High-Quality Genome Resource of Ustilaginoidea virens (UV2_4G), Causal Agent of an Emerging False Smut Disease in Rice.

Ustilaginoidea virens is the fungal pathogen causing an emerging false smut disease that affects crop yield as well as deteriorates quality of the grains by producing mycotoxins. A high quality genome of U. virens isolate UV2_4G was sequenced using Nanopore and Illumina HiSeq 2,000 sequencing platforms. The total assembled genome of Indian isolate UV2_4G was 35.9 Mb, which comprised 89 scaffolds with N50 of 700,296 bp. A total of 358,697 variants were identified in the genome, out of which 355,173 were SNPs and 3,524 were INDELS. Further, 7,390 SSRs belonging to different repeat types were also identified in the genome. Out of 7,444 proteins predicted, 7,206 were functionally annotated. A total of 1,307 CAZymes, 501 signal peptides, 1,876 effectors, and 2,709 genes involved in host-pathogen interactions were identified. Comparative analysis revealed isolate UV2_4G is distinct with 31 unique clusters and placed distantly in phylogenetic analysis. Taken together, this high-quality genome assembly and sequence annotation resource can give an improved insight for characterizing the biological and pathogenic mechanisms of U. virens.

Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice (Oryza sativa L.).

Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.

Seed Biopriming With Trichoderma Strains Isolated From Tree Bark Improves Plant Growth, Antioxidative Defense System in Rice and Enhance Straw Degradation Capacity.

This study is a unique report of the utilization of Trichoderma strains collected from even tree barks for rice plant growth, its health management, and paddy straw degradation. Seven different spp. of Trichoderma were characterized according to morphological and molecular tools. Two of the isolated strains, namely Trichoderma hebeiensis and Trichoderma erinaceum, outperformed the other strains. Both of the strains controlled four important rice pathogens, i.e., Rhizoctonia solani (100%), Sclerotium oryzae (84.17%), Sclerotium rolfsii (66.67%), and Sclerotium delphinii (76.25%). Seed bio-priming with respective Trichoderma strains reduced the mean germination time, enhanced the seedling vigor and total chlorophyll content which could be related to the higher yield observed in two rice varieties; Annapurna and Satabdi. All the seven strains accelerated the decomposition of rice straw by producing higher straw degrading enzymes like total cellulase (0.97-2.59 IU/mL), endoglucanase (0.53-0.75 IU/mL), xylanase (145.35-201.35 nkat/mL), and laccase (2.48-12.60 IU/mL). They also produced higher quantities of indole acetic acid (19.19-46.28 µg/mL), soluble phosphate (297.49-435.42 µg/mL), and prussic acid (0.01-0.37 µg/mL) which are responsible for plant growth promotion and the inhibition of rice pathogen populations. Higher expression of defense enzymes like catalase (≥250% both in shoot and root), peroxidase (≥150% in root and ≥100% in shoot), superoxide dismutase (≥ 150% in root and ≥100% in shoot), polyphenol oxidase (≥160% in shoot and ≥120% in shoot), and total phenolics (≥200% in root and ≥250% in shoot) as compared to the control indicates stress tolerance ability to rice crop. The expression of the aforementioned enzymes were confirmed by the expression of corresponding defense genes like PAL (>3-fold), DEFENSIN (>1-fold), POX (>1.5-fold), LOX (>1-fold), and PR-3 (>2-fold) as compared to the non-treated control plants. This investigation demonstrates that Trichoderma strains obtained from tree bark could be considered to be utilized for the sustainable health management of rice crop.

Identification of siderophore producing and cynogenic fluorescent Pseudomonas and a simple confrontation assay to identify potential bio-control agent for collar rot of chickpea.

In soil, plant roots coexist with bacteria and fungi that produce siderophores capable of sequestering the available iron. Microbial cyanogenesis has been demonstrated in many species of fungi and in a few species of bacteria (e.g., Chromobacterium and Pseudomonas). Fluorescent Pseudomonas isolates P29, P59, P144, P166, P174, P187, P191 and P192 were cyanogenic and produced siderophores in the presence of a strong chelater 8-Hydroxyquinoline (50 mg/l). A simple confrontation assay for identifying potential antagonists was developed. Fluorescent Pseudomonas isolates P66, P141, P144, P166 and P174 were antagonistic against both Rhizoctonia solani and Sclerotium rolfsii. Vigorous plant growth was observed following seed bacterization with P141, P200 and P240. In field experiments, seed bacterization with selected bacterial isolates resulted in reduced collar rot (S. rolfsii) incidence.

Crop specific plant growth promoting effects of ACCd enzyme and siderophore producing and cynogenic fluorescent Pseudomonas.

Fluorescent Pseudomonas, aerobic, Gram-negative bacteria possess many traits that make them well suited as biocontrol and growth promoting agents. Our study revealed that isolates vary in mechanisms involved in the antagonist interactions against pathogen and growth stimulatory effects on host plant. Most of the potential antagonistic fluorescent Pseudomonas identified were avid iron chelators (P233, P201, 176, P76 and, P76). Wide variation in ACCd enzyme production was observed. ACCd enzyme assay tested P141 > P247 > P126, as potential ACCd enzyme producer. Cynogenic fluorescent Pseudomonas isolates P76 and P124 exerted strong inhibitory against S. rolfsii. However, another cynogenic fluorescent Pseudomonas P179 had no influence against R solani and S. rolfsii which remains unexplained. Noticeable crop specific plant growth stimulation exerted by different fluorescent Pseudomonas was observed on wheat (P124), chickpea (P72), lathyrus (P85, P216), greengram (P11), blackgram (P99, P233); bottlegourd (P248, P167); rice (P176, P247).