Understanding plant-microbe interactions to improve the cultivation of biofuels

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AMI Global Ambassador Ashley Shade and colleagues Nicole Geerdes and Adina Howe examine how plant-associated microbes can be leveraged to support crops grown on marginal lands for use as biofuel feedstocks.

The production of clean energy alternatives to fossil fuels is crucial to meeting the current climate change goal of net zero emissions by 2050. To meet the demand for clean energy, the production of biofuels is projected to increase by 30% over the next five years alone (IEA, 2023).

Panicum_virgatum_Shenandoah_2zz (1)

Source: David J. Stang

Panicum virgatum ‘Shenandoah’ or Red Switch Grass

Perennial grasses, such as switchgrass and miscanthus, are second-generation bioenergy feedstocks that provide additional ecosystem services beyond bioenergy compared to first-generation bioenergy feedstocks such as corn or sugarcane.

These second-generation feedstocks have relatively deeper root systems that hold the soil and its nutrients in place year-round, improving soil health and reducing the agricultural impacts of nutrient leaching and run-off on the environment.

Abiotic stress

Cultivating plants that are resilient to abiotic stress has become an increasing need across agriculture, and this need is also true for the sustainable production of biofuel feedstocks, which aims to use nonoptimal lands for food production and requires minimal water and nutrient inputs.

Because of this, crops cultivated on so-called “marginal” lands can have high water and nutrient variability – both forms of abiotic stress that can reduce yield. Leveraging plant-associated microbes to support the abiotic stress tolerance of plants is a possible solution for cultivating resilient and high-yielding biofuel feedstocks on marginal lands.

Microbiome management

Microbes offer many benefits for plants, such as improved nutrient uptake, plant growth, and resilience to abiotic and biotic stress. Given the diversity of benefits that microbes can provide for plants, there is optimism around the possibilities for microbial applications to improve biofuel feedstock production.

Thus, precise microbiome management for plants is an active and broad area of research. Several general approaches are used first to understand and then test the benefits for plants. These approaches range in biological complexity and ease of potential utility in the field. Here, we discuss two types of potential bioinoculants: single beneficial strains and multiple-strain consortia.

The application of microbes as bioinoculants (also called “biologicals” or, in some specific cases, “biofertilizers”) can be a sustainable way to improve and maintain yield under abiotic stress for many cropping systems. Applying a microbial strain to a biofuel feedstock as a bioinoculant could improve how much bioenergy is subsequently produced per acre of land, helping to meet bioenergy goals. Different bioinoculants may support different plant health outcomes, such as growth promotion or stress tolerance.

The approach to develop single-strain bioinoculants generally involves enriching and isolating putatively beneficial microbes based on the presence of plant-supportive functions, screening isolates for plant benefit in controlled conditions, and then testing the transfer of efficacy and trialing modes of optimal bioinoculant delivery to the plant under field conditions.

Key players

Given the diversity of the plant-associated microbiome, identifying the most effective and competitive players associated with the plant can be challenging. It is unlikely that a single microbe can provide everything a plant may need for growth promotion and myriad stress tolerances.

Thus, there is also research to develop and understand how consortia of multiple microbes could be used together instead of as single inoculants. These consortia are sometimes called synthetic communities.

The general approach is to construct synthetic communities based on their complementary plant-supportive traits and non-exclusive growth conditions. Field-to-field variations in biofuel feedstock yield may decrease when synthetic communities of microbes that together provide diverse benefits to the plant are used as bioinoculants.

Harnessing microbes

Like humans, who have different compositions of microbes living on our different body parts, plants have different compositions of microbes living on their leaves, roots, and inside their tissues. Some of these microbes provide specific benefits to their plant host by which they can directly or indirectly enhance plant growth and reduce negative responses to abiotic stress. Thus, another possible way to support plants facing climate change is to learn how to harness these naturally occurring, plant-associated beneficial microbes for sustainable biofuel feedstock production.

Biofuel feedstock production is facing uncertainty in yield due to the increased environmental variability resulting from climate change. Second-generation feedstocks additionally provide ecosystem services to maintain soil health and are expected to achieve a high standard of sustainable production.

Along with improving plant feedstocks and precision agriculture, microbiome management is a promising tool to support biofuel feedstocks that could offer sustainable solutions. From understanding the plant-beneficial mechanisms of single bioinoculants to complex field rhizosphere interactions, there is a lot of potential in advancing understanding toward applying microbial solutions for biofuel feedstock production.

Related works from the authors

1. Bandopadhay S, X Li, AW Bowsher, RL Last and A Shade. Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought. In press, Nature Communications

2. Howe AC, Bonito, M-Y Chou, MA Cregger, A Fedders, JL Field, HG Martin, JL Labbé, ME Mechan Llontop, TR Northern, A Shade and TJ Tschaplinski. 2022. Frontiers and opportunities in bioenergy crop microbiome research networks. Phytobiomes Journal. 6:2471-2906. https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-05-21-0033-MR

3. Howe A, N Stopnisek, SK Dooley, FM Yang, KL Grady and A Shade. 2023. Seasonal activities of the phyllosphere microbiome of perennial crops. Nature Communications. 14:1039. https://doi.org/10.1038/s41467-023-36515-y

4. Shade A and N Stopnisek. 2019. Abundance-occupancy distributions to prioritize core plant microbiome membership. Current Opinion in Microbiology. 49:50-58. https://doi.org/10.1016/j.mib.2019.09.008

5. Zhalnina K, C Hawkes, A Shade, MK Firestone, and J Pett-Ridge. 2021. Managing microbiomes for sustainable biofuel production. Phytobiomes Journal. 5:2471-2906. https://doi.org/10.1094/PBIOMES-12-20-0090-E

Nicole Geerdes, Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA

Adina Howe, Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA;

Department of Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Ames, IA, 50011, USA

AMI Global Ambassador Ashley Shade, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d’Ecologie Microbienne LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, F-69100 France