Rhizosphere Soil Research Articles

Effect of grafted scion varieties on apple root growth, carbon and nitrogen metabolism and microbiome in roots and rhizosphere soil

Effect of grafted scion varieties on apple root growth, carbon and nitrogen metabolism and microbiome in roots and rhizosphere soil

Insect residual streams supplement improves chili pepper growth: Insights into the role of rhizosphere soil microbiome and metabolome

Insect residual streams supplement improves chili pepper growth: Insights into the role of rhizosphere soil microbiome and metabolome

Arbuscular mycorrhizal fungi enhance drought resistance and alter microbial communities in maize rhizosphere soil

Although the benefits of inoculation with arbuscular mycorrhizal fungi (AMF) for mitigating drought stress and enhancing plant growth of host are well‐studied, our understanding of their interactions with soil attributes and rhizosphere microbial communities remains limited. In the present study, we conducted a pot experiment to explore how AMF affects maize growth, antioxidant activity, soil properties, and the rhizosphere microbial communities under drought stress. The results showed that AMF inoculation during drought stress resulted in improved maize seedling growth, significantly increasing plant biomass (42.7%), chlorophyll content (13.4%), and antioxidant capacity. It also enhanced soil nutrient availability and microbial biomass. We observed significant shifts in the structure and composition of the rhizosphere microbial community with AMF inoculation under drought conditions when compared to those under well-watered conditions. Significantly, bacterial diversity and composition showed greater sensitivity to drought stress than fungal communities. This was attributed to plants preferentially reducing the supply of carbon sources to bacterial rather than to fungal communities under drought conditions. AMF inoculation also enhanced the complexity (e.g., degree) and stability of the rhizosphere microbial ecological network, suggesting closer ecological interactions within the soil microbial community. Furthermore, bacterial diversity and richness played a more important role in soil function than those of fungal communities under drought stress, particularly with AMF inoculation. Overall, our findings suggest that AMF inoculation alters soil microbial diversity and interactions, highlighting their key roles in enhancing plant stress tolerance and mitigating the negative effects of drought on agricultural ecosystems.

Isolation and characterization of plant growth promoting actinobacteria, Amycolatopsis samaneae (AM75), from the rice rhizosphere in mirza area, Assam, India

This study aimed to isolate plant growth-promoting actinobacteria from the rhizosphere of rice. Rhizospheric soil samples were collected from the Aijung variety of rice in the Mirza area, Kamrup district, Assam, India. The isolate AM75 identified as Amycolatopsis samaneae, was characterized as gram-positive and non-motile. It exhibited varied colony characteristics on different selective media. The isolate produce several enzymes including urease, nitrate reductase, lipase, catalase, and amylase but did not demonstrate cellulase or gelatinase activity. Notably, isolate AM75 displayed various plant growth-promoting activities such as siderophore activity, hydrogen cyanide (HCN) production, indole-3-acetic acid (IAA) production, and zinc solubilization. However, it did not produce hydrogen sulfide (H2S) or solubilize phosphate. The optimal growth conditions for AM75 were pH 7.2, 30ºC temperature, and NaCl 2.5% concentration. Additionally, AM75 exhibited inhibitory activity against the plant pathogens Erwinia chrysanthemi ATCC11660, Aspergillus niger ATCC6275, and Fusarium oxysporum ATCC62506. The isolate was resistant to standard antibiotics, including rifampcin, streptomycin, ampicillin, and nalidixic acid.

Effect of molybdenum supply on crop performance through rhizosphere soil microbial diversity and metabolite variation

Effect of molybdenum supply on crop performance through rhizosphere soil microbial diversity and metabolite variation

Plant Growth-Promoting Effect and Complete Genomic Sequence Analysis of the Beneficial Rhizosphere Streptomyces sp. GD-4 Isolated from Leymus secalinus

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria residing in the rhizosphere and are capable of enhancing plant growth through various mechanisms. Streptomyces sp. GD-4 is a plant growth-promoting bacterium isolated from the rhizosphere soil of Leymus secalinus. To further elucidate the molecular mechanisms underlying the beneficial effects of the strain on plant growth, we evaluated the growth-promoting effects of Streptomyces sp. GD-4 on forage grasses and conducted comprehensive genome mining and comparative genomic analysis of the strain. Strain GD-4 effectively colonized the rhizosphere of three forages and significantly promoted the growth of both plant roots and leaves. Genome sequence functional annotation of GD-4 revealed lots of genes associated with nitrogen, phosphorus, and sulfur metabolism. Additionally, genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, and phosphate solubilization were annotated. Whole-genome analysis revealed that GD-4 may possess molecular mechanisms involved in soil nutrient cycling in rhizosphere soil and plant growth promotion. The bacteria also possess genes associated with adaptability to abiotic stress conditions, further supporting the ability of Streptomyces sp. GD-4 to colonize nutrient-poor soils. These findings provide a foundation for further research into soil remediation technologies in plateau regions.

Effect of Peanut Intercropping on Arsenic Uptake and Remediation Efficiency of Plants in Arsenic-Contaminated Soil

Phytoremediation is an economically viable and environmentally friendly technique among various arsenic-contaminated soil remediation technologies. Field plot experiments were conducted to investigate the effects of peanut intercropping with sunflower, lucerne, and jute on the growth and development of intercropped crops and the efficiency of arsenic (As) remediation in polluted soil within the intercropping system. The results indicate that intercropping peanuts with other crops can enhance the biomass and yield of the crops. The land equivalent ratios (LER) of the three intercropping patterns were 1.03, 1.70, and 1.17, respectively. The intercropping pattern also influences the absorption and accumulation of As in crops. Total arsenic accumulation in peanuts intercropped with jute reached 493 μg·plant−1, which was significantly higher by 29.5% compared to peanut monoculture. Additionally, the translocation factor (TF) and bioaccumulation factor (BCF) of peanut seeds were significantly higher in peanut-jute intercropping compared to other treatments, but the As content of peanut seeds in all treatments complied with national food safety standards (GB2762-2022, 0.5 mg·kg−1). Intercropping of peanuts altered the pH and Eh values of rhizosphere soil, further influencing the percentage content of various forms of As in the soil, and reducing the mobility and effectiveness of As. The metal removal equivalent ratios (MRER) for the three intercropping patterns were 1.30, 2.11, and 1.26, respectively. The intercropping of peanuts and lucerne resulted in an MRER of 2.11. It indicates that peanut intercropping has a significant promotion and high restoration efficiency on the growth and development of lucerne. Therefore, among the three patterns, the peanut intercropping lucerne pattern has the best effect in applying to contaminated soil, and can better realize the integration of economic and ecological benefits.

Ecological filters shape arbuscular mycorrhizal fungal communities in the rhizosphere of secondary vegetation species in a temperate forest.

The community assembly of arbuscular mycorrhizal fungi (AMF) in the rhizosphere results from the recruitment and selection of different AMF species with different functional traits. The aim of this study was to analyze the relationship between biotic and abiotic factors and the AMF community assembly in the rhizosphere of four secondary vegetation (SV) plant species in a temperate forest. We selected four sites at two altitudes, and we marked five individuals per plant species at each site. Soil rhizosphere samples were collected from each SV plant species, during the rainy and dry seasons. Soil samples from the rhizosphere of each plant species were analyzed for AMF spores, organic matter (OM), pH, soil moisture, and available phosphorus, and nitrogen. Three ecological filters influenced the AMF community assembly: host plant identity, abiotic factors, and AMF species co-occurrence. This assembly consisted of 61 AMF species, with different β-diversity values among plant species across seasons and altitudes. Canonical correspondence analysis revealed that AMF community composition is linked to OM and available P and N, with only a few AMF species co-occurring, while most do not. Our study highlights how ecological filters shape AMF structure, which is essential for understanding how soil and environmental factors affect AMF in SV plant species across seasons and altitudes.

Insights and applications of Arbuscular mycorrhizal fungi

In natural ecosystems, rhizospheric soils are teeming with diverse biological organisms that enhance plant growth, nutrient absorption, stress tolerance and disease prevention. Among these organisms, arbuscular mycorrhizal (AM) fungi are particularly significant due to their symbiotic relationships with plants. Their application extends beyond natural ecosystems into agricultural and horticultural practices, where they contribute to improved soil health and plant productivity. This review discusses the benefits of incorporating AM fungi into modern agricultural systems to improve nutrient uptake, soil structure and plant resilience. It emphasizes the need for strategies to restore and maximize AM fungi's efficacy, ensuring sustainability and productivity in agriculture, industry and natural ecosystems.

Microbial Communities in Permafrost, Moraine and Deschampsia antarctica Rhizosphere Soils near Ecology Glacier (King George Island, Maritime Antarctic)

Microbial Communities in Permafrost, Moraine and Deschampsia antarctica Rhizosphere Soils near Ecology Glacier (King George Island, Maritime Antarctic)

Identification, Genome Characterization, and Growth Optimization of Paenibacillus Peoriae MHJL1 for Biocontrol and Growth Promotion of Cotton Seedlings

Fusarium and verticillium wilt are the primary diseases affecting cotton plants, significantly reducing both the yield and quality of cotton. Paenibacillus spp. are crucial biocontrol strains for controlling plant diseases. In this study, Paenibacillus peoriae MHJL1, which could prevent the pathogenic fungi of fusarium and verticillium wilt and promote cotton growth, was isolated from the rhizosphere soil of cotton plants. Whole-genome analysis of strain MHJL1 identified 16 gene clusters for secondary metabolite synthesis, including fusaricidins with potent antifungal properties. By optimizing the fermentation process, the cell and spore numbers of MHJL1 were increased to 2.14 × 108 CFU/mL and 8.66 × 108 CFU/mL, respectively. Moreover, the antifungal ability of MHJL1 was also increased by 31.48%. In pot experiments conducted with healthy soil, the control rates for MHJL1 against fusarium and verticillium wilt were found to be 44.83% and 58.27%, respectively; in experiments using continuously cropped soil, the control rates were 55.22% against fusarium wilt and 48.46% against verticillium wilt. Our findings provide valuable insights for the biocontrol application and fermentation of P. peoriae MHJL1, while also contributing a new resource for the development of microbial agents.

Legumes reduce the effects of salt stress on co-existing grass.

Nitrogen (N) fixing legumes typically enhance the ability of coexisting non-N-fixing species to resist disease and drought, but whether legumes enhance their ability to resist salt stress remains unknown, restricting our ability to explore the potential of legumes to rehabilitate salt-affected ecosystems. We conducted a simulation experiment to examine whether and how legumes influence the response of coexisting grass to salt stress. We compared the effects of salt stress on the plant biomass, root cell viability, antioxidant enzyme activities, soil extracellular enzyme activities and microbial functional gene abundances associated with N and phosphorus (P) cycling between pure grass communities and legume-grass mixtures. We found that salt stress decreased grass biomass and the abundance of most N and P cycling genes in rhizosphere soils. However, these negative effects were smaller in legume-grass mixtures than in pure grass community. Additionally, salt stress increased the activities of soil N and P cycling enzymes, with greater positive effects observed in legume-grass mixtures than in the pure grass community. The structural equation modelling results showed that the most direct and indirect path coefficients of salt stress effects on biomass were smaller in legume-grass mixtures than in the pure grass community. Our findings provide direct evidence that legumes can reduce the negative impact of salt stress on co-existing grass community, highlighting the potential of including legumes with high N fixation abilities to restore salt-affected ecosystems.

Diversity, characterization, and biotechnological potential of plant growth-promoting bacteria from Bryophyllum pinnatum (Lam.) (Crassulaceae) roots and rhizosphere soil.

Cultivable microbial communities associated with plants inhabiting extreme environments have great potential in biotechnological applications. However, there is a lack of knowledge about these microorganisms from Bryophyllum pinnatum (which survives in severely barren soil) and their ability to promote plant growth. The present study focused on the isolation, identification, biochemical characterization, and potential applications of root endophytic bacteria and rhizosphere bacteria. A total of 73 bacterial isolates were obtained, with 50 derived from rhizospheric soil and 23 from root tissue. The identified strains were categorized into 16 genera, with Bacillus, Priestia, Pseudarthrobacter, Neobacillus, Mesobacillus, and Arthrobacter being the most species-rich genera. Heat stress experiments indicated that almost half (50.7%) of the selected isolates were tolerant to heat stress. Furthermore, most strains present diverse capabilities for biotechnological applications, including the potential for indole-3-acetic acid (IAA) production, organic phosphorus solubilization, inorganic phosphorus solubilization, and nitrogen fixation. Some isolates (21.92%) exhibited broad-spectrum antagonistic activity against various phytopathogenic fungi, including Fusarium spp. Agar plate assays revealed that the Cellulomonas hominis strain LS43 and Bacillus inaquosorum strain LS77 significantly increased the total fresh weight of Arabidopsis (P < 0.05), yet these strains did not significantly affect the primary root length or the number of leaves. Notably, a subset of the strains tested did not significantly increase the growth of Arabidopsis and, in fact, had inhibitory effects on certain growth parameters. This is the first investigation highlighting the potential of root endophytic bacteria and rhizosphere bacteria in association with B. pinnatum in barren soils. Thus, these isolated strains positively influence plant nutrient uptake, stress resilience, and biocontrol to reduce chemical inputs in conventional agricultural practices, highlighting the importance of their development as biofertilizers for improving the quality of barren soil.

Assessment of Ecological Recovery Potential of Various Plants in Soil Contaminated by Multiple Metal(loid)s at Various Sites near XiKuangShan Mine

Soil metal(loid) pollution is a threat to ecological and environmental safety. The vegetation recovery in mining areas is of great significance for protecting soil resources. In this study, (1) we first gathered four types of soils to analyse their contamination degree, including tailings mud (TM), wasteland soil (TS) very near TM, as well as non-rhizosphere soils of pepper (PF) and maize (MF) in a farmland downstream from the TM (about 5 km). Geo-accumulation and potential ecological risk indices indicated that the soil samples were mainly polluted by antimony (Sb), arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), and copper (Cu) to different degrees. Leachates of TM resulted in increased Sb, As, and Cd accumulation in TS. (2) Then, we sampled six local plants growing in the TS to assess the possibilities of using these plants as recovery vegetation in TS, of which Persicaria maackiana (Regel) Nakai ex T. Mori absorbed relatively high Sb concentrations in the leaves and roots. (3) After that, we collected rhizosphere soil and tissue samples from eight crops on the above farmland to assess their capacities as recovering vegetation of contaminated farmland soil, of which the fruits of maize accumulated the lowest concentrations of most monitored metal(loid)s (except for Pb). Further, we compared the differences in the bacterial community structure of MF, PF, TM, and TS to assess capacities of cultivating pepper and maize to improve soil microbial community structure. The MF displayed the best characteristics regarding the following attributes: (1) the highest concentrations of OMs and total P; (2) the highest OTU numbers and diversity of bacteria; and (3) the lowest abundance of bacteria with potentially pathogenic and stress-tolerant phenotypes.

Variations of microbiota and metabolites in rhizosphere soil of Carmona microphylla at the co-contaminated site with polycyclic aromatic hydrocarbons and heavy metals.

Co-contamination with organic/inorganic compounds is common in industrial area and poses a great risk to local soil ecological environment. In this study, an operating ink factory site co-contaminated with polycyclic aromatic hydrocarbons (PAHs, mild to moderate pollution level) and heavy metals (HMs, heavy pollution level) was selected and screened for native vegetation, Carmona microphylla. High-throughput sequencing and metabolomics were mainly used to investigate the responses of soil bacteria and metabolites to the composite pollution and rhizosphere effect. As the results showed, among three pollution levels, a medium level of pollution was favorable to increase the richness and diversity of soil bacterial community, while high level of pollution greatly decreased special OTUs number. In addition, HMs were the most significant factors driving bacterial community structure, especially for Cd. The influence of medium molecular weight PAHs with 4 rings (MMW-PAHs) on dominant bacteria was greater than low molecular weight PAHs with 2-3 rings (LMW-PAHs) and high molecular weight PAHs with 5-6 rings (HMW-PAHs). Soil bacterial function was affected mainly by pollution level, but not rhizosphere effect, in which high pollution level changed α diversity and structure and composition of C- and N-cycling bacteria. Rhizosphere promoted network complexity by increasing the connection densities among bacterial communities, metabolites, soil properties and the involved number of metabolites. Compared to HMs, PAHs played a more important role in shaping bacterial community through affecting metabolites in non-rhizosphere soil, which was different from rhizosphere soil with a more significant effect of HMs than PAHs. Some key bacterial taxa have established resistance to HMs in rhizosphere soils, whereas they were sensitive to compound contamination in non-rhizosphere soils. Some key bacterial taxa are resistant to HMs in rhizosphere soils, whereas they are susceptible to complex contamination in non-rhizosphere soils, which could be a consequence of the rhizosphere by regulating soil metabolism. It also provides a valuable reference for how co-contaminants and rhizosphere effect shape together soil bacterial community through the changes of soil metabolites.

Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage.

Rice (Oryza sativa L.), Poaceae family, forms staple diet of half of world's population, and brinjal (Solanum melongena L.), an important solanaceous crop, are consumed worldwide. Rhizosphere research is gaining importance towards application of knowledge for improving productivity, sustainable agricultural practice, and rhizoremediation for nature restoration. While there are reports on rhizobacteriome of rice, studies comparing structural, functional and metabolomic traits of microbial communities in rhizospheres of rice and brinjal are not yet available. We demonstrated, in Oryza sativa (1144-Hybrid, Dhiren, Local Saran cultivars) and Solanum melongena (Jhiloria, Chandtara, Jotshna cultivars) rhizospheres from Malda, India, using integrated approach of 16S ribosomal sequencing, shotgun metagenomics, and microbial metabolomics to decipher microbial diversity, association with soil physicochemical characteristics, key genes and pathways. Ectoine biosynthesis was significantly expressed in brinjal (Jhiloria), but not in rice rhizosphere. The dominant brinjal rhizobacteriome-specific bacteria comprised Thermus sp., Petrobacter succinatimandens, Thermoanaerobacter sp., and Diaphorobacter sp., that were involved in house-keeping functions including pentose phosphate pathway, biosynthesis of amino acids, lipopolysaccharide, and photosynthesis. The dominant bacteria unique to rice rhizobacteriome (Local Saran) consisted of Aeromonas sp., associated with catechol meta-cleavage, while Clostridium sp., Faecalibacterium prausnitzii, and Roseburia sp. were involved with lysine biosysnthesis in rice (1144-Hybrid). Our results imply novel information for improved breeding of brinjal specific cultivar with enhanced ectoine production associated with osmotic stress tolerance, rice specific cultivars with enhanced lysine production significant to human nutrition and catechol removal for the maintenance of environmental quality.

Effects of different microplastics on the physicochemical properties and microbial diversity of rice rhizosphere soil

Effects of different microplastics on the physicochemical properties and microbial diversity of rice rhizosphere soil

Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages.

Crop plant microbiomes are increasingly seen as important in plant nutrition and health, and a key to maintaining food productivity. Currently, little is known of the temporal changes that occur in the wheat rhizosphere microbiome as the plant develops, and how this varies among different sites. We used a pot-based mesocosm experiment with the same modern wheat cultivar grown in eight soils from across the North China Plain, a major wheat producing area. DNA from rhizosphere soil was taken from wheat plants, from seedling up to grain harvesting stage, and amplicon sequenced for prokaryotes and microeukaryotes, followed by community analysis. Our results showed that rhizosphere diversity of prokaryotes and microeukaryotes increased over time in most sites. While there was turnover between earlier- and later-arriving species, the predominant successional model was accumulation, with early arrivals remaining in place as others colonized the rhizosphere. Rhizosphere community network modularity and stability increased during the development and maturation of the wheat plant. The abundances of certain stage-specific keystone species were correlated with eventual grain yield - suggesting a potentially important role in wheat production. Some keystone species belonged to groups previously implicated in various functions. This study provides a basis for further experimental investigation of the wheat rhizosphere microbiome, its role in determining crop yields, and the potential for microbiome engineering to promote yields. The sequential arrival and accumulation of microbiota suggests that deliberate inoculation might accelerate this process.

Health Risk of Heavy Metal and Implication for Ecological Threat in Soils Weathered from the Black Shale.

Heavy metals were analyzed in rhizosphere soils and rice grains collected from typical black shale areas. The concentrations of As, Cd, Cu, and Zn in the rhizosphere soil exceeded the current soil environmental quality standards. Cd exhibited the highest bioaccumulation capacity, with 45% of rice grains exceeding food safety limit. Structural equation modeling (SEM) revealed that soil organic matter indicated that 34.79% of rice Cd accumulation and approximately 10%-25% of other metals were inhibited. Multiple regression modelling showed that in areas with high geological background of black shales, the screening and intervention values for soil Cd were adjusted to 0.24mg kg-1 and 0.42mg kg-1 for pH ≤ 5.5 and 0.27mg kg-1 and 1.66mg kg-1 for pH 5.5 - 6.5 respectively. Primary exposure pathways for non-carcinogenic risks were identified as food ingestion and skin contact. This study provides fundamental information for land use application and development in region with high geological background.

The Isolation of Lead-Tolerant PGPR from Red Clover Soil and Its Role in Promoting the Growth of Alfalfa.

Alfalfa (Medicago sativa L.) is an outstanding species used for the remediation of heavy metal-contaminated soil, and our previous research has shown that PGPR can promote plant growth under high-concentration lead stress. This discovery has forced scientists to search for PGPR strains compatible with alfalfa to develop an innovative bioremediation strategy for the remediation of lead-contaminated soil. This study used lead-tolerant rhizosphere soil of red clover as experimental material; cultured, isolated, and screened 52 excellent lead-tolerant bacteria that promote rhizosphere growth; and then inoculated them into alfalfa. Marked differences existed in the secretion of auxin, protease, and ACC deaminase among these strains. The results indicated that Pseudomonas spp. (strain Y2), Pseudomonas spp. (strain Y22), and Bacillus spp. (strain Y23) exhibited a strong growth-promoting ability in alfalfa, and there was no antagonistic reaction among the three strains, enabling their coexistence. The pot experiment manifested that strains Y2, Y22, Y23, and YH (a mixture of Y2, Y22, and Y23) could increase the plant height, root length, fresh and dry weight above ground, and fresh and dry weight below ground of alfalfa. They could all significantly raise the chlorophyll content and antioxidant enzyme activity in alfalfa (p < 0.05) and the content of malondialdehyde (MDA) in alfalfa. Furthermore, the concurrent inoculation of three distinct types of plant growth-promoting rhizobacteria (PGPR) significantly diminished lead (Pb) concentrations in rhizosphere soil, enhanced the levels of available potassium (AK) and available phosphorus (AP), and augmented the capacity of plants to absorb Pb. The results imply that PGPR can be employed to facilitate plant growth and microbial-assisted remediation of lead and other heavy metal-contaminated soil and establish a basis for further research on the growth-promoting mechanism of PGPR in plants.