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1. The Impact of Soybean Genotypes on Rhizosphere Microbial Dynamics and Nodulation Efficiency

   https://doi.org/10.3390/ijms26072878  

   Thingujam, Doni; Majeed, Aqsa; Sivarathri, Bala Subramanyam; Narayana, Nisarga Kodadinne; Bista, Mohan K; Cowart, Katie E; Knight, Adelle J; Pajerowska-Mukhtar, Karolina M; Bheemanahalli, Raju; Mukhtar, M Shahid (April 2025, International Journal of Molecular Sciences)

   Rhizosphere microbiome exerts a significant role in plant health, influencing nutrient availability, disease resistance, and overall plant growth. Establishing a robust and efficient nodulation process is essential for optimal nitrogen fixation in legumes like soybeans. Different soybean genotypes exhibit variations in their rhizosphere microbiome, potentially impacting nitrogen fixation through nodulation. However, a detailed understanding of how specific soybean genotypes influence rhizosphere microbial communities and nodulation patterns remains limited. Our study aims to investigate the relationship between rhizosphere microbial abundance and plant growth in four soybean genotypes. We evaluated plant growth parameters, including biomass, leaf area, and stomatal conductance, and identified significant genotypic differences in nodulation. Specifically, genotypes PI 458505 and PI 603490 exhibited high levels of nodulation, while PI 605839A and PI 548400 displayed low nodulation. 16S rRNA gene amplicon sequencing revealed diverse bacterial communities in the rhizosphere, with Proteobacteria as the dominant phylum. High-nodulation genotypes harbored more diverse microbial communities enriched with Actinobacteria and Acidobacteriota, while low-nodulation genotypes showed higher abundances of Firmicutes and Planctomycetota. Alpha and beta diversity analyses confirmed distinct microbial community structures between high- and low-nodulation groups. Our findings suggest that the rhizosphere microbiome significantly influences soybean growth and nodulation, highlighting the potential for genotype-driven strategies to enhance plant-microbe interactions and improve soybean productivity. 

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2. Evolution of manipulative microbial behaviors in the rhizosphere

   https://doi.org/10.1111/eva.13333  

   Klein, Malin; Stewart, Justin D.; Porter, Stephanie S.; Weedon, James T.; Kiers, E. Toby (January 2022, Evolutionary Applications)

   Abstract The rhizosphere has been called “one of the most complex ecosystems on earth” because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed aplant‐centric perspective when trying to harness the potential of microbiome‐derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, amicrobe‐centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context‐dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production. 

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3. Phytomicrobiome systems affect plant health and crop production

   Flowers, L. (February 2023, International Journal of Science and Research Archive)

   The sustainability of plant life is intimately connected to its evolution with microbial life. Based on experimental evidence, microbial assemblages benefit plants on molecular, cellular, and ecological levels. The plant microbiome or phytomicrobiome are the microbes closely associated with a particular plant species. Distinct plant microbial ecosystems are in the phyllosphere, rhizosphere, soil, and endosphere. Plant-associated microbes affect plants in numerous ways and participate in various physiological functions essential for the plant, including nutrient recycling, the breakdown and synthesis of critical molecules, and other phytoprotective functions. While studying plant-microbe interactions is not new, recent developments in metagenomic sequencing and high-throughput pathway identification techniques have allowed scientists to explore unculturable microbes associated with plants. This review primarily focuses on the significant role of the phytomicrobiome and describes the prevalent taxonomic units found in association with plants. Plants are suitable tractable model systems to study plant-microbe interactions and can be grown under different experimental conditions to examine other characteristics of the phytomicrobiome. This article also provides a systematic review of the current research on the phytomicrobiome. It explores the extent to which the phytomicrobiome participates in an essential process that promotes plant fitness and sustainabilityand reviews research that focuses on microbiome community shifts in response to abiotic and biotic stress. Genetic engineering of plant-associated microbes to enhance plant growth and protection is addressed. The use of nanofertilizers and phytomicrobiome transplantation to restore plant health and improve the success of agriculturally beneficial crops is also discussed. 

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4. The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa

   https://doi.org/10.1111/mec.16782  

   DeWolf, Ella; Brock, Marcus T.; Calder, William John; Kliebenstein, Daniel J.; Katz, Ella; Li, Baohua; Morrison, Hilary G.; Maïgnien, Lois; Weinig, Cynthia (February 2023, Molecular Ecology)

   Abstract The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) ofBrassica rapathat differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet‐multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from six genera and the concentration of five GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant–microbe interactions mediated by GLS; that is, GLS compounds produced by the host plant “feed‐down” to influence rhizosphere microbial community and rhizosphere microbes “feed‐up” to influence GLS production. 

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5. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B.; Goodwillie, Carol; Peralta, Ariane L. (June 2020, mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways. 

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