). The gala dinner was a more formal affair held in the stunning Mural Hall. I met a wonderful range of researchers over dinner and was introduced to some people I wouldn’t have met otherwise.

I’m very grateful for the support of APPS which allowed me to attend the conference, present my PhD research and meet so many fantastic scientists. Thank-you as well to the organising committee for supporting gender equality and making sure that there was gender balance in the presenters at every level.

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).

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.

Google Scholar is Filled with Junk Science

An interesting commentary on the state of Google Scholar’s search results.

I haven’t personally experienced the junk science results in Google Scholar that this author discusses, but then again my current research may not be attractive for predatory publishers. I’m focusing on plant physiology and biochemistry, which may be less prone to junk science when compared with more controversial areas or topics.

But this problem is very important to keep at the front of your mind if you’re researching a new area and may not have the skills to evaluate the research and determine ‘good science’ from ‘bad science’.

Drought vs Deluge – How Will Grasslands Cope with Climate Change?

Climate change due to human activities is predicted to change many aspects of the environment, from atmospheric carbon dioxide to temperature and rainfall1. Modellers are confident in the projected temperature increases, but the predictions about rainfall are much less certain. Changes in rainfall patterns will impact on many aspects of ecosystems, including how nutrients move.

Associate Professor Sally Power studies how these nutrient cycles are being affected by human-induced changes in the environment. She took up a position two years ago at the Hawkesbury Institute of the Environment, University of Western Sydney after completing her studies and working at the Imperial College in London. She previously completed a post-doctoral position at La Trobe University, Melbourne and loved Australia, so now she’s here permanently. Associate Professor Power is passionate about the understanding the interactive impact of multiple climate drivers on ecosystems.

At a recent seminar at Macquarie University Associate Professor Power spoke about three projects she is involved with at the moment:

  1. Drought and diversity in the UK (DIRECT)
  2. Rainfall extremes (DRI-grass)
  3. Elevated CO2 impacts on forest nutrient cycling (EucFACE)

The DIRECT project (Diversity, Rainfall and Elemental Cycling in a Terrestrial Ecosystem) aims to answer questions about how grassland ecosystems will respond to predicted rainfall changes and whether biodiversity will buffer these effects of a rainfall pattern change2. To test these ideas the research team constructed an array of grassland plots with a range of plants functional groups – perennials, caespitose grasses and annual plants (Figure 1)3.

Figure 1. Plant traits selected for the DIRECT experiment Image: Grantham Institute, Imperial College London (4).

Figure 1. Plant traits selection for the DIRECT experiment
Image: Grantham Institute, Imperial College London (4).

Rainfall predicted for the year 2100 (down 30% in summer, up 15% in winter) was applied to these plots to see how different vegetation communities might respond to rainfall changes2. Key ecosystem processes (such as respiration rate and nutrient cycling) were faster when there were a range of perennial plants present. Process rates in vegetation plots dominated by annual plants or caespitose grasses were not strongly affected by changes in rainfall2. This research showed that plant functional groups are important for maintaining grassland ecosystem function and they need to be considered in future management plans2.

In addition, the researchers used different plots in the same area and changed the rainfall pattern to see if drought and deluge impact differently on the grassland ecosystem. The rainfall treatments used were5:

  • Current levels;
  • Prolonged drought – 30% drop in rainfall; and
  • Reduced frequency – same amount of rain, concentrated into heavier falls less frequently.

The key findings were that changing the frequency of rainfall affected the number of species, especially the perennial species5. Surprisingly the number of species was not affected by the change in the total amount of rain (prolonged drought). The reduced rainfall frequency also lead to an increase in respiration and the grassland ecosystem switched from being a net carbon sink to net carbon source (from overall absorbing carbon to overall emitting carbon; Figure 2)5. The results of this experiment suggest that grassland ecosystems are relatively resistant to predicted rainfall changes5.

Figure 2. Change from carbon sink to carbon source for each of the  rainfall treatments (A = ambient; PD = prolonged drought; RF = reduced frequency). (Adapted from image presented by Associate Professor Sally Power)

Figure 2. Change from carbon sink to carbon source for each rainfall treatment (A = ambient; PD = prolonged drought; RF = reduced frequency; adapted from image presented by Associate Professor Power)

Associate Professor Power is also in the preliminary stages of some large scale experiments in western Sydney. The first of these experiments is DRI-grass (Drought & Root Herbivore Interactions in a Grassland Ecosystem). This study asks whether Australian grassland ecosystems have stronger responses to the amount or frequency of rain and whether these responses are affected by root herbivores6. Associate Professor Power emphasised that root herbivores are very abundant and their weight can exceed the weight of the sheep in a hectare7. Root herbivores can respond directly and indirectly to changes in rainfall patterns and can make it harder for plants to cope with climate change impacts8.

The research team has set up five different rainfall treatments: +50% rain; -50% rain; 3 week rainfall cycle with the same total amount of rain; summer drought; and the ambient conditions (Figure 3). The rainfall treatments only began in June 2013 and the root herbivores are not yet in place. So far the researchers have observed there are lower species abundances under drought conditions and an increase in summer rain has led to the dominance of African lovegrass.

Figure 3. Rainfall shelters for the DRI-grass experiment in the foothills  of the Blue Mountains (Image: The Hermon Slade Foundation; 6)

Figure 3. Rainfall shelters for the DRI-grass experiment in the foothills
of the Blue Mountains (Image: The Hermon Slade Foundation; 6)

The second project in western Sydney is being conducted in the EucFACE facility (Eucalyptus Free Air CO2 Enrichment)9 located in an intact Cumberland Plain Woodland ecosystem. Associate Professor Power and her team are looking at how elevated CO2 increases rates of nutrient cycling in the ecosystem. So far they have noticed there is an increase in available phosphorus, but no change in the amount of available nitrogen in elevated CO2 conditions.

Once the data is collected from these long term experiments, Associate Professor Power aims to understand some of the impacts of climate change on grassland ecosystems and make recommendations about how these systems should be managed to mitigate these impacts.

 

Learn more:

  1. IPCC (2013). Summary for Policymakers. In: Climate Change 2013: The Physical Science Basis. Working Group I Contribution to the IPCC Fifth Assessment Report. Cambridge University Press, Cambridge.
  2. Fry EL, Manning P, Allen DGP, Hurst A, Everwand G, Rimmler M & Power SA (2013). Plant Functional Group Composition Modifies the Effects of Precipitation Change on Grassland Ecosystem Function. PLoS ONE, 8(2): e57027. doi: 10.1371/journal.pone.0057027.
  3. Fry EL, Power SA & Manning P (2014b). Trait-based classification and manipulation of plant functional groups for biodiversity-ecosystem function experiments. Journal of Vegetation Science, 25, 248–261. doi: 10.1111/jvs.12068.
  4. Fry E, Hurst A, Everwand G, Rimmler M, Manning P & Power S (2009). Poster: “Diversity, Rainfall and Elemental Cycling in a Terrestrial ecosystem, (DIRECT)” presented at Committee for Atmospheric Pollution Effects Research AGM. https://workspace.imperial.ac.uk/climatechange/public/pdfs/CAPER_poster.pdf, accessed 25 May 2014.
  5. Fry EL, Manning P & Power SA (2014a). Ecosystem functions are resistant to extreme changes to rainfall regimes in a mesotrophic grassland. Plant Soil, doi: 10.1007/s11104-014-2137-2.
  6. The Hermon Slade Foundation (2014). Drought, deluge and diversity decline – How do root herbivores affect grassland resilience to predicted changes in rainfall patterns? http://www.hermonslade.org.au/projects/HSF_13_12/hsf_13_12.html, accessed 25 May 2014.
  7. Britton E (1978). A revision of the Australian chafers (Coleoptera: Scarabaeidae: Melolonthinae) Vol. 2. Tribe Melolonthini. Australian Journal of Zoology, 26, 1–150, Supplementary Series.
  8. Bardgett RD & Wardle DA (2003). Herbivore-mediated linkages between aboveground and belowground communities. Ecology, 84, 2258-2268. doi: 10.1890/02-0274.
  9. Hawkesbury Institute of the Environment (2014). EucFACE, http://www.uws.edu.au/hie/facilities/face, accessed 25 May 2014.

Synaesthesia – a ‘mixing of the senses’

The 2014 winner of the Paul Bourke Award was Associate Professor Anina Rich, a researcher from Macquarie University. This honour is awarded annually by the Academy of the Social Sciences in Australia to an early researcher who has achieved excellence in their field. As part of the award the winner presents their recent research in a public lecture at their home university. Dr Anina Rich studies how the brain integrates sensory information, particularly focusing on synaesthesia.

People with synaesthesia (synaesthetes) perceive sensory information in a different way. They can experience colours in association with letters, sounds or smells. The most common type of synaesthesia is letter-colour (Figure 1) but there are also other types such as auditory-visual and olfactory-visual synaesthesia. Chiou & Rich (2014) define synaesthesia as a ‘concurrent and distinct experience in a separate or the same modality’.

Figure 1. A representation of the colours one synaesthetes associates with each letter and number.

Figure 1. A representation of the colours one synaesthete associates with each letter and number.

Synaesthesia is present is 0.05-4% of the population and may have a genetic link. Relatives with synaesthesia are common and it is more prevalent in females than males. Many people don’t realise they are a synaesthete as their synaesthetic experience is constant over time and normal for them (perception in general is subjective).

Dr Rich is interested in studying synaesthesia as it may provide information about how information is normally integrated. Synaesthesia is not a medical disorder, there are no deficits associated with it. Many synaesthetes report that the extra sensory information they receive can be used to improve their memory and learning. Dr Rich is interested in seeing if synaesthetes have extra connections in the brain or are just using their connections between brain sections in a different way to the rest of the population.

To test this idea, Dr Rich and her team asked seven auditory-visual synaesthetes to describe the location on a grid of colours and shapes in response to auditory stimulus (Figure 2). Using functional MRI, Dr Rich and her team were able to work out that the occipital lobe in the back of the brain is stimulated when auditory-visual synaesthetes are presented with auditory information.

Figure 2. Examples of the stimuli presented to the auditory-visual synaesthetes (Chiou et al. 2013).

Figure 2. Examples of the stimuli presented to the auditory-visual synaesthetes (Chiou et al. 2013).

In addition, Dr Rich’s team has been investigating the areas of the brain non-synaesthetes use to process information about objects and colours. For example, a lemon is instantly recognisable as a lemon due to its yellow colour. When this colour is changed to something incongruent, like a red lemon, it becomes harder to identify. This object-colour binding is centralised in the anterior temporal lobe of the brain. Dr Rich is now conducting research to see if the same brain location of object-colour binding is seen in synaesthetes and what happens to their synaesthetic experience if the activity of this brain region is temporarily disrupted (Chiou et al. 2014).

Studying synaesthesia and how the brain processes sensory information is important as it can provide information about how learning and experience can alter our perception. As Dr Rich said in her presentation “what we already know has huge influence on what we think we see”. This work has implications for designing environments where people are required to process multiple sources of information, such as airplane cockpits.

To learn more:

Chiou R & Rich AN (2014). The role of conceptual knowledge in understanding synaesthesia: Evaluating contemporary findings from a “hub-and-spokes” perspective. Frontiers in Psychology, 5(105), 2-18. doi:  10.3389/fpsyg.2014.00105.

Chiou R, Stelter M & Rich AN (2013). Beyond colour perception: Auditory-visual synaesthesia induces experiences of geometric objects in specific locations. Cortex, 49(6), 1750-1763.

Chiou R, Sowman PF, Etchell AC & Rich AN (2014).A Conceptual Lemon: Theta Burst Stimulation to the Left Anterior Temporal Lobe Untangles Object Representation and Its Canonical Color. Journal of Cognitive Neuroscience, 26(5) 1066-1074. doi:10.1162/jocn_a_00536.