Rice Rhizosphere Soil Research Articles

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides.

Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

Effects of Cotton Stalk Biochar on the Structure and Function of Fungi Community in Alkaline Rhizosphere Soil of Rice Under Cadmium Pollution

To study the effects of cotton stalk biochar on the regulation of fungal diversity, the structure and function of alkaline rice rhizosphere soil under cadmium pollution was investigated. An outdoor pot experiment was conducted by adding cotton stalk biochar (0%, 1%, and 5%) to an alkaline paddy soil with a cadmium concentration of 0.1 and 8 mg·kg-1. Taking rice rhizosphere soil as the research object, Illumina HiSeq sequencing was used to analyze the effects of cotton stalk biochar and cadmium pollution on the diversity, structure, abundance, and function of fungi in an alkaline rhizosphere soil, and to explore the correlation between soil environmental factors and the fungal community under the control of cotton stalk biochar. The results showed that:① the application of cotton stalk biochar significantly increased the soil pH, available nutrients, and organic matter, and reduced the content of reducible cadmium in the soil (P<0.05). ② The distribution of rice rhizosphere soil fungi was mainly Ascomycota, Aphelidiomycota, and Chytridiomycota, which accounted for 57% of all mycophytes. The genus was mainly Mortierella, Alternaria, and Fusarium. There was a significant difference in the α-diversity of the fungal community among the treatments (P<0.05). In the absence of cotton stalk biochar (C0), the increase in the cadmium concentration reduced the relative abundance and fungal diversity index (Shannon index) of Chytridiomycota, Mortierella, and Alternaria in the soil. Under different concentrations of cadmium (Cd0, Cd1, and Cd8), increasing cotton stalk biochar reduced the fungal community richness index (Chao1 index) and Shannon index. Cadmium pollution resulted in an increase in the relative abundance of Chytridiomycota in the soil, but decreased the abundance of Alternaria. The application of cotton stalk biochar could significantly increase the relative abundance of Chytridiomycota (P<0.05). Cadmium pollution reduced the abundance of Mortierella and Alternaria, but the application of cotton stalk biochar could increase the relative abundance of Alternaria. Increasing cotton stalk biochar means that soil will have more endophytes, plant pathogens, and saprophytes; while increasing cadmium pollution will reduce endophytes, plant pathogens, and saprophytes in the soil. ③ The main environmental factors affecting the diversity and structure of fungal communities are the available potassium, organic matter, and pH of the soil. The reducible cadmium content, which comprises the largest proportion of cadmium in rice soil, was significantly positively correlated to Rotifera, Aphelidiomycota, and Ascomycota (P<0.05), but negatively correlated to other mycophytes (P<0.05). The results indicate that cotton stalk biochar plays a certain role in the microecological regulation of alkaline cadmium-contaminated soil.

Watering techniques and zero-valent iron biochar pH effects on As and Cd concentrations in rice rhizosphere soils, tissues and yield

Zero-valent iron amended biochar (ZVIB) has been proposed as a promising material in immobilizing heavy metals in paddy fields. In this study, the impacts of pH of ZVIB (pH 6.3 and pH 9.7) and watering management techniques (watering amount in the order of CON (control, 5/72)>3/72>1–3/72>3/100>1/72, with 5/72, for example, representing irrigation given to 5 cm above soil surface in 72 hr regular interval) on As and Cd bioavailability for rice and its grain yield (YieldBR) were investigated in a pot experiment. Brown rice As (AsBR) content was irrelative to the watering treatments, while significantly decreased (>50%) with the addition of both ZVIB materials. The diminutions of brown rice Cd (CdBR) content as well as the YieldBR were highly dependent on both the soil amendment materials’ pH and watering amount. Among all the watering treatments, 3/72 treatment (15% less irrigation water than the CON) with ZVIB 6.3 amendment was the optimum fit for simultaneous reduction of AsBR (50%) and CdBR contents (19%) as well as for significant increment (12%) of the YieldBR. Although high pH (9.7) ZVIB application could also efficiently decrease As and Cd contents in brown rice, it might risk grain yield lost if appropriate (e.g. 3/72 in our study) watering management technique was not chosen. Therefore, ZVIB would be an environmentally friendly option as an amendment material with proper selection of watering management technique to utilize As and Cd co-contaminated arable soils safely for paddy cultivation.

Endophytic Bacillus megaterium triggers salicylic acid-dependent resistance and improves the rhizosphere bacterial community to mitigate rice spikelet rot disease

Endophytes have been demonstrated to trigger salicylic acid-dependent resistance and alter rhizosphere bacterial communities. However, few comprehensive studies have been conducted to elucidate the interactions between the direct (systemic resistance) and indirect (rhizosphere microbiome) defenses triggered by endophytes. The present study aimed to illuminate the possible roles of endophytic Bacillus megaterium in rice resistance against rice spikelet rot disease (SRD), and to make inferences on the potential interactions between plant defenses and the rhizosphere microenvironment. An outdoor pot experiment was conducted to explore the degree to which endophytes mitigate disease in rice, where four combination treatments were designed (inoculation and non-inoculation with B. megaterium, and infection with and without Fusarium proliferatum). Rice plants and rhizosphere soil, at the heading stage, were sampled to measure the accumulation of defense-related enzymes, including L-phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), β-1,3-glucanase and chitinase, and to perform 16S rRNA Illumina sequencing. Defense-related enzyme activities in rice plants inoculated with B. megaterium showed local or systemic increases. Plant-beneficial bacteria were found to be enriched when rice plants were treated with the endophyte. A correlation between plant resistance and the rhizosphere microbiome was also observed. The present study highlights the significance of B. megaterium for plant defenses against SRD through dual mechanism — systemic resistance and rhizosphere microbiome. Inferences of this study elucidate correlations between plant defenses and the rhizosphere microenvironment, which were attributed to the presence of B. megaterium.

Water management impact on denitrifier community and denitrification activity in a paddy soil at different growth stages of rice

Rice is one of the largest water-consuming crops. Alternate wetting and drying (AWD) is now an effective water-saving practice for rice cultivation that has been widely applied across the world. AWD may increase denitrification loss. However, the underlying mechanism remains unclear. This study investigated denitrifier activity, abundance and community structure in the rice rhizosphere and bulk soil in response to water management at the internode elongation (IE) and flowering (F) stages. The results revealed that at the IE stage, AWD significantly increased denitrification capacity (DC) in the rhizosphere compared with continuously flooded practice (CF). DC was significantly and positively related to electrical conductivity (EC) and the abundance of nirS-harboring denitrifiers. AWD led to higher EC in the 0–20 cm soil layer than CF. Although AWD lowered nirS abundance by 15 % compared with CF, the activity of nirS-harboring denitrifiers was enhanced by 1.89-folds of CF. At the F stage, AWD significantly decreased DC relative to CF. AWD had lower dissolved organic carbon (DOC) than CF, and DOC was significantly correlated with DC. Compared with CF, AWD also markedly changed the structure and network stability of nirS and nirK communities, resulting in sharp decreases in the total number of links in nirK and nirS networks of rhizosphere. The soil pH and EC were the key factors shaping the structure of nirS and nirK communities. Overall, the increase in denitrification losses due to AWD occurred primarily at the IE rather than F stage, and this increase was attributed to a rise in EC and changes in the activity and structure of nirS community. These findings provide a new insight into the mechanism of impact of the water-saving practice on denitrification loss for rice cultivation.

Estimation and optimization of exopolysaccharide production from rice rhizospheric soil and its interaction with soil carbon pools

Exopolysaccharides (EPS) the high molecular weight microbial substances play an important role in enhancing soil aggregation as well as maintaining water holding capacity around the rhizosphere. Therefore, looking into the fact that rice is one of the important food crops for most of the people of the world and the ability of EPS to increase the uptake of nutrients by plants and protect from drought stress. The present investigation was carried out to study the EPS production by bacteria isolated from rice cultivar Naveen with four treatments viz., aerobic (−5 kPa), saturation (0 kPa), submerged (2 cm standing water) and control (without any water treatment) and their interaction with soil labile carbon pools. Soil (0–15 cm depth) was collected from panicle initiation stage of the crop growth to isolate EPS producing bacteria. Different parameters like microbial biomass carbon (MBC), readily mineralizable carbon (RMC) and organic carbon (OC) alongwith total and colloidal EPS were estimated. The total and colloidal EPS increased 26.0% and 9.0% among the treatments over saturation. The MBC, RMC and OC were found to increase 30.0%, 19.0% and 4.0% among the treatment over saturation. These findings indicated a positive correlation between carbon pools and total and colloidal EPS production. Similarly, in this study, 22 EPS producing bacteria were isolated from the rice rhizospheric region and amongst 4 isolates were found to tolerate maximum level of water stress (−0.73 MPa). Further, optimization studies indicated that all these 4 bacterial isolates produced EPS at 37 °C, 80 mM salt concentration and pH value 7.5 within 3 days of incubation. Further, among different carbon sources, sucrose followed by glucose was found to be best for production of EPS. Further work is going on to evaluate the efficacy of these potential EPS producing bacterial isolates under field conditions.

Rhodococcus oryzae sp. nov., a novel actinobacterium isolated from rhizosphere soil of rice (Oryza sativa L.).

A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67T, belonged to the genus Rhodococcus and formed a cluster with Rhodococcus maanshanensis DSM 44675T, Rhodococcus kronopolitis NEAU-ML12T and Rhodococcus tukisamuensis JCM 11308T (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C16 : 0, 10-methyl C18 : 0, C18 : 1 ω9c and C16 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H2). Whole-cell hydrolysates contained meso-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67T was 64.6 mol%. Strain NEAU-CX67T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with R. maanshanensis DSM 44675T (92.1 and 45.4 %) and R. tukisamuensis JCM 11308T (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67T is considered to represent a novel species of the genus Rhodococcus for which the name Rhodococcus oryzae sp. nov. is proposed. The type strain is NEAU-CX67T (=DSM 107701T=CCTCC AB 2018233T).

Microbial carbon source utilization in rice rhizosphere and nonrhizosphere soils with short-term manure N input rate in paddy field

Carbon (C) plays a vital role in regulating soil nutrient cycling and increasing soil microbial community, but there is still limited information on how C source utilization characteristics responds to soil physical and chemical properties changes under double-cropping rice (Oryza sativa L.) paddy field in southern China. Therefore, the effects of different short-term manure nitrogen (N) input rate managements on C source utilization characteristics in rice rhizosphere and non-rhizosphere soils under double-cropping rice field in southern China were studied by using 18O-H2O method. Therefore, a field experiment were established in Ningxiang city of Hunan Province, and five different fertilizer treatments were applied: (1) 100% N of chemical fertilizer (M0), (2) 30% N of organic manure and 70% N of chemical fertilizer (M30), (3) 50% N of organic manure and 50% N of chemical fertilizer (M50), (4) 100% N of organic manure (M100), and (5) without N fertilizer input as control (CK). The results showed that soil microbial biomass C content, soil microbial growth rate, and soil microbial basal respiration with application of organic manure treatments (M30, M50, M100) were significantly higher (p < 0.05) than that of CK treatment. And the soil C utilization efficiency with M0 treatment were significantly higher (p < 0.05) than that of M100 treatment. Compared with CK and M0 treatments, the metabolic capacity of soil microorganisms to exogenous C sources with M30, M50 and M100 treatments were increased. The largest types of exogenous C source was carboxylic acids, followed by amino acid and carbohydrate, and complex compounds was the smallest. The RDA analysis results indicated that fertilizer treatments significantly changed the utilization characteristics of soil microorganisms to exogenous C sources. As a result, this study found that characteristics of soil C source utilization were significantly affected by different short-term manure N input rate managements.

Burkholderia sp. Y4 inhibits cadmium accumulation in rice by increasing essential nutrient uptake and preferentially absorbing cadmium

Microbial remediation of heavy metal-polluted soil is a commonly used method. Burkholderia sp. Y4, isolated from cadmium (Cd)-contaminated rice rhizosphere soil, was investigated for its direct and indirect effects on Cd accumulation in rice by SEM-EDS, FITR and sequencing analysis of the soil bacterial community. Burkholderia sp. Y4 inoculation reduced Cd accumulation in rice roots, rachises, and grains of the two rice varieties T705 and X24 and increased levels of essential elements, especially Fe and Mn, which competitively inhibited Cd transport through cationic channels. Living Burkholderia sp. Y4 cells, rather than non-living ones, could colonize the surface of rice roots and accumulated more Cd through direct biosorption associated with –CO and –NH/−CO bonds of amino acids and proteins. The results of soil microbial community showed that the colonization of externally added Burkholderia sp. Y4 could be maintained over some time to impact the total rhizospheric environment. Burkholderia sp. Y4 inoculation decreased the abundance of microbes involved in the iron cycle (Acidobacteria) as well as of those mediating the transformation of ammonium nitrogen to nitrate nitrogen (Nitrosomonadaceae and Nitrospira). So Burkholderia sp. Y4 inoculation may indirectly change the availability of micronutrients and Cd in rice rhizosphere soil through iron-nitrogen coupled cycles to increase essential nutrient uptake and inhibit Cd accumulation in rice by preferential Cd-biosorption. Therefore, Burkholderia sp. Y4 is potentially suitable for the bioremediation of Cd-contaminated paddy soil.

Migration and transformation of cadmium in rice - soil under different nitrogen sources in polymetallic sulfide mining areas

We conducted pot experiments to assess the bioavailability of cadmium (Cd) in contaminated rhizosphere soil and accumulation in rice organs in response to nitrogen (N) supply ((NH4)2SO4, NH4NO3, NH4Cl). The results showed that the concentration of bioavailable Cd in rice rhizosphere soil was (NH4)2SO4 treatment > NH4Cl treatment > NH4NO3 treatment at the same level of N application and growth period; the Cd concentration in rice roots was (NH4)2SO4 treatment > NH4NO3 treatment > NH4Cl treatment; and the Cd concentration in rice straw was NH4NO3 treatment > NH4Cl. The Cd concentration in rice roots, straws, and seeds at the maturity stage was (NH4)2SO4 treatment > NH4Cl treatment. With the same N fertilizer, excessive N promoted Cd accumulation in rice at later growth stages. This suggested that sulfate (SO42−) influenced Cd concentration in rice. NH4Cl application maintained a low Cd level in different rice organs with the same N level. This confirmed that NH4Cl is a safe N source for rice planting in polymetallic sulfide mining areas. The study concludes that appropriate NH4Cl levels for Cd-contaminated paddy soil with high-S-content could obtain rice grains with Cd concentrations below the food safety standards (0.2 or 0.4 mg·kg−1).

Microbial carbon use efficiency, biomass turnover, and necromass accumulation in paddy soil depending on fertilization

Microbial anabolism relative to catabolism, reflected by the C use efficiency (CUE), determines the fate of C transformation in soil. Understanding how the microbial CUE and microbial necromass respond to fertilization is crucial for the evaluation of the C sequestration potential in intensively managed paddy soils. We examined the microbial CUE, microbial biomass turnover, and necromass accumulation in rice rhizosphere and bulk soils subjected to long-term (31 years) fertilizations: no fertilizers (control), mineral fertilizers alone (NPK), mineral fertilizers plus rice straw incorporation (NPK-Straw), and mineral fertilizers combined with a low or a high amount of organic manure (NPK-lowM or NPK-highM). The microbial CUE was determined by 18O incorporation into DNA. Microbial necromass accumulation was quantified by the biomarker analysis of amino sugars. Rice straw and manure incorporation reduced the microbial CUE in the rhizosphere soil, whereas the CUE remained constant in the bulk soil. CUE was lower in the rhizosphere soil than in the bulk soil due to nutrients uptake and root exudate release by rice plants, leading to a higher C/nutrient ratio in the rhizosphere. Organic inputs strengthened these rhizosphere processes and could thus weaken the relative potential of C sequestration. The microbial CUE decreased with the increase of the available C/N ratio in the rhizosphere but not in the bulk soil. The microbial CUE mainly depended on the respiration in the bulk soil and on the microbial growth in the rhizosphere soil, indicating the divergent microbial utilization of organic substrates between rhizosphere and bulk soils. In both rhizosphere and bulk soils, organic inputs promoted the microbial biomass growth rate and further increased the amount of microbial necromass by 27–52 % compared with NPK alone, which was highly correlated with the soil organic C pools. Despite enhancing rhizosphere respiration, our findings highlight that rice straw and manure applications increase C sequestration in paddy soils by enhancing the net flux of microbial biomass formation, and consequently promoting necromass accumulation.

Streptomyces oryziradicis sp. nov., a novel actinomycete isolated from rhizosphere soil of rice (Oryza sativa L.).

A novel actinobacterium, designated strain NEAU-C40T, was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and was characterized using a polyphasic approach. On the basis of results of 16S rRNA gene sequence analysis, strain NEAU-C40T belongs to the genus Streptomyces, and shares highest sequence similarities with Streptomyces polygonati CGMCC 4.7237T (97.9%) and Streptomyces abietis DSM 42080T (97.9%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Streptomyces. Cell walls contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose, rhamnose and ribose. The major menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16:0, anteiso-C15:0, C16:0 and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified lipid. The genomic DNA G+C content of strain NEAU-C40T was 71.8 mol%. Moreover, multilocus sequence analysis based on five other housekeeping genes (atp D, gyr B, rpo B, rec A and trp B) and the low level of DNA-DNA relatedness allowed the isolate to be differentiated from its most closely related strains. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-C40T can be characterized to represent a novel species of the genus Streptomyces, for which the name Streptomyces oryziradicis sp. nov. is proposed. The type strain is NEAU-C40T (=DSM 107943T=CCTCC AA 2018038T).

Sheath blight and drought stress management in rice (Oryza sativa) through Trichoderma spp.

Sheath blight of rice caused by Rhizoctonia solani Kuhn is a major rice diseases worldwide, and cause up to 50% yield losses depending upon its severity. Native biocontrol agents were isolated from rice rhizospheric soil of different region and NADEP compost. Fourteen strains of Trichoderma were isolated and screened in vitro against Rhizoctonia solani causing sheath blight of rice through dual culture technique. Among all tested isolates under in vitro conditions Trichoderma BHU-11, T-4 and BHU-8 showed the maximum inhibition for Rhizoctonia solani (71.48%, 67.28% and 63.89%, respectively). These strains of Trichoderma were also taken for checking drought tolerance in rice crop. Trichoderma strains when applied as seed + root dip treatment showed reduction of disease incidence. It also acted as plant growth promoter and increased the number of tillers/hill, plant height and yield of the crop. Trichoderma alters the drought response including drought avoidance through different morpho-physiological and biochemical adaptations, and enhanced drought recovery. The root colonization by Trichoderma increased the growth of roots and plant productivity. Biochemical studies showed the ability of Trichoderma BHU-11, T-4 and BHU-8 to produce high level phenol and proline contents in Trichoderma treated stress challenged plants and higher accumulation of chlorophyll in Trichoderma treated plants.

Cadmium-resistant rhizobacterium Bacillus cereus M4 promotes the growth and reduces cadmium accumulation in rice (Oryza sativa L.)

Rice farmland cadmium pollution is an increasing problem for food safety. Cd-resistant bacterial strain was isolated from rice rhizosphere soil and identified as Bacillus cereus M4. Treatment with M4 fermentation broth increased rice seedlings growth in vermiculite, while reduced Cd accumulation in grains of rice grown in Cd-contaminated potted soil from 0.309 to 0.186 mg/kg. Indoleacetic acid (IAA) was detected in M4 metabolites and in potted soil solutions supplemented with M4 broth. M4 broth increased the abundance of Bacillus from 0.54% to 0.95% and changed the soil bacterial community composition. These findings indicate that M4 promotes rice growth by secreting IAA and altering the rhizospheric soil microenvironment, via soil solution composition and microbial community, which may affect Cd translocation from soil to rice roots, thereby decreasing grain Cd accumulation. Therefore, B. cereus M4 is potentially suitable for the bioremediation of Cd-contaminated paddy soils.

Study on the efficiency of free-living nitrogen fixing bacteria isolated from rice rhizospheresoil on auxin and giberellin production

Study on the efficiency of free-living nitrogen fixing bacteria isolated from rice rhizospheresoil on auxin and giberellin production

Dissipation of chlorantraniliprole in contrasting soils and its effect on soil microbes and enzymes

An experiment was set up to determine the rate of dissipation of chlorantraniliprole (CTP) from two soils with contrasting properties. The other objective of the study was to find out the effect of CTP on soil microorganisms (population, microbial biomass carbon and soil enzymes) under controlled environment. CTP residues when applied at recommended dose ((RD) (at 40 g a.i./ha)) could not be recovered either from alluvial soil or red soil at 60 days post application of CTP in a microcosm study. Higher clay content led to higher half-life in alluvial soil compared to red soil. CTP could not be recovered from RD treatment at 30 days after pesticide application under controlled environment. Faster dissipation of CTP was observed in rice rhizosphere soil with 23.89 and 34.65 days dissipation half-lives for RD and double the recommended dose (DRD) treatments, respectively. Different doses of chlorantraniliprole did not have considerable negative effect on actinomycetes, fungi, biological nitrogen fixers and phospahte solubilising bacteria except the bacteria population. Among the treatments, DRD recorded the lowest activity of dehyrodeganse, fluoresein diacetate hydrolase, acid and alkaline phosphatases followed by RD treatment. Microbial biomass carbon, β –glycosidase and urease did not vary significantly among the different doses of CTP. In general, RD did not have negative effcts on soil microbes. Hence, CTP can be recommeded in rice pest managment maintaining existing soil microbes and soil enzymes activity.

Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization

Urea is widely used in rice farming systems to improve the nitrogen (N) availability and crop yield, yet its influence on CH4 emissions remains unclear. The present study aimed to identify the potential microbial mechanisms resulting in the N fertilizer-induced effects on CH4 emissions from paddies. A field experiment was conducted with (N1, 100 kg N ha−1) and without (N0) N fertilization. CH4 emission rate was measured every 3–7 day using the static chamber-gas chromatography method. Quantitative PCR (qPCR) and Illumina MiSeq sequencing approaches were employed to investigate the community composition and structure of methanogenic archaea and methanotrophic bacteria in rice rhizosphere soil at three time points (tillering stage 17d, heading stage 47d and mature stage 67 d). Urea application significantly stimulated the CH4 emissions from paddies, partially due to the decrease of redox potential (Eh) around the root region and the reduction of dissolved oxygen (DO) concentration at the soil-water interface. qPCR indicated a sharp increase in methanogenic archaeal 16S rRNA and methanotrophic bacterial pmoA gene copies with urea fertilization. Next-generation sequencing of these amplicons revealed that the diversity of both methanogenic and methanotrophic communities was decreased by urea input. Additionally, urea fertilization stimulated the genera Methanoregula (methanogen) and Methylococcus (type I methanotrophs) and inhibited the genus Methylocystis (type II methanotrophs). Urea fertilization changed oxygen state of the paddy soil and water and thus changed the community structure of methanogens and methanotrophs, which resulted in increased CH4 emissions.

Phenolic acids and terpenoids in the soils of different weed-suppressive circles of allelopathic rice

ABSTRACTAllelopathic rice ‘PI312777’ (PI) and non-allelopathic rice ‘Lemont’ (Le) were used to assess phenolic acids and terpenoids in the soils of different circles using inhibitory-circle method. The rhizosphere soils of rice (inner circle) and barnyard grass at a 12 cm distance from rice (outer circle) were collected for analyses. The results showed total content of phenolic acids in outer circle of PI was significantly higher than that of Le, while the outer soil of PI contained a higher total content of benzoic acid derivatives and a lower total content of cinnamic acid derivatives than the inner soil. Total terpenoid and monoterpene contents in inner and outer circle soils of PI were significantly higher than that of Le, and the ratio of oxygenated monoterpenes in outer soil of PI was higher than that of Le. Furthermore, phenolic acid mixtures showed a more obvious inhibitory effect on root length than on shoot length of the receptor, while oxygenated monoterpenes were opposite, and a low concentration of oxygenated monoterpenes enhanced inhibitory effect of phenolic acids mixtures on shoot length of the receptor. All results suggested oxygenated monoterpenes participated in the weed-suppressive effect together with phenolic acids of allelopathic rice.

Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management.

Carbon (C) plays an important role in the interaction between plant and rhizosphere microbial communities, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under the double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term (33 years) fertilizer regimes on the characteristics of C utilization in both rhizosphere and nonrhizosphere soils under double-cropping rice fields in Southern China were investigated by using the metagenome sequencing technology. The experiment began in 1986, and included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter, and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and nonrhizosphere soils was increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira was promoted by application of inorganic fertilizers. The largest group of clusters of orthologous groups of proteins categories was "amino acid transport and metabolism" with 16.46% unigenes, followed by "general function prediction only" (12.23%). Regarding the gene ontology categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%), and molecular function (110 353, 29.26%). The principal coordinate analysis indicated that different parts of the root zone were the most important factors affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significant effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices significantly increases the C source utilization of soil microorganisms in double-cropping rice fields.

Microbial Carbon Source Metabolic Profile in Rice Rhizosphere and Non-rhizosphere Soils with Different Long-term Fertilization Management

Rhizosphere and non-rhizosphere soil samples under different long-term fertilization treatments including control without fertilizer (CK), chemical fertilization alone (NPK), rice residues combined with NPK (NPKS), 30% manure plus 70% chemical fertilizers (LOM), and 60% manure plus 40% chemical fertilizers (HOM) were collected from a paddy field in a red soil hilly area in Ningxiang City, Hunan Province, China. The characteristics of microbial carbon utilization in the soils were studied. Results of 18O-H2O tracer analysis showed that both soil microbial biomass carbon content (MBC) and microbial growth rate (CGrowth) were highest in the HOM treatment, whereas they were lowest in CK. In the rhizosphere soil, the highest basal respiration was observed in HOM, and the lowest values were in CK and NPK. Microbial carbon utilization efficiency (CUE) was highest in NPK but lowest in the LOM and HOM treatments. In non-rhizosphere soil, no significant differences between basal respiration and CUE were observed among the fertilization treatments. Results from MicroRespTM showed that the ability of microorganisms to metabolize exogenous carbon sources was higher in non-rhizosphere soil than in rhizosphere soil. The application of organic materials (rice residues or manure) increased the microbial metabolic rate of carboxylic acids, amino acids, and carbohydrates in the order carboxylic acids > amino acids and carbohydrates > complex compounds. Redundancy analysis of the microbial metabolism patterns of various carbon substrates showed that:① CK was well separated from the fertilization treatments; ② NPK was grouped with NPKS, whereas LOM and HOM were grouped together and were separate from NPK and NPKS. This indicates that the fertilization treatments changed the microbial carbon metabolism patterns. The above-mentioned results indicated that the fertilization treatments did not affect microbial CUE and basal respiration. However, exogenous carbon source input (such as root exudates) and the application of organic materials can increase microbial basal respiration, and thus, reduce microbial CUE.