Rice Rhizosphere Soil Research Articles

Migration and Transformation of Arsenic in Rice and Soil under Different Nitrogen Sources in Polymetallic Sulfide Mining Areas.

Nitrogen (N) fertilizer affects the migration and transformation of arsenic (As) in soil and rice. We conducted pot experiments and studied the effects of 0.1, 0.2, and 0.4 g∙kg−1 N levels of NH4Cl, (NH4)2SO4, and NH4NO3 fertilizers on the As bioavailability in the As-contaminated inter-rhizosphere soil and As accumulation in the rice organs. The results showed that the concentration of bioavailable As in the rice rhizosphere soil was significantly negatively correlated with pH under the 0.4 g∙kg−1 N level of each fertilizer. At the same N level, while the As concentration was maturity stage > tillering stage in rice stems and leaves treated with NH4Cl and (NH4)2SO4, it was the opposite in roots. This suggests that the transfer of As from roots to stems and leaves mainly occurs in the late stage of rice growth under the condition of only NH4+-N fertilizer applying. The As concentration in rice aboveground organ (grains and stems–leaves) decreased with the increasing N application under the same N fertilizer treatment condition during the mature stage. In addition, the As concentration in rice grains treated with (NH4)2SO4 was the lowest. This result indicated that SO42− and NH4+-N had a significant synergistic inhibition on the As accumulation in rice grains. It was concluded that appropriate (NH4)2SO4 levels for As-contaminated paddy soils with high sulfur (S) contents would obtain rice grains with inorganic As concentrations below 0.2 mg·kg−1.

Effects of nitrogen application after abrupt drought-flood alternation on rice root nitrogen uptake and rhizosphere soil microbial diversity

Abrupt drought-flood alternation is a frequent meteorological disaster that occurs during the summer in southern China. This study sought to clarify the composition of the bacterial community in the rhizosphere soil of rice under nitrogen (N) application after abrupt drought-flood alternation and to provide more basic data for understanding N absorption by the roots system under N application after abrupt drought-flood alternation. The activity of N metabolism enzymes and the N content and N accumulation in various organs improved under N application after abrupt drought-flood alternation. Between the T1_N and T1 comparison groups, 1758 differentially expressed genes were identified, including 1027 upregulated and 731 downregulated genes. Transcriptomic GO and KEGG analyses indicated that nitrate assimilation, response to bacterium, defence response to bacterium, and N compound metabolic processes were enriched. At the phylum level, Proteobacteria, Acidobacteria, Nitrospirota, and Gemmatimonadota were the dominant flora. The root glutamine synthetase activity was significantly negatively correlated with Nitrospirota. Nitrospirota is a key taxon regulating rice root N absorption under N application after abrupt drought-flood alternation. N application after abrupt drought-flood alternation promoted the rapid recovery ability of plants and improved the microbial environment in rice. This study preliminarily clarified the role of microorganisms in the root uptake of rice under N application after abrupt drought-flood alternation. • This study was subjected to RNA-seq and 16S rRNA gene technology. • Abrupt drought-flood alternation changed rice rhizosphere soil microbial environment. • The nitrospirota of T1_N is the dominant flora at the phylum level. • Response to bacterium, nitrogen compound metabolic processes were enriched between T1_N and T1.

Improvement of the Cd and Zn phytoremediation efficiency of rice (Oryza sativa) through the inoculation of a metal-resistant PGPR strain.

Cadmium (Cd) and zinc (Zn) in contaminated soil inhibit rice yield and produce toxic effects on human body through rice accumulation. Plant growth promoting rhizobacteria (PGPR) assisted phytoremediation is an effective ecological measure to improve the remediation efficiency of heavy metal contaminated soil. The purpose of this study was to investigate the efficiency of the combination of rice and Cd/Zn-tolerant PGPR strain Bacillus sp. ZC3-2-1 for the remediation of Cd-Zn contaminated soil. Moreover, the effects of inoculations on rhizosphere bacterial communities and ion homeostasis of rice under Cd-Zn exposure will also be explored. The results showed that compared with the treatment without inoculation, ZC3-2-1 decreased the bioavailable Cd and Zn concentrations in soil by 39.3% and 32.0%, respectively, and increase the phytoextraction of Cd2+ and Zn2+ by rice to 48.2% and 8.0%, respectively. This inoculation process significantly increased the rice biomass, resulting that the contents of Cd2+ and Zn2+ per biomass unit of rice didn't change significantly. This fact meant that ZC3-2-1 could improve the phytoremediation efficiency of Cd-Zn contaminated soil by promoting the phytoextraction and immobilization of the metal, while might not affect the crop food safety. Besides, through regulation of the Na+ and Mg2+ concentration in rice, ZC3-2-1 played a positive role in maintaining ion homeostasis which was disrupted by Zn or Cd. Moreover, ZC3-2-1 could modulate the beneficial bacterial communities in rice rhizosphere soil, and then enhanced Cd-Zn immobilization and enzyme activities in soil, leading to the enhancement of rice growth and phytoremediation efficiency. Above all, this study provided novel insights into developing an efficient phytoremediation system and safe production of rice in Cd-Zn contaminated soil with the application of Bacillus sp. ZC3-2-1, as well as advance our understanding of the principles of rhizosphere bacterial community assemble and maintaining ion homeostasis in rice during this phytoremediation process.

High Levels of Zinc Affect Nitrogen and Phosphorus Transformation in Rice Rhizosphere Soil by Modifying Microbial Communities.

Due to global industrialization in recent decades, large areas have been threatened by heavy metal contamination. Research about the impact of excessive Zn on N and P transformation in farmland has received little attention, and its mechanism is still not completely known. In this study, we planted rice in soils with toxic levels of Zn, and analyzed the plant growth and nutrient uptake, the N and P transformation, enzyme activities and microbial communities in rhizosphere soil to reveal the underlying mechanism. Results showed high levels of Zn severely repressed the plant growth and uptake of N and P, but improved the N availability and promoted the conversion of organic P into inorganic forms in rice rhizosphere soil. Moreover, high levels of Zn significantly elevated the activities of hydrolases including urease, protease, acid phosphatase, sucrase and cellulose, and dehydrogenase, as well as the abundances of Flavisolibacter, Sphingomonas, Gemmatirosa, and subgroup_6, which contributed to the mineralization of organic matter in soil. Additionally, toxic level of Zn repressed the nitrifying process by decreasing the abundance of nitrosifying bacteria Ellin6067 and promoted denitrification by increasing the abundance of Noviherbaspirillum, which resulted in decreased NO3− concentration in rice rhizosphere soil under VHZn condition.

Bi-Directional Pollution Characteristics and Ecological Health Risk Assessment of Heavy Metals in Soil and Crops in Wanjiang Economic Zone, Anhui Province, China.

Understanding the extent of contamination, sources and various carcinogenic and non-carcinogenic risks associated with different heavy metals in soil-crop systems is crucial for the prevention of heavy metal pollution. A survey was undertaken to determine heavy metal concentrations and degree of pollution in soil-crop systems (rice, wheat, and corn) using various indices such as pollution factor (CF), geo-accumulation index (Igeo), enrichment coefficients and transfer coefficient, and to determine the source of heavy metals pollution in the Wanjiang Economic Zone, Anhui Province, China. A total of 308 pairs of soil-crop samples were collected in this study, comprising 245 pairs of soil-rice samples, 53 pairs of soil-wheat samples, and 10 pairs of soil-corn samples. The concentrations of cadmium (Cd) and nickel (Ni) in the soil of the study area exceeded the national limitation of heavy metals in the soil of China (GB 15618-2018, Soil Environmental Quality: Risk Control Standard for Soil Contamination of Agricultural Land. Ministry of Environmental Protection of China. Beijing. China). The concentrations of copper (Cu), zinc (Zn) and lead (Pb) were also above the national limits to a lesser extent. All eight heavy metals (Cd, Cu, Ni, Pb Zn, arsenic (As), chromium (Cr), and mercury (Hg)) exceeded the background values in the study area. The enrichment coefficients of rice, wheat and maize to Cd, Cu and Zn were higher than those to other elements. On the basis of Igeo, it can be indicated that the rhizosphere soil of rice was slightly polluted by Cd and Hg, while the concentrations of the other heavy metals were below the safety limits. The CF and pollution load index (PLI) indicated that the soil in the study area was heavily contaminated with heavy metals. A principal component analysis identified different sources of soil heavy metal pollution, that is, Cu, Pb, Zn and Cd from industrial sources, Cr and Ni from natural sources, and As and Hg from agricultural sources. The carcinogenic risk of heavy metals was related to the intake of crops. Residents in the study area ingest rice, wheat, and corn on a daily basis. On the basis this study, it is suggested that local governments should pay attention to the carcinogenic risk of heavy metals in rice.

Zinc application promotes nitrogen transformation in rice rhizosphere soil by modifying microbial communities and gene expression levels

Application of Zn fertilizers to agricultural field is a simple and effective way for farmers to manage Zn deficient stress in soils to avoid yield lose. Although a synergistic effect of Zn on N transformation in soil has been reported, the mechanism is not fully understood yet. In this study, we planted rice in soils with different combinations of Zn and N supply, and analyzed the plant growth and N uptake, the N transformation, microbial communities, enzyme activities and gene expression levels in rhizosphere soil to reveal the underlying mechanism. Results showed that Zn application promoted the rice growth and N uptake, increased the soil alkali-hydrolyzed N and NH4+, but decreased NO3− and inhibited NH3 volatilization from the rhizosphere soil under optimal N condition. Zn supply significantly increased the relative abundances of Sphingomonas, Gaiella, subgroup_6, and Gemmatimonas, but decreased nitrosifying bacteria Ellin6067; while increased saprophytic fungi Schizothecium and Mortierella, but decreased pathogenic fungi Gaeumannomyces, Acremonium, Curvularia, and Fusarium in the rhizosphere soil under optimal N condition. Meanwhile, Zn application elevated the activities of protease, cellulase and dehydrogenase, and up-regulated the expression levels of napA, nirS, cnorB, and qnorB genes involved in the denitrification process in rice rhizosphere soil under optimal N condition. These results indicated Zn application could facilitate the soil N transformation and improved its availability by modifying both bacterial and fungal communities, and altering the soil enzyme activities and functional gene expression levels, ultimately promoted the N uptake and biomass of rice plant. However, this synergistic effect of Zn on rice growth, N uptake and soil N transformation strongly depended on the external N conditions, as no significant changes were observed under high N condition. Our results indicated that Zn co-fertilized with appropriate application of N is a useful strategy to improve the N bioavailability in rice rhizosphere soil and enhance the N uptake in rice plant.

Metarhizium robertsii as a promising microbial agent for rice in situ cadmium reduction and plant growth promotion

The toxic chemical element cadmium (Cd) in paddy fields triggered increasing problems of growth inhibition and food security in rice consistently. In this study, we found Metarhizium robertsii, which is widely used as a bioinsecticide and biofertilizer in agriculture and recently found to be resistant to Cd, developed intraradical and extraradical symbiotic hyphae in rice seedlings, and successfully colonized in the rice rhizosphere soil to more than 103 CFUs g−1 soil at harvesting. M. robertsii colonization significantly reduced Cd accumulations in both hydroponically cultured seedlings and the matured rice cultured in Cd contaminated potting soil (2 ppm). Notably, Cd accumulation reduction of the roots, stems, leaves, husks and grains of the matured rice induced by the fungus were 44.3%, 32.1%, 35.3%, 31.9% and 24.7%, respectively. It was caused by the M. robertsii-induced suppression of Cd intake transporter gene osNramp5 in the rice roots, and the chemical stabilizing of Cd to the residual fraction in the rhizosphere soil. In addition, the colonization of M. robertsii significantly promoted the growth characters and the photosynthesis of the rice plants. This is achieved by the increase of endogenous hormone levels of indole-3-acetic, gibberellin A3 and brassinolide induced by M. robertsii. Furthermore, the fungus enhanced the antioxidative capacities via increasing enzyme activities of catalase, peroxidase and the production of glutathione, ascorbic acid, proline in the rice plants. Our work provides theoretical basis for expanding the use of M. robertsii as in situ Cd accumulation reduction and detoxification agents for rice in contaminated paddy fields.

Pseudonocardia terrae sp. nov., an actinobacterium isolated from rice rhizosphere soil in Thailand.

A novel actinomycete, designated strain RS11V-5T, was isolated from rhizosphere soil of Oryza sativa L. collected from Roi Et Province, Thailand, and its taxonomic position was evaluated. Cells of strain RS11V-5T were Gram-stain-positive, aerobic, and non-motile. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose. MK-8(H4) was detected as the predominant menaquinone of this strain. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid. The major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain RS11V-5T belonged to the genus Pseudonocardia and had high 16S rRNA sequence similarity of 99.3 % to Pseudonocardia kujensis KCTC 29062T and less than 98.4 % to other members of the genus Pseudonocardia. The DNA G+C content of the strain RS11V-5T was 73.3 mol%. Strain RS11V-5T showed 46.5 % digital DNA-DNA hybridization, 92.2 % orthologous average nucleotide identity (OrthoANI), 90.2 % ANI based on blast and 92.7 % ANI based on MUMmer to P. kujensis KCTC 29062T. Based its phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain RS11V-5T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia terrae sp. nov. is proposed. The type strain is RS11V-5T (=TBRC 15286T=NBRC 115296T).

Rhizosphere bacteria community shift from vegetative to reproductive stage of Indonesia aromatic rice var. Pulut mandoti EMAS

The popular Indonesian aromatic rice, var. Pulut Mandoti Emas (PME) is produced with high economic value in Salukanan Village, Enrekang Regency, however, the best aroma quality of mandoti rice is restricted to the village. Therefore, this study aims to analyze the rhizosphere microbial group and the nutrients of the Mandoti rice paddy field in Salukanan Village at the vegetative and reproductive phases. Metagenome analysis was carried out with 16S rRNA amplification and Library preparation to examine the macro and micronutrients. The results showed that the most dominant taxa in the rhizosphere soil of vegetative mandoti rice was phylum Acidobacteria (35%), Proteobacteria (30%), and Firmicutes (12%), while in the reproductive phase, it was Phylum Firmicutes (42%), Proteobacteria (29%), and Planctomycetes (14%), respectively. The most dominant genus in vegetative phase was Candidatus koribacter, while at the reproductive phase was Aquisphaera. The analysis of macronutrients P, K, Mg, Ca, and micronutrients Fe, Mn, Cu, Na, Zn showed a reduction in the nutrient concentration at the reproductive phase compared to the vegetative phase excluding S element. Furthermore, the concentration of S element affects the abundance of bacteria in the reproductive phase, while the other elements of nutrients affect the vegetative phase. Based on these results, further strategies can be formulated to increase yield and guide breeding of mandoti aromatic rice.

Bioaccumulation and Risk Assessment of Potentially Toxic Elements in Soil-Rice System in Karst Area, Southwest China

The accumulation of potentially toxic elements (PTE) in a soil–rice system poses a significant issue of concern in agricultural soils, particularly in the polluted or high PTE geological background regions, such as karst areas. The source identification, bioaccumulation factors of PTE, and its health risk were investigated by correlation analysis, principal components analysis, and single/comprehensive assessments in a soil-rice system in Mashan County, Guangxi Province. The results showed that the mean contents of PTE in rice rhizosphere soil samples were higher than Guangxi surface soil, but lower than Mashan background. Of the samples, 84.21% have Cd content exceeding the soil environmental quality -- risk control standard for soil contamination of agricultural land in China (GB 15618-2018) risk screening value. The Nemerow comprehensive pollution index indicated that 21.05 and 26.32% of the soil samples were moderately and heavily polluted. The contents of pH-related exchangeable Ca, exchangeable Mg, and redox-related available Fe and available Mn in soil affected the bioaccumulation of PTE in rice. In all the rice samples, 55.26% of Cd and 31.58% of Pb exceed the maximum allowable value of contaminants in rice recommended by the national food safety standard for maximum levels of contaminants in foods in China (GB 2762-2017). The average targeted hazard quotient values (THQ) of PTE decreased in an order of As > Cd > Cr > Cu > Zn > Pb > Hg, and the degree of health risk it posed to the population was Children > Female > Male. The hazard index (HI) of all samples was greater than one due to all THQAs and the THQCd of more than half samples were above 1, which implied that the residents were exposed to non-carcinogenic risk by rice ingestion. Therefore, the PTE in the karst area with a high geological background can be absorbed and migrated by crops, leading to a greater health risk to humans, which should be paid attention to in future research and agricultural management.

Effects of Nitrogen Fertilizer Ratio on Microbial Diversity of Rice Rhizosphere Soil in Cold Region.

The experiment was conducted in the paddy field of a scientific and technological park of an agricultural reclamation farm in Xinxiang province from 2017 to 2019. The soil quality of the experimental field was the rhizosphere soil of rice in the cold region, and Longjing 31 was used as the experimental material. The effects of nitrogen application ratio on microbial diversity of rice rhizosphere soil in the cold region were studied. The aim is to provide a theoretical basis for rational fertilization, improving soil environment and high yield and efficiency. The results showed that: (a) the microbial diversity index of rice rhizosphere soil in the cold region was the best after the second nitrogen application; (b) under the ratio of N4 nitrogen application, the activity of bacteria, fungi and actinomycetes in rice rhizosphere soil in a cold region and their survival were the best; (c) under intensive cultivation conditions, the microbial diversity was the highest under SF1 treatment. SF0 treatment had the highest fungal diversity and SF3 treatment had the highest actinomycete diversity. (d) There was no significant effect on the microbial diversity of rice rhizosphere soil in the cold region without nitrogen fertilizer application in a single season.

Diversity of rice rhizosphere microorganisms under different fertilization modes of slow-release fertilizer

The application of slow-release fertilizer is an effective way to satisfy the demand for nutrients of crops. The objective of present study was to investigate the microbial community characteristics in rice rhizosphere soil under different fertilization modes of slow-release fertilizer. Three fertilization modes of slow-release fertilizer, i.e., (CK) manually broadcasted on the soil surface at 300 kg·ha−1 before transplanting and then same fertilizer rate was applied at the same way one week after transplanting; (SF) 10 cm depth mechanized placement at 600 kg·ha−1 during the transplanting; (DSF) 10 cm depth mechanized placement at 480 kg·ha−1 during the transplanting, were adopt in the field experiment. The results showed that SF and DSF treatments promoted richness (ACE and Chao1 values) and diversity (Shannon value) of rice rhizosphere microorganisms compared with CK treatment. Compared with CK, SF treatment increased relative abundances of Planctomycetes and decreased relative abundance of Nitrospirae, DSF treatments increased relative abundances of Deltaproteobacteria. Moreover, higher relative abundances of Paenibacillus and Sphingomonas were recorded in DSF treatment than CK. In addition, the partial factor productivity (PFP) deep placement of slow-release fertilizer treatment was significantly higher than that of CK treatment. DSF treatment increased the yield by 16.61% compared with CK treatment while reducing fertilizer input by 20%. In conclusion, compared with broadcasting, deep placement of slow-release fertilizer could improve the structure, distribution, and diversity of the microbial community in rice rhizosphere soil, and increase the utilization rate of fertilizers, and increase rice yield.

Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.

Predatory activity of Acanthamoeba sp genotype T4 on different plant growth-promoting bacteria and their combined effect on rice seedling growth

Heterotrophic protists play a crucial role in plant growth promotion via nutrient cycling and shift in microbial community composition in the soil ecosystem. Selective predation pressure by protists contributes to the evaluation of plant beneficial traits in rhizospheric bacteria. However, not always all plant growth-promoting bacterial (PGPB) strains are benefitted by predation. This study aimed to examine the predatory effect of Acanthamoeba sp genotype T4 on a range of PGPB strains and their combined impact on early rice seedling growth. Acanthamoeba sp isolated from rice rhizosphere soils were used to assess predation against several PGPB such as Pseudomonas, Bacillus, Enterobacter, Morganella, Stenotrophomonas, Providencia, and Lysinibacillus on Nutrient Yeast Extract agar (NYE) plate. The controlled experiment on the germinated rice seeds (Oryza sativa L.) grown in Petri dishes containing each PGPB strain and Acanthamoeba sp was performed to evaluate the combined impact on plant performance. The PGPB-Acanthamoeba combined treatments in Petri dishes showed significant rice seedling growth compared to PGPB alone, non-PGPB and control. Our results indicated the positive but different impact of Acanthamoeba sp with different PGPB species on early rice plant growth. Further in-depth research should be carried out with diverse protists and PGPB species to assess which protist species can be linked to enhancement of indigenous soil PGPB for improved plant growth.

Assembly and co-occurrence patterns of rare and abundant bacterial sub-communities in rice rhizosphere soil under short-term nitrogen deep placement

Nitrogen (N) deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields. However, relatively little is known how bacterial consortia, especially abundant and rare taxa, respond to N deep placement, which is critical for understanding the biodiversity and function of agricultural ecosystem. In this study, Illumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields. The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples. Abundant bacteria showed ubiquitous distribution; while rare taxa exhibited uneven distribution across all samples. Stochastic processes dominated community assembly of both abundant and rare bacteria, with dispersal limitation playing a more vital role in abundant bacteria, and undominated processes playing a more important role in rare bacteria. The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer (BN) and no N fertilizer (NN) treatments in abundant and rare taxa of rhizosphere soil; while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa. Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa. Nevertheless, most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability. Overall, these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.

Characterization and low-cost preservation of Chromobacterium violaceum strain TRFM-24 isolated from Tripura state, India

BackgroundChromobacterium species, through their bioactive molecules, help in combating biotic and abiotic stresses in plants and humans. The present study was aimed to identify, characterize and preserve in natural gums the violet-pigmented bacterial isolate TRFM-24 recovered from the rhizosphere soil of rice collected from Tripura state. ResultsBased on morphological, biochemical and 16S rRNA gene sequencing, the isolate TFRM-24 was identified as Chromobacterium violaceum (NAIMCC-B-02276; MCC 4212). The bacterium is saprophytic, free living and Gram negative. The strain was found positive for production of IAA, cellulase, xylanase and protease, and showed tolerance to salt (2.5%) and drought (-1.2 MPa). However, it showed poor biocontrol activity against soil-borne phytopathogens and nutrient-solubilizing abilitiets. C. violaceum strain TRFM-24 did not survive on tryptic soya agar (TSA) beyond 12 days between 4 and 32 °C temperature hence a method of preservation of this bacterium was attempted using different natural gums namely Acacia nilotica (babul), Anogeissus latifolia (dhavda), Boswellia serrata (salai) and Butea monosperma (palash) under different temperature regime (6–32 °C). The bacterium survived in babul gum (gum acacia), dhavda and salai solution at room temperature beyond a year. ConclusionBased on polyphasic approach, a violet-pigmented isolate TRFM-24 was identified as Chromobacterim violaceum which possessed some attributes of plant and human importance. Further, a simple and low-cost preservation method of strain TRFM-24 at room temperature was developed using natural gums such as babul, dhavda and salai gums which may be the first report to our knowledge.

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, which can effectively explore the interaction relationship or co-occurrence model of different microbial species in different environments. The purpose of this manuscript is to provide details on how to use the weighted correlation network algorithm to analyze different co-occurrence networks that may occur in microbial communities due to different ecological environments. All analysis of the experiment is performed in the WGCNA package. WGCNA is an R package for weighted correlation network analysis. The experimental data used to demonstrate these methods were microbial community data from the NCBI (National Center for Biotechnology Information) database for three niches of the rice (Oryza sativa) root system. We used the weighted correlation network algorithm to construct co-abundance networks of microbial community in each of the three niches. Then, differential co-abundance networks among endosphere, rhizoplane and rhizosphere soil were identified. In addition, the core genera in network were obtained by the "WGCNA" package, which plays an important regulated role in network functions. These methods enable researchers to analyze the response of microbial network to environmental disturbance and verify different microbial ecological response theories. The results of these methods show that the significant differential microbial networks identified in the endosphere, rhizoplane and rhizosphere soil of rice.

Rhizosphere-Associated Microbiomes of Rice (Oryza sativa L.) Under the Effect of Increased Nitrogen Fertilization.

Crops assemble and rely on rhizosphere-associated microbiomes for plant nutrition, which is crucial to their productivity. Historically, excessive nitrogen fertilization did not result in continuously increasing yields but rather caused environmental issues. A comprehensive understanding should be developed regarding the ways in which crops shape rhizosphere-associated microbiomes under conditions of increased nitrogen fertilization. In this study, we applied 16S and 18S ribosomal RNA gene profiling to characterize bacterial and fungal communities in bulk and rhizosphere soil of rice subjected to three levels of nitrogen fertilization for 5 years. Soil biochemical properties were characterized, and carbon-, nitrogen-, and phosphorus-related soil enzyme activities were investigated, by assays. Increasing nitrogen fertilization led to a decreasing trend in the variation of microbial community structures and demonstrated a more definite influence on fungal rather than bacterial community compositions and functions. Changes in the level of nitrogen fertilization significantly affected chemical properties such as soil pH, nutrient content, and microbial biomass levels in both rhizosphere and bulk soil. Soil enzyme activity levels varied substantially across nitrogen fertilization intensities and correlated more with the fungal than with the bacterial community. Our results indicated that increased nitrogen input drives alterations in the structures and functions of microbial communities, properties of soil carbon, nitrogen, and phosphorus, as well as enzyme activities. These results provide novel insights into the associations among increased nitrogen input, changes in biochemical properties, and shifts in microbial communities in the rhizosphere of agriculturally intensive ecosystems.

Massilia rhizosphaerae sp. nov., a rice-associated rhizobacterium with antibacterial activity against Ralstonia solanacearum.

A novel rhizobacterium, designated strain NEAU-GH312T, with antibacterial activity against Ralstonia solanacearum was isolated from rhizosphere soil of rice (Heilongjiang Province, PR China) and characterized with a polyphasic approach. Cells of strain NEAU-GH312T were Gram-stain-negative, aerobic, non-spore-forming, motile with peritrichous flagella and rod-shaped. Colonies were light orange, convex and semi-translucent on Reasoner's 2A (R2A) agar after 2 days of incubation at 28 °C. Growth was observed on R2A agar at 10-40 °C, pH 4.0-8.0 and with 0-5 % (w/v) NaCl. The respiratory quinone was ubiquinone Q-8. The major cellular fatty acids of strain NEAU-GH312T were C16 : 1 ω7c and/or C16 : 1 ω6c, C16 : 0 and C18 : 1 ω7c and/or C18 : 1 ω6c. The main polar lipids were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analyses confirmed the well-supported affiliation of strain NEAU-GH312T within the genus Massilia, close to the type strains of Massilia arvi THG-RS2OT (98.7 %), Massilia norwichensis NS9T (98.7 %) and Massilia kyonggiensis TSA1T (98.6 %). Strain NEAU-GH312T had a genome size of 6.68 Mb and an average DNA G+C content of 66.3 mol%. Based on the genotypic, phenotypic and chemotaxonomic data obtained in this study, strain NEAU-GH312T could be classified as representative of a novel species of the genus Massilia, for which the name Massilia rhizosphaerae sp. nov. is proposed, with strain NEAU-GH312T (=DSM 109722T=CCTCC AB 2019142T) as the type strain.

Elucidating the impact of three metallic nanoagrichemicals and their bulk and ionic counterparts on the chemical properties of bulk and rhizosphere soils in rice paddies

Growing applications of nanoagrichemicals have resulted in their increasing accumulation in agricultural soils, which could modify soil properties and affect soil health. A greenhouse pot trial was conducted to determine the effects of three metallic nanoagrichemicals on several fundamental chemical properties of a rice paddy soil, including zinc oxide nanoparticles (ZnO NPs) and copper oxide nanoparticles (CuO NPs) at 100 mg/kg, and silicon oxide nanoparticles (SiO2 NPs) at 500 mg/kg, as well as their bulk and ionic counterparts. The investigated soil amendments displayed significant and distinctive impact on the examined soil chemical properties relevant to agricultural production, including soil pH, redox potential, soil organic carbon (SOC), cation exchange capacity (CEC), and plant available As. For example, all amendments increased the bulk soil pH at day 47 to some extent, but the increase was substantially higher for SiO32− (37.7%) than other amendments (5.8%–13.7%). Soil Eh was elevated markedly at day 47 after the addition of soil amendments in both the bulk soil (45.9%–74.4%) and rice rhizosphere soil (20.3%–68.9%). CuO NPs and Cu2+ generally exhibited greater impact on soil chemical properties than other agrichemicals. Significantly different responses to soil amendments were observed between bulk and rhizosphere soils, suggesting the essential role of plants in affecting soil properties and their responses to environmental disturbance. Overall, our results confirmed that the tested amendments could have remarkable impacts on the fundamental chemical properties of rice paddy soils.