Plant growth-promoting and biocontrol traits of endophytic Bacillus licheniformis against soft rot causing Pythium myriotylum in ginger plant.

Bacterial endophytes from plants harbor diverse metabolites that play major roles in biocontrol and improve plant growth. In this study, a total of 12 endophytic bacteria were isolated from the ginger rhizome. The strain K3 was highly effective in preventing mycelia growth of Pythium myriotylum (78.5 ± 1.5% inhibition) in dual culture. The cell-free extract (2.5%) of endophyte K3 inhibited 76.3 ± 4.8% mycelia growth, and 92.4 ± 4.2% inhibition was observed at a 5% sample concentration. The secondary metabolites produced by Bacillus licheniformis K3 showed maximum activity against Pseudomonas syringae (24 ± 1 mm zone of inhibition) and Xanthomonas campestris (28 ± 3 mm zone of inhibition). The strain K3 produced 28.3 ± 1.7 IU mL-1 protease, 28.3 ± 1.7 IU mL-1 cellulase, and 2.04 ± 0.13 IU mL-1 chitinase, respectively. The ginger rhizome treated with K3 in the greenhouse registered 53.8 ± 1.4% soft rot incidence, and the streptomycin-treated pot registered 78.3 ± 1.7% disease incidence. The selected endophyte K3 improved ascorbate peroxidase (1.37 ± 0.009 µmole ASC min-1 mg-1 protein), catalase (8.7 ± 0.28 µmole min-1 mg-1 protein), and phenylalanine ammonia-lyase (26.2 ± 0.99 Umg-1) in the greenhouse. In addition, K3 treatment in the field trial improved rhizome yield (730 ± 18.4 g) after 180 days (p < 0.01). The shoot length was 46 ± 8.3 cm in K3-treated plants, and it was about 31% higher than the control treatment (p < 0.01). The lytic enzyme-producing and growth-promoting endophyte is useful in sustainable crop production through the management of biotic stress.

Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development.

Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.

Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species.

BACKGROUND: Bacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum. Even though ginger (Zingiber officinale) and mango ginger (Curcuma amada) are from the same family Zingiberaceae, the latter is resistant to R. solanacearum infection. MicroRNAs have been identified in many crops which regulates plant-pathogen interaction, either through silencing genes or by blocking mRNA translation. However, miRNA's vital role and its targets in mango ginger in protecting bacterial wilt is not yet studied extensively. In the present study, using the "psRNATarget" server, we analyzed available ginger (susceptible) and mango ginger (resistant) transcriptome to delineate and compare the microRNAs (miRNA) and their target genes (miRTGs). RESULTS: A total of 4736 and 4485 differential expressed miRTGs (DEmiRTGs) were identified in ginger and mango ginger, respectively, in response to R. solanacearum. Functional annotation results showed that mango ginger had higher enrichment than ginger in top enriched GO terms. Among the DEmiRTGs, 2105 were common in ginger and mango ginger. However, 2337 miRTGs were expressed only in mango ginger which includes 62 defence related and upregulated miRTGs. We also identified 213 miRTGs upregulated in mango ginger but downregulated in ginger, out of which 23 DEmiRTGS were defence response related. We selected nine miRNA/miRTGs pairs from the data set of common miRTGs of ginger and mango ginger and validated using qPCR. CONCLUSIONS: Our data covered the expression information of 9221 miRTGs. We identified nine miRNA/miRTGs key candidate pairs in response to R. solanacearum infection in ginger. This is the first report of the integrated analysis of miRTGs and miRNAs in response to R. solanacearum infection among ginger species. This study is expected to deliver several insights in understanding the miRNA regulatory network in ginger and mango ginger response to bacterial wilt.

Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens.

Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.

Elucidation of antibacterial effect of calcium chloride against Ralstonia pseudosolanacearum race 4 biovar 3 infecting ginger (Zingiber officinale Rosc.).

Bacterial wilt incited by Ralstonia pseudosolanacearum (Rps) race 4 biovar 3 is a serious threat to ginger (Zingiber officinale Rosc.) cultivation throughout the ginger growing tracts and warrants effective remedial measures since most of the strategies failed at field level implementation. After a series of experiments, calcium chloride was found to be effective against Rps both in vitro and in planta and its prophylactic effect has been successfully demonstrated under field conditions. CaCl2 at a concentration of > 2% significantly inhibited Rps under in vitro conditions. Calcium is an important nutritional element imparts a major role in plant disease resistance, and numerous studies have demonstrated the mitigating effect of calcium for disease management. CaCl2 being inhibitory to Rps, the mechanism of inhibition by CaCl2 against Rps was elucidated by a series of in vitro assays including swarming motility and biofilm formation. Direct inhibition was also studied using Scanning Electron Microscopy (SEM). The minimum bactericidal concentration and minimum inhibitory concentration were found to be around 3% while the EC 90 value was found to be 2.25%. The SEM analysis revealed the destruction of cell structure by making perforations on the cell surface. CaCl2 at the targeted concentrations inhibited biofilm formation as well as swarming motility of Rps. These findings suggest that CaCl2 exhibits strong antibacterial activity against Rps and has the potential to be used as an effective bactericide for Rps in managing bacterial wilt in ginger.

Phyllosphere-associated Methylobacterium: a potential biostimulant for ginger (Zingiber officinale Rosc.) cultivation.

Methanol, a by-product associated with plant metabolism, is a substrate for pink pigmented facultative methylotrophs (PPFMs) of phyllosphere. The symbiotic interaction of PPFMs has many desirable effects on plant growth and disease resistance. The present study investigated the potential of native PPFMs for mitigating biotic stress and plant growth promotion in ginger. PPFMs were isolated from ginger phyllosphere by leaf imprint technique and screened against major fungal phytopathogens of ginger viz. Macrophomina phaseolina, Sclerotium rolfsii, Pythium myriotylum, Colletotrichum gloeosporioides and Fusarium oxysporum. Among the 60 PPFMs, IISRGPPFM13 was selected for its highly inhibitory activity against the target pathogens. The isolate was useful for mineral solubility, production of IAA, siderophores and hydrolytic enzymes like cellulase, pectinase, lipase, amylase and chitinase. On in planta experiments revealed that IISRGPPFM13 considerably increased plant growth parameters when the bacterium was applied as soil drenching cum foliar spraying. Methanol utilization potential of the isolate was confirmed by mxaF gene analysis where the sequence showing 95.51% identity towards Methylobacterium platani and M. iners. Further, 16S rRNA gene sequence showing 98.73% identity with M. komagatae 002-079 T (AB252201). This is the first report of its kind that a genus of Methylobacterium with biostimulant potential isolated from the phyllosphere of ginger.

Assessing the Efficacy of Broad-Spectrum Antibiotics in Controlling Bacterial Contamination in the In Vitro Micropropagation of Ginger (Zingiber officinale Rosc).

Ginger (Zingiber officinale Rosc) (Zingiberaceae) is a livelihood and commercial crop in Ethiopia. But, the availability of clean and healthy planting materials has become a problem due to wilt disease, caused by Ralstonia solanacearum Biovar 3 Race 4. This problem obliged growers to seek for tens of millions of vigorous and disease-free planting materials very quickly via in vitro micropropagation of shoot tip explants. For this purpose, protocols of sterilizing shoot tip explants and controlling bacterial contamination of one Ethiopian ginger cultivar called Deribo were tested. Hence, this article reports the finding of a study that aimed at testing the (a) effectiveness of three sterilization agents, namely, 0.25% w/v RBK (composed of ridomile, bayleton, and kocide at 1 : 1 : 1 ratio), 0.50% v/v NaOCl, and 70% v/v ethanol at three different treatment times in combination with 0.25% HgCl2; (b) efficacy of four broad-spectrum antibiotics and their combinations in controlling bacterial contaminants of ginger shoot tip explants and in vitro micropropagation media; and (c) effects of the antibiotics on the shooting performances of the explants of the cultivar. A 0.50% v/v NaOCl at exposure time of 20 min followed by 0.25% HgCl2 has resulted in 80% contamination-free and 70% live explants after three weeks of incubation. Likewise, cefotaxime at 50, 100, and 200 mg/L and cefotaxime plus streptomycin at 25, 50, and 100 mg/L yielded 87 to 93% contamination-free microshoots after three weeks of culturing. The number of explants killed by the antibiotics increased with increasing the concentration of the antibiotics. Cefotaxime at 50 mg/L and cefotaxime plus streptomycin at 25 mg/L yielded significantly highest mean microshoots per explant (7.10 ± 0.36 and 7.51 ± 0.27, respectively) and mean shoot length (4.2 ± 0.26 and 3.56 ± 0.17 cm, respectively). Some of the microshoots showed some yellowing. But, they turned green and grew normal after subcultured into fresh, antibiotics-free culture media. These findings are important foundations towards developing more optimized protocols of sterilizing explants and controlling bacterial contaminants for large-scale in vitro micropropagation of the Deribo ginger cultivar.

Development of a colloidal gold strip-based immunochromatographic assay for rapid detection of Fusarium oxysporum in ginger.

BACKGROUND: Rhizome rot, caused primarily by Fusarium oxysporum, is one of the most destructive diseases leading to significant loss in ginger worldwide. The loss can be greatly reduced by proper disease management practices steered by accurate and early diagnosis of pathogens. Pathogen detection at an early stage of infection can also reduce the incidence of disease epidemics. Classical methods are often time consuming, relying on culturing the putative pathogens and the availability of expert taxonomic skills for accurate identification, which leads to the delayed application of control measures. The development of a simple, rapid, sensitive and cost-effective point-of-care diagnostic tool is thus one of the major research priorities for rhizome rot. RESULTS: The 65 kDa, immunoreactive protein band was selected as a diagnostic marker and was subjected to MS analysis followed by blastp. Based on blast result, a synthetic antigenic peptide was synthesized, and used to generate pAbs. The peptide-specific antibodies were used to develop a colloidal gold immunochromatographic assay (ICA). The sensitivity, specificity, and accuracy of ICA were 92.59%, 81.25%, and 90%, respectively. The ICA has a visual detection limit of 2.122 µg mL-1 for infected rhizome samples and 5.065 µg mL-1 for leaf samples with optimal detection time within 5 min. Moreover, the ICA also detected early stage infected samples, of which 71.42% (50/70) were true positives. CONCLUSION: Findings from this study indicated that the assay can be utilized as a tool for the investigation of rhizome rot infection in field samples. © 2019 Society of Chemical Industry.

Effective management of soft rot of ginger caused by Pythium spp. and Fusarium spp.: emerging role of nanotechnology.

Ginger (Zingiber officinale Rosc.) is a tropical plant cultivated all over the world due to its culinary and medicinal properties. It is one of the most important spices commonly used in food, which increases its commercial value. However, soft rot (rhizome rot) is a common disease of ginger caused by fungi such as Pythium and Fusarium spp. It is the most destructive disease of ginger, which can reduce the production by 50 to 90%. Application of chemical fungicides is considered as an effective method to control soft rot of ginger but extensive use of fungicides pose serious risk to environmental and human health. Therefore, the development of ecofriendly and economically viable alternative approaches for effective management of soft rot of ginger such diseases is essentially required. An acceptable approach that is being actively investigated involves nanotechnology, which can potentially be used to control Pythium and Fusarium. The present review is aimed to discuss worldwide status of soft rot associated with ginger, the traditional methods available for the management of Pythium and Fusarium spp. and most importantly, the role of various nanomaterials in the management of soft rot of ginger. Moreover, possible antifungal mechanisms for chemical fungicides, biological agents and nanoparticles have also been discussed.

Differential Modulation of Endophytic Microbiome of Ginger in the Presence of Beneficial Organisms, Pathogens and Both as Identified by DGGE Analysis.

Endophytic microorganisms play a significant role in plants response to beneficial organisms and pathogens. In the current study, endophytic microorganisms from Zingiber officinale were screened for in vitro inhibition against Pythium myriotylum. From this, Burkholderia vietnamiensis ZoB74 was selected as an organism with remarkable antifungal effect. Further, the study focussed on analysis of in vivo changes in endophytic bacterial community of Z. officinale in presence of selected organisms and the pathogen P. myriotylum by PCR-DGGE. 16S rDNA sequencing of bacterial community after DGGE has resulted in the identification of a group of uncultured bacteria as the predominant microbial community of rhizome under various conditions of treatment. High frequency dominance of these endophytic bacteria suggests their role in disease resistance to soft rot in ginger. This also revealed the variation of endophytic microbiome of Z. officinale under biotic stress. Hence the study provides molecular insight into uncultured microbiome and its stress-inducible variation in ginger rhizome.

Culturable Endophytic Bacteria of Ginger Rhizome and their Remarkable Multi-trait Plant Growth-Promoting Features.

Functional contribution of endophytic bacteria towards plant growth is highly impressive due to their species diversity and array of probiotic mechanisms. In the study, 96 endophytic bacteria isolated from rhizome of ginger (Zingiber officinale) were screened for phosphate solubilisation, 1-amino cyclopropane-1-carboxylate (ACC) deaminase activity, nitrogen fixation, ammonia and IAA production. Among these, sixteen endophytes with multiple plant growth-promoting activities were identified by 16S rDNA sequencing and all of them showed growth enhancement in Vigna unguiculata var Lola which make the study remarkably significant. The result was a clear indication of consistent, reliable and broad spectrum plant probiotic features of all the selected isolates. However, strain-specific effects on soil parameters represent the unique and distinguishable role of each of the selected isolates in the chemobiology of ginger rhizome. The study provided deeper insight into microbiomics of ginger rhizome with its agricultural promises.

Endophytic Paraconiothyrium sp. from Zingiber officinale Rosc. Displays Broad-Spectrum Antimicrobial Activity by Production of Danthron.

The bioactivity spectrum of fungal endophytes isolated from Zingiber officinale was analyzed against clinical pathogens and against the phytopathogen Pythium myriotylum, which causes Pythium rot in ginger. One of the isolates GFM13 showed broad bioactivity against various pathogens tested including P. myriotylum. The spore suspension as well as the culture filtrate of the endophytic fungal isolate was found to effectively protect ginger rhizomes from Pythium rot. By molecular identification, the fungal endophyte was identified as Paraconiothyrium sp. The bioactive compound produced by the isolate was separated by bioactivity-guided fractionation and was identified by GC-MS as danthron, an anthraquinone derivative. PCR amplification showed the presence of non-reducing polyketide synthase gene (NR-PKS) in the endophyte GFM13, which is reported to be responsible for the synthesis of anthraquinones in fungi. This is the first report of danthron being produced as the biologically active component of Paraconiothyrium sp. Danthron is reported to have wide pharmaceutical and agronomic applications which include its use as a fungicide in agriculture. The broad-spectrum antimicrobial activity of danthron and the endophytic origin of Paraconiothyrium sp. offer immense applications of the study.

Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease.

Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.

Simultaneous determination of four aflatoxins and ochratoxin A in ginger after inoculation with fungi by ultra-fast liquid chromatography-tandem mass spectrometry.

BACKGROUND: Aflatoxins (AFs) and ochratoxin A (OTA) have been detected frequently in food, agricultural products and traditional Chinese medicines, and their presence poses serious health and economic problems worldwide. Ginger can easily be polluted with mycotoxins. In this study, ginger samples were cultivated for 15 days after inoculation with fungi and were prepared based on ultrasound-assisted solid-liquid extraction using methanol/water followed by immunoaffinity column clean-up and analysed by ultra-fast liquid chromatography-tandem mass spectrometry (UFLC-MS/MS) for AFs and OTA. RESULTS: The limits of detection and quantification of AFs and OTA were 0.04-0.30 µg mL(-1) and 0.125-1.0 µg mL(-1) , respectively. The recoveries were 82.0-100.2%. After 15 days' cultivation, no macroscopic mildew was found in ginger. But, the content of AFB1 expressed an increasing trend in ginger, peel [less than the limit of quantification (LOQ)] to the innermost layer (51.86 µ mL(-1) ), AFB2 was only detected in the innermost layer at the level of 0.87 µ mL(-1) . A small amount (

Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis.

We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.

Diversity and potential application of endophytic bacteria in ginger.

Here, 248 endophytic bacterial strains were isolated to assess the distribution and population diversity of endophytic bacteria in ginger plants. A total of 10.4 x 10(4) to 20.2 x 10(4) CFU/g fresh weight endophytic bacteria of different growth stages were isolated. Maximum bacterium numbers were obtained at the seedling stage. A total of 107 functional strains were screened, including 17 antibacterial strains and 90 indole acetic acid-producing strains. Based on 16S rDNA sequence restriction fragment length polymorphism and 16S rDNA sequences, these 107 strains were mapped and grouped into 16 genera. Bacillus and Pseudomonas were the dominant genera; however, the bacteria belonged to a tremendous range of genera, with the highest species richness being observed at the seedling stage. Sixteen strains exhibited antimicrobial activity against Pythium myriotylum Drechsler, while 7 strains exhibited antimicrobial activity against Phyllosticta zingiberi Hori. Bacillus was the dominant antibacterial strain. Pseudomonas fluorescens, B. megaterium, and Enterobacter ludwigii produced remarkably high levels of IAA. Only a few endophytic bacterial strains were inhibited in fresh ginger juice. Most of these strains were present during seedling stage, including Roseateles depolymerans, Chryseobacterium taiwanense, E. ludwigii, Agrobacterium larrymoorei, P. fluorescens, and Bacillus amyloliquefaciens. This study indicates that the community of endophytic bacteria in ginger changes with the synthesis of antibacterial substances.

Phenazine carboxylic acid production and rhizome protective effect of endophytic Pseudomonas aeruginosa isolated from Zingiber officinale.

Ginger (Zingiber officinale) is cultivated commercially in most parts of the world especially in India for its culinary and medicinal applications. One of the major challenges that limit the yield of ginger is rhizome rot disease caused by organisms including Pythium myriotylum. A feasible ecofriendly method is yet to be devised to prevent the plant from this threatening disease. Recent studies on plant microbiome show the possibility of having endophytic organisms with plant protective characteristics associated with the plants. Because of the uniquely evolved underground nature of the ginger rhizome and its peculiar survival in soil for a long time, many interesting endophytic microbes with plant protective characters can be well expected from it. In the current study, previously isolated endophytic Pseudomonas aeruginosa from ginger was investigated in detail for its effect on Pythium myriotylum. The rhizome protective effect of the organism was also studied by co-inoculation studies, which confirmed that Pseudomonas aeruginosa has very potent inhibitory effect on Pythium myriotylum. On further studies, the active antifungal compound was identified as phenazine 1-carboxylic acid.

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot.

BACKGROUND: Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. RESULTS: Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. CONCLUSIONS: Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Characterization of major hydrolytic enzymes secreted by Pythium myriotylum, causative agent for soft rot disease.

Pythium myriotylum, an oomycetous necrotroph is the causal agent of soft rot disease affecting several crops. Successful colonization by necrotrophs depends on their secretion of a diverse array of plant cell wall degrading enzymes (CWDEs). The induction dynamics of CWDEs secreted by P. myriotylum was analysed as little information is available for this pathogen. Activities of CWDEs that included pectinase, cellulase, xylanase and protease were detected using radial diffusion assay and differential staining. In Czapek Dox minimal medium supplemented with respective substrates as carbon source, the increase in CWDE activities was observed till 8 days of incubation after which a gradual decline in enzymatic activities was observed. With sucrose as sole carbon source, all the enzymes studied showed increase in activity with fungal growth while with cell wall material derived from ginger rhizome as sole carbon source, an initial spurt in cellulase, xylanase and pectinase activities was observed 3 days post incubation while protease activity increased from three days of incubation and reached maximum at 13 days of incubation. To further evaluate the role of CWDEs in pathogenicity, UV-induced mutants (pmN14uv1) were generated wherein significant reduction in cellulase, pectinase and protease activities were observed while that of xylanase remained unchanged compared to wild type isolate (RGCBN14). Bioassays indicated changes in infection potential of pmN14uv1 thereby suggesting the crucial role played by P. myriotylum CWDEs in initiating the rotting process. Hence appropriate strategies that target the production/activity of these secretory hydrolytic enzymes will help in reducing disease incidence/pathogen virulence.