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Molybdenum plays an important role as a nutrient for plants. It has an important role in the process of plant growth and fixing nitrogen for the plant. A field experiment conducted in the autumn of 2023 aimed to study how different fertilizer treatments affected the availability of molybdenum in maize (Zea mays L.) rhizosphere and non-rhizosphere soils. The treatments included sheep manure at a rate of 8 tons per hectare, urea at 400 kg per hectare, humic acid at 500 cm³ per liter per dunum, and a control group. The experiment followed a randomized complete block design (RCBD) with three replications, using local maize seeds planted in 3 m by 3 m plots. After applying the treatments, the concentration of available molybdenum was measured in both soil regions at 70 and 100 days after planting. Results indicated that adding fertilizers (sheep manure, humic acid, and nitrogen) increased the concentration of available molybdenum in both soil regions. Specifically, the humic acid treatment had the highest concentration of available molybdenum at both 70 and 100 days, while the nitrogen treatment had the lowest. This highlights the importance of humic acid and organic materials in improving molybdenum availability. Furthermore, molybdenum concentration increased at the 100-day mark for all treatments outside the rhizosphere, except for the control, showing that all treatments enhanced molybdenum content both within and beyond the rhizosphere.

Abstract Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.

Abstract The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu’ er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Abstract Background Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content. Results In this study, we present a novel approach, RhizoMAP, in which the rhizosphere molecules are imprinted on selected polymer membranes and then spatially profiled using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). We enhanced the performance of RhizoMAP by combining the use of two thin (

Diphenyl ether herbicides are extensively utilized in agricultural systems, but their residues threaten the health of sensitive rotation crops. Functional microbial strains can degrade diphenyl ether herbicides in the rhizosphere of crops, facilitating the restoration of a healthy agricultural environment. However, the interplay between microorganisms and plants in diphenyl ether herbicides degradation remains unclear. Thus, the herbicide-degrading strain Bacillus sp. Za and the sensitive crop, maize, were employed to uncover the interaction mechanism. The degradation of diphenyl ether herbicides by strain Bacillus sp. Za was promoted by root exudates. The strain induced root exudate re-secretion in diphenyl ether herbicide-polluted maize. We further showed that root exudates enhanced the rhizosphere colonization and the biofilm biomass of strain Za, augmenting its capacity to degrade diphenyl ether herbicide. Root exudates regulated gene fliZ, which is pivotal in biofilm formation. Wild-type strain Za significantly reduced herbicide toxicity to maize compared to the ZaΔfliZ mutant. Moreover, root exudates promoted strain Za growth and chemotaxis, which was related to biofilm formation. This mutualistic relationship between the microorganisms and the plants demonstrates the significance of plant-microbe interactions in shaping diphenyl ether herbicide degradation in rhizosphere soils. [Graphic: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Abstract Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05–80.63% for PMTSA13T and 74.02–80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13T ranged from 19 to 39%, and 19.1–38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to ‘carbohydrate metabolism and transport (G)’, according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant–microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13T (= KCTC 59028T = GDMCC 1.4451T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.

Abstract Background The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. Results Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi – a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. Conclusions This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.

Leguminous shade trees are ubiquitous parts of tea plantations of the Terai region. However, their shed leaves might have an effect on the soil microflora under those shade trees, so it is important to find out how leaf litter affect the soil microflora. Isolation of soil microbial consortia followed by downstream experiments were conducted to observe the tolerance/susceptible pattern of those soil microflora against the fallen leaves. Sample from under Albizia odoratissima has higher organic carbon, organic matter and nitrogen content but the same property was found to be low in the sample collected under Melia azedarach. Isolation of consortia was done on nutrient agar. In vitro tolerance assay was conducted to find out the tolerance pattern against leaf extracts, heavy metal salts, pesticides, antibiotics and antifungals. Heavy metals salts like Arsenic trioxide (AS2O3) and Cupric chloride (CuCl2); and pesticides like Thiamethoxam; Spiromesifen; Phorate etc. showed no inhibition against all the isolated consortia. Co-Trimoxazole and Augmentin have not showed any inhibition except consortia under Derris robusta, whereas no antifungals but Itraconazole had an impact over all the consortia. Shade trees, being a crucial member of the tea plantations, cannot be removed but replacement of these with other species could be a probable option, besides this limited use of chemical pesticides and fertilizers should be taken into consideration strictly to restrain the microbial population in tea garden soil. So, this study has disclosed the acceptability of each and every shade tree used in this region.

The Korean fir tree (Abies koreana), an endemic species of South Korea, is experiencing a severe decline in population due to climate change. Studies on the conservation of Korean fir have been extensive, yet research regarding its correlation with rhizosphere bacterial communities remains scarce, warranting further investigation. In this study, metagenome amplicon sequencing targeting the 16S rRNA V4 region was conducted to examine the presence of specific bacterial communities in Korean fir and to investigate potential differences based on habitat types (rhizosphere of native or cultivated trees, soil of dead trees, and bulk soil) and seasonal variations (April, June, September, November). Here we show that although we could not identify specific taxa highly specifically with Korean fir, the rhizosphere bacterial community in native trees exhibited less variability in response to seasonal changes compared to that in bulk soils. Suggesting the establishment of relatively stable bacterial populations around the Korean fir natural habitat. Further research on other types of rhizosphere and/or microbes is necessary to investigate the distinct relationship of Korean fir with microbial communities.

In order to explore the effects of ecological landscaping tree species Taxodium ‘Zhongshanshan 118’ on soil microbial ecosystem in Huaihe Plain of north Anhui Province, the differences in soil nutrients levels, microbial communities structures and their influencing factors between the rhizosphere (R) and non-rhizosphere (NR) were analyzed. The results were as follows: (1) The 4-year-old Taxodium ‘Zhongshanshan 118’ rhizosphere had a low enrichment capacity for macronutrients, resulting in a deficiency of hydrolyzable nitrogen and available phosphorus. The R had similar levels of total nitrogen, and lower levels of total phosphorus, total potassium and available potassium than the NR soil. The R had a strong enrichment ability for microelements (iron, copper, manganese). And the available manganese content in the R was significantly higher than that in the NR. Both the R and the NR soils of Taxodium ‘Zhongshanshan 118’ were alkaline. The R had a slightly lower pH and a higher electrical conductivity than the NR. The R had a certain degree of enrichment for available sodium, available magnesium and available calcium, as well as for organic carbon and organic matter. (2) Based on the Anosim analysis of community structure between groups, the R value was 0.224 (P=0.022), which was significantly greater than 0, indicating significant differences between the bacterial communities of the R and the NR of Taxodium ‘Zhongshanshan 118’. The total number of OTUs in the R and the NR was 5 283. There were 1 307 unique OTUs in R and 1 265 OTUs in NR. (3) The R had a slightly lower bacterial diversity than the NR. The dominant phylum in both the R and the NR were Firmicutes, Proteobacteria, Acidobacteriota, Bacteroidetes, Chloroflexi, Myxococcota, Actinobacteria, and Crenarchaeota. Among them, only Acidobacteriota showed a significant positive correlation with available phosphorus. The R had higher abundances of Firmicutes (17.94%) and Bacteroidetes (5.21%) than the NR (1.84% and 3.90%), respectively. Neither of them had a significant correlation with environmental factors. The R had higher abundances of Clostridia, Bacteroidia and Bacilli than the NR by 14.05%, 1.32% and 2.06%, respectively. (4) The UPGMA clustering analysis showed that R4 was isolated from the other samples. NR4 and NR5 formed a cluster, NR1, NR2 and NR3 clusted with R1, R2, R3 and R5. R4 had lower species diversity and abundance than the other samples, and had an uneven distribution of taxa. In conclusion, despite the weak rhizosphere effect of young Taxodium ‘Zhongshanshan 118’, it was the main factor for the enrichment of Firmicutes and Bacteroidetes in the rhizosphere. And more microelements and a moderate amount of macroelements should be applied in the cultivation process.

Abstract Background Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps−TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. Results qPCR revealed that the B. subtilis UD1022eps−TasA− strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. Conclusion This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.

Bacteria play critical roles in regulating soil phosphorus (P) cycling. The effects of interactions between crops and soil P-availability on bacterial communities and the feedback regulation of soil P cycling by the bacterial community modifications are poorly understood. Here, six soybean (Glycine max) genotypes with differences in P efficiency were cultivated in acidic soils with long-term sufficient or deficient P-fertilizer treatments. The acid phosphatase (AcP) activities, organic-P concentrations and associated bacterial community compositions were determined in bulk and rhizosphere soils. The results showed that both soybean plant P content and the soil AcP activity were negatively correlated with soil organic-P concentration in P-deficient acidic soils. Soil P-availability affected the α-diversity of bacteria in both bulk and rhizosphere soils. However, soybean had a stronger effect on the bacterial community composition, as reflected by the similar biomarker bacteria in the rhizosphere soils in both P-treatments. The relative abundance of biomarker bacteria Proteobacteria was strongly correlated with soil organic-P concentration and AcP activity in low-P treatments. Further high-throughput sequencing of the phoC gene revealed an obvious shift in Proteobacteria groups between bulk soils and rhizosphere soils, which was emphasized by the higher relative abundances of Cupriavidus and Klebsiella, and lower relative abundance of Xanthomonas in rhizosphere soils. Among them, Cupriavidus was the dominant phoC bacterial genus, and it was negatively correlated with the soil organic-P concentration. These findings suggest that soybean growth relies on organic-P mineralization in P-deficient acidic soils, which might be partially achieved by recruiting specific phoC-harboring bacteria, such as Cupriavidus.

The rhizosphere of a plant is home to helpful microorganisms called plant growth-promoting rhizobacteria (PGPR), which play a crucial role in promoting plant growth and development. The significance of PGPR for long-term agricultural viability is outlined in this review. Plant growth processes such as nitrogen fixation, phosphate solubilization, and hormone secretion are discussed. Increased plant tolerance to biotic and abiotic stress, reduced use of chemical fertilizers and pesticides, and enhanced nutrient availability, soil fertility, and absorption are all mentioned as potential benefits of PGPR. PGPR has multiple ecological and practical functions in the soil’s rhizosphere. One of PGPR’s various roles in agroecosystems is to increase the synthesis of phytohormones and other metabolites, which have a direct impact on plant growth. Phytopathogens can be stopped in their tracks, a plant’s natural defenses can be bolstered, and so on. PGPR also helps clean up the soil through a process called bioremediation. The PGPR’s many functions include indole acetic acid (IAA) production, ammonia (NH3) production, hydrogen cyanide (HCN) production, catalase production, and more. In addition to aiding in nutrient uptake, PGPR controls the production of a hormone that increases root size and strength. Improving crop yield, decreasing environmental pollution, and guaranteeing food security are only some of the ecological and economic benefits of employing PGPR for sustainable agriculture.

Microorganisms (MOs) are prominent in ecological functioning and balance. The rhizosphere is considered one of the most diverse ecosystems on Earth and serves as a breeding spot for many MOs. Rhizosphere microbial diversity changes according to plant species, genotype, and the nature of the soil. The current study reports the possible use of bacteria isolated from the rhizosphere of Azadirachta indica for synthesizing silver nanoparticles (AgNPs). The physicochemical characterization and antibacterial activity of these green synthesized AgNPs are also reported. The gene (16S rRNA) sequence of bacteria isolated from the rhizosphere showed a maximum similarity of 99.25% with Bacillus subtilis. After incubation, the colorless reaction mixture transformed to brown, which indicates the formation of AgNPs, and UV-vis spectral analysis also confirmed the biosynthesis of AgNPs. Compared to lower temperatures, the efficiency of AgNP synthesis was high at the higher temperature. The scanning electron microscope image demonstrated spherical-shaped AgNPs with sizes ranging from 18 to 21 nm. Energy-dispersive X-ray analysis established the elemental analysis of synthesized AgNPs. The synthesized AgNPs showed strong bactericidal properties against pathogenic bacteria Klebsiella pneumonia, Pseudomonas aeruginosa, Escherichia coli, and methicillin-resistant Staphylococcus aureus.

Rhododendron simsii plays important roles in maintaining ecological system stability in the north temperate zone. However, its natural growth is greatly affected by soil microorganisms, particularly rhizosphere microbes. In this study, a comparative analysis was conducted of the bacterial community structure in the rhizosphere of R. simsii at the old, adult, juvenile, and seedlings stages. The results showed that Proteobacteria (38.53%‒47.63%), Actinobacteria (23.45%‒34.03%), and Acidobacteria (10.33%‒17.79%) were the dominant phyla in the R. simsii rhizosphere. In particular, 3, 5, 42, and 33 OTUs were unique to the soil samples of ‘old trees’, ‘adult trees’, ‘juvenile trees’, and ‘seedlings’, respectively. Across four sets of R. simsii rhizosphere microbes sampled from seedlings to old trees, the OTUs first increased, then decreased, and finally increased. Overall, alpha diversity (Chao, ACE, and Sobs) revealed similar trends with the highest value i‒n recorded for the rhizosphere sample of ‘adult trees’ and the lowest for the ‘seedlings’ sample. The bacterial genera in the rhizosphere samples from ‘old trees’ and ‘adult trees’ exhibited close clustering. Notably, the R. simsii population of ‘juvenile trees’, demonstrating the highest genetic diversity, were rich in Bradyrhizobium and Streptomycetes. This research serves to benefit the domestication of wild R. simsii and other Rhododendron resources.

IntroductionCorm rot in saffron (Crocus sativus L.) significantly impacts yield and quality. Non-toxic fungi, particularly Trichoderma species, are valuable for biological control due to their production of diverse and biologically active secondary metabolites.MethodsThis study aimed to isolate an effective antagonistic fungus against the pathogenic fungi causing corm rot in saffron. Four pathogenic fungi (Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, and Penicillium citrinum) were isolated from diseased saffron bulbs in Chongming. Initial screening through dual culture with these pathogens re-screening from rhizosphere soil samples of C. sativus based on its inhibitory effects through volatile, nonvolatile, and fermentation broth metabolites. The inhibitory effect of biocontrol fungi on pathogenic fungi in vitro was evaluated by morphological observation and molecular biology methods.ResultsAntagonistic fungi were identified as Trichoderma brevicompactum DTN19. F. oxysporum was identified as the most severe pathogen. SEM (scanning electron microscope) and TEM (transmission electron microscope) observations revealed that T. brevicompactum DTN19 significantly inhibited the growth and development of F. oxysporum mycelium, disrupting its physiological structure and spore formation. Additionally, T. brevicompactum DTN19 demonstrated nitrogen fixation and production of cellulase, IAA (Indole acetic acid), and siderophores. Whole-genome sequencing of strain DTN19 revealed genes encoding protease, cellulase, chitinase, β-glucosidase, siderophore, nitrogen cycle, and sulfate transporter-related proteinsDiscussionT. brevicompactum DTN19 may inhibit the propagation of pathogenic fungi by destroying their cell walls or producing antibiotics. It can also produce IAA and iron carriers, which have the potential to promote plant growth. Overall, T. brevicompactum DTN19 showed the development prospect of biological agents.

Allelopathy, a biological phenomenon involving the production and release of secondary metabolites known as allelochemicals, plays a critical role in plant interactions and agroecosystem dynamics. Phenolic compounds are a significant class of allelochemicals that profoundly affect plant competition, soil health, and microbial communities. When released into the soil, their action depends on the soil's physico-chemical characteristics and microbial communities. This review comprehensively inspects phenolic allelochemicals’ structure-function relationship, their direct combat with root cells in the rhizosphere, ecological functions, and their role in plant succession and stress tolerance. Phenolic allelochemicals, characterized by their diverse structures and ecological roles, offer a sustainable alternative to synthetic herbicides due to their minimal residual impact on the environment and rapid biodegradation. Additionally, the review addresses the challenges and future directions in applying phenolic allelochemicals, aiming to bridge the gap between ecological theory and practical agricultural applications for environmental protection and crop productivity enhancement.

The use of microbes capable of beneficially interacting with plants is essential for advancing climate-smart agriculture. This approach aims to reduce chemical use while simultaneously enhancing crop productivity. This implies efforts to optimize the criteria for selecting potential plant growth promoters (PGPs), focusing also on yeasts, only recently investigated for their PGP potential. The present study employed a set of Ascomycetes and Basidiomycetes yeasts to test their PGP properties on zucchini (Cucurbita pepo L.), chosen as a fast-growing plant with a vast economical interest. Yeasts were tested alone and as consortium. Seed inoculation with yeasts boosted the early phase of growth of the zucchini plants, primarily affecting the root development. Three strains belonging to the species Schwanniomyces etchellsii, Zygotorulaspora florentina and Holtermanniella festucosa induced a strong and significant enhancement of weight and length of both epi- and hypogeal parts of the plant. Furthermore, the presence of yeasts induced strain-specific modulations in the biochemical profiles of soil, primarily detected in the rhizosphere. This suggests an active interaction between the roots and the inoculated yeast cultures.

Nitrogen (N) shortage often hinders the bioremediation of mining-generated tailings. For pioneer plants living in mine tailings, biological N fixation (BNF) is an essential source of N. However, the diazotrophs in the rhizosphere of pioneer plants are rarely investigated. In this study, the pioneer plant Miscanthus sinensis samples were collected from four different tailings across Southwest China, and the 16S rRNA amplicon sequencing, multivariable statistical tools, 15N2 DNA-SIP, metagenomic-binning, cultural screening methods, and pot experiment were applied to analyze the roles of diazotrophs in rhizosphere of M. sinensis. Firstly, genera Stenotrophomonas and Pseudomonas were identified as keystone taxa in the rhizosphere of M. sinensis cultivated in the tailings. Furthermore, 15N2 DNA-SIP demonstrated that Stenotrophomonas and Pseudomonas were the rhizospheric diazotrophs. The metagenome-assembled genomes of Stenotrophomonas and Pseudomonas contained some genes involved in BNF, plant growth promotion, and metal(loid) resistance (As, Sb, Ni, Co, Zn, Mn, Cu, and Cd). Subsequent diazotrophic isolation was conducted, and two diazotrophic strains (Pseudomonas sp. R21 (nitrogenase activities, 1,161.9 nmol C2H4 mg−1 protein h−1) and Stenotrophomonas sp. R30 (1,890.2 nmol C2H4 mg−1 protein h−1)) were isolated from the rhizosphere soil of M. sinensis. Pot assay demonstrated that inoculation with Pseudomonas sp. R21 and Stenotrophomonas sp. R30 could promote plant growth, N content, and metal(loid) (arsenic and antimony) accumulation, which confirmed nitrogenase activity and plant growth-promoting ability of the two identified keystone taxa, highlighting the exciting opportunities of applying some keystone rhizospheric diazotrophs in the pioneer plants through microbiome manipulation for the bioremediation of tailings.

IntroductionHorizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.MethodsAmong the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.Results and discussionK. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10−3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain’s ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq-pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.

ABSTRACT The current and ongoing challenges brought on by climate change will require future scientists who have hands-on experience using advanced molecular techniques, can work with large data sets, and can make correlations between metadata and microbial diversity. A course-embedded research project can prepare students to answer complex research questions that might help plants adapt to climate change. The project described herein uses plants as a host to study the impact of climate change-induced drought on host-microbe interactions through next-generation DNA sequencing and analysis using a command-line program. Specifically, the project studies the impact of simulated drought on the rhizosphere microbiome of Fast Plants rapid cycling Brassica rapa using inexpensive greenhouse supplies and 16S rRNA V3/V4 Illumina sequencing. Data analysis is performed with the freely accessible Python-based microbiome bioinformatics platform QIIME 2.

Capsaicinoids are produced uniquely in pepper fruits, and its level determines the commercial quality and health-promoting properties of pepper. So, it is particularly important to increase capsaicinoids content in pepper. Rhizosphere microbiota is critical to plant growth and performance, and affected by plant varieties. However, the impact of pepper varieties with different capsaicinoids yields on the rhizosphere microbiota is poorly understood. Using high-throughput sequencing of the 16S rRNA and internal transcribed spacer (ITS) region, we investigated the rhizosphere microbial community among five pepper varieties containing different capsaicinoids. Our results demonstrated that pepper variety significantly influenced the diversity and structure of rhizosphere microbial community. Bacterial diversity in varieties with high capsaicinoids content was significantly higher than in varieties with low capsaicinoids content, while fungal diversity was opposite to bacterial diversity. The correlation analysis revealed that 19 dominant bacterial genera (e.g., Chujaibacter, Rhodanobacter, and Gemmatimonas) were significantly correlated with capsaicinoids content, and nine of them were also significantly associated with soil nutrients, whereas only one fungal genus (Podospora) was significantly correlated with capsaicinoids content. Additionally, almost all genera which significantly correlated to capsaicinoids content were biomarkers of the five pepper varieties and the correlation was well corresponding to the capsaicinoids content. Overall, our results confirmed that the variety of pepper significantly affected the rhizosphere microbial community in the fields, and bacteria and fungi responded differently to capsaicinoids, which may affect the biosynthesis of capsaicinoids and contribute to further improvement of capsaicinoids production in pepper fruits.

IntroductionDespite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health.MethodsWe therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits.ResultsBacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth.DiscussionThis study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.

Cadmium (Cd) contamination poses a significant threat to agricultural soils and food safety, necessitating effective remediation strategies. Salix species, with their high coverage and Cd accumulating capacity, hold promise for remediation efforts. The rhizosphere microbiome is crucial for enhancing Cd accumulating capacity for Salix. However, the mechanisms by how Salix interacts with its rhizosphere microbiome to enhance Cd extraction remains poorly understood. In this study, we compared the remediation performance of two Salix ecotypes: 51–3 (High Cd-accumulating Ecotype, HAE) and P646 (Low Cd-accumulating Ecotype, LAE). HAE exhibited notable advantages over LAE, with 10.80 % higher plant height, 43.80 % higher biomass, 20.26 % higher Cd accumulation in aboveground tissues (93.09 μg on average), and a superior Cd translocation factor (1.97 on average). Analysis of the rhizosphere bacterial community via 16S rRNA amplicon sequencing revealed that HAE harbored a more diverse bacterial community with a distinct composition compared to LAE. Indicator analysis identified 84 genera specifically enriched in HAE, predominantly belonging to Proteobacteria, Actinobacteria, and Firmicutes, including beneficial microbes such as Streptomyces, Bacillus, and Pseudomonas. Network analysis further elucidated three taxa groups specifically recruited by HAE, which were highly correlated with functional genes that associated with biosynthesis of secondary metabolites, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins. These functions contribute to enhancing plant growth, Cd uptake, and resistance to Cd in Salix. Overall, our findings highlight the importance of the rhizosphere microbiome in facilitating Cd extraction and provide insights into microbiome-based strategies for sustainable agricultural practices.

Modern agriculture’s goal of improving crop resource acquisition efficiency relies on the intricate relationship between the root system and the soil. Root and rhizosphere traits play a critical role in the efficient use of nutrients and water, especially under dynamic environments. This review emphasizes a holistic perspective, challenging the conventional separation of nutrient and water uptake processes and the necessity for an integrated approach. Anticipating climate change-induced increase in the likelihood of extreme weather events that result in fluctuations in soil moisture and nutrient availability, the study explores the adaptive potential of root and rhizosphere traits to mitigate stress. We emphasize the significance of root and rhizosphere characteristics that enable crops to rapidly respond to varying resource availabilities (i.e. the presence of water and mobile nutrients in the root zone) and their accessibility (i.e. the possibility to transport resources to the root surface). These traits encompass for example root hairs, mucilage and extracellular polymeric substance (EPS) exudation, rhizosheath formation and the expression of nutrient and water transporters. Moreover, we recognize the challenge of balancing carbon investments, especially under stress, where optimized traits must consider carbon-efficient strategies. To advance our understanding, the review calls for well-designed field experiments, recognizing the limitations of controlled environments. Non-destructive methods such as mini rhizotron assessments and in-situ stable isotope techniques, in combination with destructive approaches such as root exudation analysis, are proposed for assessing root and rhizosphere traits. The integration of modeling, experimentation, and plant breeding is essential for developing resilient crop genotypes capable of adapting to evolving resource limitation.

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).

Les plantes, au travers de leur système racinaire, sont des ingénieurs du sol qui sont capables de modifier les propriétés biologiques, chimiques et physiques du sol qu’elles colonisent. Cependant, si les propriétés du sol sont généralement étudiées et considérées pour leur impact sur les plantes (prélèvement hydrominéral, croissance et rendement), le fait qu’à l’inverse la plante agisse sur les propriétés du sol à travers son système racinaire, et sa rétroaction sur la plante, est beaucoup moins investigué. Une grande partie de ces interactions plante-sol se déroule dans la rhizosphère, zone ténue de sol entourant les racines et impactée par leur activité, qui se révèle être un « hotspot » d’activité biologique entretenu par l’apport de carbone racinaire (exsudats, mucilages) comprenant des composés polymériques spécifiques. Nous argumentons ici que l’effet racines/rhizosphère sur le sol est un levier pour agir sur la tolérance au déficit hydrique des cultures au travers de quelques exemples de nos travaux récents. Vu plus globalement, dans le cadre des systèmes de cultures et rotations, les systèmes racinaires peuvent s’avérer être un outil dans la gestion des propriétés hydrauliques du sol pour optimiser le bilan hydrique à l’échelle de la parcelle (partage ruissellement/infiltration, stockage de l’eau, drainage et recharge des nappes).

IntroductionThe importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.MethodsHere the “cry-for-help” hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.ResultsArabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography–mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the “cry-for-help” event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6’h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.DiscussionThese findings expand the knowledge on PCB-triggered “cry-for-help” and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.

The rapid global emergence of antibiotic resistance genes (ARGs) is a substantial public health concern. Livestock manure serves as a key reservoir for tetracycline resistance genes (TRGs), serving as a means of their transmission to soil and vegetables upon utilization as a fertilizer, consequently posing a risk to human health. The dynamics and transfer of TRGs among microorganisms in vegetables and fauna are being investigated. However, the impact of different vegetable species on acquisition of TRGs from various manure sources remains unclear. This study investigated the rhizospheres of three vegetables (carrots, tomatoes, and cucumbers) grown with chicken, sheep, and pig manure to assess TRGs and bacterial community compositions via qPCR and high-throughput sequencing techniques. Our findings revealed that tomatoes exhibited the highest accumulation of TRGs, followed by cucumbers and carrots. Pig manure resulted in the highest TRG levels, compared to chicken and sheep manure, in that order. Bacterial community analyses revealed distinct effects of manure sources and the selective behavior of individual vegetable species in shaping bacterial communities, explaining 12.2% of TRG variation. Firmicutes had a positive correlation with most TRGs and the intl1 gene among the dominant phyla. Notably, both the types of vegetables and manures significantly influenced the abundance of the intl1 gene and soil properties, exhibiting strong correlations with TRGs and elucidating 30% and 17.7% of TRG variance, respectively. Our study delineated vegetables accumulating TRGs from manure-amended soils, resulting in significant risk to human health. Moreover, we elucidated the pivotal roles of bacterial communities, soil characteristics, and the intl1 gene in TRG fate and dissemination. These insights emphasize the need for integrated strategies to reduce selection pressure and disrupt TRG transmission routes, ultimately curbing the transmission of tetracycline resistance genes to vegetables.

In this study, a six-month pot experiment was conducted to explore the effects of nanoparticles (NPs), including CeO2, TiO2 and SiO2 NPs at 200 and 800 mg/kg, on the growth and quality of model medicinal plant Salvia miltiorrhiza. A control group was implemented without the application of NPs. Results showed that NPs had no significant effect on root biomass. Treatment with 200 mg/kg of SiO2 NPs significantly increased the total tanshinone content by 44.07 %, while 200 mg/kg of CeO2 NPs were conducive to a 22.34 % increase in salvianolic acid B content. Exposure to CeO2 NPs induced a substantial rise in the MDA content in leaves (176.25 % and 329.15 % under low and high concentration exposure, respectively), resulting in pronounced oxidative stress. However, TiO2 and SiO2 NPs did not evoke a robust response from the antioxidant system. Besides, high doses of CeO2 NP-amended soil led to reduced nitrogen, phosphorus and potassium contents. Furthermore, the NP amendment disturbed the carbon and nitrogen metabolism in the plant rhizosphere and reshaped the rhizosphere microbial community structure. The application of CeO2 and TiO2 NPs promoted the accumulation of metabolites with antioxidant functions, such as D-altrose, trehalose, arachidonic acid and ergosterol. NPs displayed a notable suppressive effect on pathogenic fungi (Fusarium and Gibberella) in the rhizosphere, while enriching beneficial taxa with disease resistance, heavy metal antagonism and plant growth promotion ability (Lysobacter, Streptomycetaceae, Bacillaceae and Hannaella). Correlation analysis indicated the involvement of rhizosphere microorganisms in plant adaptation to NP amendments. NPs regulate plant growth and quality by altering soil properties, rhizosphere microbial community structure, and influencing plant and rhizosphere microbe metabolism. These findings were beneficial to deepening the understanding of the mechanism by which NPs affect medicinal plants.

The aim of this study was to determine the diversity of aerobic halotolerant Bacillus plant growth promoting rhizobacteria (PGPR), their production of hydrolytic exo-enzymes and their inoculation effect on two cowpea plants. The soil dilution plate technique was performed on tryptic soy agar complemented with thermal pretreatment to select Bacillus strains associated with the Phoenix dactylifera rhizosphere growing in hypersaline and arid soil in Algeria (In Salah, Tamanrasset). The inoculation effect of these strains on cowpea plant growth was assessed based on biometric and physiological parameters. As a result, thirteen halophilic, halotolerant and non-halophilic Bacillus strains were isolated. Upon screening, all strains were capable of producing at least two hydrolytic enzymes under saline conditions and most of the strains (n=10/13) showed at least two plant growth promoting (PGP) traits. Strains were identified as members of Bacillus genera based on their phenotypic and biochemical characteristics. The inoculation of these strains in cowpeas significantly improved biometrics and physiological growth parameters of the inoculated plants. Based on their PGP effects, five strains were identified: RP 7 (B. coagulans), RP 8 (B. circulans), RP 10 (Paenibacillus polymyxa), RP 12 (B. circulans) and RP 13 (B. cereus). The isolation and characterization of halophilic and halotolerant Bacillus strains increased knowledge about the microflora in the rhizosphere associated with date palms in saline and arid soils. Bacillus-PGPR strains proved to be highly effective to improve cowpea plant growth and development.

Abstract Background Macrophytes may modify benthic biodiversity and biogeochemistry via radial oxygen loss from roots. This condition contrasts sediments anoxia, allows roots respiration, and facilitates aerobic microbial communities and processes in the rhizosphere. Simultaneously, the rhizosphere can stimulate anaerobic microorganisms and processes via exudates or by favoring the build-up of electron acceptors as nitrate. As eutrophication often results in organic enrichment in sediments and large internal nutrients recycling, an interesting research question is to investigate whether plants maintain the capacity to stimulate aerobic or anaerobic microbial communities and processes also under elevated organic pollution. Methods A manipulative experiment was carried out under laboratory-controlled conditions. Microcosms containing bare sediments and sediments transplanted with the macrophyte Vallisneria spiralis L. were created. The effect of the plant was investigated on sediments with moderate (8%) and elevated (21%) organic matter content, after an acclimatization period of 30 days. Chemical and physical parameters, microbial community composition and the potential rates of nitrification, denitrification and nitrate ammonification were measured at two different depths (0–1 and 1–5 cm) after the acclimatization period to evaluate the role of roots. Results Vallisneria spiralis grew and assimilated pore water nutrients at the two organic matter levels and vegetated sediments had always nutrient-depleted porewaters as compared to bare sediments. Nitrifying microbes had a lower relative abundance and diversity compared to denitrifying bacteria. However, regardless of the organic content, in vegetated sediments nitrifiers were detected in deeper horizons as compared to bare sediments, where nitrification was confined near the surface. In contrast, potential denitrification rates were not affected by the presence of roots, but probably regulated by the presence of nitrate and by root-dependent nitrification. Potential nitrate ammonification rates were always much lower (

Abstract Background The rhizosphere environment regulated by root secretory activity and rhizosphere microbial interactions plays an essential role in resisting soil-borne diseases, while the host species is an important factor that affects the composition of root exudates and rhizosphere microbiomes. However, few studies have been done on the characteristics of root exudates and bacterial communities in terms of composition, diversity, and functional potential when host plants of different species are subjected to the same disease. Results In this study, we examined the rhizosphere soil bacteria and root exudates of both healthy and diseased tomatoes and peppers employing metabolomics and amplicon techniques. Our findings indicated that variations existed in both root exudates and the bacterial community among different host species and health states. The diversities of both rhizosphere metabolites and bacterial communities were significantly reduced in different diseased plants. Although pepper and tomato resisted the invasion of Ralstonia by recruiting different potentially beneficial bacteria, their rhizosphere bacterial communities had the same functional potential. In comparison to diseased rhizosphere soil, healthy rhizosphere soil had many more functional pathways associated with disease suppression and plant growth. Conclusions This study highlighted the crucial role of host plants in shaping the rhizosphere environment and revealed the variation characteristics of root exudates and rhizosphere bacteria of different host plants induced by the same disease. Graphical Abstract

Abstract Background The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. Results Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). Conclusions Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering “beneficial keystone biome” to develop more resilient and productive crops under climate change. Video Abstract

Exuded plant metabolites play an important role in fostering beneficial interactions with the surrounding soil microbiota, thereby helping plants to better adjust to changing environmental conditions. These metabolites act as signals to attract or enhance the colonization of plant roots with specific groups of beneficial microbes and they modulate the dynamics of plant–microbe interactions in fulfilling plant niche-based requirements, directly and/or indirectly. This review emphasizes the expression, levels, modes of action, and net effects of the signaling metabolites that help food crop plants to become colonized by microbes that promote plant growth and development under periods of biotic stress.

Abstract Background Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system. Results Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species. Conclusion The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.

Abstract Background Biochar is mainly used to enhance soil fertility, microbial activity, improve plant performance and reduce disease incidence. Methods A greenhouse experiment was designed to investigate the response of biochar on rhizosphere soil chemical properties, enzyme activity, microbial communities, and sugarcane Pokkah boeng disease (PB). Two sugarcane varieties Zhongzhe 9 (Z9) and ROC22, susceptible/resistant to PB, were cultivated and treated with: no biochar, 15 t ha−1 biochar, and 30 t ha−1 biochar. Results The amendment of 30 t ha−1 of biochar (B2) significantly improve soil pH by 1.50% and 9.61% compared with that of B1 and B0, followed by 0.51% increase by 15 t ha−1 of biochar (B1) compared with that of control (B0). The application of 15 t ha−1 biochar significantly increased available phosphorus (AP) and ammonium nitrogen (NH4 +–N) by 209.93 mg kg−1 and 12.1 mg kg−1, while the application of 30 t ha−1 of biochar significantly increased 241.04 mg kg−1 of available potassium (AK) (P

Abstract Background Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors. Results Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones. Conclusions Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract

Abstract Background Chickpea (Cicer arietinum L.) production is affected by many biotic factors, among them Fusarium wilt caused by Fusarium oxysporum f. sp. ciceri and Botrytis gray mold caused by Botrytis cinerea led to severe losses. As fungicide application is not advisable, biological management is the best alternative for plant protection. The rhizosphere-dwelling antagonistic bacteria are one of the important successful alternative strategy to manage these diseases of chickpea. Rhizosphere dwelling bacteria serve as biocontrol agents by different mechanisms like producing antibiotics, different enzymes, siderophores against pathogens and thereby reducing the growth of pathogens. Results The present study aimed to isolate rhizospheric bacteria from the soils of different chickpea fields to evaluate biocontrol efficacy of the isolated bacteria to manage Fusarium wilt and Botrytis gray mold in chickpea. A total of 67 bacteria were isolated from chickpea rhizosphere from Bundelkhand region of India. Study revealed the isolated bacteria could reduce the Fusarium oxysporum f. sp. ciceris and Botrytis cinerea infection in chickpea between 17.29 and 75.29%. After screening of all the bacteria for their biocontrol efficacy, 13 most promising bacterial isolates were considered for further study out of which, three bacterial isolates (15d, 9c and 14a) have shown the maximum in vitro antagonistic effects against Fusarium oxysporum f. sp. ciceri and Botrytis cinerea comparable to in vivo effects. However, Isolate (15d) showed highest 87.5% and 82.69% reduction in disease against Fusarium wilt and Botrytis gray mold respectively, under pot condition. Three most potential isolates were characterized at molecular level using 16S rRNA gene and found to be Priestia megaterium (9c and 14a) and Serratia marcescens (15d). Conclusion This study identified two native biocontrol agents Priestia megaterium and Serratia marcescens from the rhizospheric soils of Bundelkhand region of India for control of Fusarium wilt, Botrytis gray mold. In future, efforts should be made to further validate the biocontrol agents in conjugation with nanomaterials for enhancing the synergistic effects in managing the fungal diseases in chickpea. This study will definitely enhance our understanding of these bioagents, and to increase their performance by developing effective formulations, application methods, and integrated strategies.

Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the saline-alkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO42–, K+ and Mg2+ concentrations. The electrical conductivity (EC), soluble ions (Na+, CO32– + HCO3–, K+, Ca2+, Mg2+, and SO42+), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes.

Cadmium (Cd) pollutes 7.0 % of China’s land area. This study examined the potential of Houttuynia cordata for Cd phytoremediation because of its ability to accumulate Cd in its growth matrix. H. cordata were planted in plastic pots filled with paddy field soils having low (LCd), medium (MCd), and high (HCd) Cd levels of 0.19, 0.69, and 2.91 mg/kg, respectively. After six months of growth, harvested plant parts were evaluated for Cd uptake and tolerance mechanisms. Metabolomics and metagenomics approaches were employed to investigate the soil rhizosphere mechanism. Results showed that the average plant biomass increased as soil Cd increased. The biomass Cd contents surpassed the allowable Cd limits for food (≤ 0.2 mg/kg) and medicinal uses (≤ 0.3 mg/kg). Cd contents were higher in H. cordata roots (30.59–86.27 mg/kg) than in other plant parts (0.63–2.90 mg/kg), with significantly increasing values as Cd soil level increased. Phenolic acids, lipids, amino acids and derivatives, organic acids, and alkaloids comprised the majority (69 in MCd vs HCd and 73 % in LCd vs HCd) of the shared upregulated metabolites. In addition, 13 metabolites specific to H. cordata root exudates were significantly increased. The top two principal metabolic pathways were arginine and proline metabolism, and beta-alanine metabolism. H. cordata increased the abundance of Firmicutes and Glomeromycota across all three Cd levels, and also stimulated the growth of Patescibacteria, Rozellomycota, and Claroideoglomus in HCd. Accordingly, H. cordata demonstrated potential for remediation of Cd-contaminated soils, and safety measures for its production and food use must be highly considered.

Pectobacterium atrosepticum (Pba) is a gram-negative bacterium that causes blackleg and tuber soft rot of potato but can also asymptomatically colonise other (non-host) plant species. The aim of this study was to investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions. To achieve this, we used total mRNA-sequencing to measure the gene expression patterns from all three species: Pba, potato and radish. We employed an end-point dual transcriptome approach. We used hydroponically grown potato (Solanum tuberosum var. Estima) and oil radish (Raphanus sativa var. Bento) roots inoculated with Pba SCRI1039 for 14 days compared to un-inoculated control plants or cultured bacteria. Total RNA was extracted from replicates of the two plant species and the bacterium using a Macherey-Nagel Nucleospin Plant RNA kit. The RNA from the 17 samples was then subjected to total mRNA-sequencing (paired-end) on an Illumina NovaSeq 6000™ sequencing platform. This gave between 39.2-58.1M reads per sample. The high-quality reads obtained were mapped to the corresponding reference genomes using Bowtie2 and the percentages of bacterium and plant transcripts calculated. This dataset constitutes the raw read fastq files and can be used to inform on genes active in plant rhizosphere-microbe interactions.

IntroductionMicrobial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.MethodsTherefore, we conducted a field experiment that covered sugarcane–peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.ResultsOur results showed that sugarcane–peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%–35%) and the interactions of rare and abundant taxa (65%–93%).ConclusionThis study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Ectomycorrhizal fungi and non-ectomycorrhizal fungi are responsive to changes in environmental and nutrient availabilities. Although many species of ectomycorrhizas are known to enhance the uptake of phosphorus and other nutrients for Pinus taeda, it is not understood how to optimize these communities to have tangible effects on plantation silviculture and P use efficiency. The first step of this process is the identification of native fungi present in the system that are associated with P. taeda and influence P uptake efficiency. We used sand-filled mesh bags baited with finely ground apatite to sample ectomycorrhizal and non-ectomycorrhizal fungi associated with the rhizosphere of P-responsive P. taeda under several field conditions. Mesh bags were assessed for biomass accumulation over three years using a single three-month burial period pre-harvest and three six-month burial periods post-planting. Amplicon sequencing assessed ectomycorrhizal and non-ectomycorrhizal communities between phosphorus treatments, sites, mesh bags, and the rhizosphere of actively growing P. taeda in the field. We found biomass accumulation within the mesh bags was inversely related to increasing phosphorus fertilization (carryover) rates from pre-harvest to post-planting. Up to 25% increases in total biomass within the bags were observed for bags baited with P. Taxonomic richness was highest in Alfisol soils treated with phosphorus from the previous rotation and lowest in the Spodosol regardless of phosphorus treatment.

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar–bacteria–plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

Abstract Mangroves buffer metals transfer to coastal areas though strong accumulation in sediments making necessary to investigate metals’ bioavailability to plants at the rhizosphere. This work evaluates the effect of mangrove root activity, through iron plaque formation, on the mobility of iron and copper its influence on metals’ uptake, and translocation through simultaneous histochemical analysis. The Fe2+ and Fe3+ contents in porewaters ranged from 0.02 to 0.11 µM and 1.0 to 18.3 µg.l-1, respectively, whereas Cu concentrations were below the method’s detection limit (

The application of plant growth-promoting rhizosphere (PGPR) and Gamma-polyglutamic acid (γ-PGA) has a potential role in improving plant tolerance under abiotic stress, while their combined effects remain largely unexplored. This study aimed to evaluate the effects of the joint effects of PGPR and γ-PGA on maize growth and rhizosphere microbial communities under salt stress. A pot experiment consisting of two strain treatments (CK, M10), two γ-PGA treatments (γ0, γ1) and two salt treatments (S1, S2) was performed for this purpose. The results showed that under S1 treatment, the combined application of M10 and γ-PGA could increase plant height, leaf area and dry weight by 11.27%, 36.45% and 8.39% respectively (P