Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

York, Larry M.; Cumming, Jonathan R.; Trusiak, Adrianna; Bonito, Gregory; Haden, Adam C. von; Kalluri, Udaya C.; Tiemann, Lisa K.; Andeer, Peter F.; Blanc‐Betes, E.; Diab, Jonathan H.; Favela, Alonso; Germon, Amandine; Gomez‐Casanovas, Nuria; Hyde, Charles A.; Kent, Angela D.; Ko, Dae Kwan; Lamb, Austin; Missaoui, Ali; Northen, Trent; Pu, Yunqiao; Ragauskas, Arthur J.; Raglin, Sierra S.; Scheller, Henrik Vibe; Washington, Lorenzo; Yang, Wendy H.

doi:10.1002/ppj2.20028

Cited by 15 publications

(10 citation statements)

References 279 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…. While not captured in this study, future work needs to delineate and find methods to capture growth and temporal variation belowground to meaningfully incorporate the microbiome and ecosystem processes into the agricultural setting (York et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Genetic variation exists withinZea maysto influence unsustainable nitrogen cycling microbiome function

Favela,

Bohn,

Kent

2023

Preprint

Self Cite

View full text Add to dashboard Cite

Overuse of synthetic nitrogen fertilizers in agroecosystems causes environmental pollution and human harm at a global level. Nitrogenous fertilizers provide a short-lived benefit to crops in the agroecosystem, but stimulate microbially-mediated nitrification and denitrification, processes that result in N pollution, greenhouse gas (GHG) production, and reduced soil fertility. Recent advances in plant microbiome science suggest that plants can modulate the composition and activity of rhizosphere microbial communities. These rhizosphere communities act as an extended phenotype, primed by genetic variation in the plant host. Genetic variation in traits (e.g., plant secondary metabolites, root architecture, immune system, etc.) act as mechanistic selective agents on the composition of the microbiome. Here we attempted to determine whether genetic variation exists inZea maysfor the ability to influence the extended phenotype of rhizosphere soil microbiome composition and function. Specifically, we determined whether plants’ influence on soil nitrogen cycling activities was altered by plant genetics and thereby allowing it to be incorporated into breeding practices. To capture an extensive amount of genetic diversity within maize we sampled the rhizosphere microbiome of a germplasm chronosequence that included ex-PVP inbreds, hybrids, and teosinte (Z. maysssp. mexicanaandZ. maysssp.parviglumis). We observed that potential N cycling processes were influenced by plant genetics. Teosinte and some hybrid genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbreds stimulated/did not inhibit these undesirable N-cycling activities. These potential differences translated to functional differences in N2O production, with teosinte plots producing less GHG than maize plots. Furthermore, within theseZeacultivars we found that plant genetics explained a significant amount of variation in the microbiome, particularly among different nitrification and denitrification functional genes within the community. We found that potential nitrification, potential incomplete denitrification, and overall denitrification rates, but not abundance of N-cycling genes of rhizosphere soils were influenced by growth stage and plant genetics. Taken together, these results suggest that crop selection can lead to changes in root phenotypes that could suppress unsustainable N-cycling processes. Reintroducing stress-adapted and “wild” root characteristics into modern germplasm may be a way to manipulate soil microbiomes at both a composition and functional level to improve sustainability.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic variation exists withinZea maysto influence unsustainable nitrogen cycling microbiome function

Favela,

Bohn,

Kent

2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…While most of the work on bioenergy crops has focused on monoculture, which could have a negative impact on biodiversity (169), although abandoned and degraded soils can become breeding grounds for invasive plant species (170), there is an emerging interest in intercropping with bioenergy crops (171, 172) (Figure 4). Despite the obvious importance of root and microbiome traits in determining the sustainable productivity of bioenergy cropping systems, little attention has been focused on belowground traits (173). Bioenergy crops have many outlets, such as mulch and bedding for farms (174), amendments (175), biochar (176), and bioplastics (177), which are used in the circular economy of sustainable production.…”

Section: Perennial Bioenergy Cropmentioning

confidence: 99%

Restoring Soil Functions and Agroecosystem Services Through Phytotechnologies

Dessureault‐Rompré

2022

Front. Soil Sci.

View full text Add to dashboard Cite

Phytotechnology has traditionally been considered as a tool to remediate contaminated soils. While phytotechnology has been generally defined as the application of science and engineering to study problems and provide solutions involving plants, the practical applications go far beyond restoring contaminated land. This review aims to broaden the way we think about phytotechnologies while highlighting how these living technologies can restore, conserve and regenerate the multiple functions and ecosystem services provided by the soil, particularly in the context of agroecosystems. At first, the main problems of soil degradation in agroecosystems are shortly underlined. Subsequently, the importance of plants and their living roots as engines of restoration are reviewed. This paper demonstrates the importance of root traits and functions for soil restoration. It also demonstrates that plant and root diversity together with perenniality are key component of an efficient soil restoration process. Then, a phytotechnology toolbox which includes three pillars for agroecosystems restoration is presented. The three pillars are agricultural practices and land management (1), rhizosphere engineering (2) and ecological intensification (3). This paper also highlights the importance of developing targeted phytotechnology-based restoration strategies developed from root functions and knowledge of rhizosphere processes. More work is needed to evaluate the potential benefits of incorporating phytotechnology-based restoration strategies in the context of grain or vegetable crop productions as most of the studies for agroecosystem restoration strategies were intended to mimic natural prairies.

show abstract

“…A major challenge in identifying appropriate SynCom inoculants is the scarcity of comparable datasets. The lack of comparable datasets is, in part, due to the absence of standardized systems and protocols (Meisner et al 2022;York et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Lin

Torres

Adams

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

show abstract

Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

Cited by 15 publications

References 279 publications

Genetic variation exists withinZea maysto influence unsustainable nitrogen cycling microbiome function

Genetic variation exists withinZea maysto influence unsustainable nitrogen cycling microbiome function

Restoring Soil Functions and Agroecosystem Services Through Phytotechnologies

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Contact Info

Product

Resources

About