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. DOI: 10.1128/mSphere.00340-20. Article.


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.

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.


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.

A living soil inoculum increases soil microbial diversity, crop and weed growth using soil from organic and conventional farms in northeastern Montana.

What began as a simple data analysis project for me in the Yeoman lab turned into a publication, a conference presentation, a post-doc position, and a long-term, multi-project collaboration with the Menalled lab at Montana State University investigating soil microbial communities in agricultural settings and plant-soil feedbacks.

This study was part of a larger investigation on farming system (conventional or organic), and wheat-weed competition, as part of a master’s thesis by Stephen Johnson.  The publication on plant competition and crop performance can be found here.

The larger project involved soil collected from the fields of four farms around Montana which had both conventionally-managed and a USDA-certified organically-managed plots growing wheat.  Soil was brought back to Montana State University, where half of each field sample was sterilized to destroy living microorganisms.  A greenhouse study was performed using either the sterile or the living soil, and the soil was conditioned by growing either Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat) for 16 weeks.  Following this plant growth phase, soil was collected and the bacterial community analyzed using Illumina MiSeq sequencing of the 16S rRNA gene.  The larger study then went on to study the performance of wheat crops in that preconditioned soil.

The strongest driving factor in soil bacterial communities was whether that soil had been sterile (purple) or living (green) in the greenhouse experiment, as seen below.  After that, farming system was the next strongest determinant of that community.  Interestingly, organically-sourced soil that had been sterilized was more similar to any living soil than conventionally-sourced sterile soil.  This indicates that organic soil was more favorable in recruiting a new soil community.

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When comparing only the living soil samples, the samples reclustered by farming system; either organic or conventional.

Which weed species was growing was also an important factor, although much weaker.  A number of soil bacteria were more abundant in the soil around of the roots of one or the other plant.  Plants are known to associate with, and even recruit, different microbial communities, and this interaction can be plant-species-specific.

Ishaq, S.L., Johnson, S.P., Miller, Z.J., Lehnhoff, E.A., Olivo, S.K., Yeoman, C.J., Menalled, F.D. 2017. A living soil inoculum increases soil microbial diversity, crop and weed growth using soil from organic and conventional farms in northeastern Montana. Microbial Ecology 73(2): 417-434. Impact 3.630. Article


Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthusretroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.


Poster: Ishaq*, S.L., Johnson, S.P., Miller, Z.J., Lehnhoff, E.A., Olivo, S.K., Yeoman, C.J., Menalled, F.D. Farming Systems Modify The Impact Of Inoculum On Soil Microbial Diversity. American Society for Microbiology (ASM), Boston, MA, June 2016.

Poster presentation at ASM 2016.

Ishaq et al ASM 2016 poster