Root exudates from citrus plants subjected to abiotic stress conditions have a positive effect on rhizobacteria

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Effects of salinity on iron-organic carbon binding in the rhizosphere of Kandelia obovata: Insights from root exudate analysis

Iron (Fe) oxides in wetland soils are crucial for stabilizing soil organic carbon (SOC) by forming stable Fe-OC complexes, thus protecting SOC from microbial breakdown and aiding its preservation. This study delves into the response of Fe (hydr-)oxides to salt stress, a relatively unexplored area, by examining Kandelia obovata, a key mangrove species. Through controlled climate chamber experiments, we investigated how salt stress affects the interactions between Fe (hydr-)oxides and SOC in root exudates (REs) and rhizosphere soils. Our results demonstrate that salinity at 30 ppt significantly increases the release of sugars, amino acids, inorganic nutrients (NH4+, NO3-), and phosphorus in K. obovata's REs, while reducing crystalline and amorphous Fe (hydr-)oxides and increasing complexed Fe (hydr-)oxide levels, thereby reducing their crystallinity in rhizosphere soils. Importantly, at elevated salinity (30 ppt), the Fe-OC bond in the rhizosphere shows greater stability, indicating enhanced resilience to salt stress compared to bulk soil. Salt stress also raises the carbon to nitrogen (C/N) ratio in REs. Testing artificial REs (AREs) with different C/N ratios showed that Fe (hydr-)oxide content decreases at C/N ratios of 10 and 30 compared to the control, whereas Fe-OC content increases with higher C/N ratios. Introduction of AREs with a C/N ratio of 20 significantly affected rhizosphere crystalline Fe (hydr-)oxide and Fe-OC content, highlighting AREs' impact on the binding of Fe (hydr-) oxides and OC. The presence of soil microorganisms was critical for the binding of Fe (hydr-) oxides and OC, as sterilized soil exhibited significantly lower levels of Fe (hydr-) oxides and Fe-OC compared to unsterilized soil. This research reveals that under salt stress, mangrove plants play a crucial role in stabilizing rhizosphere SOC by influencing Fe (hydr-) oxide crystallinity and promoting the formation of stable Fe-OC complexes, highlighting the complex interactions between plant REs, salt stress, and soil minerals.

Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance

Introduction

Knowledge on spatiotemporal heterogeneity of plant root microbiomes is lacking. The diversity of the root microbiome must be revealed for understanding plant-microbe interactions and the regulation of functionally crucial microbial taxa.

Methods

We here investigated the dynamics of microbial group characteristics within each soil ecological compartment [rhizoplane (B), rhizosphere (J), and bulk soil (T)] across different cultivation years (year 4: F4 and year 5: F5) by using high-throughput sequencing (16S and ITS).

Results

According to the species diversity, microbiome diversity and the ASV (amplified sequence variant) number in the rhizoplane ecotone increased significantly with an increase in the planting years. By contrast, the microbiome diversity of the rhizosphere soil remained relatively stable. PCoA and PERMANOVA analyses revealed that microbial taxa among different planting years and ecological compartments varied significantly. Planting years exerted the least effect on the rhizosphere microbiome, but their impact on fungi in the rhizoplane and bacteria in the bulk soil was the most significant.

Discussion

Planting years influenced the microbial community composition in various ecological compartments of ginseng root soil. Potentially harmful fungi such as Cryptococcus (2.83%), Neonectria (0.89%), llyonectria (0.56%), Gibberella (0.41%), Piloderma (4.44%), and Plectosphaerella (3.88%) were enriched in F5B with an increase in planting years, whereas the abundance of potentially beneficial Mortierella increased. Correlation analysis indicated associations between bacterial taxa and soil pH/S-CAT, and between fungal taxa and soil moisture content/total potassium. Our study highlights the significance of changes in rhizoplane fungi and the stability of the rhizosphere microbial community in comprehending plant ecological sustainability.

Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives

Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment

Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches

Introduction

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear.

Methods

We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS).

Results

Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years.

Discussion

In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

Prediction of cadmium and zinc phytoextraction by the hyperaccumulator Sedum plumbizincicola using a dynamic geochemical mechanical combination model

Phytoextraction with hyperaccumulators is an environmentally friendly and cost-effective technique for soil remediation but remediation time is largely dependent on experience due to variations in soil properties which restrict the application of this technique. Here, a novel dynamic multi-surface model (MSM) framework is proposed to predict the efficiency and duration of cadmium (Cd) and zinc (Zn) phytoextraction using the hyperaccumulator Sedum plumbizincicola. First, the application of MSM to S. plumbizincicola was investigated using 95 naturally contaminated soils. Using the 'default' settings and considering the pH and DOC content in the rhizosphere, the dissolved Cd/Zn predicted by MSMs showed strong correlations with metal uptake by shoots (R2 = 0.825/0.802 for Cd/Zn, n = 95) and outperformed chemical extraction methods. Then the MSMs were further integrated with time and Cd and Zn interactions to form dynamic-MSM combined (D-MSM-C) models to evaluate and predict phytoextraction efficiency and duration based on a six-season continuous pot experiment. The D-MSM-C models well predicted metal contents remaining in soils after each season with mean absolute percentage error (MAPE) = 20.4 % (Cd) and 2.46 % (Zn) (n = 66). This model is a powerful tool for assessing and predicting phytoremediation efficiency and duration and is applicable across diverse soil properties and multiple metal-contamination scenarios.

Impact of PGPR inoculation on root morphological traits and root exudation in rapeseed and camelina: interactions with heat stress

Root exudation is involved in the recruitment of beneficial microorganisms by trophic relationships and/or signalling pathways. Among beneficial microorganisms, Plant Growth-Promoting Rhizobacteria (PGPR) are known to improve plant growth and stress resistance. These interactions are of particular importance for species that do not interact with mycorrhizal fungi, such as rapeseed (Brassica napus L.) and camelina (Camelina sativa (L.) Crantz). However, heat stress is known to have a quantitative and qualitative impact on root exudation and could affect the interactions between plants and PGPR. We aimed to analyse the effects of PGPR inoculation on root morphology and exudation in rapeseed and camelina at the reproductive stage. The modulation of the effects of these interactions under heat stress was also investigated. The plants were inoculated twice at the reproductive stage with two different Pseudomonas species and were exposed to heat stress after the second inoculation. In non-stressing conditions, after bacterial inoculation, rapeseed and camelina exhibited two contrasting behaviours in C root allocation. While rapeseed plants seemed to suffer from the interactions with the bacteria, camelina plants appeared to control the relationship with the PGPR by modifying the composition of their root exudates. Under heat stress, the plant-PGPR interaction was unbalanced for rapeseed, for which the C allocation strategy is mainly driven by the C cost from the bacteria. Alternatively, camelina plants prioritized C allocation for their own above-ground development. This work opens up new perspectives for understanding plant-PGPR interactions, especially in an abiotic stress context.

Secondary metabolites responses of plants exposed to ozone: an update

Tropospheric ozone (O3) is a secondary pollutant that causes oxidative stress in plants due to the generation of excess reactive oxygen species (ROS). Phenylpropanoid metabolism is induced as a usual response to stress in plants, and induction of key enzyme activities and accumulation of secondary metabolites occur, upon O3 exposure to provide resistance or tolerance. The phenylpropanoid, isoprenoid, and alkaloid pathways are the major secondary metabolic pathways from which plant defense metabolites emerge. Chronic exposure to O3 significantly accelerates the direction of carbon flows toward secondary metabolic pathways, resulting in a resource shift in favor of the synthesis of secondary products. Furthermore, since different cellular compartments have different levels of ROS sensitivity and metabolite sets, intracellular compartmentation of secondary antioxidative metabolites may play a role in O3-induced ROS detoxification. Plants' responses to resource partitioning often result in a trade-off between growth and defense under O3 stress. These metabolic adjustments help the plants to cope with the stress as well as for achieving new homeostasis. In this review, we discuss secondary metabolic pathways in response to O3 in plant species including crops, trees, and medicinal plants; and how the presence of this stressor affects their role as ROS scavengers and structural defense. Furthermore, we discussed how O3 affects key physiological traits in plants, foliar chemistry, and volatile emission, which affects plant-plant competition (allelopathy), and plant-insect interactions, along with an emphasis on soil dynamics, which affect the composition of soil communities via changing root exudation, litter decomposition, and other related processes.

Domestication shapes the endophytic microbiome and metabolome of Salicornia europaea

AIMS

We aim at understanding the effect of domestication on the endophytic microbiome and metabolome of Salicornia europaea and collecting evidence on the potential role of microbial populations and metabolites in the adaptation of plants to different ecological contexts (wild vs crops).

METHODS AND RESULTS

Samples were collected from a natural salt marsh (wild) and an intensive crop field (crop). High-throughput sequencing of the 16S rRNA gene, gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) were used to analyze the endophytic bacterial communities and the metabolite profiles of S. europaea roots, respectively. The elemental analysis of the plant shoots was performed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS).Overall, significant differences were found between the microbiome of wild and cultivated plants. The later showed a higher relative abundance of the genera Erythrobacter, Rhodomicrobium, and Ilumatobacter than wild plants. The microbiome of wild plants was enriched in Marinobacter, Marixanthomonas, and Thalassospira. The metabolite profile of crop plants revealed higher amounts of saturated and non-saturated fatty acids and acylglycerols. In contrast, wild plants contained comparatively more carbohydrates and most macroelements (i.e. Na, K, Mg, and Ca).

CONCLUSIONS

There is a strong correlation between plant metabolites and the endosphere microbiome of S. europaea. In wild populations, plants were enriched in carbohydrates and the associated bacterial community was enriched in genes related to primary metabolic pathways such as nitrogen metabolism and carbon fixation. The endosphere microbiome of crop plants was predicted to have higher gene counts related to pathogenesis. Crop plants also exhibited higher amounts of azelaic acid, an indicator of exposure to phytopathogens.

Grapefruit Root and Rhizosphere Responses to Varying Planting Densities, Fertilizer Concentrations and Application Methods

Huanglongbing (HLB) disease has caused a severe decline in citrus production globally over the past decade. There is a need for improved nutrient regimens to better manage the productivity of HLB-affected trees, as current guidelines are based on healthy trees. The aim of this study was to evaluate the effects of different fertilizer application methods and rates with different planting densities on HLB-affected citrus root and soil health. Plant material consisted of 'Ray Ruby' (Citrus × paradisi) grapefruit trees grafted on 'Kuharske' citrange (Citrus × sinensis × Citrus trifoliata). The study consisted of 4 foliar fertilizer treatments, which included 0×, 1.5×, 3× and 6× the University of Florida Institute of Food and Agriculture (UF/IFAS) recommended guidelines for B, Mn and Zn. Additionally, 2 ground-applied fertilizer treatments were used, specifically controlled-release fertilizer (CRF1): 12-3-14 + B, Fe, Mn and Zn micronutrients at 1× UF/IFAS recommendation, and (CRF2): 12-3-14 + 2× Mg + 3× B, Fe, Mn and Zn micronutrients, with micronutrients applied as sulfur-coated products. The planting densities implemented were low (300 trees ha-1), medium (440 trees ha-1) and high (975 trees ha-1). The CRF fertilizer resulted in greater soil nutrient concentrations through all of the time sampling points, with significant differences in soil Zn and Mn. Grapefruit treated with ground-applied CRF2 and 3× foliar fertilizers resulted in the greatest bacterial alpha and beta diversity in the rhizosphere. Significantly greater abundances of Rhizobiales and Vicinamibacterales were found in the grapefruit rhizosphere of trees treated with 0× UF/IFAS foliar fertilizer compared to higher doses of foliar fertilizers.

Relieving your stress: PGPB associated with Andean xerophytic plants are most abundant and active on the most extreme slopes

Introduction

Plants interact with plant growth-promoting bacteria (PGPB), especially under stress condition in natural and agricultural systems. Although a potentially beneficial microbiome has been found associated to plants from alpine systems, this plant- PGPB interaction has been scarcely studied. Nevados de Chillán Complex hold one of the southernmost xerophytic formations in Chile. Plant species living there have to cope with drought and extreme temperatures during the growing season period, microclimatic conditions that become harsher on equatorial than polar slopes, and where the interaction with PGPB could be key for plant survival. Our goal was to study the abundance and activity of different PGPB associated to two abundant plant species of Andean xerophytic formations on contrasting slopes.

Methods

Twenty individuals of Berberis empetrifolia and Azorella prolifera shrubs were selected growing on a north and south slope nearby Las Fumarolas, at 2,050 m elevation. On each slope, microclimate based on temperature and moisture conditions were monitored throughout the growing period (oct. - apr.). Chemical properties of the soil under plant species canopies were also characterized. Bacterial abundance was measured as Log CFU g^-1 from soil samples collected from each individual and slope. Then, the most abundant bacterial colonies were selected, and different hormonal (indoleacetic acid) and enzymatic (nitrogenase, phosphatase, ACC-deaminase) mechanisms that promote plant growth were assessed and measured.

Results and Discussion

Extreme temperatures were observed in the north facing slope, recording the hottest days (41 vs. 36°C) and coldest nights (-9.9 vs. 6.6°C). Moreover, air and soil moisture were lower on north than on south slope, especially late in the growing season. We found that bacterial abundance was higher in soils on north than on south slope but only under B. empetrifolia canopy. Moreover, the activity of plant growth-promoting mechanisms varied between slopes, being on average higher on north than on south slope, but with plant species-dependent trends. Our work showed how the environmental heterogeneity at microscale in alpine systems (slope and plant species identity) underlies variations in the abundance and plant growth promoting activity of the microorganisms present under the plant canopy of the Andean xerophytic formations and highlight the importance of PGPB from harsh systems as biotechnological tools for restoration.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Introduction

Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.

Methods

This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.

Results and Discussion

Compared to the control (treated with ddH₂O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

Adaptive regulation of activated sludge's core functional flora based on granular internal spatial microenvironment

A great deal of efforts has been put into studying the influence of the external macroenvironment for activated sludge to survive on microbial community succession, while granular internal spatial microenvironment should be given equal attention, because it is more directly involved in the information exchange and material transfer among microorganisms. This study systematically investigated the effects of granular microenvironment on spatial colonization and composition of sludge's core functional flora, and the corresponding difference of biological treatment performance. High content of extracellular-proteins (67.53 mg/gVSS) or extracellular-polysaccharide (65.02 mg/gVSS) stimulated the microbial flocculation and aggregation of 0.5-1.5 mm granules (GS) or 1.5-3.0 mm granules (GM), respectively, which was resulted from excellent cell hydrophobicity (59.26%) or viscosity (3.47 mPa s), therefore, constituted relatively dense porous frame. More hollow space existed in 3.0-5.0 mm granules (GL), which formed loose skeleton with 0.213 mL/g of total pore volume and 17.21 nm of average pore size. Combining scanning electron microscope images and fluorescent in-situ hybridization based microbiological analysis, aerobic nitrifiers were observed to wrap or surround anaerobic bacteria, or facultative/anaerobic bacteria were self-encapsulated, which created granule's unique microenvironment with alternating aerobic and anaerobic zones. GS has the most rich organic matter degrading bacteria and anaerobic heterotrophic denitrifiers, while GM and GL presented the greatest relative abundance of facultative and aerobic denitrifiers, respectively. The activity of dehydrogenase and nitrogen invertase of GM showed be 1.32-3.09 times higher than those of GS and GL, contributing to its higher carbon and nitrogen removal. These findings highlight the importance of granular microenvironment to adaptive regulation of activated sludge's core functional flora and corresponding pollutant removal performance.

Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress

When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.

Kalanchoë blossfeldiana naturally transformed with Rhizobium rhizogenes exhibits superior root phenotype

Plant transformation with root oncogenic loci (rol) genes and open reading frames (ORFs) from Rhizobium rhizogenes have not yet targeted the underground root phenotype of these transformants. Hence, there is a need to develop plants with more efficient root system architecture (RSA). Here, RSA was assessed in naturally transformed (NT) and single rol/ORF Kalanchoë blossfeldiana 'Molly' lines in an aeroponic growth system combined with gene expression analysis. Three NT lines; 306, 324 and 331; exhibited better-developed RSA with longer roots and increased root biomass. In line 306, longest root was 6.3 ± 0.3 cm while WT had 4.8 ± 0.1 cm. However, root length of all overexpressing lines was ca. 30% shorter than WT. Root fresh weight of NT lines was 4.5-fold higher than WT. The expression of rolB, ∆ORF13a and ORF14 in the leaves of overexpressing lines was many folds higher than in NT lines. Increased expression of ∆ORF13a and ORF14 in leaves and roots may contribute more to a stronger compact phenotype than previously assumed. The moderate compact phenotype of NT lines combined with improved RSA compared to the overexpressing lines and WT strongly indicate that the use of R. rhizogenes has great potential to produce Kalanchoë phenotypes with enhanced RSA.

Plant-Microbiota Interactions in Abiotic Stress Environments

Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

Effects of Trichoderma asperellum 6S-2 on Apple Tree Growth and Replanted Soil Microbial Environment

Trichoderma asperellum strain 6S-2 with biocontrol effects and potential growth-promoting properties was made into a fungal fertilizer for the prevention of apple replant disease (ARD). 6S-2 fertilizer not only promoted the growth of Malus hupehensis Rehd seedlings in greenhouse and pot experiments, but also increased the branch elongation growth of young apple trees. The soil microbial community structure changed significantly after the application of 6S-2 fertilizer: the relative abundance of Trichoderma increased significantly, the relative abundance of Fusarium (especially the gene copy numbers of four Fusarium species) and Cryptococcus decreased, and the relative abundance of Bacillus and Streptomyces increased. The bacteria/fungi and soil enzyme activities increased significantly after the application of 6S-2 fertilizer. The relative contents of alkenes, ethyl ethers, and citrullines increased in root exudates of M. hupehensis Rehd treated with 6S-2 fertilizer and were positively correlated with the abundance of Trichoderma. The relative contents of aldehydes, nitriles, and naphthalenes decreased, and they were positively correlated with the relative abundance of Fusarium. In addition, levels of ammonium nitrogen (NH₄-N), nitrate nitrogen (NO₃-N), available phosphorus (AP), available potassium (AK), organic matter (SOM), and pH in rhizosphere soil were also significantly related to changes in the microbial community structure. In summary, the application of 6S-2 fertilizer was effective in alleviating some aspects of ARD by promoting plant growth and optimizing the soil microbial community structure.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

Effect of neonicotinoid dinotefuran on root exudates of Brassica rapa var. chinensis

Root exudates are released by plant roots and are important carrier substances for material exchange and information transmission among plants and the rhizosphere. In the present study, the effect of dinotefuran on root exudates of Chinese cabbage (Brassica rapa var. chinensis) was investigated. The physiological activities revealed that dinotefuran uptake caused oxidative stress in vegetable tissues even at low dinotefuran exposure levels. The metabolic profile of plant root exudates acquired by LC-QTOF/MS was clearly changed by dinotefuran, where the numbers of both up- and down-regulated MS peaks increased with increasing dinotefuran concentration. Under dinotefuran stress, some osmotic adjustment substances (proline and betaine) and defence-related metabolites (spermidine, phenylalanine and some phenolic acids) were significantly upregulated, which may help plants adapt to adverse environmental conditions. Specifically, the contents of some phenylalanine-derived secondary metabolites increased with increasing dinotefuran concentration, which may increase the external detoxification ability of plants. Moreover, respiration metabolism was significantly affected, where some intermediates in the TCA cycle (succinic acid and malic acid) were upregulated with low-level dinotefuran exposure; however, anaerobic respiration products (lactic acid and 3-phenyllactic acid) were accumulated at high exposure levels. In addition, the release of glucosinolates was significantly inhibited in both dinotefuran treatment groups.

Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices.

IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

Rice root exudates enhance desorption and bioavailability of phthalic acid esters (PAEs) in soil associating with cultivar variation in PAE accumulation

Phthalic acid esters (PAEs) is a class of prevalent pollutants in agricultural soil, threating food safety through crop uptake and accumulation of PAEs. Accumulation of PAEs varies largely among crop species and cultivars. Nevertheless, how root exudates affect PAE bioavailability, dissipation, uptake and accumulation is still not well understood. In the present study, desorption and pot experiments were designed to investigate how root exudates from high-(Peizataifeng) and low-(Fengyousimiao) PAE accumulating rice cultivars affect soil PAE bioavailability, dissipation, and accumulation variation. Rice root exudates including low molecular weight organic acids (LMWOAs) of Peizataifeng and Fengyousimiao could enhance desorption of two typical PAE compounds, di-n-butyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP), from aged soil to their available fractions by increasing soil dissolved organic carbon (DOC), thus improving their bioavailability in soil. Peizataifeng produced twice higher amounts of oxalic acid, critic acid and malonic acid in root exudates, and exhibited stronger effects on enhancing desorption and bioavailability of DBP and DEHP than Fengyousimiao. Higher (by about 50%) total organic carbon contents of root exudates from Peizataifeng led to higher (by 10-30%) soil microbial biomass carbon and nitrogen than Fengyousimiao, and thus promoted more PAE dissipation from soil than Fengyousimiao. Nevertheless, higher (by 20-50%) soil DOC and significantly higher PAE bioavailability in the soils planted Peizataifeng resulted in greater (by 53-93%) PAE accumulation in roots and shoots of Peizataifeng than Fengyousimiao, confirming by higher (by 1.82-3.48 folds) shoot and root bioconcentration factors of Peizataifeng than Fengyousimiao. This study reveals that the difference in root exudate extent and LMWOAs between Peizataifeng and Fengyousimiao differentiates PAE accumulation.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

A novel biosensor to monitor proline in pea root exudates and nodules under osmotic stress and recovery

BACKGROUND AND AIMS

Plant and bacteria are able to synthesise proline, which acts as a compound to counteract the negative effects of osmotic stresses. Most methodologies rely on the extraction of compounds using destructive methods. This work describes a new proline biosensor that allows the monitoring of proline levels in a non-invasive manner in root exudates and nodules of legume plants.

METHODS

The proline biosensor was constructed by cloning the promoter region of pRL120553, a gene with high levels of induction in the presence of proline, in front of the lux cassette in Rhizobium leguminosarum bv. viciae.

RESULTS

Free-living assays show that the proline biosensor is sensitive and specific for proline. Proline was detected in both root exudates and nodules of pea plants. The luminescence detected in bacteroids did not show variations during osmotic stress treatments, but significantly increased during recovery.

CONCLUSIONS

This biosensor is a useful tool for the in vivo monitoring of proline levels in root exudates and bacteroids of symbiotic root nodules, and it contributes to our understanding of the metabolic exchange occurring in nodules under abiotic stress conditions.

Root Growth Adaptation to Climate Change in Crops

Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.

Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

Pine wilt disease (PWD) caused by the nematode Bursaphelenchusxylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.

Root exudates: from plant to rhizosphere and beyond

This article describes the composition of root exudates, how these metabolites are released to the rhizosphere and their importance in the recruitment of beneficial microbiota that alleviate plant stress. Metabolites secreted to the rhizosphere by roots are involved in several processes. By modulating the composition of the root exudates, plants can modify soil properties to adapt and ensure their survival under adverse conditions. They use several strategies such as (1) changing soil pH to solubilize nutrients into assimilable forms, (2) chelating toxic compounds, (3) attracting beneficial microbiota, or (4) releasing toxic substances for pathogens, etc. In this work, the composition of root exudates as well as the different mechanisms of root exudation have been reviewed. Existing methodologies to collect root exudates, indicating their advantages and disadvantages, are also described. Factors affecting root exudation have been exposed, including physical, chemical, and biological agents which can produce qualitative and quantitative changes in exudate composition. Finally, since root exudates play an important role in the recruitment of mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR), the mechanisms of interaction between plants and the beneficial microbiota have been highlighted.

Salt stress alleviation in citrus plants by plant growth-promoting rhizobacteria Pseudomonas putida and Novosphingobium sp

This work reveals the protective role of two rhizobacteria, Pseudomonas putida and Novosphingobium sp., on citrus plants subjected to salt stress conditions. Detrimental salt stress effects on crops are likely to increase due to climate change reducing the quality of irrigation water. Plant growth-promoting rhizobacteria (PGPRs) can mitigate stress-induced damage in plants cultivated under high salinity conditions. In this work, Citrus macrophylla (alemow) plants inoculated with the rhizobacteria Pseudomonas putida KT2440 or Novosphingobium sp. HR1a were subjected to salt stress for 30 days. Results showed that in absence of salt stress, Novosphingobium sp. HR1a induced a decrease of transpiration (E) and stomatal conductance (g_s). Both rhizobacteria reduced salt stress-induced damage. Levels of abscisic acid (ABA) and salicylic acid (SA) were lower in inoculated plants under salt stress conditions. Similarly, under stress conditions maximum efficiency of photosystem II (F_v/F_m) in inoculated plants decreased to a lower extent than in non-inoculated ones. In stressed plants, Novosphingobium sp. HR1a also induced leaf accumulation of 3-indole acetic acid (IAA) and a delay in the decrease of quantum yield (ΦPSII). P. putida KT2440 inhibited root chloride and proline accumulation in response to salt stress. Although both bacterial species had beneficial effects on salt-stressed citrus plants, Novosphingobium sp. HR1a induced a better plant performance. Therefore, both strains could be candidates to be used as PGPRs in programs of inoculation for citrus protection against salt stress.