Conducting the Rhizosphere Symphony: How Much Do Plants Change Their Tune?
Published in Microbiology
The rhizosphere has long been described as the zone of influence of plant roots1, but roots are not the only influence on soil microorganisms in this important region. Agricultural management practices such as fertilization and crop rotation shape soil physical and chemical properties and influence which bacteria and fungi survive and thrive. Upon establishment, plant roots then recruit a subset of microorganisms from bulk soil, establishing the unique microbial community that will inhabit the rhizosphere in a sort of one-time “rhizosphere snapshot” driven by host selection. At least, that’s how the story was thought to go.
However, while sampling for other projects at the Russell Ranch Century Experiment, a long-term agricultural system trial initiated 25 years ago, we started to question whether complex, dynamic rhizosphere processes are really established in such a static manner. For example, this trial has shown differences in the amount of soil organic matter and the soil microbial communities between conventional, organic, and integrated management systems. It has also shown variation in the availability of nutrients such as nitrogen from organic and synthetic sources even when the total amount applied is constant2. Wouldn’t plants require different root-associated microbial communities, then, in organic systems where nutrients must be obtained through mineralization of cover crops and compost rather than readily available synthetic fertilizer? Instead of a “rhizosphere snapshot”, what if plant roots are active conductors of an ongoing “rhizosphere symphony”, with each plant genotype upregulating specific microbial taxa and functions as a conductor brings together different sections of instruments?
We hypothesized that a single maize genotype would recruit management-system-specific rhizosphere communities in plots under long-term organic management as compared to the conventionally managed plots. To understand how plants shape not only which microbes are present but also how they interact with one another and what they do, we investigated microbial taxonomic composition, co-occurrence networks, and nitrogen-cycling functional genes.
We found that plant selection does moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently from one another. A single maize genotype recruited management-system-specific taxa and shifted N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Plant effects acted as an equalizing influence on bacterial communities, making rhizosphere microbiomes from conventional and organic systems more similar to one another in diversity and network structure than communities from their respective bulk soils. In contrast, fungal community composition was mainly affected by management practices, but network arrangements were mostly driven by plants.
Our finding that plants change their tune in different management systems highlights the essential role of roots in orchestrating rhizosphere microbiome assembly and processes. With further research into the underlying mechanisms, we may be able to manipulate the sound of the symphony by talking to the conductor: plant-driven strategies may be instrumental in maximizing beneficial rhizosphere interactions for sustainable agricultural productivity.
1. Hiltner, L. Über neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter besonderer Berücksichtigung der Gründungung und Bräche. Arbeiten der Deutschen Landwirtschafts-Gesellschaft 98, 59–78 (1904).
2. Wolf, K. M. et al. The century experiment: the first twenty years of UC Davis’ Mediterranean agroecological experiment. Ecology 99, 503–503 (2018).
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Harnessing plant microbiomes to improve performance and mechanistic understanding
This is a Cross-Journal Collection with Microbiome, Environmental Microbiome, npj Science of Plants, and npj Biofilms and Microbiomes. Please click here to see the collection page for npj Science of Plants and npj Biofilms and Microbiomes.
Modern agriculture needs to sustainably increase crop productivity while preserving ecosystem health. As soil degradation, climate variability, and diminishing input efficiency continue to threaten agricultural outputs, there is a pressing need to enhance plant performance through ecologically-sound strategies. In this context, plant-associated microbiomes represent a powerful, yet underexploited, resource to improve plant vigor, nutrient acquisition, stress resilience, and overall productivity.
The plant microbiome—comprising bacteria, fungi, and other microorganisms inhabiting the rhizosphere, endosphere, and phyllosphere—plays a fundamental role in shaping plant physiology and development. Increasing evidence demonstrates that beneficial microbes mediate key processes such as nutrient solubilization and uptake, hormonal regulation, photosynthetic efficiency, and systemic resistance to (a)biotic stresses. However, to fully harness these capabilities, a mechanistic understanding of the molecular dialogues and functional traits underpinning plant-microbe interactions is essential.
Recent advances in multi-omics technologies, synthetic biology, and high-throughput functional screening have accelerated our ability to dissect these interactions at molecular, cellular, and system levels. Yet, significant challenges remain in translating these mechanistic insights into robust microbiome-based applications for agriculture. Core knowledge gaps include identifying microbial functions that are conserved across environments and hosts, understanding the signaling networks and metabolic exchanges between partners, and predicting microbiome assembly and stability under field conditions.
This Research Topic welcomes Original Research, Reviews, Perspectives, and Meta-analyses that delve into the functional and mechanistic basis of plant-microbiome interactions. We are particularly interested in contributions that integrate molecular microbiology, systems biology, plant physiology, and computational modeling to unravel the mechanisms by which microbial communities enhance plant performance and/or mechanisms employed by plant hosts to assemble beneficial microbiomes. Studies ranging from controlled experimental systems to applied field trials are encouraged, especially those aiming to bridge the gap between fundamental understanding and translational outcomes such as microbial consortia, engineered strains, or microbiome-informed management practices.
Ultimately, this collection aims to advance our ability to rationally design and apply microbiome-based strategies by deepening our mechanistic insight into how plants select beneficial microbiomes and in turn how microbes shape plant health and productivity.
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Microbiome and Reproductive Health
Microbiome is calling for submissions to our Collection on Microbiome and Reproductive Health.
Our understanding of the intricate relationship between the microbiome and reproductive health holds profound translational implications for fertility, pregnancy, and reproductive disorders. To truly advance this field, it is essential to move beyond descriptive and associative studies and focus on mechanistic research that uncovers the functional underpinnings of the host–microbiome interface. Such studies can reveal how microbial communities influence reproductive physiology, including hormonal regulation, immune responses, and overall reproductive health.
Recent advances have highlighted the role of specific bacterial populations in both male and female fertility, as well as their impact on pregnancy outcomes. For example, the vaginal microbiome has been linked to preterm birth, while emerging evidence suggests that gut microbiota may modulate reproductive hormone levels. These insights underscore the need for research that explores how and why these microbial influences occur.
Looking ahead, the potential for breakthroughs is immense. Mechanistic studies have the power to drive the development of microbiome-based therapies that address infertility, improve pregnancy outcomes, and reduce the risk of reproductive diseases. Incorporating microbiome analysis into reproductive health assessments could transform clinical practice and, by deepening our understanding of host–microbiome mechanisms, lay the groundwork for personalized medicine in gynecology and obstetrics.
We invite researchers to contribute to this Special Collection on Microbiome and Reproductive Health. Submissions should emphasize functional and mechanistic insights into the host–microbiome relationship. Topics of interest include, but are not limited to:
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