Rhizosphere Of Rice Plants Research Articles

Mechanisms of N-doped microporous biochar decreased Cd transition in rhizosphere soils and its impact on soil bacterial community composition

Soil cadmium (Cd) contamination has garnered considerable attention. This study employed batch sorption experiments and rhizobox experiments to examine the impact of nitrogen-doped microporous biochar (NBB) on the temporal and spatial distribution of Cd in the rhizosphere of rice plants, with the aim of elucidating the underlying mechanisms. The results indicated that the adsorption of Cd(II) onto NBB was predominantly governed by chemical reactions. When applied to soil, the NBB significantly hindered the migration of Cd from the bulk soil to the rhizosphere. Additionally, the application of NBB decreased the redox potential (Eh) in the rhizosphere soil and increased the relative abundance of Anaeromyxobacteraceae, Geobacteraceae, Desulfurisporaceae, and Syntrophomonadaceae, which could facilitate the reduction of soil Cd availability. Furthermore, the NBB2 treatment encouraged the formation of iron plaque on the root surface, thereby limiting the uptake of Cd from the soil into the root system. Moreover, the N-doped microporous biochar treatment resulted in lower Cd levels in the stele of root, an effect that was associated with increased sulfur (S) content in the stele and epidermis, suggesting a potential role for S in Cd sequestration. Ultimately, the application of N-doped microporous biochar resulted in diminished Cd accumulation in the rice tissues.

Biocontrol Potential of Rhizosphere Fungi Against Pyricularia Oryzae in Ciherang Rice Variety

Blast disease is an important disease of rice caused by Pyricularia oryzae. The use of antagonistic fungi from the rhizosphere of rice plants has the potential to control plant pathogens. One of them is from the genus Aspergillus. This research aims to test the ability of Aspergillus genus fungi in suppressing the intensity of P. oryzae attack on ciherang rice varieties. The research methods were isolation and identification of rhizosphere fungi, propagation of P. oryzae, antagonistic test of rhizosphere fungi against P. oryzae in vivo, and reisolation of fungi from rice plant tissues. This research used a completely randomised design (CRD) consisting of 9 treatments and 3 replications. Data obtained from this research were statistically analysed using analysis of variance (ANOVA) and Tukey's honest significant difference test at the 5% level The results showed that Aspergillus sp1 and Aspergillus sp2 fungi could significantly reduce the intensity of blast disease attack caused by P. oryzae isolates from Moncongloe and Simbang regions..

Identification of plant growth promoting antagonistic bacteria against blast disease of rice

This study aimed to isolate and identify plant growth-promoting bacteria from rhizosphere of rice plants that exhibit antagonistic properties against Magnaporthe oryzae, the causal agent of blast disease. Bacteria were isolated from the surface of rice leaves, stems, and soil attached to the roots. The antagonistic activity of the isolated bacteria was assessed using a dual culture method, and identities were determined through 16S rDNA sequencing. To evaluate their growth-promoting abilities, assays were conducted to measure indole acetic acid (IAA) production, siderophore secretion, hydrogen cyanide (HCN) production, and phosphate solubilization. The results revealed that Bacillus subtilis, identified as BDISO_01R, exhibited antagonistic behavior and the maximum inhibition of M. oryzae (81.00%) was obtained by bacterial isolate BDISO-01R. Additionally, eight bacterial isolates demonstrated IAA production, sixteen isolates produced siderophores, and nine isolates displayed phosphate solubilization capability. This research sheds light on the diverse microbial arsenal that can potentially promote rice growth while combating blast disease. Bangladesh J. Nuclear Agric, 37(1): 63-79, 2023

Biocontrol efficacy of Burkholderia pyrrocinia S17-377 in controlling rice sheath blight

Rice sheath blight, caused by Rhizoctonia solani, is a major disease of rice that significantly affects rice production. To find sustainable and effective methods to control this disease, biocontrol strains have emerged as a promising solution. In this study, a total of 28 strains were screened from the rhizosphere of rice plants in order to identify strains that are effective against rice sheath blight. Among these strains, strain S17-377 showed remarkable antifungal activity, resulting in a 10 mm diameter inhibitory band against R. solani. Furthermore, it exhibited a wide range of antimicrobial properties in vitro. Through genetic analysis using the 16S rDNA and recA genes, strain S17-377 was identified as Burkholderia pyrrocinia. Importantly, it was found to be non-pathogenic to onions and did not possess the virulence genes BCESM and cblA. Therefore, this strain is safe for both people and plants. The strain S17-377 showed an efficacy of 64.81% and 55.78% in controlling rice sheath blight in pot experiments and field trials, respectively. Strain S17-377 displayed persistent colonization ability in rice plants for up to 30 days after inoculation. It also induced the expression of several rice plant genes, including NH1, PR1a, PR10, PAL/ZB8, LOX, and AOS2, as well as enzymes such as POD, PPO, and PAL. Additionally, S17-377 produced proteases, chitinases, non-volatile metabolites, and biofilms. In terms of disease control, the aseptic fermentation solution of S17-377, when diluted with PDA medium at ratios of 1:20, 1:10, and 1:5, exhibited inhibition rates of 77.14%, 86.92%, and 98.26%, respectively, against R. solani. S17-377 also had noticeable effects on the expansion and collapse of fungal mycelium. Moreover, the bacterial culture filtrates(BCF) of S17-377 demonstrated high thermal stability with an inhibition rate of 96.16%, even after being subjected to a temperature of 121 °C for 30 min. The BCF of strain S17-377 exhibited significant inhibition of R. solani, with inhibition rates of 95.23%, 94.43%, and 75.11% for the n-butanol, crude protein, and crude lipopeptide extracts, respectively. Further analysis of the n-butanol extract using liquid chromatography-mass spectrometry (LC-MS) identified eight compounds with potent antibacterial activity. These findings highlight the potential of strain S17-377 as a biocontrol agent for the management of rice sheath blight.

Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.

Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.

CHARACTERIZATION AND EVALUATION OF ANTIFUNGAL POTENTIAL OF BACTERIAL ENDOPHYTES OF RICE AGAINST FUSARIUM MONILIFORME AND RHIZOCTONIA SOLANI

Rice (Oryza sativa L.) is one of the most important staple food crop of Pakistan as well as in the whole world. A number of phyto-pathogens including bacteria, fungi, nematodes and viruses along with abiotic stresses such as drought, salinity, nutrient deficiency and etc. have a detrimental effect on rice yield. In order to overcome the attack of pathogenic microbes, use of endophytes as bio-control agent is an attractive way to minimize the use of toxic agrochemicals. In this study, we screened seven strains of bacterial endophytes from the rhizosphere of rice plants. A colony PCR was performed using universal primers to characterize the isolated bacterial endophytes followed by sequence analysis. On the basis of molecular characterization, endophytes were identified as Pantoea sp., Burkholderiasp Bacillus megaterium, Pseudomonas flourescens, Lysinibacillus fusiformis, Delftia sp., and Acinetobacter baumnii. Additionally, endophytes were assayed for In vitro effects against Fusarium moniliforme and Rhizoctonia solani causing bakanae and sheath blight disease of rice, respectively. Pantoea sp., Burkholderia sp., Bacillus megaterium and Delftiasp moderately suppressed Fusarium moniliforme but Pseudomonas flourescens, Lysinibacillus fusiformis both showcased a strong inhibiting activity against Fusarium moniliforme. On the other hand, Pantoea sp., Burkholderia sp., Bacillus megaterium, Pseudomonas flourescens and Lysinibacillus fusiformis had a strong inhibitory effect against Rhizoctonia solani. The isolated endophytic bacteria were also found to be good producers of phyto-hormones such as hydrogen cyanide (HCN) and catalase. On the basis of our results, we conclude that the endophytic bacteria from rice rhizosphere possess antifungal activity against economic important pathogenic fungi.

Isolation and molecular identification of halotolerant diazotrophic bacteria from The Northern Coastal of Pemalang, Central Java, Indonesia

Abstract. Purwanto, Oktaviani E, Leana NWA. 2022. Isolation and molecular identification of halotolerant diazotrophic bacteria from The Northern Coastal of Pemalang, Central Java, Indonesia. Biodiversitas 23: 5814-5821. Plant Growth Promoting Bacteria can fix nitrogen, a very important macronutrient for plant growth. However, the application of urea as a source of this macronutrient has a negative impact on the environment. Therefore, developing biofertilizers using N-fixing bacteria is an environmentally friendly technology. Therefore, this research aimed to isolate and analyze the diversity of N2-fixing bacteria from saline rice fields. The soil samples were taken from the rhizosphere of rice plants in Nyamplung Sari Village, Petarukan District, Pemalang Regency. Meanwhile, 9 (nine) isolates of nitrogen-fixing bacteria have been isolated, which can fix N2. The isolates can bind to N2, but only a few can produce IAA. The nitrogen-fixing ability of diazotrophic bacteria ranged from 17.85 ppm to 29.05 ppm. Isolate Jn3 has the highest ability to fix nitrogen, reaching 29.05 ppm, while Jn3, J, J12, J5, Kn1, and A3 can produce IAA with values of 2.00, 2.69, 2.22, 1.76, 3.47, and 1.79 ppm, respectively. Based on the 16S rRNA analysis and phylogeny construction, the isolated bacteria were identified in 3 (three) clusters. The first cluster was identified as Pseudomonas stutzeri and Acinetobacter junii (Kn1 and Jn3), while the second was identified as Bacillus cereus, Bacillus tropicus, Bacillus altitudinis, and Bacillus subtilis (Jn, Jn1, A3, and K3 isolates). The third cluster was identified as Bacillus pumilus, Acinetobacter baumanii, and Acinetobacter schindleri (J12, J5, and J). In addition, our study reported the findings of Acinetobacter baumannii and Acinetobacter schindleri species that can fix nitrogen.

An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth.

Rice is a symbol of life and a representation of prosperity in South Korea. However, studies on the diversity of the bacterial communities in the rhizosphere of rice plants are limited. In this study, four bundles of root samples were collected from the same rice field located in Goyang, South Korea. These were systematically analyzed to discover the diversity of culturable bacterial communities through culture-dependent methods. A total of 504 culturable bacteria were isolated and evaluated for their plant growth-promoting abilities in vitro. Among them, Arthrobacter sp. GN70 was selected for inoculation into the rice plants under laboratory and greenhouse conditions. The results showed a significantly positive effect on shoot length, root length, fresh plant weight, and dry plant weight. Moreover, scanning electron microscopic (SEM) images demonstrated the accumulation of bacterial biofilm networks at the junction of the primary roots, confirming the root-colonizing ability of the bacterium. The strain also exhibited a broad spectrum of in vitro antimicrobial activities against bacteria and fungi. Here, we first report the rice plant growth-promoting ability of the Arthrobacter species with the biofilm-producing and antimicrobial activities against plant and human pathogens. Genome analyses revealed features attributable to enhance rice plant growth, including the genes involved in the synthesis of plant hormones, biofilm production, and secondary metabolites. This study revealed that the rhizobacteria isolated from the roots of rice plants have dual potential to be utilized as a plant growth promoter and antimicrobial agent.

Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Identification of endophytic and rhizosphere bacteria in rice (Oryza sativa L.) in the experimental field at Payakumbuh State Agriculture Polytechnic, West Sumatra, Indonesia

The decrease of soil fertility and fewer soil microorganisms will lower crop production, particularly rice, thus threatening the national food security program. This study is (a) to isolate and identify the bacteria in the endophytic and rhizosphere of rice plants (b) to study the bacteria from the endophytic and rhizosphere of rice plants which potentially stimulate plant growth. The experiment was carried out at the Laboratory of Food Crop Cultivation at Payakumbuh State Agriculture Polytechnic, Limapuluh Kota Regency, West Sumatra for four months. The sampling method was carried out by random sampling at rice planting in the Payakumbuh State Agriculture Polytechnic Experimental Field. Endophytic bacteria were taken from the root tissue of rice plants, and rhizosphere bacteria were taken from a layer of soil around rice roots. Isolation of bacteria was carried out by using the pour plate and scratchplate methods. Four bacteria were identified using the 16S rRNA sequencing method. The identification results showed that in the rice root tissue found the bacteria Chromobacterium rhizoryzae and Brevibacillus brevis. In the rice rhizosphere, Bacillus pseudomycoides and Bacillus thuringiensis are found. Bacteria are dominated by the Bacillus genera which can stimulate plant growth.

Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants.

A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4-95.6%), Aquabacterium (95.9-95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30°C in the presence of 1-6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8-76.3% and 19.4-21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosusgen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711T = NBRC 114717T).

Limnohabitans radicicola sp. nov., a slow-growing bacterium isolated from rhizosphere of rice plant and emended description of the genus Limnohabitans.

In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859T (98.2%) followed by Limnohabitans curvus KCTC 42562T (98%), Limnohabitans planktonicicus II-D5T (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2DT (97.4%). Growth of strain JUR4T occurred at 10-37 °C (optimum, 30 °C), at pH 5.5-8.0 (optimum, 6.5-7) and in the presence of 0-0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4T was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4T and closely related reference strains were 21.0-24.8% and 74.7-81.4%, respectively. Strain JUR4T contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C16:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4T represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4T (=KACC 21745T=NBRC 114484T).

Fuscibacter oryzae gen. nov., sp. nov., a phosphate-solubilizing bacterium isolated from the rhizosphere of rice plant.

An ovoid to rod shaped, white to brown pigmented, facultative anaerobic, mesophilic, non-phototrophic, Gram-staining-negative, non-motile, multiply by binary fission designated strain KVB23T, which was isolated from root of rice plant, near Ilsan, South Korea, was investigated for its taxonomic position by polyphasic approach. Optimal growth was found to occur at 30˚C, at pH 6.5 and in the absence of NaCl on R2A. Phylogenetic analysis based on the 16S rRNA gene sequence of strain KVB23T revealed that it formed a distinct lineage, as a separate deep branch within the family Rhodobacteriaceae, with < 96.5% sequence similarity to representatives of the genera Rhodobacter, Xinfangfangia, Tabrizicola, Falsirhodobacter, Haematobacter, Paenirhodobacter, Pseudorhodobacter and Pararhodobacter. Based in 16S rRNA sequences strain KVB23T was most closely related to Tabrizicola fusiformis KCTC 62105T (96.5%) and Rhodobacter thermarum KCTC 52712T (96.2%). The draft genome of strain KVB23T was 3.80bp long with a DNA G + C content of 63.1%. Genome of strain KVB23T harboured gene clusters for tryptophan and cobalamin biosynthesis. The strain contained Q-10 as the sole respiratory quinone. The predominant fatty acids were found to consist of C16:0, C18:0 and summed feature 8 (comprising C18:1 ω7c and / or C18:1 ω6). The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, seven unidentified phosphoglycolipids, two unidentified aminophosphoglycolipid, one unidentified glycolipid and four unidentified lipids. Phosphate-solubilizing bacteria have the ability to dissolve insoluble phosphates and enhance the soil fertility. Strain KVB23T can solubilize calcium phosphate tribasic. Phosphate solubilizing and tryptophan biosynthesis property of strain KVB23T could be a possible factor for the increase in growth of rice plant. Differential phenotypic, chemotaxonomic and genotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain KVB23T was found to represent a novel genus in the Rhodobacteriaceae family, for which the name Fuscibacter oryzae gen. nov., sp. nov. is proposed, with the type strain KVB23T(= KACC 21711T = NBRC 114716T).

Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant.

A novel fibrillar matrix-producing, rod-shaped, red-orange, asporogenous, aerobic bacterium, designated DK36T, was isolated from roots of a rice plant in the Ilsan region near Dongguk University, South Korea. Cells of strain DK36T were Gram-stain-negative and motile by means of gliding. The temperature and pH ranges for growth were 7-35 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7.0). The strain did not require NaCl for growth but tolerated up to 8 % (w/v) NaCl. Phylogenetic anlaysis of the 16S rRNA gene sequence revealed that DK36T formed a monophyletic clade with Adhaeribacter aerophilus 6425 S-25T, Adhaeribacter aerolatus 6515 J-31T and Adhaeribacter swui 17mud1-7T with sequence similarities of 96.3, 95.5 and 95.2%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values of strain DK36T with the most closely related strains whose whole genomes are publicly available were 72.5-83.6% and 19-28 %, respectively. The strain showed the typical chemotaxonomic characteristics of the genus Adhaeribacter, with the presence of menaquinone MK-7 as the respiratory quinone, and C16 : 1ω5c, iso-C15 : 0 and summed feature 4 (composed of iso-C17 : 1 I/anteiso-C17 : 1 B) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminophosphoglycolipid, one unidentified phospholipid, two unidentified aminolipids and five unidentified polar lipids. The genomic DNA G+C content based on the draft genome sequence was 43.4 mol%. The results of physiological and biochemical tests and 16S rRNA gene sequence analysis clearly revealed that strain DK36T represents a novel species of the genus Adhaeribacter, for which the name Adhaeribacter rhizoryzae sp. nov. is proposed. The type strain is DK36T (=KACC 19902T=NBRC 113689T).

Genome Sequence of Pantoea sp. Strain 1.19, Isolated from Rice Rhizosphere, with the Capacity To Promote Growth of Legumes and Nonlegumes

ABSTRACTPantoea sp. 1.19, a plant growth-promoting bacterium (PGPB), was isolated from the rhizosphere of rice plants in Spain. Its genome, estimated at 3,771,065 bp, encodes 3,535 coding sequences (CDSs), carrying genes for synthesis of auxins, homoserine lactones, enzymes, siderophores, and quorum sensing. Several CDSs emphasize its biotechnological potential as an agriculture inoculant.

Molecular Diversity Assessment of Plant Growth Promoting Rhizobacteria Using Denaturing Gradient Gel Electrophoresis (DGGE) of 16s rRNA Gene

The rhizobacteria were isolated from rhizosphere of rice plant of different fields of 4 districts of Nepal and 5 districts of Bihar and Uttar Pradesh, adjoining states of India with Nepal. The DGGE analysis was performed for diversity analysis. For the construction of dendrogram, 16S rRNA gene was amplified by two different sets of primers. The DGGE ladder consisting of PCR amplified products of nine pure bacterial cultures were obtained. The first DGGE ladder was prepared by 400 bp fragment of 16S rDNA with GC clamp and the second DGGE ladder was prepared with 200 bp fragment of 16S rDNA with GC clamp. The perpendicular DGGE of these amplicons based on their melting behavior clearly demonstrated separation of different isolates. The 16S rDNA fragment amplified with primer set of V2-V3 regions with GC clamp showed separation between 40-60% of denaturant. The DGGE profile based on primer set F352T and 519r for various bacteria present in soil samples of 5 districts of India and 4 districts of Nepal revealed that the number of bands which might be specific for diazotrophic isolates varied from 2 to 11. The dendrogram constructed based on DGGE profile of various samples of 5 districts of India and 4 districts of Nepal showed that all the samples could be clustered in nine groups with 58-96% similarity to each other. Among all these 37 samples, only Var-4 and Var-5 showed 100% similarity, no other samples from any site showed 100% similarity. Int. J. Appl. Sci. Biotechnol. Vol 5(1): 72-80

Microbial Community Structure in the Rhizosphere of Rice Plants.

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.

Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon.

Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment.

Morfología y bioactividad de la cianobacteria Leptolyngbya en los campos de cultivo de arroz

The genus Leptolyngbya comprises filamentous cyanobacteria that are important in rice fields. In the rhizosphere, cyanobacteria produce a variety of secondary metabolites such as auxins that are important in agriculture soil performance. To assess this, Leptolyngbya strain MMG-1, was isolated from the rhizosphere of rice plants and described. For this, the morphology of this strain was studied by light microscopy as well as by confocal laser scanning microscopy. Besides, the ability of this strain to synthesize an auxin-like bioactive com- pound was demonstrated under various culture conditions (different amounts of tryptophan; pH; different alter- nating light:dark periods; duration of the incubation). The auxin-like compound was extracted from the culture of Leptolyngbya strain MMG-1 and identified as indole-3-acetic acid (IAA) by thin layer chromatography (TLC) as well as by high performance liquid chromatography (HPLC). Our results showed that the strain required the precursor L-tryptophan for the synthesis of IAA. Leptolyngbya strain MMG-1 accumulated IAA intracellularly. The IAA secreted by Leptolyngbya strain MMG-1 was significantly correlated with the initial concentration of L-tryptophan in the medium, as well as with the duration of the incubation. The bioactivity of the secreted IAA was determined by its effect on the rooting pattern of Pisum sativum seedlings. The culture supernatant of Leptolyngbya strain MMG-1 stimulated the seedling lateral rooting, while it decreased root length. Hence, rhizospheric Leptolyngbya produced auxin under different conditions and affected the plants rooting pattern.

Beneficial rhizobacteria from rice rhizosphere confers high protection against biotic and abiotic stress inducing systemic resistance in rice seedlings

The present study reports a screening for PGPR in a highly selective environment, the rhizosphere of rice plants, in southwestern of Spain. Among the 900 isolates, only 38% were positive for at least one of the biochemical activities to detect putative PGPR. The best 80 isolates were selected and identified by 16S rRNA partial sequencing. Among these, 13 strains were selected for growth promotion assays. Only one strain (BaC1-38) was able to significantly increase height, while nine strains significantly inhibited it. Five strains significantly increased dry weight, and only BaC1-21 significantly decreased it. Based on significant modifications in growth, three bacteria (BaC1-13, BaC1-21 and BaC1-38) were tested for systemic induction of resistance against stress challenge (salt and Xanthomonas campestris infection). Protection against salt stress and pathogen infection was similar; BaC1-38 protected by 80%, BaC1-13 by 50% and BaC1-21 only by 20%. Toxicity of salt stress to the plants was evaluated by photosynthetic efficiency of seedlings. Fv/Fm only decreased significantly in plants inoculated with BaC1-13. ΦPSII also decreased significantly in plants inoculated with BaC1-21, but increased significantly with BaC1-38. NPQ decreased significantly in plants inoculated with BaC1-21. The two strains able to induce systemic resistance against Xanthomonas campestris seem to work by different pathways. BaC1-13 primed enzymes related with the detoxification of reactive oxygen species (ROS). However, BaC1-38 primed pathogenesis-related proteins (PRs), and this pathway was more effective, both improved chlorophyll index confirming the priming state of the plant.