USDA AFRI NIFA Agricultural Production Systems grant awarded to Menalled et al.

In 2016, I was a post-doc in the Menalled Lab, which studies plant and weed ecology in the context of agricultural production and sustainability.  There, I assessed soil bacterial communities under different farming management practices and climate scenarios.  I also helped to develop a grant proposal, which was just accepted by the USDA AFRI NIFA Agricultural Production Systems!  Leading this project is Dr. Fabian Menalled (as Principal Investigator, or PI), along with a number of other PIs; Dr. Amy Trowbridge, Dr. David Weaver, Dr. Tim Seipel, Dr. Maryse Bourgault, and Dr. Carl Yeoman, and collaborators Dr. Darrin Boss, Dr. Kate Fuller, Dr. Ylva Lekberg, and myself as a subaward PI.  I will again be providing microbial community analysis for this project, and collectively the project investigators will bring expertise in plant ecology, agronomy, economics, soil and plant chemistry, microbial ecology, agroecosystems, and more.

This research and extension project focuses on the needs of dryland agricultural stakeholders and it was designed in close collaboration with the NARC Advisory Board. While I was only able to attend one meeting, other team members regularly meet with Montana producers to discuss current issues and identify locally-sourced needs for agricultural research.  During this project, we will continue to meet with the NARC Advisory Board to share our results, evaluate implications, and better serve the producer community.

Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield and economic returns.

Project summary

The semi-arid section of the Northern Great Plains is one of the
largest expanses of small grain agriculture and low-intensity livestock
production. However, extreme landscape simplification, excessive reliance on
off-farms inputs, and warmer and drier conditions hinder its agricultural
sustainability. This project evaluates the potential of diversifying this region
through the integration of cover crops and targeted grazing. We will complement
field and greenhouse studies to appraise the impact of system diversity,
temperature, and precipitation on key multi-trophic interactions, yields, and
economic outputs. Specifically, we will 1) Assess ecological drivers as well as
agronomic and economic consequences of integrating cover crops and livestock
grazing in semi-arid systems, 2) Evaluate how climate variability modify the
impacts of cover crops and livestock grazing on agricultural outputs. Specifically,
we will 2.1) Compare the effect of increased temperature and reduced moisture
on agronomic and economic performance of simplified and diversified systems,
2.2.) Assess the impact of climate and system diversity on associated biodiversity
(weeds, insect, and soil microbial communities) and above- and belowground
volatile organic (VOC) compound emissions, and 2.3) Evaluate how changes in
microbially induced VOCs influence multitrophic plant-insect interactions.

Objectives

  1. Assess key ecological drivers as well as agronomic and economic consequences of integrating cover crops and livestock grazing in semi-arid production systems
    • Compare the agronomic and economic performance of simplified and diversified systems
    • Assess the impact of cover crops and livestock grazing on the associated biodiversity (weeds, insects, and the soil microbiota)
  2. Evaluate how climate conditions modify the impacts of cover crops and livestock grazing on semi-arid production systems
    • Compare the effect of temperature and soil moisture on agronomic and economic performance of simplified and diversified systems
    • Assess the impact of climate and system diversity on associated biodiversity and above- and belowground volatile organic compound (VOC) emissions
    • Evaluate how changes in VOCs emissions influence important multitrophic interactions such as resistance to wheat stem sawfly and natural enemy host location cues
  3. Integrate the knowledge generated into an outreach program aimed at improving producers’ adoption of sustainable diversified crop-livestock systems

Menalled lab at MSU seeking graduate students

The Menalled lab has MS and PhD opportunities in agroecology, “Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield, and economic returns”.

Last year, I did a post-doc in Dr. Fabian Menalled’s weed ecology lab at MSU exploring the effect of farming system and climate change on bacteria in the wheat rhizosphere.  If you love friendly lab groups, early morning field work, and being outside, then working in the Menalled lab in Bozeman, Montana might be the place for you.

Of course, in Montana, it helps if you also love winter…

What is academic Outreach/Extension?

Service can be a vaguely defined expectation in academia, but it’s an expectation to give back to our community; this can be accomplished in different ways and is valued differently by institutions and departments.  Outreach is an easily neglected part of science, because so often it is considered non-essential to your research.  It can be difficult to measure the effectiveness or direct benefit of outreach as a deliverable, and when you are trying to hoard merit badges to make tenure and your time is dominated by other responsibilities, you often need to prioritize research, teaching, advising, or grant writing over extension and service activities.  Nevertheless, public outreach is a vital part to fulfilling our roles as researchers.  Academic work is supported by public funding in one way or another, and much of our research is determined by the needs of stakeholders, who in this sense are anyone who has a direct interest in the problem you are trying to solve.

Depending on your research field, you may work very closely with stakeholders (especially with applied research), or not at all (with theoretical or basic research).  If you are anywhere in agriculture, having a relationship with your community is vital.  More importantly, working closely with the public can bring your results directly to the people out in the real world who will benefit from it.

A common way to fulfill your outreach requirement is to give public presentations.  These can be general presentations that educate on a broad subject, or can be specifically to present your work.  Many departments have extension specialists, who might do some research or teaching but whose primary function is to connect researchers at the institution with members of the public.  In addition to presentations, extension agents generate newsletters or other short publications which summarize one or more studies on a specific subject.  They are also a great resource for networking if you are looking for resources or collaborations, for example if you are specifically looking for farms in Montana that grow wheat organically and are infested with field bindweed.

For my new job, I’m shifting gears from agricultural extension to building science and health extension.  In fact, the ESBL and BioBE teams at the University of Oregon have recently created a Health + Energy Research Consortium to bring university researchers and industry professionals together to foster collaborations and better disseminate information.  The goals of the group at large are to improve building sustainability for energy and materials, building design to serve human use better, and building microbiology and its impact on human health. I have a few public presentations coming up on my work, including one on campus at UO on Halloween, and one in February for the Oregon Museum of Science and Industry Science Pub series in February.  Be sure to check my events section in the side bar for details.

Even when outreach or extension is not specified in your job title, most academics have some level of engagement with the public.  Many use social media outlets to openly share their current work, what their day-to-day is like, and how often silly things go wrong in science.  Not only does this make us more approachable, but it’s humanizing.  As hard as scientists work to reach out to the public, we need you to reach back.  So go ahead, email us (please don’t call because the stereotype is true: we really do hate talking on the phone), tweet, post, ping, comment, and engage with us!!

 

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Fort Ellis inoculation day

Today was a big day out in the field at Fort Ellis: virus inoculation day for the project I’ve been part of, on how farming system can alter reactions to adverse growing conditions (like climate change, weed competition, and disease).  This is the second year of the project, and the fifth year of the larger crop rotation study, so a lot is riding on being able to keep to the schedule.

Spring has been cool and wet here in Montana, which has presented us from being able to do work in the muddy fields but hasn’t slowed down the wheat or the weeds.  If the wheat is too developed when the virus is sprayed, the infection won’t manifest well enough to measure.  Thanks to carefully prepared protocols, seasoned personnel, and a stretch of sunny, dry days, we treated our plots and went home early!

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Harvesting a feast of data

My greenhouse trial on the legacy effects of farming systems and climate change has concluded!  Over this past fall and winter, I maintained a total of 648 pots across three replicate trials (216 trials per).  In the past few weeks, we harvested the plants and took various measurements: all-day affairs that required the help of several dedicated undergraduate researchers.

In case you were wondering why research can be so time and labor intensive, over the course of the trials we hand-washed 648 pot tags twice, 648 plant pots twice, planted 7,776 wheat seeds across two conditioning phases, 1,944 wheat seeds and 1,944 pea seeds for the response phase.  We counted seedling emergence for those seeds every day for a week after each of the three planting dates in each of the three trials (9 plantings all together).  Of those 11,664 plants, we hand-plucked 7,776 seedlings and grew the other 3,888 until harvesting which required watering nearly every day for over four months.  At harvest, we counted wheat tillers or pea flowers, as well as weighed the biomass on those 3,888, and measured the height on 1,296 of them.  And this is only a side study to the larger field trial I am helping conduct!  All told, we have a massive amount of data to process, but we hope to have a manuscript ready by mid-summer – stay tuned!

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Expanding Your Horizons for Girls workshop, MSU 2017

Yesterday I participated in the Expanding Your Horizons for Girls workshop at Montana State University!  EYH brings almost 300 middle-school aged girls from all over Montana for a one-day conference in STEM fields.  Twenty-seven instructors, including myself and other female scientists and educators, ran workshops related to our current research.  My presentations were on “Unlocking the Hidden World of Soil Bacteria”, with the help of undergraduate Genna Shaia from the Menalled Lab.

I gave the girls a brief presentation on microbial ecology, and how bacteria and fungi can affect plants in agricultural soil.  We talked about beneficial versus pathogenic microorganisms, and how different farming strategies can influence soil microbiota.  This was followed by two hands-on activities that they were able to talk home with them.  First, the girls made culture plates from living or sterile soil that was growing wheat or peas to see what kind of microbes they could grow.  Then, they planted wheat seeds in either living or sterile soil so they could track which soil made the seeds germinate faster.

 

The girls were enthusiastic to learn, asked lots of insightful questions, and it was awesome being able to share microbiology with kids who hadn’t given it much thought before!  If you are a woman in STEM, and have the opportunity to participate in a workshop or mentor a young scientist,  it is not only rewarding but can make a huge impact on encouraging women into STEM.

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Slideshow photos: Genna Shaia, reproduced with student permission.

Draft twice, submit once: the grant writing process

Today, the research team that I am a part of submitted a grant which I co-wrote with Dr. Tim Seipel, along with Dr. Fabian Menalled, Dr. Pat Carr, and Dr. Zach Miller. We submitted to the Organic Transitions Program (ORG) through the US Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA).  The culmination of months of work, and some 12+ hour days this past week to meet today’s deadline, this grant will hopefully fund some very exciting work in agriculture!

Research relies on grant money to fund projects, regardless of the type of institution performing the research, though commercial research centers may partially self-fund projects.  Most new research hires to universities will receive a “start-up package” which includes some funding for a few years to buy equipment, pay for a small, preliminary project, or temporarily hire a technician. Start-up funds are designed to hold a researcher over for a year or two until they may apply for and receive grant funding of their own.  Sooner or later, everyone in academia writes a grant.

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Grants may be available for application on a regular basis throughout the year, but some grant calls are specific to a topic and are made annually.  These have one submission date during the year, and a large number of federal grants are due during in the first quarter of the year, a.k.a. Grant Season.  University researchers find themselves incredibly pressed for time from January to March and will hole up in their office for days at a time to write complex grants.  Despite the intention of starting your writing early, and taking the time to thoroughly discuss your project design with all your co-PDs well before you start writing to avoid having to rewrite it all again, most researchers can attest that these 20-30 pages grants can get written over from scratch 2 or 3 times, even before going through a dozen rounds of group editing.

The Bright Idea

Most large grants, providing several hundred thousand to over a million in funding over several years, require project teams with multiple primary researchers (called Principal Investigators or Project Directors) to oversee various aspects of research, in addition to other personnel (students, technicians, subcontractors).  One researcher may conceptualize the project and approach other researchers (usually people they have worked with in the past, or new hires) to join the project.  Project ideas may get mulled over for several years before they mature into full grant submissions, or go through multiple versions and submissions before they are perfected.

The grant I just co-wrote investigates the use of cover crops in Montana grain production.  Briefly, cover crops are plant species which improve the soil quality but which you aren’t necessarily intending to eat or sell.  They are grown in fields before or after the cash crop (ex. wheat) has been grown and harvested.  Legumes like peas, beans, or alfalfa, are a popular choice because they fix nitrogen from its gaseous form in the atmosphere into a solid form in soil which other plants (like wheat) can use.  Other popular cover crop plants are great at bio-remediation of contaminated soils, like those in the mustard family (1, 2, 3). Planting cover crops in an otherwise empty (fallow) field can out-compete weeds that may grow up later in the year, and they can prevent soil erosion from being blown or washed away (taking the nutrients with it).  For our project, we wanted to know how different cover crop species affect the soil microbial diversity, reduce weeds, put nutrients back into soil, and improve the production of our crop.

We designed this project in conjunction with the Montana Organic Association, the Organic Advisory and Research Council, and Montana organic wheat farmers who wanted research done on specific cover crops that they might use, in order to create a portfolio of cover crops that each farmer could use in specific situations.  As these organizations comprise producers from across the state, our research team was able to get perspective on which cover crops are being used already, what growing conditions they will and won’t work in (as much of Montana is extremely dry), and what production challenges growers face inherent to planting, managing, and harvesting different plant types.

Drafting Your Team

When you assemble a research team, you want to choose Project Directors who have different experiences and focuses and who will oversee different parts of the project.  A well-crafted research team can bring their respective expertise to bear in designing a large and multi-faceted project.  For our grant, I am the co-PD representing the microbial ecology and plant-microbe interaction facet, about a third of the scope of the grant.  We will also be investigating these interactions under field settings, which requires a crop production and agroecology background, as well as expanding the MSU field days to include organic-specific workshops and webinars, which requires an extension specialty.

Because grant project teams are made up of researchers with their own projects and goals, in addition to providing valuable perspective they may also change the scope or design of your project.  This can be extremely beneficial early on in the grant-writing phase, especially as you may not have considered the limitations of your study, or your goals are too unambitious or too lofty.  For example, the cover crop species you want to test may not grow well under dry Montana conditions, do you have a back-up plan?  However, as the submission deadline looms larger, changing the focus of your study can cost you precious writing time.  Working in a research team requires a high degree of organization, a flair for communication, and an ability to work flexibly with others.

Identifying the research question

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All grants center around a Project Narrative, and funding agencies will provide detailed instructions on how to format your project grant.  Pay strict attention- in very competitive pools your grant can be flagged or rejected for not having the appropriate file names or section headers.  The Narrative gives introductory background on your topic that details the research that has previously been published.  Ideally, it also includes related studies that you and your team have published, and/or preliminary data from projects you are still working on.  The aim is to provide a reasoned argument that you have correctly identified a problem, and that your project will fill in the knowledge gaps to work towards a solution.  Grant panels are made up of researchers in a related field, but they may not be intimately aware of your type of research.  So, you need to be very specific in explaining  your reasoning for doing this study.  If your justification seems weak, your project may be designated as “low priority” work and won’t get funded.

In our case, cover crops have been used by farmers already, but not much basic research has been done on the impacts of picking one species over another to plant.  Thus, when cover crops fail, it may be unclear if it was because of unfavorable weather, because the previous crop influenced the soil in ways which were detrimental to your new crop, because you seeded your crop too sparsely and weeds were able to sneak in and out-compete, because you seeded too densely and your crop was competing with itself, or something else entirely.

You also need to identify the specific benefits of your project.  Will you answer questions? Will you create a new product for research or commercial use?  Will organic producers be able to use what you have learned to improve their farm production?  Will you teach students?  When you are identifying a need for knowledge and describing who or what will benefit from this study, you need to identify “stakeholders”.  These are people who are interested in your work, not people who are directly financially invested.  For us, our stakeholders are organic wheat farmers in Montana and the Northern Great Plains who want to integrate cover crops into their farming as an organic and sustainable way to improve crops and reduce environmental impact.  Not only did our stakeholders directly inform our project design, but we will be working closely with them to host Field Day workshops, film informative webinars, and disseminate our results and recommendations to producers.

Crafting Your Experimental Plan

Once you have identified a problem or research question, you need to explain exactly how you will answer it.  For experiments in the laboratory or field, you need to be incredibly specific about your design.  How many samples will you take and when?  Will you have biological replicates?  Biological replicates are identical treatments on multiple individual organisms (like growing a single cover crop species in four different pots) to help you differentiate if the results you see are because of variation in how the individual grows or because of the treatment you used.  Do you have technical replicates?  Technical replication is when you analyze the same sample multiple times, like sequencing it twice to make sure that your technology creates reproducible results.  Will you collect samples which will provide the right type of information to answer your question?  Do your collection methods prevent sample deterioration, and how long will you keep your samples in case you need to repeat a test?

In addition to describing exactly what you will do, you need to explain what might go wrong and how you will deal with that.  This is called the Pitfalls and Limitations section.  Because basic research needs to be done in controlled environments, your study may be limited by a “laboratory effect”: plants grown in a greenhouse will develop differently than they will in a field.  Or, you might not be able to afford the gold-standard of data analysis (RNA sequencing of the transcriptome still costs hundreds of dollars per sample and we anticipate over 1,200 samples from this project) so you need to justify how other methods will still answer the question.

Supporting Documents

Even after explaining your research question in the Narrative and your design in the Methods sections, your grant-writing work is still far from complete.  You will need to list all of the Equipment and research Facilities currently available to you to prove that your team can physically perform the experiment.  If you will have graduate students, you need a Mentoring Plan to describe how the research team will train and develop the career of said student.  If you will be working with people outside of the research team, you will need Letters of Support to show that your collaborators are aware of the project and have agreed to work with you, or that you have involved your stakeholders and they support your work.  I was delighted by the enthusiasm shown towards this project by Montana organic producers and their willingness to write us letters of support with only a few days’ notice!  You’ll also need a detailed timeline and plan for disseminating your results to make sure that you can meet project goals and inform your stakeholders.

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Poster presentation at ASM 2016.

Perhaps the most difficult accessory document is the Budget, for which you must price out almost all the items you will be spending money on.  Salary, benefits (ex. health insurance), tuition assistance, travel to scientific conferences, journal publication costs, travel to your research locations, research materials (ex. seeds, collection tubes, gloves, etc.), cost to analyze samples (ex. cost of sequencing or soil nutrient chemical analysis) cost to produce webinars, and every other large item must be priced out for each year of the grant.  The Budget Narrative goes along with that, where you explain why you are requesting the dollar amount for each category and show that you have priced them out properly.  For large pieces of equipment, you may need to include quotes from companies, or for travel to scientific conferences you may need airline and hotel prices to justify the costs.

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On top of what you need to complete the study, called Direct Costs, you also need to request money for Indirect Costs.  This is overhead that is paid to the institution that you will be working at to pay for the electricity, water, heating, building space, building security, or other utilities that you will use, as well as for the administrative support staff at the institution. Since nearly all grants are submitted through an organization (like universities), instead of as an individual, the university will handle the money and do all the accounting for you. Indirect costs pay for vital research support, but they run between 10-44% of the dollar amount that you ask for depending on the type of grant and institution, potentially creating a hefty financial burden that dramatically reduces the available funding for the project.  On a $100,000 grant, you may find yourself paying $44,000 of that directly to the university.

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Draft Twice, Submit Once

The Budget is by far the most difficult piece to put together, because the amount of money you have available for different experiments will determine how many, how large, and how intensive they are.  Often, specific methods or whole experiments are redesigned multiple times to fit within the financial constraints you have.  If you factor in the experimental design changes that all your co-PDs are making on the fly, having to balance the budget and reconstruct your narrative on an hourly basis to reflect these changes, and the knowledge that some grants only fund 6-8 projects a year and if you miss this opportunity you may not have future salary to continue working at your job, it’s easy to see why so many researchers find Grant Season to be extremely stressful.

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Plowing Forward: Montana Agriculture in a Changing Climate

Agriculture is consistently Montana’s largest economic sector, but as an arid state we need to prepare for the challenges brought on by changing weather patterns.  Yesterday, agricultural producers, scientists, special interest groups, lawmakers, and the general public came together at the Bozeman Public Library to talk about the future of climate change and what it means for people in the agricultural industry and research sector.  The event was organized by Plowing Forward, a collaborative group to coordinate local Ag. education efforts.

“If you’ve eaten today, then you’re involved in agriculture.”  -Chris Christiaens at the Plowing Forward meeting in Bozeman, MT, Feb 10, 2017

Opening remarks were led by Chris Christiaens, lobbyist and Project Specialist for the Montana Farmers Union, based in Great Falls, MT. Chris gave us some perspective on how Montana farming and ranching has changed over time, especially over the last 10 years,including changes to the growing season, harvest times, water usage, the types of plants which are able to survive here.  He reminded us that the effect of climate on agriculture affects all of us.

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Chris Christiaens, Project Specialist for Montana Farmers Union.

Next, we heard from Montana’s Senator Jon Tester, who runs a farm in northern Montana that has been in his family since 1912.  The Senator spoke to his personal experiences with farming and how his management practices had adapted over the years to deal with changing temperature and water conditions.  Importantly, he spoke about how agriculture is a central industry to the United States in ways that will become even more apparent in the coming years as the negative effects of climate change affect more and more areas.  Food security, a peaceful way of life, and economic vitality (not just in Montana or the United States, but globally), were contingent upon supporting agricultural production under adverse events.  He assured agricultural stakeholders that he continues to support production, research, and education, including the work we do in the laboratory as well as out in the field to promote agriculture.

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Montana Senator Jon Tester

Next, we heard from three professors from Montana State University.  Dr. Cathy Whitlock, a Professor of Earth Sciences, who is also the Director for the MSU Institute on Ecosystems, and a Lead Coordinator for the Montana Climate Assessment.  The Montana Climate Assessment seeks to assemble past and current research on Montana climate in order to assess trends, make predictions about the future, and help both researchers and producers to tailor their efforts based on what is happening at the regional level.  The Assessment is scheduled for release in August, 2017, and will allow for faster dissemination of research information online.

Dr. Whitlock’s introduction to the MCA was continued by  Dr. Bruce Maxwell, a Professor of Agroecology, as well as the Agriculture Sector Lead for the Montana Climate Assessment.  He summarized current research on the present water availability in Montana, as well as what we might see in the future.  He warned that drier summers were likely, and while winters may get wetter, if they continue to get warmer that snow runoff will flow into rivers before the ground has thawed.  This means snow melt will flow out of the region more quickly and not be added to local ground water sources for use here.  To paraphrase Bruce, a longer growing season does you no good if you don’t have any water.

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Dr. Bruce Maxwell, Montana State University

We also heard from my current post-doctoral advisor, Dr. Fabian Menalled, Professor of Weed Ecology Management and Cropland Weed Specialist (Extension).  He presented some of the results from our ongoing project at Fort Ellis on the interactions between climate change (hot and dry conditions), farm management system (conventional or organic), disease status, and weed competition on wheat production.  Increased temperatures and decreased moisture reduced wheat production but increased the amount of cheatgrass (downy brome), a weed which competes with wheat and can reduce wheat growth.  My work on the soil bacterial diversity under these conditions didn’t make it into the final presentation, though.  I have only just begun the data analysis, which will take me several months due to the complexity of our treatments, but here is a teaser: we know very little about soil bacteria, and the effects we are seeing are not exactly what we predicted!

Here is the video of Dr. Menalled’s presentation (just under 9 minutes):

Lastly, we heard from a local producer who spoke to his experience with ranching on a farm that had been run continuously for well over 100 years.  His talk reflected the prevailing sentiment of the presentations: that farm practices had changed over the last few decades and people in agriculture were already responding to climate change, even if previously they wouldn’t put a name to it.  The presentations concluded with a question and answer session with the entire panel, as well as a reminder that we all have the right and the obligation to be invested in our food system.  Whether we grow produce or raise livestock for ourselves or others, whether we research these biological interactions, whether we set the policy that affects an entire industry, or whether we are just a consumer, we owe it to ourselves to get involved and make sure our voice is heard.  To that end, I wrote a letter to my legislators (pictured below), and in the next few weeks I’ll be writing posts about how I participate in science (and agriculture) on the local and national level.

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Make your voice heard.