Soil bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system.

This is the second paper from Tindall’s master’s work at Montana State University in the Menalled Lab has been accepted for publication! Tindall defended her master’s in August 2021, and has been working at a plant production company in Bozeman since then.

Ouverson, T., Boss, D., Eberly, J., Sepiel, T.,  Menalled, F.D., Ishaq, S.L. 2022. Soil bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. Frontiers in Sustainable Food Systems.

Abstract

Soil microbial communities are integral to highly complex soil environments, responding to changes in aboveground plant biodiversity, influencing physical soil structure, driving nutrient cycling, and promoting both plant growth and disease suppression. Cover crops can improve soil health, but little is known about their effects on soil microbial community composition in semiarid cropping systems, which are rapidly becoming warmer and drier due to climate change. This study focused on a wheat-cover crop rotation near Havre, Montana that tested two cover crop mixtures (five species planted early season and seven species planted mid-season) with three different termination methods (chemical, grazed, or hayed and baled) against a fallow control under ambient or induced warmer/drier conditions. Soil samples from the 2018 and 2019 cover crop/fallow phases were collected for bacterial community 16S rRNA gene sequencing. The presence and composition of cover crops affected evenness and community composition. Bacterial communities in the 2018 ambient mid-season cover crops, warmer/drier mid-season cover crops, and ambient early season cover crops had greater richness and diversity than those in the warmer/drier early season cover crops. Soil microbial communities from mid-season cover crops were distinct from the early season cover crops and fallow. No treatments affected bacterial alpha or beta diversity in 2019, which could be attributed to high rainfall. Results indicate that cover crop mixtures including species tolerant to warmer and drier conditions can foster diverse soil bacterial communities compared to fallow soils.

Contribution to Field Statement
Semiarid, dryland agriculture makes up a significant portion of global crop production and understanding how cropping systems modify soil bacterial communities is crucial for global agricultural security. We evaluated soil bacterial community responses to contrasting cropping systems and soil temperature and moisture in a semiarid agroecosystem close to Havre, Montana. This study focused on a wheat-cover crop rotation that tested two cover crop mixtures (five species planted early season and seven species planted mid-season) with three different termination methods (chemical, grazed, or hayed and baled) against a fallow control under ambient or induced warmer/drier conditions. We hypothesized that 1) the mid-season and early season cover crop mixtures would have more diverse soil bacterial communities than fallow, 2) on average, ambient conditions would support higher soil bacterial diversity than warmer/drier conditions, and 3) there would be a gradient in soil microbial community diversity from warmer/drier fallow plots terminated by glyphosate (lowest) to ambient cover crop plots terminated by grazing (highest). Overall, results indicate that cover crop mixtures that include species tolerant to the predicted warmer and drier conditions may result in diverse soil bacterial communities compared to fallow soils.

Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains.

This project was part of the graduate research for master’s student Tindall Ouverson, and is her first manuscript!

Photo of woman in front of mountains

Tindall is a Master’s of Science in the Department of Land Resources and Environmental Sciences at Montana State University. Her graduate advisers are Drs. Fabian Menalled and Tim Seipel. Her research focuses on the response of soil microbial communities to cropping systems and climate change in semiarid agriculture. 

I have been mentoring Tindall as a graduate committee member since she began in fall 2019, teaching her laboratory and analytical skills in microbial ecology, DNA sequencing, and bioinformatic analysis. We first met when she came to visit when I was working in Oregon, and since then have connected remotely. She has a flair for bioinformatics analysis, and a passion for sustainable agricultural development. She plans to defend her thesis in spring 2021, and then to further her career in sustainable agriculture in Montana.

In the Northern Great Plains of the United States, cereal crops, such as wheat, are important economic staples. In this area, climate change is forecasted to increase temperature and decrease precipitation during the summer, which is expected to negatively affect crop production and the management of pests (insects and microbes).  There are numerous reports on the current effects of climate change on agricultural production, as well as how they will be predicted to worsen, such as:


Ouverson, T.,  Eberly, J., Seipel, T., Menalled, F., Ishaq, S.L.2021.Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains.  Frontiers in Sustainable Food Systems 5:75No Impact Factor. Article. This is an invited submission to Plant Growth-Promoting Microorganisms for Sustainable Agricultural Production  special collection.

Abstract

Industrialized agriculture results in simplified landscapes where many of the regulatory ecosystem functions driven by soil biological and physicochemical characteristics have been hampered or replaced with intensive, synthetic inputs. To restore long-term agricultural sustainability and soil health, soil should function as both a resource and a complex ecosystem. In this study, we examined how cropping systems impact soil bacterial community diversity and composition, important indicators of soil ecosystem health. Soils from a representative cropping system in the semi-arid Northern Great Plains were collected in June and August of 2017 from the final phase of a five-year crop rotation managed either with chemical inputs and no-tillage, as a USDA-certified organic tillage system, or as a USDA-certified organic sheep grazing system with reduced tillage intensity. DNA was extracted and sequenced for bacteria community analysis via 16S rRNA gene sequencing. Bacterial richness and diversity decreased in all farming systems from June to August and was lowest in the chemical no-tillage system, while evenness increased over the sampling period. Crop species identity did not affect bacterial richness, diversity, or evenness. Conventional no-till, organic tilled, and organic grazed management systems resulted in dissimilar microbial communities. Overall, cropping systems and seasonal changes had a greater effect on microbial community structure and diversity than crop identity. Future research should assess how the rhizobiome responds to the specific phases of a crop rotation, as differences in bulk soil microbial communities by crop identity were not detectable.

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

In the Northern Great Plains of the United States, cereal crops, such as wheat, are important economic staples. In this area, climate change is forecasted to increase temperature and decrease precipitation during the summer, which is expected to negatively affect crop production and the management of pests (insects and microbes).  There are numerous reports on the current effects of climate change on agricultural production, as well as how they will be predicted to worsen, such as:

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, 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.

These factors had varying effects on soil bacteria, and interacted with each other. Unsurprisingly, the more stressful things that wheat had to contend with, the more the bacterial community was affected.


Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20. 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 evennessSoil 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.

Soil bacterial communities of wheat vary across the growing season and among dryland farming systems.

For my post-doctoral research project in the Menalled lab in 2016/2017, I was investigating the effect of farming system, weed competition, and season, on wheat production and soil bacteria during a growing season in Montana. All of these represent potentially stressful conditions, which can hamper plant growth, as well as whether and how they will interact with soil microbial communities. In particular, the element of time is missing from many studies on soil microbial ecology, often because of cost. Because plant-microbial interactions change depending on the needs of the plant, we wondered if soil communities would change as the wheat (and weeds) grew, matured, and then senesced (aged and died).

This publication is part of a series, from data collected from a long-term farming experiment in Bozeman, MT, including:


Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358:113989. Article.

Abstract

Despite knowledge that management practices, seasonality, and plant phenology impact soil microbiota; farming system effects on soil microbiota are not often evaluated across the growing season. We assessed the bacterial diversity in soil around wheat roots through the spring and summer of 2016 in winter wheat (Triticum aestivium L.) in Montana, USA, from three contrasting farming systems: a chemically-managed no-tillage system, and two USDA-certified organic systems in their fourth year, one including tillage and one where sheep grazing partially offsets tillage frequency. Bacterial richness (range 605–1174 OTUs) and evenness (range 0.80–0.92) peaked in early June and dropped by late July (range 92–1190, 0.62–0.92, respectively), but was not different by farming systems. Organic tilled plots contained more putative nitrogen-fixing bacterial genera than the other two systems. Bacterial community similarities were significantly altered by sampling date, minimum and maximum temperature at sampling, bacterial abundance at date of sampling, total weed richness, and coverage of Taraxacum officinaleLamium ampleuxicaule, and Thlaspi arvense. This study highlights that weed diversity, season, and farming management system all influence soil microbial communities. Local environmental conditions will strongly condition any practical applications aimed at improving soil diversity, especially in semi-arid regions where abiotic stress and seasonal variability in temperature and water availability drive primary production. Thus, it is critical to incorporate or address seasonality in soil sampling for microbial diversity.

Agroecosystem resilience is modified by management system via plant–soil feedbacks

For my post-doctoral research project in the Menalled lab in 2016/2017, I was investigating the effect of farming system, weed competition, disease status, and climate change, on wheat production and soil bacteria during a growing season in Montana. All of these represent potentially stressful conditions, which can hamper plant growth, as well as the amount and type of root exudates they secrete into soil. Plants have a complex relationship with bacteria and fungi in the soil, and will provide sugars in exchange for microbial products. When conditions are harsh enough to threaten plant survival, like during droughts, plants may cut off support to soil microbes, which can cause the community to crash. Similarly, microbial communities may be unsupportive or pathogenic towards plants, and can hamper seed germination, as well as growth or health of plants.

We also wanted to know if adverse conditions during even just a single growing season would affect the microbial community enough to cause a change in plant growth during the next growing season – even if other conditions went back to normal. We took soil from the field at the end of the growing season and set up a greenhouse trial. To examine the impact of the microbial community, we set up paired comparisons where one half had the living field soil, and the other had field soil which had been autoclaved first to kill any microbes. The greenhouse trial involved hundreds of plant pots and thousands of data, and the seed germination and plant growth data was used to evaluate the legacy of stress.

This publication is part of a series, from data collected from a long-term farming experiment in Bozeman, MT, including:


Seipel, T., Ishaq, S.L., Menalled, F.D. 2019. Agroecosystem resilience is modified by management system via plant–soil feedbacks. Basic and Applied Ecology 39:1-9. Article.

Abstract

Designing resilient cropping systems is essential to sustain agricultural production in the face of changing environmental and social pressures. However, the extent to which changes in farm management systems could alter resistance and resilience is largely unknown, especially in response to climate change. Plant and soil microbial community interactions are a vital component of functioning and resilient agroecosystems. The aim of our study was to use winter wheat (Triticum aestivum L.) and pea (Pisum sativum L.) plant–soil feedbacks (i.e. plant species-specific effects on soil biotaand their impacts on subsequent plant growth) as a metric of system resilience and resistance to climate variability in three different farming management systems: 1) a chemical no-till system, 2) an USDA-certified organic system reliant on tillage and 3) an USDA-certified organic system that included sheep grazing with the overall goal of minimizing tillage intensity. Climate conditions soil experienced were ambient, warmer, and warmer and drier and were manipulated in the field using open-top chamber and rain-out shelters. Plant–soil feedbacks were negative for wheat and positive for pea but varied among farming management systems but were less sensitive to climate conditions. Plant–soil feedbacks were lower in magnitude in the tilled organic system indicating more resistance to the accumulation of pathogenic soil microbiotaresulting from repeated cropping of wheat. However, recovery was lower when the crop was pea in the tilled organic indicating slower recovery and less resilience. Results indicate that while increases in crop diversity may promote more resilient agroecosystems, farming management will affect agroecosystem resilience.