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Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil. [ABSTRACT FROM AUTHOR]

Currently, there are no standard management practices to counteract the adverse effects of fumigation on the soil microbiome. In this study, a variety of pre-plant soil amendments were examined for their ability to recruit and maintain apple rhizosphere microbiomes that are suppressive to pathogen re-infestation of fumigated orchard soils. The capacity of these amendments to improve other characteristics of soil productivity was also evaluated. Results suggest that composted chicken manure and liquid chitin are likely to be detrimental to plant and soil health when used as a post-fumigation soil amendment. In comparison, insect frass (IF) resulted in a significant increase in tree trunk diameter relative to the fumigated control. Following pathogen re-infestation of fumigated soil, however, IF induced a significant increase in Pythium ultimum in the rhizosphere. Therefore, IF can benefit the growth of young apple trees in fumigated soil but may stimulate pathogen activity upon re-infestation. To date, the possibility of using soil amendments to suppress pathogen re-infestation of fumigated soils has not been tested. Results from this study ground support the use of soil amendments as an intervention strategy for "steering" the soil and rhizosphere microbiome in more beneficial and/or prophylactic directions following fumigation. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops. [ABSTRACT FROM AUTHOR]

High crop diversity can potentially enhance farmland productivity and ecosystem services, through direct or indirect effects, particularly belowground. Intercropping is a powerful technique to increase crop diversity and belowground biodiversity. It has attracted long-term global attention. However, little is known about the impacts of belowground microbiota on intercropping-driven increases in crop productivity. This study was an 8-year experiment involving five maize planting patterns, which aimed to distinguish the contributions of rare and abundant microbiota (bacteria, fungi, and eukaryotes) in rhizosphere soil to support maize production. The results indicated that the richness and phylogenetic diversity of rare microbial taxa were significantly higher than those of abundant taxa across all soil samples. Maize and soybean intercropping increased the diversity of rare taxa rather than abundant taxa. Plant growth stages significantly altered the community composition of both rare and abundant microbial taxa. The assembly of the rare and abundant communities is mainly driven by deterministic processes and, in particular, the abundant taxa rather than the rare taxa mainly contributed to maize productivity gain. The changes in maize productivity were significantly associated with many core species in the abundant microbial communities mainly belonging to bacterial Actinomycetales and Rhodocyclaceae, fungal Tausonia and Curvularia, and eukaryotic Leptophyryidae and Ochromonadaceae. The network complexity of abundant fungi and eukaryotic communities also exerted notable effects on maize productivity. Overall, these findings underscored the importance of the core taxa and network stability of abundant microbiota in intercropping systems. This suggests the potential of intercropping to improve crop production by regulating belowground microbial effects in intensive agroecosystems.

The accumulation of microplastics in agricultural soil brings unexpected adverse effects on crop growth and soil quality, which is threatening the sustainability of agriculture. Biochar is an emerging soil amendment material of interest as it can remediate soil pollutants. However, the mechanisms underlying biochar alleviated the toxic effects of microplastics in crops and soil were largely unknown. Using a common economic crop, peanut as targeted species, the present study evaluated the plant physiologica and molecular response and rhizosphere microbiome when facing microplastic contamination and biochar amendment. Transcriptome and microbiome analyses were conducted on peanut root and rhizosphere soil treated with CK (no microplastic and no biochar addition), MP (1.5% polystyrene microplastic addition) and MB (1.5% polystyrene microplastic+2% peanut shell biochar addition). The results indicated that microplastics had inhibitory effects on plant root development and rhizosphere bacterial diversity and function. However, biochar application could significantly promote the expressions of key genes associated with antioxidant activities, lignin synthesis, nitrogen transport and energy metabolism to alleviate the reactive oxygen species stress, root structure damage, nutrient transport limitation, and energy metabolism inhibition induced by microplastic contamination on the root. In addition, the peanut rhizosphere microbiome results showed that biochar application could restore the diversity and richness of microbial communities inhibited by microplastic contamination and promote nutrient availability of rhizosphere soil by regulating the abundance of nitrogen cycling-related and organic matter decomposition-related microbial communities. Consequently, the application of biochar could enhance root development by promoting oxidative stress resistance, nitrogen transport and energy metabolism and benefit the rhizosphere microecological environment for root development, thereby improved the plant-soil system health of microplastic-contaminated agroecosystem.

Soil biosolarization (SBS) is an alternative technique for soil pest control to standard techniques such as soil fumigation and soil solarization (SS). By using both solar heating and fermentation of organic amendments, faster and more effective control of soilborne pathogens can be achieved. A circular economy may be created by using the residues of a given crop as organic amendments to biosolarize fields that produce that crop, which is termed circular soil biosolarization (CSBS). In this study, CSBS was employed by biosolarizing soil with amended tomato pomace (TP) residues and examining its impact on tomato cropping under conditions of abiotic stresses, specifically high salinity and nitrogen deficiency. The results showed that in the absence of abiotic stress, CSBS can benefit plant physiological performance, growth and yield relative to SS. Moreover, CSBS significantly mitigated the impacts of abiotic stress conditions. The results also showed that CSBS impacted the soil microbiome and plant metabolome. Mycoplana and Kaistobacter genera were found to be positively correlated with benefits to tomato plants health under abiotic stress conditions. Conversely, the relative abundance of the orders RB41, MND1, and the family Ellin6075 and were negatively correlated with tomato plants health. Moreover, several metabolites were significantly affected in plants grown in SS- and CSBS-treated soils under abiotic stress conditions. The metabolite xylonic acid isomer was found to be significantly negatively correlated with tomato plants health performance across all treatments. These findings improve understanding of the interactions between CSBS, soil ecology, and crop physiology under abiotic stress conditions.

Abstract Background Numerous chemical pesticides have been used in agricultural production to combat crop diseases and pests. Despite ensuring certain economic advantages, they have also resulted in issues like environmental contamination, declining soil quality, and pesticide residues. Because biological control is environmentally friendly and difficult to acquire resistance to, it has been used in practice recently. Methods In this study, we isolated the endophytic fungus Purpureocillium lilacinum from Portulaca oleracea L., which was previously found to have inhibitory effects on soil pathogens in tobacco fields. To find out how the biocontrol agent P. lilacinum affects soil microorganisms and plant metabolism in tobacco cultivation, we used amplicon sequencing technology and gas chromatography-mass spectrometry to look at the structure of soil microbial communities and the networks of interactions between microorganisms and metabolites in the inter-rhizosphere soil of tobacco fields treated with different amounts of P. lilacinum. Results The findings showed that there was a trend toward less microbial diversity among inter-root microorganisms as solid-state fermentation (SSF) products of P. lilacinum increased; however, submerged fermentation (SmF) had no discernible impact on microbial diversity when compared to the direct use of SSF. Additionally, the relationship between inter-root fungi and volatile compounds in tobacco leaves was dominated by a negative correlation. Conclusions The result demonstrated that P. lilacinum’s antagonistic interaction in the inter-rhizosphere microbial community was dominant and valuable for biopesticide application. P. lilacinum can work more effectively on tobacco roots by using SSF products. P. lilacinum’s opposition to fungal colonies may enhance the volatile chemicals in tobacco leaves. These provide some implications for the biocontrol application of P. lilacinum.

Cupressus gigantea is an endangered species mainly distributed on beach land, down-slope, and middle-slope positions along the Yarlung Zangbo River on the Tibet Plateau of China, with an altitude ranging from 3000 to 3400 m. We investigated the rhizosphere and fine root microbiomes of C. gigantea at these three slope positions through metagenomic analysis. Slope positions had a greater influence on microbiome composition in the rhizosphere than that in the fine roots. Down- and middle-slope positions presented higher microbial richness indeces and community similarity, while a more complex co-occurrence network was observed in the beach land samples. Rhizosphere bacterial community assembly was determined via deterministic processes in the beach land and via stochastic processes in the down- and middle-slope positions. Archaeal and fungal community assemblies were both dominated by stochastic processes in the rhizosphere and fine roots at the three slope positions. Nitrogen (N) functional genes were more sensitive to changes in slope positions than phosphorus (N) functional genes. Soil properties explained more than 60% and 34% of the variations in the N and P functional genes and more than 30% and 10% of the variations in the microbiomes in the rhizosphere and fine roots, respectively. Variation in the microbiome was significantly driven by total nirtogen, total potassium, pH, and soil moisture in rhizosphere, and by pH and soil moisture in fine roots. Our observations suggest that the effect of slope position on the microbiomes of C. gigantea was greater for the rhizosphere than the fine roots, with down- and middle-slope positions presenting higher community similarity.

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria–fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.

Abstract Background The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits. Methods This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform. Results The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality. Conclusions The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.

ABSTRACT Rice bacterial leaf blight (BLB) is the most destructive phyllosphere bacterial disease caused by Xanthomonas oryzae pv. oryzae. The effect of soil-borne diseases on the rhizosphere microbiome has been extensively investigated. However, the regulatory role of the phyllosphere disease BLB on the rhizosphere microbiome remains unclear. Here, we observed that BLB significantly altered the composition of the bacterial-fungal community in the rhizosphere, decreasing bacterial diversity but not fungal diversity. The scale of inter-kingdom networks in the rhizosphere microbiome of BLB-infected plants was more complex and broader than in healthy plants, while the bacterial community was more vulnerable to BLB than the fungal community. Indeed, the relative abundance of Streptomyces, Chitinophaga, Sphingomonas, and Bacillus was higher in the BLB rhizosphere, which can be explained by their keystone hub taxa status in the rhizosphere co-occurrence network. Null model analysis showed that the deterministic assembly of bacterial communities increased while that of fungi decreased. Additionally, the assembly of bacterial and fungal communities was significantly related to variations in BLB and soil nutrients, especially pH and available phosphorus. Random forest model results showed that the bacterial community in the rhizosphere had a strong potential for predicting BLB. Metagenomic analysis revealed that BLB had a considerable impact on the functional adaptation of the rhizosphere microbiome. Interestingly, the abundance of some functional genes involved in carbon, phosphorus, and methane metabolism increased drastically. IMPORTANCE Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.

Microorganisms play an important role in the growth and development of a plant throughout its entire life cycle. Recent advances in the methods of molecular biological analysis have expanded our understanding of the composition and functions of plant microbiota (epiphytic, rhizosphere, and endosphere) and the molecular mechanisms associated with specific processes that govern plant-microorganism interactions. This article reviews the types of plant microbial communities, their sources of origin, and species composition, as well as the critical role they play in modulating the plant immune response against phytopathogens, improving the elemental nutrition of plants, scaring away herbivorous animals, producing phytohormones, and enabling plants to thrive under extreme environmental conditions.

Background: Numerous chemical pesticides have been used in agricultural production to combat crop diseases and pests. Despite ensuring certain economic advantages, they have also resulted in issues like environmental contamination, declining soil quality, and pesticide residues. Because biological control is environmentally friendly and difficult to acquire resistance to, it has been used in practice recently. Methods: In this study, we isolated the endophytic fungus Purpureocillium lilacinum from Portulaca oleracea L., which was previously found to have inhibitory effects on soil pathogens in tobacco fields. To find out how the biocontrol agent P. lilacinum affects soil microorganisms and plant metabolism in tobacco cultivation, we used amplicon sequencing technology and gas chromatography-mass spectrometry to look at the structure of soil microbial communities and the networks of interactions between microorganisms and metabolites in the inter-rhizosphere soil of tobacco fields treated with different amounts of P. lilacinum. Results: The findings showed that there was a trend toward less microbial diversity among inter-root microorganisms as solid-state fermentation (SSF) products of P. lilacinum increased; however, submerged fermentation (SmF) had no discernible impact on microbial diversity when compared to the direct use of SSF. Additionally, the relationship between inter-root fungi and volatile compounds in tobacco leaves was dominated by a negative correlation. Conclusions: The result demonstrated that P. lilacinum's antagonistic interaction in the inter-rhizosphere microbial community was dominant and valuable for biopesticide application. P. lilacinum can work more effectively on tobacco roots by using SSF products. P. lilacinum's opposition to fungal colonies may enhance the volatile chemicals in tobacco leaves. These provide some implications for the biocontrol application of P. lilacinum. [ABSTRACT FROM AUTHOR]

Introduction: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichodermabased products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses. Methods: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont. Results and discussion: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species. [ABSTRACT FROM AUTHOR]

The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota. The RIPENING-INHIBITOR (RIN) gene in tomato is well known for its role in regulating hormone metabolism and fruit ripening. This study shows that RIN is also important for plant immunity through root exudation-mediated recruitment of disease-suppressive microbiota. [ABSTRACT FROM AUTHOR]

Hydrocarbonoclastic bacterial strains were isolated from rhizosphere of plants growing in crude oil-contaminated sites of Assam, India. These bacteria showed plant growth-promoting attributes, even when exposed to crude oil. Two independent pot trials were conducted to test the rhizodegradation ability of the bacterial consortium in combination of plants Azadirchta indica or Delonix regia in crude oil-contaminated soil. Field experiments were conducted at two crude oil-contaminated agricultural field at Assam (India), where plants (A. indica or D. regia) were grown with the selected bacterial consortium consisting of five hydrocarbonoclastic bacterial isolates (Gordonia amicalis BB-DAC, Pseudomonas aeruginosa BB-BE3, P. citronellolis BB-NA1, Rhodococcus ruber BB-VND, and Ochrobactrum anthropi BB-NM2), and NPK was added to the soil for biostimulation. The bacterial consortium-NPK biostimulation led to change in rhizosphere microbiome with enhanced degradation of petroleum hydrocarbons (PHs) in soils contaminated with crude oil. After 120 days of planting A. indica + consortium + NPK treatment, degradation of PHs was found to be up to 67%, which was 55% with D. regia with the same treatment. Significant changes in the activities of plant and soil enzymes were also noted. The shift is bacterial community was also apparent as with A. indica, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria increased by 35.35%, 26.59%, and 20.98%, respectively. In the case of D. regia, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria were increased by 39.28%, 35.79%, and 9.60%, respectively. The predicted gene functions shifted in favor of the breakdown of xenobiotic compounds. This study suggests that a combination of plant-bacterial consortium and NPK biostimulation could be a productive approach to bioengineering the rhizosphere microbiome for the purpose of commercial bioremediation of crude oil-contaminated sites, which is a major environmental issue faced globally. [ABSTRACT FROM AUTHOR]

An ever-growing collection of commercial biostimulants is becoming available in a wide variety of forms and compositions to improve crop performance. Given the intricate nature of deciphering the underlying mechanisms of commercial products, which typically comprise various biological components, it is crucial for research in this area to have robust tools to demonstrate their effectiveness in field trials. Here, we took a multi-attribute approach to evaluating the impact of biostimulants on crop performance. First, we assessed the impact of a biostimulant on the soil and rhizosphere microbiomes associated to crops in eight reference farms, including corn (3 farms), soybean (2), cotton (2) and sugarcane (1), in different biomes and production contexts in Brazil and Paraguay. Second, we modeled a set of integrated indicators to measure crop responses to biostimulant application, including five analytical themes as follows: i) crop development and production (9 indicators), ii) soil chemistry (9), iii) soil physics (5), iv) soil biology (6) and v) plant health (10). Amplicon 16S rRNA and ITS sequencing revealed that the use of the biostimulant consistently changes the structure of bacterial and fungal communities associated with the production system for all evaluated crops. In the rhizosphere samples, the most responsive bacterial taxa to biostimulant application were Prevotella in cotton; Prauserella and Methylovirgula in corn; and Methylocapsa in sugar cane. The most responsive fungal taxa to biostimulant use were Arachnomyces in soybean and cotton; and Rhizophlyctis in corn. The proposed integrated indicators yielded highly favorable positive impact indices (averaging at 0.80), indicating that biostimulant-treated fields correlate with better plant development and crop performance. Prominent indices were observed for indicators in four themes: soil biology (average index 0.84), crop production (0.81), soil physics (compaction reduction 0.81), and chemical fertility (0.75). The multi-attribute approach employed in this study offers an effective strategy for assessing the efficacy of biostimulant products across a wide range of crops and production systems. [ABSTRACT FROM AUTHOR]

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of cooccurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production. [ABSTRACT FROM AUTHOR]

Summary: Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly.To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots.Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response.Our results indicate a central role of root caps in microbiome assembly with ripple‐on effects affecting higher trophic levels and microbiome composition on older root zones. [ABSTRACT FROM AUTHOR]

Introduction: Root-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment. Methods: In this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis. Results and discussion: The results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs. [ABSTRACT FROM AUTHOR]

Drought stress poses a serious threat to Pinus massoniana seedling growth in southern China. Trichoderma species, as beneficial microorganisms, have been widely used in agriculture to enhance plant growth and drought tolerance, but the interaction mechanisms remain unclear. To investigate the effect of drought-resistant Trichoderma longibrachiatum inoculation on P. massoniana growth under drought stress, the plant physiological indicators and rhizosphere microbiome diversity were measured to identify Trichoderma-activated mechanisms. Trichoderma longibrachiatum inoculation significantly promoted P. massoniana growth under drought treatment, and enhanced nitrogen, phosphorus, and potassium absorption compared with those of non-inoculated seedlings. Trichoderma longibrachiatum treatment alleviated the damage to cell membranes and needle tissue structure, and significantly increased antioxidant enzyme activities, osmotic substance contents, and photosynthesis in P. massoniana in response to drought stress. Soil nutrient contents, activities of sucrase, phosphatase, and urease as well as the relative abundances of the dominant genera Burkholderia, Rhodanobacter, and Trichoderma were elevated in the rhizosphere soil of P. massoniana inoculated with T. longibrachiatum under drought stress. A network analysis showed that certain crucial dominant taxa driven by T. longibrachiatum inoculation, including Penicillium, Trichoderma, Simplicillium, Saitozyma, Burkholderia, Bradyrhizobium, Sinomonas, and Mycobacterium, had more correlations with other microorganisms in the soil. Trichoderma longibrachiatum enhanced P. massoniana seedling growth under drought stress by regulating physiological responses and soil microbial community. [ABSTRACT FROM AUTHOR]

Agricultural cropping systems and pasture comprise one third of the world's arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.

For decades chlorine dioxide has been used in water disinfection with excellent results. As the scope of application expands, chlorine dioxide has the potential for soil disinfection. We used amplicon sequencing and gas chromatography-mass spectrometry to compare the changes of four mixed rhizosphere microbial community samples and 12 tobacco leaf volatile samples four months after the flood irrigation with chlorine dioxide in different concentrations (0, 2, 4, 8 mg/l). Phenotypic data of 60 tobacco plants were also collected. The effects of chlorine dioxide on rhizosphere microorganisms were positively correlated with dose gradients. Bacteria responded more strongly in both community structure and metabolic pathways than fungi. Five new bacterial phyla (Firmicutes, Bacteroidota, Myxococcota, Patescibacteria, Verrucomicroboata) appeared in chlorine dioxide treatment groups, while the fungal community only appeared as one new fungal phylum (Basidomycota). Alterations in 271 predicted metabolic bacterial pathways were found. However, in the fungal community were only 10 alternations. The correlations between leaf volatile compounds and rhizosphere microorganisms under the influence of chlorine dioxide treatment could be observed based on network results. However, natural connectivity had already been declining rapidly when less than 20% of the network’s nodes were removed. Therefore, the microbe-metabolite network is not stable. It might be why chlorine dioxide treatments did not significantly affect tobacco quality (p = 0.754) and phenotype (p = 0.867). As a comprehensive investigation of chlorine dioxide in agriculture, this study proves the effectiveness and safety of chlorine dioxide soil disinfection and widens the application range of chlorine dioxide.

Coronarin (COR), an analog of jasmonic acid, has been shown to enhance the tolerance of plants to drought. However, the effects of COR on the interactions among microorganisms associated with plant roots and their implications for enhancing the drought tolerance of plants remain unclear. Here, we studied the effects of applying COR on the microorganisms associated with plant roots and the rhizosphere metabolome. Treatment with COR affected the fungal community of the rhizosphere by inducing changes in the rhizosphere metabolome, which enhanced the drought tolerance of plants. However, treatment with COR had no significant effect on root microorganisms or rhizosphere bacteria. Specifically, the application of COR resulted in a significant reduction in the relative abundance of metabolites, such as mucic acid, 1,4-cyclohexanedione, 4-acetylbutyric acid, Ribonic acid, palmitic acid, and stearic acid, in maize roots under drought conditions; COR application also led to increases in the abundance of drought-resistant fungal microorganisms, including Rhizopus, and the assembly of a highly drought-resistant rhizosphere fungal network, which enhanced the drought tolerance of plants. Overall, the results of our study indicate that COR application positively regulates interactions between plants and microbes and increases the drought tolerance of plants.

Abstract Background The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. Results The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. Conclusion Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.

Astragalus is a medicinal plant with obvious rhizosphere effects. At present, there are many Astragalus plants with high application value but low recognition and resource reserves in the northwestern area of Yunnan province, China. In this study, metagenomics was used to analyze the microbial diversity and community structure of rhizosphere soil of A. forrestii, A. acaulis, and A. ernestii plants grown in a special high-cold environment of northwestern Yunnan, China, at different altitudes ranging from 3225 to 4353 m. These microbes were taxonomically annotated to obtain 24 phyla and 501 genera for A. forrestii, 30 phyla and 504 genera for A. acaulis, as well as 39 phyla and 533 genera for A. ernestii. Overall, the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Acidobacteria, while the dominant fungal ones were Ascomycota and Basidiomycota. At the genus level, Bradyrhizobium, Afipia, and Paraburkholderia were the most prevalent bacteria, and Hyaloscypha, Pseudogymnoascus, and Russula were the dominant fungal genera. Some of them are considered biocontrol microbes that could sustain the growth and health of host Astragalus plants. Redundancy analysis revealed that pH, TN, and SOM had a significant impact on the microbial community structures (p < 0.05). Finally, triterpene, flavonoid, polysaccharide, and amino acid metabolisms accounted for a high proportion of the enriched KEGG pathways, which possibly contributed to the synthesis of bioactive constituents in the Astragalus plants.

Phosphorous (P) is widely used in agriculture; yet, P fertilizers are a nonrenewable resource. Thus, mechanisms to improve soil P bioavailability need to be found. Legumes are efficient in P acquisition and, therefore, could be used to develop new technologies to improve soil P bioavailability. Here, we studied different species and varieties of legumes and their rhizosphere microbiome responses to low-P stress. Some varieties of common beans, cowpeas, and peas displayed a similar biomass with and without P fertilization. The rhizosphere microbiome of those varieties grown without P was composed of unique microbes displaying different levels of P solubilization and mineralization. When those varieties were amended with P, some of the microbes involved in P solubilization and mineralization decreased in abundance, but other microbes were insensitive to P fertilization. The microbes that decreased in abundance upon P fertilization belonged to groups that are commonly used as biofertilizers such as Pseudomonas and Azospirillum. The microbes that were not affected by P fertilization constitute unique species involved in P mineralization such as Arenimonas daejeonensis, Hyphomicrobium hollandicum, Paenibacillus oenotherae, and Microlunatus speluncae. These P-insensitive microbes could be used to optimize P utilization and drive future sustainable agricultural practices to reduce human dependency on a nonrenewable resource.

IntroductionThe use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.MethodsIn this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.Results and discussionAn overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.

An ever-growing collection of commercial biostimulants is becoming available in a wide variety of forms and compositions to improve crop performance. Given the intricate nature of deciphering the underlying mechanisms of commercial products, which typically comprise various biological components, it is crucial for research in this area to have robust tools to demonstrate their effectiveness in field trials. Here, we took a multi-attribute approach to evaluating the impact of biostimulants on crop performance. First, we assessed the impact of a biostimulant on the soil and rhizosphere microbiomes associated to crops in eight reference farms, including corn (3 farms), soybean (2), cotton (2) and sugarcane (1), in different biomes and production contexts in Brazil and Paraguay. Second, we modeled a set of integrated indicators to measure crop responses to biostimulant application, including five analytical themes as follows: i) crop development and production (9 indicators), ii) soil chemistry (9), iii) soil physics (5), iv) soil biology (6) and v) plant health (10). Amplicon 16S rRNA and ITS sequencing revealed that the use of the biostimulant consistently changes the structure of bacterial and fungal communities associated with the production system for all evaluated crops. In the rhizosphere samples, the most responsive bacterial taxa to biostimulant application were Prevotella in cotton; Prauserella and Methylovirgula in corn; and Methylocapsa in sugar cane. The most responsive fungal taxa to biostimulant use were Arachnomyces in soybean and cotton; and Rhizophlyctis in corn. The proposed integrated indicators yielded highly favorable positive impact indices (averaging at 0.80), indicating that biostimulant-treated fields correlate with better plant development and crop performance. Prominent indices were observed for indicators in four themes: soil biology (average index 0.84), crop production (0.81), soil physics (compaction reduction 0.81), and chemical fertility (0.75). The multi-attribute approach employed in this study offers an effective strategy for assessing the efficacy of biostimulant products across a wide range of crops and production systems.

It is aimed to screen phosphate-solubilizing rhizobacteria（PSB）and to clarify its growth-promoting effect on Pinus massoniana seedlings and the mechanism . The soil-dilution plate method was used to isolate and purify the PSB strains. The PSB strains were identified by morphology and 16s rDNA sequencing methods. Finally, the masson pine seedlings were inoculated with PSB strains for 60 d, then the seedling growth and physiological indexes, soil physical and chemical properties, and rhizosphere bacterial community were determined. The results showed that three PSB strains（WJ10, WJ25 and WJ41）with strong phosphate-solubilizing abilities were isolated from the P. massoniana rhizosphere soil and belonged to Paraburkholderia spp. The three PSB strains had the strongest phosphate-solubilizing abilities to aluminum phosphate, followed by tricalcium phosphate, calcium monophosphate and ferric phosphate. Based on the pot experiment, the three PSB strains effectively promoted seedlings growth, with the best effects on the seedling height and root length promotion for WJ25, followed by WJ41 and WJ10. The main mechanisms of seedling promotion of the three PSB strains include: 1）The PSB strains increased the root activity, chlorophyll b, soluble protein, nitrogen, phosphorus and potassium contents in masson pine seedlings; 2）meanwhile, PSBs enhanced the contents of available phosphorus, available potassium, active nitrogen, soil urease and phosphatase in rhizosphere soil; 3）in addition, the addition of three PSB strains also affected the composition and diversity of the rhizosphere bacterial community, and promoted the significant enrichment of beneficial bacteria such as Bacillus, Nitrosospira, Gemmata and Cytophaga in the rhizosphere soil. In conclusion, the three Paraburkholderia spp. strains could promote masson pine seedlings growth by regulating plant physiology and changing rhizosphere microenvironment. This study provides a theoretical basis for the development and application of rhizosphere PSB fertilizer of P. massoniana. [ABSTRACT FROM AUTHOR]

The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field. [ABSTRACT FROM AUTHOR]

Apple leaf characteristics are the most important vegetative growth and development traits. The apple rhizosphere is also indirectly responsible for apple growth and development. It provides roots with elements and compounds that improve roots' and shoots' growth and development. The application of exogenous plant growth regulators such as strigolactones (SLs) has become one of the main trends for improving vegetative growth and enhancing the rhizosphere microbiome. This study aimed to investigate the effect of the exogenous SLs on some leaf characteristics, such as leaf area, angle, nitrogen content, chlorophyll content, and apical area diameter, in addition to the composition of the rhizosphere microbiome of apple M9 rootstock. The apple rootstocks were treated with various concentrations of GR24, an analog of SLs; the concentrations were 0, 1, 5, and 10 µM. The study found that the treatments of 5 µM increased the leaf–stem angles and leaf length while decreasing the apical diameter. The treatments of 1 and 5 µM increased leaf nitrogen content; however, this effect was not observed when using the higher concentration of 10 µM. The lower concentration (1 µM) led to a different abundance and diversity of microorganisms compared to the higher concentration (10 µm). [ABSTRACT FROM AUTHOR]

Background: The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits. Methods: This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform. Results: The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality. Conclusions: The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role. Key message: It observed the Bourbon and Castillo coffee varieties to have a distinct microbial profile, indicating the presence of a diverse assemblage of soil and phyllosphere microorganisms, including non-culturable bacterial species. [ABSTRACT FROM AUTHOR]

Abstract Background Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome from soil to resist Rs. However, whether this recruitment is inheritable from resistant parent to progeny has not been determined. Results In the present study, we investigated the rhizosphere microbiomes of tomatoes with clear kinship and different resistance against Rs. Resistant tomatoes grown with the additions of natural soil or its extract showed lower disease indexes than those grown in the sterile soil, demonstrating the importance of soil microbiome in resisting Rs. The results of 16S ribosomal RNA gene amplicon sequencing revealed that the resistant cultivars had more robust rhizosphere microbiomes than the susceptible ones. Besides, the resistant progeny HF12 resembled its resistant parent HG64 in the rhizosphere microbiome. The rhizosphere microbiome had functional consistency between HF12 and HG64 as revealed by metagenomics. Based on multi-omics analysis and experimental validation, two rhizobacteria (Sphingomonas sp. Cra20 and Pseudomonas putida KT2440) were enriched in HF12 and HG64 with the ability to offer susceptible tomatoes considerable protection against Rs. Multiple aspects were involved in the protection, including reducing the virulence-related genes of Rs and reshaping the transcriptomes of the susceptible tomatoes. Conclusions We found promising bacteria to suppress the tomato bacterial wilt in sustainable agriculture. And our research provides insights into the heritability of Rs-resistant tomato rhizobacteria, echoing the inheritance of tomato genetic material. Video Abstract

Bacterial wilt caused by Ralstonia solanacearum is considered one of the most harmful diseases of pepper plants. Recently, research on plant disease control through the rhizosphere microbiome has been actively conducted. In this study, the relationship with disease occurrence between the neighboring plant confirmed by analyzing the physicochemical properties of the rhizosphere soil and changes in the microbial community. The results confirmed that the microbial community changes significantly depending on the organic matters, P2O5, and clay in the soil. Despite significant differences in microbial communities according to soil composition, Actinobacteriota at the phylum level was higher in healthy plant rhizosphere (mean of relative abundance, D: 8.05 ± 1.13; H: 10.06 ± 1.59). These results suggest that Actinobacteriota may be associated with bacterial wilt disease. In this study, we present basic information for constructing of healthy soil in the future by presenting the major microbial groups that can suppress bacterial wilt.

Abstract Background The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. Results Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. Conclusion We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract

The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops. [ABSTRACT FROM AUTHOR]

Root exudates shape the rhizosphere microbiome, but little is known about the specific compounds in root exudates that are important. Here, we investigated the impacts of the plant-synthesized phytohormones indole-3-acetic acid (IAA) and abscisic acid (ABA) exuded by roots on the maize rhizobacterial communities. To identify maize genotypes that differed in the root exudate concentrations of IAA and ABA, we screened hundreds of inbred lines using a semi-hydroponic system. Twelve genotypes with variable exudate concentrations of IAA and ABA were selected for a replicated field experiment. Bulk soil, rhizosphere, and root endosphere samples were collected at two vegetative and one reproductive maize developmental stage. IAA and ABA concentrations in rhizosphere samples were quantified by liquid chromatography–mass spectrometry. The bacterial communities were analyzed by V4 16S rRNA amplicon sequencing. Results indicated that IAA and ABA concentrations in root exudates significantly affected the rhizobacterial communities at specific developmental stages. ABA impacted the rhizosphere bacterial communities at later developmental stages, whereas IAA affected the rhizobacterial communities at the vegetative stages. This study contributed to our knowledge about the influence that specific root exudate compounds have on the rhizobiome composition, showing that the phytohormones IAA and ABA exuded by roots have a role in the plant–microbiome interactions. [ABSTRACT FROM AUTHOR]

Bacillus subtilis strain NCD-2 is a promising biocontrol agent for soil-borne plant diseases and shows potential for promoting the growth of some crops. The purposes of this study were to analyze the colonization ability of strain NCD-2 in different crops and reveal the plant growth promotion mechanism of strain NCD-2 by rhizosphere microbiome analysis. qRT-PCR was used to determine the populations of strain NCD-2, and microbial communities' structures were analyzed through amplicon sequencing after application of strain NCD-2. Results demonstrated that strain NCD-2 had a good growth promotion effect on tomato, eggplant and pepper, and it was the most abundant in eggplant rhizosphere soil. There were significantly differences in the types of beneficial microorganisms recruited for different crops after application of strain NCD-2. PICRUSt analysis showed that the relative abundances of functional genes for amino acid transport and metabolism, coenzyme transport and metabolism, lipid transport and metabolism, inorganic ion transport and metabolism, and defense mechanisms were enriched in the rhizospheres of pepper and eggplant more than in the rhizospheres of cotton, tomato and maize after application of strain NCD-2. In summary, the colonization ability of strain NCD-2 for five plants was different. There were differences in microbial communities' structure in rhizosphere of different plants after application of strain NCD-2. Based on the results obtained in this study, it was concluded that the growth promoting ability of strain NCD-2 were correlated with its colonization quantity and the microbial species it recruited. [ABSTRACT FROM AUTHOR]

Purpose: Microorganisms and their metabolites suppress plant parasitic nematodes. The activity and biocontrol efficiency of antagonistic microorganisms is affected by microbial interactions. Here, the changes of rhizosphere metabolome and microbiome in Meloidogyne incognita infested soil are analysed. The differences in rhizosphere microbial community and interactions, functional genes, and metabolites of soils high or low-infested with M. incognita were compared. The keystone microorganisms and nematicidal metabolites were investigated in order to find new biocontrol agents. Methods: Microbial composition and functional genes were explored using metagenomics. Abundances of various metabolites were analysed via metabolomics. Microorganisms were isolated from soil, the enzyme activity was determined. Nematicidal activities of microbes and metabolites were detected. Results: Rhizosphere microbial composition, function, network, and metabolites differed in high and low-infested soils. Abundances of nematicidal microorganisms and metabolites, and extracellular enzymes genes in low-infested soil were higher than in high-infested soil. The network complexity of high-infested soil decreased compared to low-infested soil network. The contents of thirty-five metabolites in the low-infested soil were higher than in the high-infested soil. The acetophenone showed high nematicidal and repellent activities against Meloidogyne incognita. Abundance of Bacillus was positively correlated with content of acetophenone. Nematicidal microbial isolates produced protease, chitinase, and lipase. Bacillus amyloliquefaciens W1 produced acetophenone and killed 98.8% of Meloidogyne incognita second-stage juveniles within 24 hours. Conclusion: The composition, network structure, metabolites, and functions of rhizosphere microbiota differed in high and low-infested soils. Bacillus amyloliquefacens W1 produced acetophenone that killed Meloidogyne incognita juveniles. Acetophenone was identified as an effective nematicide. [ABSTRACT FROM AUTHOR]

Background: The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. Results: The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. Conclusion: Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting. [ABSTRACT FROM AUTHOR]

Fertilization is widely acknowledged as being an essential practice to improve forest productivity in forest ecosystems. However, too little consideration has been given to the taxonomic and functional compositions of rhizosphere soil microbes and their interactions with root exudates under different fertilizer regimes in forest plantations. Here, we investigated the effects of four typical fertilizer regimes (CK, no fertilizer; CF, compound fertilizer; OF, organic fertilizer; CMF, compound microbial fertilizer) on soil microbial communities and their potential functional groups in Phoebe bournei young plantations, as well as their associations with soil physicochemical properties and root exudates. These results showed that fertilizer regimes strikingly affected the rhizosphere soil microbial community compositions and alpha diversity indices. The pathotroph was the dominant fungal guild. With the applications of three fertilizations, the relative abundances of the plant pathogen and arbuscular mycorrhiza increased. The alpha diversity of soil bacteria was highest under the OF regime, and soil fungal diversity was more powerfully affected by the amendment of CMF. Additionally, while the fungal community was simultaneously influenced by soil physiochemical factors and root exudates, the bacterial community in the rhizosphere was mostly impacted by root exudates. More importantly, the application of OF and CF induced dramatic growths of Fusarium, while CMF treatment including Bacillus suppressed the development of Fusarium via adjusting bacterial species. Overall, our findings exhibit the divergent responses of rhizosphere bacteria and fungi to fertilizer regimes in P. bournei young plantations. The application of organic fertilizer provides benefits for rhizosphere bacteria, and microbial fertilizer can help alleviate inhibition through changing pathogens. [ABSTRACT FROM AUTHOR]

Currently, there are no standard management practices to counteract the adverse effects of fumigation on the soil microbiome. In this study, a variety of pre-plant soil amendments were examined for their ability to recruit and maintain apple rhizosphere microbiomes that are suppressive to pathogen re-infestation of fumigated orchard soils. The capacity of these amendments to improve other characteristics of soil productivity was also evaluated. Results suggest that composted chicken manure and liquid chitin are likely to be detrimental to plant and soil health when used as a post-fumigation soil amendment. In comparison, insect frass (IF) resulted in a significant increase in tree trunk diameter relative to the fumigated control. Following pathogen re-infestation of fumigated soil, however, IF induced a significant increase in Pythium ultimum in the rhizosphere. Therefore, IF can benefit the growth of young apple trees in fumigated soil but may stimulate pathogen activity upon re-infestation. To date, the possibility of using soil amendments to suppress pathogen re-infestation of fumigated soils has not been tested. Results from this study ground support the use of soil amendments as an intervention strategy for “steering” the soil and rhizosphere microbiome in more beneficial and/or prophylactic directions following fumigation.