Rice Rhizosphere Soil Research Articles

Little environmental adaptation and high stability of bacterial communities in rhizosphere rather than bulk soils in rice fields

The rhizosphere harbors complex bacterial communities, which are critical for plant growth and health. Significant differences exist between bacterial communities in the rhizosphere and bulk soils, however, limited research has explored co-occurrence patterns, environmental adaptations, and assembly mechanisms of rhizosphere bacterial communities. Using 16S rRNA high-throughput sequencing, we investigated the taxonomic and phylogenetic diversity of bacterial communities in both rhizosphere and bulk soils from a rice cropping experimental system in China. In addition to investigating differences in bacterial composition, we examined co-occurrence patterns, estimated environmental breadth and phylogenetic signals, and analyzed community assembly processes in these environments. Significant differences were observed between rhizosphere composition and bulk soil (p < 0.05) even some bacteria in the rice rhizosphere may come from the bulk soil around roots. The distribution patterns and ecological functions between communities in the rice rhizosphere and bulk soil were also significantly different. Lower β-diversity values among bacterial communities in the rice rhizosphere indicated that they had a higher stability than those in the bulk soils. In addition, rice rhizosphere communities had a wider phylogenetic diversity and lower functional redundancy when compared with bulk soils. Moreover, the results of environmental breadth analysis revealed that communities in bulk soils were more environmentally constrained than rhizosphere communities. Our null model revealed that deterministic processes drove community assembly in bulk soils (59.57%), whereas stochastic processes determined those in the rice rhizosphere (53.85%). Available potassium was decisive in determining the balance between stochasticity and determinism in both communities. Our study provides insights on the mechanisms underlying the assembly and maintenance of bacterial diversity in rice cropping soils, in response to environmental changes.

Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis

A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang Province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1T (98.46%) and Massilia putida 6NM-7T (98.41%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11T formed lineage related to M. phosphatilytica 12-OD1T and M. putida 6NM-7T. The major fatty acids of the strain were C16:0, C17:0-cyclo and C16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11T and M. phosphatilytica 12-OD1T and M. putida 6NM-7T were 45.4 and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11T was 66.2%. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to have the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, we conclude that strain NEAU-DD11T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11T (= CCTCC AB 2019141T = DSM 109721T).

Manure application accumulates more nitrogen in paddy soils than rice straw but less from fungal necromass

Microbial processes involving in nitrogen (N) assimilation mediate the continuous supply of mineral N for crop growth and the reactive N loss in intensively managed agriculture soils. This study aimed to reveal the microbial assimilation role in N accumulation in paddy soils under partial substitution of mineral fertilizer with organic materials (straw or manure), by quantifying the microbial N derived from living biomass and necromass. Rice rhizosphere and bulk soils were collected at a 31-year field trial including five fertilization treatments: no fertilizer (Control), mineral fertilizer alone (NPK), 20% mineral fertilizer substituted by rice straw (NPKS), and 30% and 60% mineral fertilizer substituted by manure (NPKLM and NPKHM, respectively). Incorporation of organic materials increased the total soil N by 22–76% compared to NPK, with a greater increase under manure- than rice straw-treated soils. Both organic inputs enhanced the amounts of living biomass and necromass N by 1.1–1.5 times via stimulating the activity of N cycling genes (chiA, AOA, narG, nirK, nirS, nosZ, nifH) in bulk soils. Although the pools of living biomass and necromass N in soils with manure amendments were 12–34% and 13–22% higher, than those with rice straw incorporation, their corresponding contributions to total N were 7.2–7.4% and 6.2–15% lower, respectively, suggesting a weaker relative microbial contribution in soil N accrual with manure amendments. Rice rhizosphere processes strengthened the role of microbial participation in soil N accumulation, particularly with organic inputs. The relative contribution of fungal necromass N to total N as well as the ratios of fungi to bacteria in both living biomass and necromass were lower under manure amendments than rice straw incorporation. As a whole, as compared with the incorporation of rice straw, the greater N accumulation in paddy soil with manure amendments is associated with the relatively weaker accumulation of fungal necromass and stronger retention of organic debris without microbial processing.

Periphytic biofilm and rice rhizosphere phosphate-solubilizing bacteria and fungi: A possible use for activating occluded P in periphytic biofilms in paddy fields

Periphytic biofilm is a complex mixture of algae, cyanobacteria, heterotrophic microbes, and detritus that is attached to submerged surfaces in most aquatic ecosystems. They have been shown to assimilate and store bio-available phosphorus (P) in paddy fields. However, it is necessary to make the occluded P available to the rice plant in the final stage of the plant growth. It has been reported that phosphate-solubilizing bacteria and fungi have a role in activating the occluded P in the periphytic biofilms. However, the ability of the bacteria and fungi isolated from the periphytic biofilms to solubilize sparingly soluble phosphates has not been reported. The aim of this study was to investigate the ability of bacterial and fungal isolates isolated from periphytic biofilms and rice rhizosphere soil, as an origin of bacteria and fungi present in periphytic biofilms, to dissolve different sparingly soluble phosphate sources as single and in combination. In addition, effective phosphate-solubilizing bacterial and fungal isolates and the organic acids produced by these microbes were also identified. The isolated bacterial and fungal isolates had different ability to solubilize various P sources. The order of P dissolution from different P sources by bacterial and fungal isolates was as follows: Ca3PO4 ˃ Ca5(PO4)3(OH) ˃ mixed medium (a combination of 7 different P sources) ˃ Ca5(PO4)3Cl ̴ C6H17NaO24P6 ˃ Ca5(PO4)3F ˃ AlPO4 ˃ FePO4. The type and amount of the organic acids produced by these isolates depended on the type of microbe (bacterial isolate or fungal isolate), used P source, microbial inoculation (single or consortium), and type of the microbe used in consortium (bacterium-bacterium, bacterium-fungus, and fungus-fungus). Based on this assay, it was found that the bacterial and fungal consortiums, due to diversity in the production of different organic acids, showed a better ability to dissolve different forms of P. Based on the sequence of 16S rRNA gene and ITS region, the effective rhizosphere isolates of 8BR15, 8BR17, 2FR3, and 2FR18 and the effective periphytic biofilm isolates of 6BP11, 13BP25, 8FP12, and 6FP9 showed the most similar to Burkholderia vietnamiensis, Arthrobacter luteolus, Talaromyces minioluteus and Talaromyces pinophilus, and Acinetobacter calcoaceticus, Bacillus cereus, Talaromyces stipitatus and Talaromyces minioluteus, respectively. According to these results, periphytic biofilms and rice rhizosphere soil can be as a potential repository for isolating bacteria and fungi effective in solubilizing various P source. In general, the results suggest that the effective phosphate-solubilizing microorganisms have the potential to be used as microbial inoculants to release the bio-available P assimilated and stored in periphytic biofilms for sustainable rice cultivation in paddy lands.

Influence of elemental sulfur on cadmium bioavailability, microbial community in paddy soil and Cd accumulation in rice plants

Cadmium (Cd) is highly toxic to living organisms and the contamination of Cd in paddy soil in China has received much attention. In the present study, by conducting pot experiment, the influence of S fertilizer (S0) on rice growth, iron plaque formation, Cd accumulation in rice plants and bacterial community in rice rhizosphere soil was investigated. The biomass of rice plants was significantly increased by S0 addition (19.5–73.6%). The addition of S0 increased the formation of iron plaque by 24.3–45.8%, meanwhile the amount of Cd sequestered on iron plaque increased. In soil treated with 5 mg/kg Cd, addition of 0.2 g/kg S0 decreased the diffusive gradients in thin films (DGT) extractable Cd by 60.0%. The application of S0 significantly decreased the concentration of Cd in rice grain by 12.1% (0.1 g/kg) and 36.6% (0.2 g/kg) respectively. The addition of S0 significantly increased the ratio of Acidobacteria, Bacteroidetes in rice rhizosphere soil. Meanwhile, the ratio of Planctomycetes and Chloroflexi decreased. The results indicated that promoting Fe- and S-reducing and residue decomposition bacterial in the rhizosphere by S0 may be one biological reason for reducing Cd risk in the soil-rice system.

Isolation and characterization of N-fixing and IAA producing rhizobacteria from two rice field agro-ecosystems in South Sulawesi, Indonesia

Abstract. Haerani N, Syam’un E, Rasyid B, Feranita. 2021. Isolation and characterization of N-fixing and IAA producing rhizobacteria from two rice field agro-ecosystems in South Sulawesi, Indonesia. Biodiversitas 22: 2497-2503. Nitrogen-fixing bacteria that live in the rhizosphere are microorganisms that can increase N availability for rice plants in a non-symbiotic manner. Nitrogen-fixing bacteria also support growth through the production of growth hormones. These abilities are mainly influenced by the environment and their association with plants. This research aims to determine the microbial characteristics from two different rice fields agro-ecosystems (rainfed and irrigated) in South Sulawesi. Bacteria isolated from the rhizosphere soil of rice in six districts were cultured and isolated using Burk's N-free media for screening purposes. A total of 20 isolates were observed for their morphological and biochemical properties, determined their ability to fix nitrogen and produce IAA. The results showed that all isolates could grow on nitrogen-free media, in which 13 isolates were isolated from rainfed rice fields, and 7 isolates were from irrigated rice fields with various physical and biochemical properties, all other qualities tested also varied. NG4 isolate from Gowa Regency (rainfed rice field) produced the highest nitrogen (0.157%), and NB13 isolate from Barru (rainfed rice field) had the highest concentration of growth hormone (IAA) (1,835 mg L-1). All isolates obtained from rainfed rice fields showed a better ability to fix nitrogen and produce growth hormone than those from irrigated rice fields. Bacteria isolates from rainfed rice fields have higher biofertilizers and biostimulant capacity to develop environmentally-friendly rice cultivation.

Elevated Atmospheric CO2 and Nitrogen Fertilization Affect the Abundance and Community Structure of Rice Root-Associated Nitrogen-Fixing Bacteria.

Elevated atmospheric CO2 (eCO2) results in plant growth and N limitation, yet how root-associated nitrogen-fixing bacterial communities respond to increasing atmospheric CO2 and nitrogen fertilization (eN) during the growth stages of rice is unclear. Using the nifH gene as a molecular marker, we studied the combined effect of eCO2 and eN on the diazotrophic community and abundance at two growth stages in rice (tillering, TI and heading, HI). Quantitative polymerase chain reaction (qPCR) showed that eN had no obvious effect on nifH abundance in rice roots under either ambient CO2 (aCO2) or eCO2 treatment at the TI stage; in contrast, at the HI, nifH copy numbers were increased under eCO2 and decreased under aCO2. For rhizosphere soils, eN significantly reduced the abundance of nifH under both aCO2 and eCO2 treatment at the HI stage. Elevated CO2 significantly increased the nifH abundance in rice roots and rhizosphere soils with nitrogen fertilization, but had no obvious effect without N addition at the HI stage. There was a significant interaction [CO2 × N fertilization] effect on nifH abundance in root zone at the HI stage. In addition, the nifH copy numbers in rice roots were significantly higher at the HI stage than at the TI stage. Sequencing analysis indicated that the root-associated diazotrophic community structure tended to cluster according to the nitrogen fertilization treatment and that Rhizobiales were the dominant diazotrophs in all root samples at the HI stage. Additionally, nitrogen fertilization significantly increased the relative abundance of Methylosinus (Methylocystaceae) under eCO2 treatment, but significantly decreased the relative abundance of Rhizobium (Rhizobiaceae) under aCO2 treatment. Overall, the combined effect of eN and eCO2 stimulates root-associated diazotrophic methane-oxidizing bacteria while inhibits heterotrophic diazotrophs.

Light exposure mediates circadian rhythms of rhizosphere microbial communities

Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light–dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light–dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.

Rice Rhizospheric Effects on the Bioavailability of Toxic Trace Elements during Land Application of Biochar.

Land application of biochar, the product of organic waste carbonization, can improve soil fertility as well as sequester carbon to mitigate climate change. In addition, biochar can greatly influence the bioavailability of toxic trace elements (TTEs) in soils resulting from its large internal surface areas, abundance in organic carbon, and ability to modify soil pH. Most research to date employs batch leaching tests to predict how biochar addition impacts TTE bioavailability, but these ex situ tests rarely considered the rhizospheric effect which might offset or intensify the changes induced by organic residue addition. This is especially so in rice rhizospheres because of strong clines in localized redox conditions. In this study, we adopted in situ high-resolution (HR) diffusive gradients in thin films (DGT) as well as rhizo-bag porewater sampling experiments to depict an overall picture of the difference in TTE (As, Cd, Cu, Ni, and Pb) bioavailability between the rice rhizosphere and bulk soils during land application of biochar. Porewater sampling experiments revealed that biochar additions stimulated TTE release due to the increase of dissolved organic carbon (DOC) and H+ concentrations. In the rhizosphere, although biochar still promoted As, Cd, and Ni release into porewaters, the rhizospheric effect was one of dampening/reduction compared with the bulk soil. When we focused on the localized changes of TTE bioavailability in the rhizosphere using an in situ HR-DGT approach, on the contrary, flux maxima of Cd, Cu, and Ni occurred near/on the root surface, and hot spots of As can be observed at peripheries of the rooting zone, which demonstrated the high heterogeneity and complexity of the rhizosphere's influence on TTE bioavailability.

Microbial carbon source utilization in rice rhizosphere soil with different tillage practice in a double cropping rice field

Carbon (C) plays an important role in maintaining soil fertility and increasing soil microbial community, but there is still limited information about how source utilization characteristics respond to soil fertility changes under double-cropping rice (Oryza sativa L.) system in southern China paddy field. Therefore, the effects of different short-term (5-years) tillage management on characteristics of C utilization in rice rhizosphere and non-rhizosphere soils under double-cropping rice field in southern China were investigated by using 18O incorporation into DNA. Therefore, a field experiment were included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that soil microbial biomass C content with CT, RT, NT treatments were increased by 29.71–47.27% and 3.77–21.30% in rhizosphere and non-rhizosphere soils, compared with RTO treatment, respectively. Compared with RTO treatment, soil microbial basal respiration and microbial growth rate with CT treatment were increased 30.56%, 30.94% and 11.91%, 12.34% in rhizosphere and non-rhizosphere soils, respectively. The soil microbial C utilization efficiency were promoted with NT treatment. Compared with RTO treatment, the metabolic capacity of soil microorganism to exogenous C source with CT, RT and NT treatments were increased. The largest type of exogenous C source was saccharides, followed by amino acid and polymers, and complex compounds was the smallest. The redundancy analysis results indicated that tillage treatments significantly changed the utilization characteristics of soil microorganism to exogenous C source. Compared with RTO treatment, the grain yield of early rice and late rice with CT treatment were increased by 409.5 kg ha−1 and 387.0 kg ha−1, respectively. Therefore, the CT and RT treatments could significantly increase soil microbial biomass C content, but the NT treatment promote microbial C utilization efficiency in the double-cropping paddy field of southern China.

Cadmium-resistant and arginine decarboxylase-producing endophytic Sphingomonas sp. C40 decreases cadmium accumulation in host rice (Oryza sativa Cliangyou 513)

In this study, an cadmium (Cd)-immobilizing and arginine decarboxylase-producing endophytic Sphingomonas sp. strain C40 obtained from the seeds of Oryza sativa Cliangyou 513 was characterized for its Cd availability and Cd uptake in host rice using hydroponic and soil experiments. The Cd concentration decreased by 51–95% compared to the control, while the spermidine concentration increased by 19–25% with Cd compared with no Cd in the strain C40-inoculated solution. Strain C40 decreased the above-ground tissue Cd content by 27–37% and increased spermine and spermidine contents by 28–67% and the expression levels of genes involved in spermine and spermidine production by 29–217% in rice roots compared to the controls. Furthermore, correlation analyses showed the significantly negative correlation between rice root spermine and spermidine contents and above-ground tissue Cd content. In the Cd-added soil, strain C40 promoted the rice biomass by 29–36% and decreased rice root, above-ground tissue, and grain Cd contents by 18, 16, and 33% and total grain Cd uptake by 14% compared with the controls at the maturity stage. Strain C40 decreased the exchangeable Cd content by 27% and increased the Fe and Mn oxides-bound Cd content by 45% in the rice rhizosphere soils at the maturity stage compared with the controls. These results suggested that the endophytic bacterial strain C40 increased rice root polyamine production and their related gene expression and the transformation of available Cd to unavailable Cd, leading to reduced Cd accumulation and translocation from the rice roots to grains.

Characterization of zinc solubilization potential of arsenic tolerant Burkholderia spp. isolated from rice rhizospheric soil.

In this study, experiments were conducted to isolate, characterize, and evaluate rice rhizosphere bacteria for their arsenic (As) tolerance ability and zinc (Zn) solubilization potential in culture media and soil. Among 20 bacterial isolates recovered, six were found to solubilize inorganic Zn salt(s) efficiently under in vitro culture conditions. 16S rRNA gene sequence-based phylogenetic analysis indicated the affiliation of efficient Zn solubilizing bacteria (ZSB) to Burkholderia vietnamiensis and Burkholderia seminalis. Zinc solubilizing efficiency (ZSE) of the bacteria varied with the concentrations and types of Zn salts used in the experiments. Increasing trend in ZSE of the bacteria was noticed when the percentage of ZnO increased from 0.1 to 0.5 but the same decreased at 1.0%. Increased Zn solubilization was noticed when bacteria were incubated with lower concentration of Zn3(PO4)2 and ZnCO3. In general, Zn solubilization increased with increasing incubation time in lower volume medium, while some isolates failed to solubilize one or more tested Zn salts. However, enriched concentrated cells of the ZSB in glucose amended medium with 0.5% ZnO showed an increasing trend of Zn solubilization with time and were able to solubilize more than 300mg/L Zn. This increased rate of Zn release by the ZSB was attributed to marked decline in pH that might be due to the enhanced gluconic acid production from glucose. As evident from the decreased ZSE of the bacteria in the presence of As(V) in particular, it seems arsenic imparts a negative effect on Zn solubilization. The ZSB were also able to increase the rate of Zn release in soil. A microcosm-based soil incubation study amending the enriched bacteria and 0.5% ZnO in soil showed an elevated level of both water-soluble and available Zn compared to un-inoculated control. During Zn solubilization in microcosms, viable cells in terms of colony-forming unit (CFU) declined by the same order of magnitude both in the presence and absence of ZnO that might be due to the nutrients limiting condition aroused during the incubation period rather than Zn toxicity. The bacteria in this study also exhibited plant growth promoting traits, such as growth in nitrogen-free medium, production of indole acetic acid (IAA), and solubilization of potassium and phosphate. Our findings suggested that Burkholderia spp. could be the potential candidates for enhancing Zn dissolution in the soil that might reduce the rate of inorganic Zn fertilization in agricultural soil.

Effect of microplastics and arsenic on nutrients and microorganisms in rice rhizosphere soil

The presence of microplastics and arsenic in soil can endanger crop growth; therefore, their effects on the properties of rhizosphere soil should be evaluated. Large (10–100 µm) and small (0.1–1 µm) polystyrene (PSMP) and polytetrafluorethylene (PTFE) particles were added to soil with different arsenic concentrations (1.4, 24.7, and 86.3 mg kg−1) to investigate the combined effect of microplastics and arsenic pollution on rice rhizosphere soil. After the addition of PSMP and PTFE, pH, arsenic (V) and arsenic (III) in the soil were observed to decrease. The interaction of arsenic with PSMP and PTFE resulted in this phenomenon, leading to a decrease of arsenic bioavailability in the soil. PSMP, PTFE, and arsenic reduced the abundance of Proteobacteria, increased the abundance of Chloroflexi and Acidobacteria, and inhibited soil urease, acid phosphatase, protease, dehydrogenase, and peroxidase activity via affecting the tertiary structure of the enzyme. PSMP, PTFE, and arsenic also reduced the available nitrogen and phosphorus content in the soil. Arsenic increased the soil organic matter content, whereas PSMP and PTFE reduced the organic matter content. Furthermore, microplastics inhibited the effects of arsenic on the microbial and chemical properties of the rhizosphere soil. This study revealed the effects of microplastic and arsenic pollution on rice rhizosphere microorganisms and nutrients, and elucidated the mechanism by which these pollutants retard crop growth in the designed growth medium.

Combined Effect of Weathered Coal Based Amendments and Soil Water Management on Methylmercury Accumulation in Paddy Soil and Rice Grains

A pot experiment and field experiment were designed to study the changes in the grain methyl mercury content in paddy soil and rice yield by sowing soil amendments that contained weathered coal, CaCO3, and Na2SeO3 as the main raw materials, combined with water management in a paddy field (80% field capacity after the heading and flowering periods). The results showed that:① In pot experiment, the content of methylmercury in rice rhizosphere soil decreased by 86.6% and the content of methylmercury in the rice grains decreased by 65.2% compared with that of the control. In field experiment, the content of methylmercury in rice rhizosphere soil decreased by 77.4% and the content of methylmercury in rice grains decreased by 60.6% upon adding the amendment+water management compared with that of CK. ② The soil pH increased by more than 0.3 in the pot experiment and 0.2 in the field experiment compared with that of the control. Furthermore, rice yield and plant biomass did not decrease in the two parts of the experiment. It can be inferred that the soil amendment and agronomic regulation measures (water management) used in this study have the advantages of quick effects, convenient use, and remarkable control effects and without secondary pollution. More, they can effectively reduce the risk of rice methylmercury exposure.

Native isolates of Trichoderma as bio-suppressants against sheath blight and stem rot pathogens of rice

BackgroundSpecies belonging to the genus Trichoderma are considered as one of the most potential biocontrol agents which can be readily collected from soil and found effective against various fungal and bacterial diseases. In rice-growing areas, the major fungal pathogens affecting rice production include Rhizoctonia solani causing sheath blight and Sclerotium oryzae causing stem rot disease of rice. Due to the lack of resistant varieties and detrimental effects of chemicals, biocontrol gives a good opportunity to manage the diseases efficiently in a sustainable manner.Main bodyTrichoderma spp. from native rice rhizosphere soil were examined for their antagonistic efficiency to supress the two soil-borne rice pathogens, viz., R. solani and S. oryzae. Morphological, biochemical and molecular characterisation of the isolates led to the identification of species as T. asperellum. The isolates of Trichoderma spp. were found to be positive to IAA release and phosphate solubilisation and were screened against R. solani and S. oryzae in vitro and in vivo in pots under glass house conditions. Regression analysis indicated a positive correlation between the amount of chlamydospores produced by T. asperellum and their antagonistic potential against the two pathogens. Exposure to external stimuli, viz., light, injury and nitrogen sources in culture media triggered increased conidiation in Trichoderma isolates. Among the four isolates studied, Trichoderma asperellum IIRRCK1 (TAIK-1) was found to be the most effective in improving plant growth in rice and highly antagonistic against R. solani and S. oryzae. Sorghum grain was found to be the most suitable among different organic substrates studied to provide better growth and viability of TAIK-1 and improved the efficiency of the seed treatment and soil application. External stimuli in the form of near UV blue light, mechanical injury to the colonies and nitrogen source added to the culture media help in faster conidiation of Trichoderma.ConclusionStrain TAIK-1 showed strong competitive and antagonistic activities against fungal soil-borne pathogens, in addition with promoting healthy growth and development of rice plants. This can be a suitable and safe alternative to chemical management in the rice fields for long-term scenario.

Screening and identification of abiotic stress-responsive efficient antifungal Pseudomonas spp. from rice rhizospheric soil.

Plant growth-promoting rhizobacteria (PGPR) are a collection of microorganisms often used to support and promote plant development and combat plant infectious diseases with various biological control methods. The most significant restricting factors for agricultural productivity worldwide are abiotic constraints. In the present study, seven bacterial isolates from the rice rhizosphere were selected for detailed tests based on results obtained in experiments determining the ACC deaminase synthesis and drought tolerance at -0.30 MPa PEG level. Screening results of the stress tolerance analysis of the seven isolates for elevated temperature (50°C), alkalinity (10% NaCl), and drought (-1.2 MPa) showed that abiotic stress resistance was less prevalent in DRO2, DRO13, and DRO43 isolates than in DRO17, DRO28, DRO35, and DRO51 isolates. During the study, it was observed that DRO17, DRO28, and DRO51 tended to maintain similar cell density at -0.73 MPa PEG level, as observed at -0.30 MPa stress condition. No bacterial growth was observed at higher PEG level (-1.12 MPa) for any bacterial isolate. Four strains of Pseudomonas (DRO17, DRO28, DRO35, and DRO51) exhibited salinity and temperature tolerance. Antifungal screening using the bangle method showed that DRO35 was highly antagonistic towards Rhizoctonia solani 4633, followed by Fusarium moniliforme 4223, with an inhibition of 64.3% and 48%, respectively. The DRO28 isolate exhibited 72.5% growth inhibition for Fusarium moniliforme 4223, while the DRO51 isolate showed 38.2% growth inhibition for Bipolaris hawaiiensis 2445. DRO17 reduced the growth of Rhizoctonia solani 4633, and Curvularia lunata 350 by 36% and 31%, respectively. In conclusion, the screening of bacterial strains with promising stress tolerance and antifungal characteristics could support farmers to achieve the required positive outcomes in the agriculture field.

Soil Enzyme Activity and Microbial Metabolic Function Diversity in Soda Saline–Alkali Rice Paddy Fields of Northeast China

Western Jilin province has the most serious area of soda salinization in Northeast China, which affects and restricts the sustainable development of agriculture. The effects of physico-chemical properties of rhizosphere and non-rhizosphere soil on soil microbial diversity and enzyme activities (polyphenol oxidase, catalase, invertase, amylase) were evaluated in typical soda saline-alkali paddy field. Community-level physiological profile (CLPP) based on Biolog-ECO plates was used to assess the functional diversity of soil microorganisms. Exchangeable sodium percentage (ESP) and pH were negative correlated with the microbial activity (AWCD), soil enzyme activities (amylase, sucrose, and catalase, except for polyphenol oxidase) in rice rhizosphere and non-rhizosphere soil (P &lt; 0.05). The indexes of microbial diversity in rice rhizosphere soil were significantly higher than that of non-rhizosphere soil. The utilization of amino acids by rice rhizosphere microorganisms was relatively high, while non-rhizosphere soil had relatively high utilization of carboxylic acid, phenolic acid, and amine. Among the selected physico-chemical properties, soil organic carbon (SOC) and soil water content (SWC) had the greatest influence on the variation of microbial diversity indexes and enzyme activities in rhizosphere soil. ESP and pH showed a significant positive correlation with carbon source utilization, especially for amine (AM) and phenolic acid (PA) carbon source utilization (P &lt; 0.05) by means of RDA, and the utilization rate of AM and PA carbon sources by rice rhizosphere and non-root soil microorganisms was P1 &lt; P2 &lt; P3.

Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice.

A gammaproteobacterial methanotroph, strain GJ1T, was isolated from a rhizosphere soil sample of rice in Nanjing, China. The cells were Gram-negative, motile rods with a single polar flagellum, and they contained type I intracytoplasmic membranes. The cells formed pink colonies. The strain possessed both the particulate methane monooxygenase enzyme (pMMO) and the soluble methane monooxygenase enzyme (sMMO). pxmABC, encoding a divergent methane monooxygenase (pXMO), and nifH, which encodes dinitrogenase reductase, were also present. Methane and methanol were utilized as sole carbon sources, while other carbon sources, including acetate, pyruvate, succinate, citrate, malate, glucose, urea, methylamine, ethanol and formate, could not be utilized by strain GJ1T. Cell grew optimally at 25-33°C (range 16-37°C), pH 6.0-8.0 (range 5.5-8.5) and 0-1.2% NaCl (no growth above 1.5% NaCl). Phylogenetic analyses based on the 16S rRNA gene, pmoA and nifH showed that the isolate belongs to the genus Methylomonas of the family Methylococcaceae within the class Gammaproteobacteria. The major quinone was determined to be MQ-8, and the major fatty acids were observed to be C16:1 and C14:0. The genome size of strain GJ1T is about 4.55Mb, and the DNA G + C content of the strain was determined to be 53.67mol% within the range of the genus Methylomonas (47-58mol%) reported at present. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain GJ1T and Methylomonas koyamae Fw12E-YT among the genus Methylomonas were the highest, and they were only 74.66% and 21.40%, respectively. In consequence, results of phenotypic characterization and phylogenetic analyses support strain GJ1T as a novel species within the genus Methylomonas, namely, Methylomonas rhizoryzae sp. nov.. The type strain is GJ1T (= ACCC 61706).

Complete Genome Sequence of Rahnella aquatilis MEM40, a Plant Growth-Promoting Rhizobacterium Isolated from Rice Rhizosphere Soil, with Antagonism against Magnaporthe oryzae and Fusarium graminearum.

Rahnella aquatilis strain MEM40 is a plant growth-promoting rhizobacterium (PGPR) with antagonism against Magnaporthe oryzae and Fusarium graminearum that was isolated from rice rhizosphere soil in Hubei, China. Here, we report its complete genome sequence, which will increase our understanding of the mechanisms of plant growth promotion and biocontrol.

Dynamic analysis on weeds inhibition and phenolic acids of allelopathic rice in field test

ABSTRACT Weed suppression of allelopathic rice PI312777 (PI) and non-allelopathic rice Lemont (LE) at 3-, 5-, and 7-leaf stages were studied in field test. The results showed that inhibitory effect of rice rhizosphere soil (IR1), the soil aqueous extracts (IR2), and the mixture of phenolic acids of the soil extracts (IR3) were IR1 > IR2 > IR3. The same trend was observed in the content of total phenols (Ctp) and the phenolic acids (Cpa) in the soil aqueous extract. The qRT-PCR results showed that six genes related to biosynthesis of phenolic acids in rice leaves and roots of PI were up-regulated and the up-regulated multiplies were increased as leaf stage increased. However, four genes were up-regulated and two genes were down-regulated in rice leaves and roots of LE. The regulated multiplies were smaller in LE than that in PI. The correlation analysis showed that IR1, IR2, IR3, Ctp, and Cpa were positively correlated. There results indicated that rice allelopathic potential was enhanced in response of paddy weeds, which accompanied by up-regulation of genes in rice leaves and roots related to metabolism pathway of phenolic compounds and increase of phenolic allelochemicals in rice rhizosphere soil.