PhotosynQ Focus

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Matthew Daniel, an Arborist from Australia and one of PhotosynQ’s most active users.

matthew

Matthew is the director of Tree Preservation Australia and CEO of Global Urban Forest Pty Ltd, a company dedicated to the relationship between soil and tree health and the science of urban forestry. He travels to many cities in Australia and abroad collecting data on tree and soil health and prescribing proper health care programs to ensure that cities have happy, healthy trees. These prescriptions include compost tea’s, deep root soil injections, and vascular stem injections of specially formulated microbial plant and soil health inoculants and organic stimulants. However, his job was limited by the lack of affordable tools and the ability to share data and results with others.

How Matthew Connected with PhotosynQ

Matthew Daniel was born and raised in Tasmania, where he first developed his interest in trees and the outdoors in general. We asked him what his first memories with trees were and he told us “When I was 5 years old my uncle found me 40 feet up a tree, freaked my mum out”, no doubt this guy was destined to climb trees for a living! He would eventually receive training and certifications for arboriculture, working near high voltage power lines and in confined spaces, become a partner in Tree Preservation Australia and eventually founded Global Urban Forest Pty Ltd.

From the moment he first heard about PhotosynQ he knew “it was exactly what I needed to understand the tree health response to soil health intervention.” He has now completely integrated the PhotosynQ platform into his workflow saying “I use PhotosynQ before, during and after all the trees I work with.” That is a lot of trees!

He successfully applied to be a PhotosynQ beta tester and created his main project tree health calculator – Beta/Experts Program – 2015-2017, which has over 8,000 data points. Matthew recently received the new MultispeQ v1.0 and is working hard to build collaborations with community groups across Australia.

Now What?

Ultimately, Matthew wants to use PhotosynQ as “an international collaborative platform to be a major part in quantifying and mitigating climate change.” Matthew believes that a global arborist community that shares data on a common, open platform can do more than improve the health of individual urban trees. It can also help to mitigate one of the causative factors of the Urban Heat Island Effect, namely a lack of vegetation in cities. Lack of vegetation in cities decreases levels of both evapotranspiration and carbon dioxide removal. It has been observed over the last century that cities are significantly warmer than the rural areas that surround them. The UHI effect affects many areas of life, such as the weather, health and the environment. It will increase the production of rain clouds and thunder over your city, make you more prone to violence during heat waves, increase your electricity bill, and even kill off fish in lakes and streams just outside your city if mitigation processes are not undertaken. By going around Australian cities and learning about the trees that are present, Matthew and a global arborist community can learn which trees are most effective at mitigating the UHI effect and make your city a more enjoyable environment.

He knows this will not be easy, but it’s the potential that is driving Matthew. The potential to build a global arborist community that can collect data for cities that they can then utilize to manage their urban tree population, the potential to reduce the urban heat island effect, and finally, the potential to mitigate the effects of climate change.

Thank you to Matthew Daniel for allowing us to write about him and taking the time to answer all our questions. Hope to see you back in the US soon!

 

PhotosynQ Focus

Now that the MultispeQ v1.0 instruments are released, we want to share some stories of how the community is using PhotosynQ technolgies. Today we want to focus on Isaac Osei-Bonsu from Ghana, currently a PhD student in the Kramer Lab at Michigan State University.

 

OB_Isaac

Isaac Osei-Bonsu has been a PhotosynQ user since the early beta days in 2015. Over that time, he has collected over 13,000 measurements and created 46 PhotosynQ projects. As we worked towards releasing the new instruments, Isaac was often tasked with testing out new MultispeQ prototypes, and some iterations did not work so well! At the end of the day, Isaac collected over 3,000 measurements with MultispeQ v1.0 prototypes and his feedback helped us to modify and improve the MultispeQ throughout the design and manufacturing process.

Isaac’s background

Isaac hails from the west African nation of Ghana, where he was a research scientist for the Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI). In Isaac’s own words, “The company is a National Agricultural Research institution which focuses on research on different crop species with the aim to improve agriculture in Ghana.” He studied a wide variety of crops including cowpea, peanut, pepper, eggplants, citrus, mangoes, avocado, pear, papaya and watermelon.

Ghana, like many countries in sub-Saharan Africa, is struggling to achieve food security and develop a robust economy. This means that the government wants farmers to produce more high value crops, like cocoa, for international markets. However, this comes at the expense of land for growing food crops, which is why it is so important to improve the productivity and efficiency of important food crops.

What Isaac is doing now

Isaac arrived at MSU with the help of a Legume Scholars Award which he received from the Consultative Group on International Agricultural Research (CGIAR) in 2015. The Legume Scholars Program supports the graduate study of young scientists from developing countries so they can pursue research careers involving grain legumes  (http://legumelab.msu.edu/training/legume_scholars).

Isaac’s is studying the photosynthetic response of  grain legumes to abiotic stress in order to improve grain legume production. His interest with automatic plant phenotyping was piqued “by the simple yet powerful nature of the MultispeQ device, connected to the PhotosynQ platform, and its possible use for rapid phenotyping in the field.” Manual phenotyping can be extremely slow and not entirely accurate. The MultispeQ instrument and the PhotosynQ platform make it easy and quick. He now uses the MultispeQ in most of his experiments. He doesn’t just use PhotosynQ because it is easier, but also because it allows him to develop a deeper understanding of abiotic stress responses in grain legumes.

Thank you to Isaac for taking some time out of your busy days to answer all of our questions. Having Isaac around our lab is a pleasure and his input into the PhotosynQ platform and MultispeQ instruments have been invaluable. We hope our instruments can help him as much as he has helped us and wish him luck in his continued research.

Teachers Workshop at Kellogg Biological Station

I traveled to the MSU K-12 Partnership 2017 Spring Workshop at the Kellogg Biological Station on April 18 with Klara Schnargl. Klara is a Future Academic Scholars in Teaching fellow and she is interested in strengthening the connections between Universities and K-12 education programs. The purpose of the program on this day was to bring graduate students and postdocs from MSU together with middle and high school biology teachers.

Klara and I were going to run a session for teachers who were interested in new, hands on, methods of teaching kids about photosynthesis. We thought that the MultispeQ instrument, combined with the ease of generating simple graphs on the PhotosynQ platform, could be a great way for students to visualize how plants use the light energy they capture and how they respond and regulate photosynthesis in response to their environment.

education blog image

We conducted a really simple experiment with the teachers so they could see PhotosynQ in action. Klara brought along two orchids in small pots and it was a beautiful, sunny spring day. So, we quickly created a project (‘KBS educational module April, 2017’) on www.photosynq.org that asked which session (we had one morning and one afternoon session) was collecting data and whether the plant was inside or outside (2 minutes). Then, after a brief talk about how to connect your phone to the MultispeQ and how to take a quality measurement (4 minutes) the teachers collected some measurements from the orchids in the classroom (5 minutes). Next, we took our orchids out into the sunshine and gave them time to adjust to their new surroundings (2 minutes). After a few more MultispeQ measurements we were heading back into the classroom to check out our data (5 minutes). We logged on to our PhotosynQ project and created a couple of graphs to compare Phi2, PhiNPQ, PhiNO and LEF inside and outside (4 minutes).

In 22 minutes we went from ‘this is MultispeQ’ to ‘look how our orchids regulated incoming light in our experiment.’

The teachers that came to our session were great, with lots of fun ideas on how they could use PhotosynQ in their classrooms and we are looking forward to working with them in the future.

Science Fun – Science faire in Ukraine

A science faire was held on May 22nd in Ternopol – IV at Theater Square.  The goal of the event was to popularize science among young people and excite the next generation of scientists in Ukraine.

There were about a dozen tents where schools and universities demonstrated scientific experiments in chemistry, biology and physics to the public.  Students of the Faculty of Chemical and Biological (http://chem-bio.com.ua), part of Ternopil Volodymyr Hnatyuk National Pedagogical University, http://tnpu.edu.ua)  presented PhotosynQ, created by scientists at Michigan State University.

Schoolchildren, students, and young scientists had the opportunity to personally touch science in the truest sense of the word. With the device MultispeQ, anyone could measure the progress of biophysical processes otherwise invisible to the eye in leaves of Phaseolus vulgaris plants and share data throughout the world via the PhotosynQ platform.

The interest and excitement generated at this event shows that science can be very interesting and exciting thing that unites the world.

by Andriy and Nataliia Herts

MultispeQ in Malawi

As the development team focuses on manufacturing the MultispeQ v1.0, we’ll have a series of articles from project partners and developers we hope you find interesting. We’ve had a great response to the pre-release, so thanks to everyone! – Greg

malawi multispeq users
(left) Masters student Hellen Mwale and Kareem Longwe practice data collection with the MultispeQ to get ready for data collection on FRN’s in Central Malawi. (right) Frank Mnthambala and Margaret Chiipanthenga collect data on soybeans in a greenhouse in Bvumbwe, Malawi to identify drought tolerant cultivars.

Over the past year we have partnered with a number of researchers in Malawi who have collected over 30,000 measurements on 15 different projects using PhotosynQ. Our partners in Malawi include researchers from the Department of Agricultural Research Services (DARS), Lilongwe University of Agricultural Research Services (LUANAR), and a private seed company (Global Seeds). I just got back from 2 weeks in Malawi meeting with them and getting their feedback on PhotosynQ.

Access to high quality laboratory equipment is lacking in Malawi, so researchers are very excited about what information MultispeQ can provide to them. In many cases, field based plant breeding and cropping systems research has been limited to data that can be recorded with a scale and tape measure. With PhotosynQ, they can see beyond what happened (e.g. how the crop yielded) and can start to understand the reasons why crops performed the way they did (e.g. how plants regulated photosynthesis to adapt to their conditions).

Despite a lot of enthusiasm, there are some real challenges that need to be overcome to collect quality data. Internet infrastructure in Malawi is very poor and the internet is often too slow to work effectively on-line or doesn’t work at all. This makes it difficult for users to create projects and analyze results. But it also means that users don’t update their mobile app very often. So they may still be trying to work around bugs in an older version of the app that we have already fixed in a newer release.

Another challenge to using PhotosynQ in Malawi is frequent ‘brown-outs.’ Partners can’t count on the electricity being on when they need to recharge their phones or MultispeQ batteries. Some partners in Malawi have responded by using ‘power banks.’ A power bank is a small extra battery that can hold enough charge to recharge your phone 2-3x. They will plug it right into their phone or tablet’s usb port in the field and recharge their mobile device while taking measurements. It’s one more thing to hold onto in the field, but it solves a problem.

malawi battery pack
A student uses a power bank to keep his mobile device working in the field.

This coming year our partners have even more interesting projects planned. Everything from variety trials of soybean, sweet potato, maize, common beans, and pigeonpea to studies analyzing the effects of cropping systems on crop performance (click here to see a list of existing projects + data). These projects will take place on research stations and smallholder farms all around Malawi.

Two Master’s students from LUANAR will be using PhotosynQ on Farm Research Networks (FRN’s) to assess how different legume-based cropping systems can increase production on smallholder farms. FRN’s are research trials that are located on smallholder farms, instead of research stations, and are managed by the farmers themselves. As such, they paint a much more accurate picture of how ‘new’ cropping systems affect crop production on smallholder farmers. What’s really exciting is that these 2 students will be collecting data on FRN’s that include over 300 farms in 3 districts in Malawi. Even if they only collect PhotosynQ data on 1/3 of the farms, it will be the largest on-farm data collection using PhotosynQ to date! And it will take place with poor internet connectivity and frequent power outages!

More Malawi Projects

Dan TerAvest

Who’s using the MultispeQ? Let’s see…

As we approach the next version of the MultispeQ, I wanted to share stories from a few of our beta testers – Matt, Karen, and Kay from the MSU Kellogg Biological Station, Jeremy Harbinson from the University of Wageningen, and Jesse Traub from Michigan State University.  You can find even more stories here.  Hope this sparks some interesting ideas for applications in your lab, home, farm, work, or play 🙂

Kellogg Biological Station

Matthew Carey (REU student), Karen Stahlheber (postdoc) and Kay Gross (KBS director), Ecologists

Matthew Carey, measuring grass at Kellogg Biological Station
Matthew Carey, measuring grass at Kellogg Biological Station

Our group is interested in the response of switchgrass (Panicum virgatum) varieties to drought, and how that interacts with fertilizer use. We installed rain reduction shelters on fields planted with switchgrass ~6 years ago and managed either with or without fertilizer. These shelters reduce available soil moisture and simulate drought conditions that might occur with future global change. Throughout the summer, we monitored plant growth, chlorophyll fluorescence, xylem tension, and the abundance/diversity of mycorrhizae (fungi that live in symbiosis with plant roots). The eventual goal (after several field seasons) is to understand how the interactions between fertilizer application and arbuscular mycorrhizae diversity affect ecosystem services such as productivity, pathogen tolerance, drought tolerance, and soil carbon storage.PhotosynQ has been a great asset to our project because it allows us to measure any stress the plants may experience due to high light/low water conditions throughout the summer. By measuring Fv/Fm in the early hours of the morning we can understand if plants underneath the shelters have suffered damage to their photosynthetic machinery compared to control plants receiving ambient rainfall. We also can use the devices during the day to assess general photosynthetic performance and see if that differs between varieties or is changed by fertilizer use.

If PhotosynQ is successful, it could allow farmers of cellulosic biofuel crops like switchgrass to use the same tools to monitor their plants for stress or for responses to fertilizer.

Plant Sciences Department, University of Wageningen

Jeremy Harbinson, Plant Physiologist / University Lecturer

Jeremy Harbinson
Jeremy Harbinson

We try to understand better the operation, regulation and limitation of photosynthesis in vivo, both from physiological and genetic perspectives. We plan to use the PhotosynQ in teaching and as a tool for the more or less routine monitoring of leaf-level photosynthesis of plants in the field. The PhotosynQ concept opens many doors. In terms of eco or environmental physiology – or phenotyping, particularly that of photosynthesis, it enables large scale data collection in a way that has previously not been possible. It helps close the gap between the diversity for physiological responses encountered in the field due to environmental and genetic reasons and the time required to get good data relating to these responses. Low-cost, fast, and measuring a large number of processes makes many things possible that cannot be done with existing instruments which are expensive, often slow and limited in what they can measure. It is a revolutionary concept.

Department of Horticulture, Michigan State University

Jesse Traub, PhD candidate

Jesse Traub, MSU Horticulture
Jesse Traub, MSU Horticulture

We are investigating physiological differences among contrasting dry bean genotypes in their response to drought and heat stress. We are especially focusing on the response of photosynthetic parameters to these stresses. The PhotosynQ platform enabled us to screen large amounts of germplasm to determine at what severity of stress different bean genotypes started to become damaged.  If PhotosynQ became a standard tool for my discipline of plant physiology and plant breeding, it would provide an easy way to compare otherwise unrelated experiments and sets of data. This would be great for the reproducibility of experiments! I admire that the PhotosynQ project has been committed to making their hardware, software, and data freely accessible to all to use, learn from, and modify. I hope such sentiments continue to grow in the academic world.

This is just a few of the 100 or so people who used the MultispeQ Beta

You can find a few more stories about using PhotosynQ to develop tools for corals, identify agricultural best practices in Malawi, optimizing light in greenhouses in the Ukraine, and detect disease in soybeans in Michigan.  Next time, a progress report on the MultispeQ v1.0!

Hello Fargo, I’ve come for your beans!

Project: Bean Variety Trials at North Dakota State University
Project Leads: Juan Osorno and Ali Soltani, North Dakota State University
Goal: Collect photosynthesis and plant health data on 150 varieties of common bean for eventual QTL (genetic) mapping.

Project Page
View and analyze the data (create a login if necessary)
Juan Osorno’s NDSU page

 

Hello Fargo!
Hello Fargo!

This week I went to Fargo, North Dakota to meet with Professor Juan Osorno and post-doc Ali Soltani, bean breeders at North Dakota State University. I bet you didn’t know that NDSU has one of the premier bean breeding programs in the US – well they do!

On my flight in, I told the guy next to me I’d never been to North Dakota before, and his response was “You’re going to love it”… Love it? North Dakota? Well, yes, I did love it. People were nice, and it appeared that everyone was there because they wanted to be, which makes sense, you don’t end up in North Dakota for no reason. Agriculture is booming, and the the fields are gigantic (at least in comparison to the ones I was used to growing up in central New York). So, what were we doing there? I’ll let Ali give a recap:

So our goal is to show that you can correlate photosynthetic outcomes to actual genes or groups of genes.   This has so far proven difficult and slow to achieve for breeders especially in comparison with the dizzying pace of mapping the genome, which has been automated and has come down in cost many orders of magnitude over the last 15 years. We took measurements of 150 different varieties with 6 replicates each (900 measurements total).  Each measurement included two protocols: SPAD (a measure of leaf greenness which correlates to Nitrogen content) and Phi2 (a measure of photosynthetic efficiency).

Stephan collecting data using the Android app
Stephan collecting data using the Android app

It took us some time to get ready to collect data.  We had to go to a coffee shop to get internet to make sure everyone had an account at PhotosynQ.org and their cell phones had the PhotosynQ android app installed correctly.  But once we got to the field (a full 1.5 hours away!), taking measurements was a snap.  The only technical problems we had were swapping batteries as they needed to be recharged – that was a big success for us, and shows we’re ready to do real work with this thing!

MultispeQs charging their batteries after a hard days work.
MultispeQs charging their batteries after a hard days work.

So let’s look at some preliminary results using the online analysis tool (so you can view and play with the data too!  Note that you may have to create a login first). This tool is intended to be a Swiss Army knife of sorts – it can do lots of quick analysis, but none of them too deeply.  If you need to do multiple regression analysis… you’ll probably have to just download the data 🙂  We might to see more data in this project this week, as Ali and Stephan go back to a second field, we’ll see.  Also, Ali is working on more in depth device comparisons, to try to use statistics to parse out the variation coming from the device versus that coming from the varieties themselves.

 

We can also compare two variables on the X and Y axis. Here we have LEF (linear electron flow) a measure of energy from photosynthesis compared to light intensity. Each device has a separate series. These differences may be due to calibration, or differences in plants, hard to know yet.
We can also compare two variables on the X and Y axis. Here we have fluorescence in the steady state (normal light) versus that from a saturated state (very high light).  These differences may be due to calibration, or differences in plants, hard to know yet.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there's not perfect overlap there.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there’s not perfect overlap there.
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR - we'll have to investigate that!
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR – we’ll have to investigate that!
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.  Anything statistically significant here?… mmm… not quite yet.
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample - distribution isn't too bad!
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample – distribution isn’t too bad!  Not a lot of outliers which means the MultispeQs worked ok.
temperature by time
This graph doesn’t show much from a plant health perspective, but it does show how temperature in the device varied over time. In general we’ve found that people’s hands heat up the device the longer they hold it. You can see that effect here for each device (each series snakes upwards), and you can see how long it took us to take all our measurements. This is something else we need to address in the next version.
Here's a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct - cool!
Here’s a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct – cool!