Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes.

Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2-6 hpi) and late (16-24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03193-4.

Cellular and proteomic events associated with the localized formation of smut-gall during Zizania latifolia-Ustilago esculenta interaction.

The perennial wild rice Zizania latifolia is confined in the swampy habitat and wetland of the Indo-Burma biodiversity hotspot of India and infection by the biotrophic fungus Ustilago esculenta is hallmarked by swellings that develop to form localized smut-gall at the topmost internodal region. The cellular and proteomic events involved in the non-systemic colonization of Z. latifolia by U. esculenta leading to smut-gall formation is poorly understood. Proteins were extracted from the smut-gall region at the topmost internodal region below the apical meristematic tissue from the infected and uninfected parts of Z. latifolia. By combining transmission electron microscopy (TEM) and fluorescent microscopy (FM), we showed that U. esculenta hyphal morphological transitions and movement occurred both intercellularly and intracellularly while sporulation occurred intracellularly in selective cells. Following proteome profiling using two dimensional SDS-PAGE at different phenological phases of smut-gall development and U. esculenta infection, differentially expressed proteins bands and their relative abundance were detected and subjected to liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis. Importantly, the fungus explores at least 7 metabolic pathways and 5 major biological processes to subdue the host defense and thrive successfully on Z. latifolia. The fungus U. esculenta produces proteases and energy acquisition proteins those enhance it's defensive and survival mode in the host. The identified differentially regulated proteins shed-light into why inflorescence is being replaced by bulbous smut-gall at late stages of the disease, as well as the development of resistance in some Z. latifolia plants against U. esculenta infection.

Mapping the Bacterial Community in Digboi Oil Refinery, India by High-Throughput Sequencing Approach.

Microbial enhanced oil recovery (MOER) is a technique which uses microbes to enhance the oil recovery process. This technique is advantageous to enhance oil recovery (EOR). In this study, we analyzed the bacterial communities of Digboi oil refinery and its surroundings using Illumina MiSeq sequencing platform. A total of 12 samples were analyzed, 6 from inside the refinery areas and another 6 from the township areas. Alpha diversity studies indicated that diversity of bacterial communities in township area was higher than the refinery areas except for Sample 1. Sample 9 from the nearby pond of Digboi Centenary Park was more diverse in community composition. Proteobacteria was found to be most dominant phylum. Mantel test indicated that environmental factors had negative influence over the bacterial community structure. Among the environmental factors Fe was least significant (r2 = 0.368) as indicated by canonical correspondence analysis.

Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang.

Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome.

Investigation on the biotrophic interaction of Ustilago esculenta on Zizania latifolia found in the Indo-Burma biodiversity hotspot.

Ustilago esculenta is a uniquely flavored biotrophic smut fungus that forms a smut gall on the top internodal region of Zizania latifolia, a perennial wild rice found in the Indo-Burma biodiversity hotspot. The smut gall is an edible vegetable locally called "kambong" in Manipur, India. The life cycle of the fungus was studied in vitro and its biotrophism was observed during different stages of the plant growth starting from the bud stage to decaying stage using light, fluorescent and electron microscopy. The size of the smut gall and the number of internodes below the apical smut gall varied significantly (P < 0.05). Examination of various parts of infected plants using culture methods, microscopy and polymerase chain reaction revealed that Ustilago esculenta colonized Zizania latifolia in a non-systemic manner. Spores and fragmented hyphae of U. esculenta were present in the rhizome of infected plant throughout the year, but shoot interiors were without any fungal structures from April until September. The smut region of infected plants in early September to December were heavily sporulated with fragmented hyphae, while the nodal regions of infected plants had no spores and fragmented hyphae. Hyphae and spores were also absent in the internodes and membranes aboveground up to smut region of infected plants but were present in the old rhizomes.

Biotrophic interaction of Sporisorium scitamineum on a new host--Saccharum spontaneum.

Sporisorium scitamineum is a biotrophic smut fungus harbored inside the smut gall on the top internodal region of Saccharum spontaneum, a wild relative of sugarcane (Saccharum officinarum). The interactions of spined conidia of S. scitamineum with S. spontaneum were examined during the different stages of plant growth starting from the bud stage to the decaying stage. The spores in the soil from the polyetic inocula grew into confined epidermal cells of the buds and finally sporulated in the topmost internodal region. Hyphae invasion of the plant tissues were restricted to the point of infection. Culms of infected plants in late October sporulated, notably; hyphal sporulation produced shorter hyphal stolons. Remarkably, the nodal regions of infected plants had no spores and fragmented hyphae. On the basis of microscopic analyses, hyphae and spores were absent in all internodes above the ground till the topmost smut gall region. This result indicated that, S. scitamineum undergoes tissue-confined invasion of S. spontaneum. By associating culture medium method with polymerase chain reaction (PCR) on plant portions void of smut gall, S. scitamineum was not detected, indicating that colonization was not systemic. It was observed that the biotrophic interaction resulted in structural reorganization in the restricted region of infection forming erect cylindrical structure, in which the fungus was sandwiched between the central stalk and sheath, and possibly played a key role in preventing inflorescence. Comparatively, a significant difference in the rate of teliospores germination between reference Ustilago esculenta (26.6%, P<0.05) and S. scitamineum (62.9%, P<0.05) at 20° C was observed. This study also provides insights on the effect of different temperature regimes on the germination of S. scitamineum teliospores in vitro.

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars.

In the present study, 217 rhizobacterial isolates were obtained from six different tea estates of Assam, India and subjected to preliminary in vitro plant growth promotion (PGP) screening for indole acetic acid (IAA) production, phosphate solubilization, siderophore production and ammonia production. Fifty isolates showed all the PGP traits and five isolates did not exhibit any PGP traits. These 50 potential isolates were further analyzed for quantitative estimation of the PGP traits along with the aminocyclopropane-1-carboxylate (ACC) deaminase, protease and cellulose production. After several rounds of screening, four rhizobacteria were selected based on their maximum ability to produce in vitro PGP traits and their partial 16S rRNA gene sequence analysis revealed that they belong to Enterobacter lignolyticus strain TG1, Burkholderia sp. stain TT6, Bacillus pseudomycoides strain SN29 and Pseudomonas aeruginosa strain KH45. To evaluate the efficacy of these four rhizobacteria as plant growth promoters, three different commercially important tea clones TV1, TV19, and TV20 plants were inoculated with these rhizobacteria in greenhouse condition and compared to the uninoculated control plants. Though, all the rhizobacterial treatments showed an increase in plant growth compared to control but the multivariate PCA analysis confirmed more growth promotion by TG1 and SN29 strains than the other treatments in all three clones. To validate this result, the fold change analysis was performed and it revealed that the tea clone TV19 plants inoculated with the E. lignolyticus strain TG1 showed maximum root biomass production with an increase in 4.3-fold, shoot biomass with increase in 3.1-fold, root length by 2.2-fold and shoot length by 1.6-fold. Moreover, two way ANOVA analysis also revealed that rhizobacterial treatment in different tea clones showed the significant increase (P < 0.05) in growth promotion compared to the control. Thus, this study indicates that the potential of these indigenous plant growth promoting rhizobacteria isolates to use as microbial inoculation or biofertilizer for growth promotion of tea crops.

Psychrotolerant antifungal Streptomyces isolated from Tawang, India and the shift in chitinase gene family.

A total of 210 Streptomyces were isolated from the soil samples of Tawang, India where temperature varied from 5 °C during daytime to -2 °C during the night. Based on antifungal activity, a total of 33 strains, putatively Streptomyces spp., were selected. Optimal growth temperature for the 33 strains was 16 °C, with growth occurring down to 6 °C but not above 30 °C. Phylogenetic analysis based on 16S rDNA sequences revealed the taxonomic affiliation of the 33 strains as species of Streptomyces. To examine the relatedness of the chitinase genes from six strong antifungal Streptomyces strains, a phylogenetic tree was constructed using the catalytic domain nucleotide sequences and resulted in seven distinct monophyletic groups. A quantitative PCR study for chitinase expressing ability revealed that of the six antifungal strains tested, the strain Streptomyces roseochromogenus TSR12 was the most active producer of family 18 chitinase genes. Streptomyces strains with enhanced inhibitory potential usually encode a family 19 chitinase gene; however, our present study did not show expression of this family in the six strains tested.

Phylogenetic analysis of alkaline proteinase producing fluorescent pseudomonads associated with green gram (Vigna radiata L.) rhizosphere.

Fifty fluorescent pseudomonads were isolated from rhizospheric soil of green gram from nearby area of Kaziranga, Assam, India and assayed for their extracellular proteinase production. Out of these isolates, 20 were found to be prominent in proteinase production. Genetic diversity of the 20 isolates were analyzed through BOX-PCR fingerprinting and 16S rDNA-RFLP along with three reference strains, viz., Pseudomonas fluorescens (NCIM2099(T)), Pseudomonas aureofaciens (NCIM2026(T)), and Pseudomonas aeruginosa (MTCC2582(T)). BOX-PCR produced two distinct clusters at 56% similarity coefficient and seven distinct BOX profiles. 16S rDNA-RFLP with three tetra-cutters restriction enzymes (HaeIII, AluI, and MspI) revealed two major clusters A and B; cluster A contained only single isolate FPS9 while the rest of 22 isolates belonged to the cluster B. Based on phenotypic characters and 16S rDNA sequence similarity, all the eight highly proteinase-producing strains were affiliated with P. aeruginosa. The proteinase was extracted from two most prominent strains (KFP1 and KFP2), purified by a three-step process involving (NH(4))(2)SO(4) precipitation, gel filtration, and ion exchange chromatography. The enzyme had an optimal pH of 8.0 and exhibit highest activity at 60°C and 37°C by KFP1 and KFP2 respectively. The specific activities were recorded as 75,050 (for KFP1) and 81,320 U/mg (for KFP2). The purified enzyme was migrated as a single band on native and SDS-PAGE with a molecular mass of 32 kDa. Zn(2+), Cu(2+), and Ni(2+) ion inhibited the enzyme activity. Enzyme activity was also inhibited by EDTA established as their metallo-proteinase nature.

Terpenoid compositions and antioxidant activities of two Indian valerian oils from the Khasi Hills of north-east India.

The volatile constituents of Valeriana jatamansi Jones and V. hardwickii Wall. (Valerianaceae) collected from the Khasi Hills of north-east India were analyzed by GC and GC/MS. Twenty-seven and twenty-one compounds were characterized and identified from V. jatamansi and V. hardwickii samples, representing 90.6% and 82.7% of the total oil, respectively. Sesquiterpenes were shown to be the main constituents in both the oil samples. Maaliol (26.1%), patchouli alcohol (9.3%) and a-gurjunene (8.7%) were the major components of V. jatamansi oil, whereas valeracetate (21.3%), methyl linoleate (14.1%), bornyl acetate (13.8%) and cuparene (7.1%) were the main constituents of V. hardwickii oil. Both Indian valerian essential oils were studied for their antioxidant activities using the free radical-scavanging activity (DPPH) and ferric reducing antioxidant power (FRAP) assays. V. hardwickii oil exhibited a higher antioxidant capacity than V. jatamansi in both assays. For both the valerian oil samples, there was a concentration-dependent increase in free radical scavenging activity and ferric reducing capacity. Both valerian oils and their ingredients are potential sources of natural antioxidants.