Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistant and stripe rust-susceptible Pakistani wheat cultivars

Plant endophytes: unveiling hidden applications toward agro-environment sustainability

Endophytic microbes are plant-associated microorganisms that reside in the interior tissue of plants without causing damage to the host plant. Endophytic microbes can boost the availability of nutrient for plant by using a variety of mechanisms such as fixing nitrogen, solubilizing phosphorus, potassium, and zinc, and producing siderophores, ammonia, hydrogen cyanide, and phytohormones that help plant for growth and protection against various abiotic and biotic stresses. The microbial endophytes have attained the mechanism of producing various hydrolytic enzymes such as cellulase, pectinase, xylanase, amylase, gelatinase, and bioactive compounds for plant growth promotion and protection. The efficient plant growth promoting endophytic microbes could be used as an alternative of chemical fertilizers for agro-environmental sustainability. Endophytic microbes belong to different phyla including Euryarchaeota, Ascomycota, Basidiomycota, Mucoromycota, Firmicutes, Proteobacteria, and Actinobacteria. The most pre-dominant group of bacteria belongs to Proteobacteria including α-, β-, γ-, and δ-Proteobacteria. The least diversity of the endophytic microbes have been revealed from Bacteroidetes, Deinococcus-Thermus, and Acidobacteria. Among reported genera, Achromobacter, Burkholderia, Bacillus, Enterobacter, Herbaspirillum, Pseudomonas, Pantoea, Rhizobium, and Streptomyces were dominant in most host plants. The present review deals with plant endophytic diversity, mechanisms of plant growth promotion, protection, and their role for agro-environmental sustainability. In the future, application of endophytic microbes have potential role in enhancement of crop productivity and maintaining the soil health in sustainable manner.

Structure and Ecological Function of Fungal Endophytes from Stems of Different Mulberry Cultivars

To explore the microbial community structure and ecological function of mulberry and their potential relationship with the resistance of mulberry, the community structure and function of endophytic fungi in 18 mulberry cultivars were analyzed and predicted by using high-throughput sequencing technology and the FUNGuild database. A total of 352 operational taxonomic units of fungi were observed at a 97% similarity level, representing six phyla of fungi, Fungi_unclassified, Ascomycota, Basidiomycota, Zygomycota, Rozellomycota, and Chytridiomycota. Fungi_unclassified was dominant, and Ascomycota was relatively dominant in all cultivars. At the genus level, Ascomycota_unclassified was dominant, and Ampelomyces was relatively dominant, with a richness in TAIWANCHANGGUOSANG 16.47-8975.69 times that in the other cultivars. Classified Ascomycota_unclassified was 4.75-296.65 times more common in NANYUANSIJI than in the other cultivars. Based on the FUNGuild analysis method, we successfully annotated six nutrient types, namely, pathotroph, pathotroph-saprotroph, pathotroph-saprotroph-symbiotroph, saprotroph, saprotroph-symbiotroph, and symbiotroph, among which saprophytic-symbiotic accounted for the largest proportion and was absolutely dominant in TWC. This research suggests that community composition differs among cultivars and that the diversity and richness of endophytic fungi in resistant cultivars are higher than those in susceptible cultivars. The ecological functions of cultivars with different resistances are quite different.

Antifungal activity of Klebsiella grimontii DR11 against Fusarium oxysporum causing soybean root rot

AIMS

Soybean root rot, caused by Fusarium oxysporum, leads to significant economic and financial losses to the soybean processing industry globally. In the study, we aimed to explore a biocontrol agent to combat F. oxysporum infection in soybean.

METHODS AND RESULTS

From soybean rhizosphere soil, 48 strains were isolated. Among them, the strain DR11 exhibited the highest inhibition rate of 72.27%. Morphological, physiological, biochemical, and 16S rDNA identification revealed that the strain DR11 was Klebsiella grimontii DR11. Strain DR11 could inhibit the growth of F. oxysporum and spore formation and alter the mycelial morphology. At 5.0 × 106 CFU mL-1, pH 7, and 30°C, it exhibited the highest inhibitory rate (72.27%). Moreover, it could decrease the activity of cell-wall-degrading enzymes of F. oxysporum. Simultaneously, the activities of defense-related enzymes and content of malondialdehyde in soybean plants were increased after treatment with strain DR11. In addition, strain DR11 could form aggregates to form biofilm and adsorb on the surface of soybean roots. It inhibited F. oxysporum growth on soybean seedlings, with an inhibitory effect of 62.71%.

CONCLUSION

Klebsiella grimontii DR11 had a strong inhibitory effect on F. oxysporum and could be used as a biocontrol agent to combat F. oxysporum infection in soybean.

Why different sugarcane cultivars show different resistant abilities to smut? : Comparisons of endophytic microbial compositions and metabolic functions in stems of sugarcane cultivars with different abilities to resist smut

To elucidate the mechanisms underlying the resistance to smut of different sugarcane cultivars, endophytic bacterial and fungal compositions, functions and metabolites in the stems of the sugarcane cultivars were analyzed using high-throughput sequencing techniques and nontargeted metabolomics. The results showed that the levels of ethylene, salicylic acid and jasmonic acid in sugarcane varieties that were not sensitive to smut were all higher than those in sensitive sugarcane varieties. Moreover, endophytic fungi, such as Ramichloridium, Alternaria, Sarocladium, Epicoccum, and Exophiala species, could be considered antagonistic to sugarcane smut. Additionally, the highly active arginine and proline metabolism, pentose phosphate pathway, phenylpropanoid biosynthesis, and tyrosine metabolism in sugarcane varieties that were not sensitive to smut indicated that these pathways contribute to resistance to smut. All of the above results suggested that the relatively highly abundant antagonistic microbes and highly active metabolic functions of endophytes in non-smut-sensitive sugarcane cultivars were important for their relatively high resistance to smut.

Control of stripe rust of wheat using indigenous endophytic bacteria at seedling and adult plant stage

Stripe rust (caused by Puccinia striiformis tritici) is one of the most devastating diseases of wheat. The most effective ways to control stripe rust are the use of resistant cultivars and the timely use of an appropriate dose of fungicide. However, the changing nature of rust pathogen outwits the use of resistant cultivars, and the use of a fungicide is associated with environmental problems. To control the disease without sacrificing the environment, we screened 16 endophytic bacteria, which were isolated from stripe rust-resistant wheat cultivars in our previous study, for their biocontrol potential. A total of 5 bacterial strains Serratia marcescens 3A, Bacillus megaterium 6A, Paneibacillus xylanexedens 7A, Bacillus subtilis 11A, and Staphyloccus agentis 15A showed significant inhibition of Puccinia striiformis f. sp. tritici (Pst) urediniospores germination. Two formulations i.e., fermented liquid with bacterial cell (FLBC) and fermented liquid without bacterial cells (FL) of each bacterial strain, were evaluated against the urediniospores germination. Formulations of five selected endophytic bacteria strains significantly inhibited the uredinioospores germination in the lab experiments. It was further confirmed on seedlings of Pakistani susceptible wheat cultivar Inqilab-91 in the greenhouse, as well as in semi-field conditions. FLBC and FL formulations applied 24 h before Pst inoculation (hbi) displayed a protective mode. The efficacy of FLBC was between 34.45 and 87.77%, while the efficacy of FL was between 39.27 and 85.16% when applied 24 hbi. The inoculated wheat cultivar Inqilab-91 was also tested under semi-field conditions during the 2017–2018 cropping season at the adult plant stage. The strains Bacillus megaterium 6A and Paneibacillus xylanexedens 7A alone significantly reduced the disease severity of stripe rust with the efficacy of 65.16% and 61.11% for the FLBC in protective effect, while 46.07% and 44.47% in curative effect, respectively. Inoculated seedlings of Inqilab-91 showed higher activities of antioxidant enzymes, superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). The treated seedlings also showed higher expressions of pathogenesis-related (PR) protein genes, antifungal protein (PR-1), β-1,3-endoglucanases (PR-2), endochitinases (PR-4), peroxidase (PR-9), and ribonuclease-like proteins (PR-10). These results indicated that endophytic bacteria have the biocontrol potential, which can be used to manage stripe rust disease. High production antioxidant enzymes, as well as high expression of PR protein genes, might be crucial in triggering the host defense mechanism against Pst.

Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat

Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

A Comprehensive Analysis Using Colorimetry, Liquid Chromatography-Tandem Mass Spectrometry and Bioassays for the Assessment of Indole Related Compounds Produced by Endophytes of Selected Wheat Cultivars

Liquid chromatography–tandem mass spectrometry (LC–MS/MS), colorimetry, and bioassays were employed for the evaluation of the ability of endophytic bacterial strains to synthesize indole-related compounds (IRCs) and in particular indole-3-acetic acid (IAA). A total of 54 endophytic strains belonging to seven bacterial genera isolated from tissues of common and spelt wheat cultivars were studied. The endophytic bacteria isolated from different tissues of the tested wheat types were capable of IRCs production, including IAA, which constituted from 1.75% to 52.68% of all IRCs, in in vitro conditions via the tryptophan dependent pathway. The selected post-culture medium was also examined using a plant bioassay. Substantial growth of wheat coleoptile segments treated with the bacterial post-culture medium was observed in several cases. Our data suggest that the studied endophytic bacteria produce auxin-type compounds to support plant development. Summarizing, our approach to use three complementary methods for estimation of IRCs in different endophytic strains provides a comprehensive picture of their effect on wheat growth.