Tag: soil health

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

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The Microbes and Social Equity Working Group is delighted to make its published debut, with this collaboratively-written perspective piece introducing ourselves and our goals. You can read about us here.

This piece also debuts the special series we are curating in partnership with the scientific journal mSystems; “Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure“. Over the next few months to a year, we will be adding additional peer-reviewed, cutting edge research, review, concept, and perspective pieces from researchers around the globe on a myriad of topics which center around social inequity and microbial exposures.

Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4.

Paper published on soil microbes, climate change, and agriculture!

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I’m pleased to announce that an article was published today on soil microbes, climate change, and agriculture! As local climates continue to shift, the dynamics of above- and below-ground associated bio-diversity will also shift, which will impact food production and the need for more sustainable practices. 

This publication is part of a series, from data collected from a long-term farming experiment in Bozeman, MT, led by researchers at Montana State University with whom I have published several times, including:

In this study, cropping system (such as organic or conventional), soil temperature, soil moisture, the diversity and biomass of weed communities, and treatment with Wheat streak mosaic virus were compared as related to the bacterial community in the soil associated with wheat plant roots.

This paper is open-access, which means anyone can read the full paper.

Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities.

Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. mSphere DOI: 10.1128/mSphere.00340-20. Article.

Abstract

Little knowledge exists on how soil bacteria in agricultural settings are impacted by management practices and environmental conditions under current and predicted climate scenarios.  We assessed the impact of soil moisture, soil temperature, weed communities, and disease status on soil bacterial communities between three cropping systems: conventional no-till (CNT) utilizing synthetic pesticides and herbicides, 2) USDA-certified tilled organic (OT), and 3) USDA-certified organic with sheep grazing (OG).  Sampling date within the growing season, and associated soil temperature and moisture, exerted the greatest effect on bacterial communities, followed by cropping system, Wheat streak mosaic virus (WSMV) infection status, and weed community. Soil temperature was negatively correlated with bacterial richness and evenness, while soil moisture was positively correlated with bacterial richness and evenness.  Soil temperature and soil moisture independently altered soil bacterial community similarity between treatments.  Inoculation of wheat with WSMV altered the associated soil bacteria, and there were interactions between disease status and cropping system, sampling date, and climate conditions, indicating the effect of multiple stressors on bacterial communities in soil.  .  In May and July, cropping system altered the effect of climate change on the bacterial community composition in hotter, and hotter and drier conditions as compared to ambient conditions, in samples not treated with WSMV.  Overall, this study indicates that predicted climate modifications as well as biological stressors play a fundamental role in the impact of cropping systems on soil bacterial communities.

Image of plastic wrapped over soil to inhibit weed growth.

NE IPM funded collaborative proposal!

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I’m pleased to announce that a small grant proposal I am part of was just funded by the Northeastern Integrated Pest Management (IPM) Center! The proposal, “A Working Group on Tarping and Soil Solarization”, brings together researchers and food production professionals from across New England to identify the current use of tarping and soil solarization to prevent weed growth without the use of chemcials, as well as identify barriers to adoption of this practice, and develop research proposals to fill any knowledge gaps related to the use of these methods and their effect on crop production, weed suppression, soil microbiota, and the local ecosystem.

Led by Dr. Sonja Birthisel (UM), the working group team is comprised of Dr. Alicyn Smart (UM), myself, Master Nathalie Lounsbury (UNH), and Eva Kinnebrew (UVM). We will be joined by over a dozen other researchers across New England who perform agricultural research, along with dozens of ‘stakeholders’: producers and other food production professionals who have an interest in the group findings and would make use of any knowledge we generate.

Featured Image Credit: Soil Solarization, Wikimedia

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

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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

Field notes from my first ESA meeting

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From iDigBio
A couple of weeks ago, I attended my first Ecological Society of America meeting in Portland, which assembles a diverse community of researchers looking at system-wide processes.  It was an excellent learning experience for me, as scientific fields each have a particular set of tools to look at different problems and our collective perspectives can solve research problems in more creative ways.

In particular, it was intriguing to attend talks on the ecology of the human microbiome.  Due to the complexity of host-associated microbial communities, and the limitations of technology, the majority of studies to date have been somewhat observational.  We have mapped what is present in different animals, in different areas of the body, under different diet conditions, in different parts of the world, and in comparison between healthy and disease states.  But given the complexity of the day-to-day life of people, and ethics or technical difficulty of doing experimental studies in humans, many of the broader ecological questions have yet to be answered.

For example, how quickly do microbial communities assemble in humans?  When you disturb them or change something (like adding a medication or removing a food from your diet) how quickly does this manifest in the community structure and do those changes last? How does dysbiosis or dysfunction in the body specifically contribute to changes in the microbial community, or do seemingly harmless events trigger a change in the microbial community which then causes disease in humans? Some of the presentations I attended have begun teasing out these problems with a combination of observational in situ biological studies, in vitro laboratory studies, and in silico mathematical modeling.  The abstracts from all the meeting presentations can be found on the meeting website under Program.  I have also summarized several of the talks I went to on Give Me The Short Version.

One of my favorite parts was attending an open lunch with 500 Women Scientists, a recently-formed organization which promotes diversity and equality in science, and supports local activists to help change policy and preconceived notions about diversity in STEM.  The lunch meeting introduced the organization to the conference participants in attendance, asked us to voice our concerns or difficulties we had faced, encouraged us to reach out to others in our work network to seek advice and provide mentoring, and walked us through exercises designed to educate on how to build a more inclusive society.

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500 Women Scientists at ESA, August 2017

My poster presentation was on Wednesday, halfway through the meeting week, which gave me plenty of time to prepare.  You never know who might show up at your poster and what questions they’ll have.  In the past, I’ve always had a steady stream of people to chat with at my poster which has led to a number of scientific friendships and networking, and this year was no different.  The rather large (but detailed) poster file can be found here: Ishaq et al ESA 2017 poster .  Keep in mind that this is preliminary work, and many statistical tests have not yet been applied or verified.  I’ve been working to complete the analysis on the large study, which also encompasses a great deal of environmental data.  We hope to have manuscript drafted by this fall on this part of the project, and several more over the next year from the research team as this is part of a larger study; stay tuned!

In preparation for the ESA conference next week

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I’m counting down the days for my first Ecological Society of America (ESA) conference next week in Portland, OR.  Over the last few weeks, I’ve been diligently working to finish as much analysis as possible on the data from my recent post-doc, as I am presenting a poster on Wednesday, August 9th from 4:30 to 6:30 pm; PS 31-13 – Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus.

Several of my new colleagues will also be presenting on their recent work, including a talk from Roo Vandegrift on the built environment and the microbiome of human skin, and one from Ashkaan Fahimipour on the dynamics of food webs.

The theme for this year’s ESA meeting is “Linking biodiversity, material cycling and ecosystem services in a changing world”, and judging from the extravagant list of presenting authors, it’s going to be an extremely large meeting.  It’s worth remembering that large conferences like these bring together researchers from each rung of the career ladder, and many of the invited speakers will be presenting on work that might have been done by dozens of scientists over decades.  Seeing only the polished summary can be intimidating, lots of scientists I’ve spoken to can feel intimidated by these comprehensive meeting talks because the speakers seem so much smarter and more successful than you.  It’s something I jokingly refer to as “pipette envy”: when you are at a conference thinking that everyone does cooler science than you.  Just remember, someone also deemed your work good enough to present at the same conference!

Harvesting a feast of data

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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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Preparing for my first greenhouse trial

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As the 2016 growing season comes to a close in Montana, here in the lab we aren’t preparing to overwinter just yet.  In the last few weeks, I have been setting up my first greenhouse trial to expand upon the work we were doing in the field.  My ongoing project is to look at changes in microbial diversity in response to climate change.  The greenhouse trial will expand on that by looking at the potential legacy effects of soil diversity following climate change, as well as other agricultural factors.

First, though, we had to prep all of our materials, and since we are looking at microbial diversity, we wanted to minimize the potential for microbial influences.  This meant that the entire greenhouse bay needed to be cleaned and decontaminated.  To mitigate the environmental impact of our research, we washed and reused nearly 700 plant pots and tags in order to reduce the amount of plastic that will end up in the Bozeman landfill.

Each pot needed to be scrubbed with disinfectant soap and then soaked in bleach.
Lines of pots drying on the rack.
I scrubbed 700 labels clean in order to reuse them.

We also needed to autoclave all our soil before we could use it, to make sure we are starting with only the microorganisms we are intentionally putting in.  These came directly from my plots in the field study, and are being used as an inoculum, or probiotic, into soil as we grow a new crop of wheat.

This is trial one of three, each of which has three phases, so by the end of 2016 I’ll have cleaned and put soil into 648 pots with 648 tags; planted, harvested, dried and weighed 11,664 plants; and sampled, extracted DNA from, sequenced, and analyzed 330 soil and environmental samples!

Each pot gets six tiny winter wheat seeds planted.
Trial 1: 216 pots ready to grow!

After only a few days, seedlings are beginning to emerge.

 Stay tuned for more updates and results (eventually) from this and my field study!

Field bindweed study sampling

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Field bindweed (Convolvulus arvensis) is an invasive plant related to morning glories.  Their winding vines grow into a tangled mass which can strangle other plants, and a single plant can produce hundreds of seeds.  The plants can also store nutrients in the roots which allow them to regrow from fragments, thus it can be very difficult to get rid of field bindweed.  It will return even after chemical or physical control (tilling or livestock grazing), but it does not tolerate shade very well.  Thus, a more competitive crop, such as a taller wheat which will shade out nearby shorter plants, reduce the viability of bindweed.

Bindweed wraps around other plants.
This patch goes all the way to Lazarro.

First seen in the US in 1739, Field bindweed is native to the Mediterranean. By 1891, it had made its way west and was identified in Missoula, Montana.  As of 2016, it has been reported from all but two counties in Montana, where it has been deemed “noxious” by the state department (meaning that it has been designated as harmful to agriculture (or public health, wildlife, property).  In the field, this can be visually striking, as pictured below.  In the foreground, MSU graduate student Tessa Scott (lead researcher on this project) is standing in a patch of wheat infested with bindweed. Just seven feet away in the background, undergraduate Lazarro Vinola is standing in non-infested wheat, with soil core samplers used for height reference.

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In agricultural fields, bindweed infestations severely inhibit crop growth and health.

 

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Last week, Tessa, Lazarro, and I went to several farms in and around Big Sandy and Lewistown, Montana in order to sample fields battling field bindweed. To do so, we harvested wheat, field bindweed, and other weed biomass by cutting all above-ground plant material inside a harvesting frame.  These will be dried and weighed, to measure infestation load and the effect on wheat production.

The sampling locations are consistent with previous years to track how different farm management practices influence infestations.  This means using GPS coordinates to hike out to spots in the middle of large fields.

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It also means getting very dirty driving and walking through dusty fields!

Thalspi, or pennycress, which is dropping seeds even in my shoes!
The van did very well on rocky, uneven field roads!