Rhizobiome shields plants from infection

Manipulating rhizosphere microorganisms to improve crop yield in saline-alkali soil: a study on soybean growth and development

Introduction

Rhizosphere microorganisms can effectively promote the stress resistance of plants, and some beneficial rhizosphere microorganisms can significantly promote the growth of crops under salt stress, which has the potential to develop special microbial fertilizers for increasing the yield of saline-alkali land and provides a low-cost and environmentally friendly new strategy for improving the crop yield of saline-alkali cultivated land by using agricultural microbial technology.

Methods

In May 2022, a field study in a completely randomized block design was conducted at the Heilongjiang Academy of Agricultural Sciences to explore the correlation between plant rhizosphere microorganisms and soybean growth in saline-alkali soil. Two soybean cultivars (Hening 531, a salt-tolerant variety, and 20_1846, a salt-sensitive variety) were planted at two experimental sites [Daqing (normal condition) and Harbin (saline-alkali conditions)], aiming to investigate the performance of soybean in saline-alkali environments.

Results

Soybeans grown in saline-alkali soil showed substantial reductions in key traits: plant height (25%), pod number (26.6%), seed yield (33%), and 100 seed weight (13%). This underscores the unsuitability of this soil type for soybean cultivation. Additionally, microbial analysis revealed 43 depleted and 56 enriched operational taxonomic units (OTUs) in the saline-alkali soil compared to normal soil. Furthermore, an analysis of ion-associated microbes identified 85 mOTUs with significant correlations with various ions. A co-occurrence network analysis revealed strong relationships between specific mOTUs and ions, such as Proteobacteria with multiple ions. In addition, the study investigated the differences in rhizosphere species between salt-tolerant and salt-sensitive soybean varieties under saline-alkali soil conditions. Redundancy analysis (RDA) indicated that mOTUs in saline-alkali soil were associated with pH and ions, while mOTUs in normal soil were correlated with Ca2+ and K+. Comparative analyses identified significant differences in mOTUs between salt-tolerant and salt-sensitive varieties under both saline-alkali and normal soil conditions. Planctomycetes, Proteobacteria, and Actinobacteria were dominant in the bacterial community of saline-alkali soil, with significant enrichment compared to normal soil. The study explored the functioning of the soybean rhizosphere key microbiome by comparing metagenomic data to four databases related to the carbon, nitrogen, phosphorus, and sulfur cycles. A total of 141 KOs (KEGG orthologues) were identified, with 66 KOs related to the carbon cycle, 16 KOs related to the nitrogen cycle, 48 KOs associated with the phosphorus cycle, and 11 KOs linked to the sulfur cycle. Significant correlations were found between specific mOTUs, functional genes, and phenotypic traits, including per mu yield (PMY), grain weight, and effective pod number per plant.

Conclusion

Overall, this study provides comprehensive insights into the structure, function, and salt-related species of soil microorganisms in saline-alkali soil and their associations with salt tolerance and soybean phenotype. The identification of key microbial species and functional categories offers valuable information for understanding the mechanisms underlying plant-microbe interactions in challenging soil conditions.

Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils

A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

Effects of frequency and amount of stover mulching on soil nitrogen and the microbial functional guilds of the endosphere and rhizosphere

Stover mulching as a conservation and sustainable agricultural practice is beneficial for maintaining soil nitrogen (N) requirements and plant health. The microbial functional guilds of the root and rhizosphere are important factors in the soil nitrogen cycle. However, it is unclear how the frequency and amount of stover mulching influence microbial functional guilds in the root and rhizosphere. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching amounts (0, 1/3, 2/3, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. The bacterial functional guilds of nitrogen fixation, nitrification, and anaerobic nitrate oxidation displayed the significantly correlation with C/N, total nitrogen, NO₃⁻, and NH₄⁺. The fungal functional guilds of plant pathogens and saprotrophs showed significantly correlations with C/N, total nitrogen, and NO₃⁻. Moreover, we found that bacterial guilds play a pivotal role in maintaining N requirements at the jointing stage, whereas root endophytic fungal guilds play a more important role than bacterial guilds in regulating plant health at the mature stage. The frequency and amount of stover mulching had significant effects on the microbial functional guilds in the root and rhizosphere. Our data suggest that stover mulch application twice every 3 years is the optimal mulching frequency because it yielded the lowest abundance of nitrifying and anaerobic nitrate-oxidising bacteria and the highest abundance of nitrogen-fixing bacteria at the jointing stage, as well as the lowest abundance of fungal plant pathogens in roots at the mature stage.

Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health

Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.

Synthetic physical contact-remodeled rhizosphere microbiome for enhanced phytoremediation

Phytoremediation is a prevalent strategy to treat environmental pollution caused by heavy metals and eutrophication-related pollutants. Although rhizosphere microbiome is critical for phytoremediation, it remains a great challenge to artificially remodel rhizosphere microbiome for enhancing multiple pollutant treatment. In this study, we designed a synthetic bacterium to strengthen physical contact between natural microbes and plant roots for remodeling the Eichhornia crassipes rhizosphere microbiome during phytoremediation. The synthetic bacterium EcCMC was constructed by introducing a surface-displayed synthetic protein CMC composed of two glucan-binding domains separated by the sequence of the fluorescent protein mCherry. This synthetic bacterium strongly bound glucans and recruited natural glucan-producing bacterial and fungal cells. Microbiome and metabolomic analysis revealed that EcCMC remarkably remodeled rhizosphere microbiome and increased stress response-related metabolites, leading to the increased activity of antioxidant enzymes involved in stress resistance. The remodeled microbiome further promoted plant growth, and enhanced accumulation of multiple pollutants into the plants, with the removal efficiency of the heavy metal cadmium, total organic matters, total nitrogen, total potassium, and total phosphorus reaching up to 98%, 80%, 97%, 93%, and 90%, respectively. This study sheds a novel light on remodeling of rhizosphere microbiome for enhanced phytoremediation of water and soil systems.

Metagenomic Analyses of the Soybean Root Mycobiome and Microbiome Reveal Signatures of the Healthy and Diseased Plants Affected by Taproot Decline

Invading pathogens interact with plant-associated microbial communities, which can be altered under the pressure of pathogen infection. Limited information exists on plant–microbe interactions occurring during natural outbreaks in agricultural fields. Taproot decline (TRD) of soybean is an emerging disease caused by Xylaria necrophora. TRD disease occurrence and yield loss associated with TRD are outstanding issues in soybean production. We applied nuclear ribosomal DNA Internal Transcribed Spacers and 16S rRNA gene taxonomic marker sequencing to define the composition of the fungal and bacterial communities associated with healthy and diseased soybean roots collected from the Mississippi Delta. The plant compartment was a significant factor regulating taxonomic diversity, followed by the disease status of the plant. TRD impacted the root endophytes, causing imbalances; at the intermediate and advanced stages of TRD, X. necrophora decreased mycobiome diversity, whereas it increased microbiome richness. Networks of significant co-occurrence and co-exclusion relationships revealed direct and indirect associations among taxa and identified hubs with potential roles in assembling healthy and TRD-affected soybean biomes. These studies advance the understanding of host–microbe interactions in TRD and the part of biomes in plant health and disease.

Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

Synergistically promoting plant health by harnessing synthetic microbial communities and prebiotics

Soil-borne diseases cause serious economic losses in agriculture. Managing diseases with microbial preparations is an excellent approach to soil-borne disease prevention. However, microbial preparations often exhibit unstable effects, limiting their large-scale application. This review introduces and summarizes disease-suppressive soils, the relationship between carbon sources and the microbial community, and the application of human microbial preparation concepts to plant microbial preparations. We also propose an innovative synthetic microbial community assembly strategy with synergistic prebiotics to promote healthy plant growth and resistance to disease. In this review, a new approach is proposed to improve traditional microbial preparations; provide a better understanding of the relationships among carbon sources, beneficial microorganisms, and plants; and lay a theoretical foundation for developing new microbial preparations.

Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits

Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.