Nanjundappa Manjunatha

The most destructive pathogen of pomegranate, Xanthomonas citri pv. punicae (Xcp) , causes bacterial blight or oily spots affecting quality and quantity of pomegranate production worldwide. Different Xcp isolates obtained from geographically distant regions exhibit remarkable similarities based on multi-locus sequence analysis (MLSA) and SSR marker-based analysis. These isolates can be grouped into just four sequence types (ST1-4) highlighting the clonal nature of the pathogen. In the current study, genome of one of the isolates of Xcp (Xcp-118) belonging to ST3 (which is more prevalent and virulent) was sequenced and annotated. The results offer genomic characterization of genes potentially associated with survival and virulence in this isolate. Further, phylogenetic analysis was carried out on 23 whole genome sequences of different species and pathovars of Xanthomonas. The results reemphasize on the genetic similarity exhibited by different pathovars of X. citri indicating towards the host-specific mechanism for induction of virulence genes as these pathovars are unable to cross-infect the host plant. Thus, in future, the complete genome sequence of Xcp-118 can be exploited to unveil novel insights into the organization of genes involved in pathogenesis of Xcp on pomegranate and may assist in developing suitable blight management practices.

Bacterial blight in pomegranate, caused by Xanthomonas citri pv. punicae (Xcp), is one of the most devastating diseases, leading to substantial economic losses in pomegranate production. Methods for blight management in pomegranate production are scarce and not well established. To date, the major control strategy is targeting the pathogen with antibiotics and copper-based compounds. However, excessive use of antibiotics has resulted in the development of antibiotic resistance in the field population of Xcp. Hence, as a means of eco-friendly and sustainable management of bacterial blight, the use of native endophytes was investigated under field conditions in the current study. Endophytic bacteria were isolated from micro-propagated nodal explants of pomegranate and were identified as Bacillus haynesii, B. tequilensis, and B. subtilis. They were found to produce volatiles that inhibited Xcp growth during in vitro antibiosis assay. GC–MS-based volatile profiling revealed the presence of several bioactive compounds with reported antimicrobial activities. These endophytes (CFU of 10⁸/mL) were then spray-inoculated on leaves of 6-month-old pomegranate plants in the polyhouse. They were found to induce ROS-scavenging enzymes such as catalase and peroxidase. This alteration was a manifestation of host tissue colonization by the endophytes as ROS scavenging is one of the mechanisms by which endophytes colonize the host plants. Furthermore, two-season field trials with endophytes for blight control resulted in a reduction of disease index by 47–68%, which was considerably higher than the reduction due to the chemical immune modulator (2-bromo-2-nitro-1, 3-propanediol) currently being recommended for blight control. In addition, these endophytes also exhibited reduced sensitivity to this immune modulator; thus, the current study advocates the use of B. haynesii, B. subtilis, and B. tequilensis as biocontrol agents for bacterial blight of pomegranate either alone or as a part of integrated disease management.

In March 2022, cankers and lesions appeared on the branches of 2–3-year-old pomegranate plants grown in four orchards of Hanumangarh, Rajasthan, India. The disease incidence ranged from 5-15%. Fiel...

Fungal pathogens are a major constraint affecting the quality of pomegranate production around the world. Among them, Alternaria and Colletotrichum species cause leaf spot, fruit spot or heart rot (black rot), and fruit rot (anthracnose) or calyx end rot, respectively. Accurate identification of disease-causing fungal species is essential for developing suitable management practices. Therefore, characterization of Alternaria and Colletotrichum isolates representing different geographical regions, predominantly Maharashtra—the Indian hub of pomegranate production and export—was carried out. Fungal isolates could not be identified based on morphological characteristics alone, hence were subjected to multi-gene phylogeny for their accurate identification. Based on a maximum likelihood phylogenetic tree, Alternaria isolates were identified as within the A. alternata species complex and as A. burnsii, while Colletotrichum isolates showed genetic closeness to various species within the C. gloeosporioides species complex. Thus, the current study reports for the first time that, in India, the fruit rots of pomegranate are caused by multiple species and not a single species of Alternaria and Colletotrichum alone. Since different species have different epidemiology and sensitivity toward the commercially available and routinely applied fungicides, the precise knowledge of the diverse species infecting pomegranate, as provided by the current study, is the first step towards devising better management strategies.

With increasing human global population, increased yield under saline conditions is a desirable trait for major food crops. Use of endophytes, isolated from halophytic hosts, seems to be an exciting approach for conferring salt tolerance to a salt-sensitive crop. Therefore, in the current study, fungal endophytes were isolated from halophytic plants’ roots and their ability to withstand in vitro salt stress was evaluated. The fungal endophytes could withstand up to 1M NaCl concentrations and this tolerance was independent of their host or tissue source. When inoculated on salt-sensitive wheat seeds/seedlings, several of the endophytes showed a positive impact on germination and biomass-related parameters upon salt stress, both in vitro and under glasshouse conditions. One of the isolates from dicot plants (identified as Microsphaeropsis arundinis) could successfully colonize wheat and promote its growth under salt and no-salt conditions. Amongst the fungal isolates that are known to be natural endophytes of wheat, Chaetomium globosum was the best performing isolate and has previously been reported to be an effective biocontrol agent. Based on the results of our preliminary study, we suggest that these fungal endophytes could prove beneficial for enhancing the salt stress tolerance of wheat crop.

Background: Berseem is a highly nutritious leguminous fodder crop which is used in rotation with cereal and other fodder crops due to its beneficial effects on soil nutrients. Endophytes isolated from roots of such nutritious plants are known to promote their growth as well as that of crop it is rotated with. Methods: In the current study, screening of berseem root endophytic bacteria (REB) was carried out. Morphologically distinct colonies were evaluated for their growth promotion traits in terms of phosphate solubilization, hormone production and enzyme synthesis. Their effect on plant growth parameters was also recorded. The in vitro antifungal activity was assayed using dual culture technique. The most efficient isolate was identified based on 16s rRNA gene sequence homology and subjected to biochemical analysis. Result: All the isolates exhibited plant growth promoting traits and secreted high levels of enzymes. They showed in vitro antagonistic activities against pathogenic fungi belonging to various genera which could be due to enhanced secretion of chitinase enzyme or other bioactive molecules. The most efficient isolate was found to be Gram negative and molecularly identified as Pseudomonas fluorescens which can be used for enhanced production of berseem in future.

Xanthomonas axonopodis pv. punicae (Xap) causes bacterial blight disease in pomegranates, often leading to 60–80% economic loss. In absence of a suitable Xap-resistant variety, the near-monoculture of the susceptible variety, Bhagwa, has aggravated the problem further. In recent times, Xap has spread to different geographical regions, indicating the wide adaptability of the pathogen. Moreover, lower sensitivity of Xap towards streptocycline containing streptomycin sulphate and tetracycline sulphate (9:1) under field conditions is frequently reported. Therefore, the current study was undertaken to assess the genetic variability of Xap isolates using SSR markers, their in vitro sensitivity towards streptomycin was evaluated, and the probable molecular basis of acquired resistance was studied. Two highly diverse isolates showed extreme differences in their pathogenicity, indicating the highly evolving nature of the pathogen. Moreover, all the isolates showed less than 50% growth inhibition on media containing 1500 µg/mL streptomycin, indicating a lower level of antibiotic sensitivity. On the molecular level, 90% of the isolates showed the presence of strA-strB genes involved in streptomycin metabolism. Additionally, G to A transitions were observed in the rpsL gene in some of the isolates. The molecular data suggest that horizontal gene transfer (strAB) and/or spontaneous gene mutation (in rpsL) could be responsible for the observed lower sensitivity of Xap towards streptomycin.