Diversity and potential application of endophytic bacteria in ginger

Bio-stimulating effect of endophytic Aspergillus flavus AUMC 16068 and its respective ex-polysaccharides in lead stress tolerance of Triticum aestivum plant

Heavy metal accumulation is one of the major agronomic challenges that has seriously threatened food safety. As a result, metal-induced phytotoxicity concerns require quick and urgent action to retain and maintain the physiological activities of microorganisms, the nitrogen pool of soils, and the continuous yields of wheat in a constantly worsening environment. The current study was conducted to evaluate the plant growth-promoting endophytic Aspergillus flavus AUMC 16,068 and its EPS for improvement of plant growth, phytoremediation capacity, and physiological consequences on wheat plants (Triticum aestivum) under lead stress. After 60 days of planting, the heading stage of wheat plants, data on growth metrics, physiological properties, minerals content, and lead content in wheat root, shoot, and grains were recorded. Results evoked that lead pollution reduced wheat plants' physiological traits as well as growth at all lead stress concentrations; however, inoculation with lead tolerant endophytic A. flavus AUMC 16,068 and its respective EPS alleviated the detrimental impact of lead on the plants and promoted the growth and physiological characteristics of wheat in lead-contaminated conditions and also lowering oxidative stress through decreasing (CAT, POD, and MDA), in contrast to plants growing in the un-inoculated lead polluted dealings. In conclusion, endophytic A. flavus AUMC 16,068 spores and its EPS are regarded as eco-friendly, safe, and powerful inducers of wheat plants versus contamination with heavy metals, with a view of protecting plant, soil, and human health.

Diversity of Endophytes of Actinidia arguta in Different Seasons

The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.

Efficacy of endophytic bacteria as promising inducers for enhancing the immune responses in tomato plants and managing Rhizoctonia root-rot disease

Around the world, a variety of crops, including tomatoes, suffer serious economic losses due to the Rhizoctonia root-rot disease. Herein, Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense isolated from strawberry (Fragaria chiloensis var. ananassa) plants were pragmatic as plant growth promotors for battling the Rhizoctonia root rot disease and bringing about defense mechanisms as well as growth promotional strategies in tomato plants. These endophytic bacteria demonstrated potent antifungal activity against R. solani in vitro along in vivo. Data explained that the isolated endophytic bacteria could produce Indole acetic acid, Gibberellic acid GA, and siderophore as well as solubilize phosphate in the soil. The consortium of (Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense) increased the protection % against Rhizoctonia infection by (79.4%), followed by B. velezensis by (73.52%), H. huttiense by (70.5%), and B. megaterium by (67.64%), respectively. There was an increase in soluble proteins and carbohydrates in infected plants treated with a consortium of endophytic bacteria by 30.7% and 100.2% over untreated infected plants, respectively. Applying endophytic bacteria either alone or in combination lowered the level of malondialdehyde MDA and hydrogen peroxide H2O2 and improved the activities of antioxidant enzymes in both infected and uninfected plants. Also, bacterial endophytes have distinctive reactions regarding the number and concentrations of isozymes in both infected and uninfected plants. It could be recommended the commercial usage of a mixture of targeted bacterial endophyte strains as therapeutic nutrients against Rhizoctonia root-rot disease as well as plant growth inducer.

Endophytic Bacillus subtilis antagonize soil-borne fungal pathogens and suppress wilt complex disease in chickpea plants (Cicer arietinum L.)

The present study aimed to identify potential endophytic bacteria antagonistic against three soil-borne fungal pathogens, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum f.sp. ciceri causing root rot, collar rot, and fungal wilt diseases in chickpea plants, respectively. A total of 255 bacterial endophytes were isolated from the leaves, stems, and roots of seven different crop plants (chickpea, tomato, wheat, berseem, mustard, potato, and green pea). The dual culture-based screening for antifungal properties indicated that three endophytic isolates had strong inhibition (>50%) against all three pathogens tested. Based on morphological, biochemical, and molecular characterization, the selected isolates (TRO4, CLO5, and PLO3) were identified as different strains of Bacillus subtilis. The bacterial endophytes (TRO4 and CLO5) were positive for plant growth promoting (PGP) traits viz., ammonia, siderophore, and indole-3-acetic acid (IAA) production. The bio-efficacy of the endophytes (TRO4, CLO5, and PLO3) was tested by an in planta trial in chickpea pre-challenged with R. solani, S. rolfsii, and F. oxysporum f.sp. ciceri. The B. subtilis strains TRO4 and CLO5 were found to be effective in reducing percent disease incidence (p ≤ 0.05) and enhancing plant growth parameters. The different root parameters viz. root length (mm), surface area (cm²), root diameter (mm), and root volume (cm³) were significantly (p ≤ 0.05) increased in TRO4 and CLO5 inoculated chickpea plants. Confocal Scanning Laser Microscopy showed heavy colonization of bacteria in the roots of endophyte-inoculated chickpea plants. The inoculation of endophytic Bacillus subtilis strains TRO4 and CLO5 in chickpea plants through seed biopriming reduced the accumulation of superoxide, enhanced the plant defense enzymes, and induced the expression of Pathogenesis-Related (PR) genes. Semi-quantitative analysis of defense-related genes showed differential activation of PR genes (60srp and IFR) by endophyte inoculation. The results of the present study reveal the antagonistic potential of B. subtilis strains TRO4 and CLO5 against three major soil-borne fungal pathogens and their ability to suppress wilt complex disease in chickpea plants. This is the first report on the simultaneous suppression of three major soil-borne fungal pathogens causing wilt complex in chickpea plants by endophytic B. subtilis strains.

Effect of Plant Preservative MixtureTM on Endophytic Bacteria Eradication from In Vitro-Grown Apple Shoots

Endophytic contaminants are a common problem for the in vitro propagation of woody plants and have significant economic repercussions for the conservation of plant genetic resources and commercial micropropagation. In this study, first, the microbial contamination that appeared around the base of in vitro-grown apple shoots was identified as Bacillus megaterium. Then, plant preservative mixture (PPMTM) was used as a bactericidal agent in plant tissue culture. Its efficacy for eradicating endophytic B. megaterium in in vitro cultures of apple was tested. In vitro-contaminated shoots were grown in tissue culture medium supplemented with 0.2% v/v PPMTM for 12 weeks and then transferred to medium without any PPMTM and cultured for 24 weeks. This study showed that PPMTM is an effective agent for controlling the growth of B. megaterium. Our results highlight the species-specific response of apple shoots to PPMTM. PPMTM was effective in controlling endogenous microbial contaminations from apple varieties 'Golden Delicious', 'Landsberger Renette', 'Suislepper', and 'Aport krovavo-krasnyi'; meanwhile, in 'KG 7' and 'Gold Rush', all the plants grown in the absence of PPMTM were still bacterially contaminated, even though they were pre-treated for 12 weeks in PPMTM-supplemented medium. These results therefore suggest the essentiality of further testing of extended incubation of PPMTM in these cultivars that had outbreaks of bacterial contamination.

Plant organ- and growth stage-diversity of endophytic bacteria with potential as biofertilisers isolated from wheat (Triticum aestivum L.)

BACKGROUND

Chemical fertilisers are extensively used for crop production, which may cause soil deterioration and water pollution. Endophytic bacteria with plant-growth-promoting (PGP) activities may provide a solution to sustainably improve crop yields, including in-demand staples such as wheat. However, the diversity of the PGP endophytic bacteria in wheat across plant organs and growth stages has not been thoroughly characterised.

RESULTS

Here, we report the isolation of endophytic bacteria from root, stem, leaf and seed of three winter wheat varieties at tillering, jointing, heading and seed-filling growth stages that were identified via 16S rRNA gene sequence analysis. Strains were screened for indole-3-acetic acid (IAA) production, potassium and phosphate solubilisation and the ability to grow on a nitrogen-free medium. Strain's capacity to stimulate various plant growth parameters, such as dry root weight, dry above-ground parts weight and plant height, was evaluated in pot trials. A total of 127 strains were randomly selected from 610 isolated endophytic bacterial cultures, representing ten genera and 22 taxa. Some taxa were organ-specific; others were growth-stage-specific. Bacillus aryabhattai, B. stratosphericus, Leclercia adecarboxylata and Pseudomonas oryzihabitans were detected as wheat endophytes for the first time. The IAA production, inorganic phosphorous solubilisation, organic phosphorus solubilisation, potassium solubilisation and growth on N-free medium were detected in 45%, 29%, 37%, 2.4% and 37.8% of the 127 strains, respectively. In pot trials, each strain showed variable effects on inoculated wheat plants regarding the evaluated growth parameters.

CONCLUSIONS

Wheat endophytic bacteria showed organ- and growth-stage diversity, which may reflect their adaptations to different plant tissues and seasonal variations, and differed in their PGP abilities. Bacillus was the most predominant bacterial taxa isolated from winter wheat plants. Our study confirmed wheat root as the best reservoir for screening endophytic bacteria with potential as biofertilisers.

Influence of tissue and geographic locality on culturable endophytic bacteria of Atractylodes macrocephala

The endophytic bacterial community and their diversity are closely related to the host's growth and development. This paper explores the culturable endophytic bacteria in the stems, leaves, roots and rhizomes of Atractylodes macrocephala (AM) of four localities (Yuqian, Wenxian, Pan'an and Pingjiang) and the potential correlation between the bacteria and plant bioactive compounds. A total of 118 endophytic bacteria belonging to 3 phyla, 5 classes, 11 orders, 26 families and 48 genera were isolated and identified from the four AM tissues. Among them, Bacillus was the dominant genus. In AM, the tissue type and locality influenced the endophytic bacterial community. Approximately 29.7 and 28.8% of the endophytic bacteria exhibited tissue specificity and geographic specificity, respectively. Furthermore, high-performance liquid chromatography revealed that the sesquiterpenoid (atractylenolide I, atractylenolide Ⅱ and atractylon) content was more in the rhizomes of Wenxian than in those of Pingjiang, Yuqian and Pan'an. The multiple linear regression was used to screen the bacterial strains related to the bioactive compounds of AM. The relative frequency of Microbacterium positively correlated with atractylenolide I and atractylon content in AM but negatively correlated with atractylenolide Ⅱ content. The study also provides a theoretical framework for future research on endophytic bacteria as alternative sources of secondary plant metabolites.

Diversity of Rhizo-Bacteriome of Crocus sativus Grown at Various Geographical Locations and Cataloging of Putative PGPRs

Earlier plant growth promoting rhizo-bacteria (PGPRs) were isolated from the plants, by cultivation based techniques and the interaction was mostly thought to be bilateral. The routine bilateral study, with no information on the associated microbiome, could be one of the reasons for the limited success of PGPRs in the field conditions. Keeping in view the role of PGPRs in rhizo-bacteriome on the growth and production of plant, the present study was aimed at studying the diversity of the rhizo-bacteriome of saffron grown across three geographical locations namely Kashmir, Kishtwar and Bengaluru. Variation in the rhizo-bacteriome of saffron growing across 10 different sites from 3 geographical locations was studied using 16S rDNA amplicon metagenomic sequencing. 16 bacterial phyla, 261 genera and 73 bacterial species were cataloged from all the rhizosphere samples. Proteobacteria was a dominant phylum in all the rhizosphere samples. Rhizo-bacteriome of saffron grown in Kishtwar was found to be significantly different from the rhizo-bacteriome of saffron grown in Kashmir and Bengaluru. Interestingly, the rhizo-bacteriome of saffron grown in Bengaluru was very similar to the saffron grown in Kashmir, thereby indicating that the rhizo-bacteriome in saffron is “plant driven” as the corm sown in Bengaluru were from Kashmir. Despite variation in rhizo-bacteriome, core rhizo-bacteriome in saffron was identified that was represented by 53 genera and eight bacterial species belonging to 11 phyla irrespective of their geographical distribution. In addition, 21 PGPRs were reported for the first time from the saffron rhizosphere. The high yielding saffron field Wuyan was found to have the highest number of PGPRs; this indicates that the presence of PGPR is important for yield enhancement than diversity. The two PGPR Rhizobium leguminosarum and Luteibacter rhizovicinus were reported from all the locations except Kishtwar that had escaped isolation in our previous attempts using cultivation based techniques. It is being proposed instead of going for random isolation and screening for PGPRs from plant rhizosphere, an alternate strategy using metagenomic cataloging of the rhizo-bacteriome community and cultivation of the dominant PGPR should be undertaken. This strategy will help in the selection of dominant PGPRs, specific to the plant in question.

Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China

Endogenous bacteria are important for maintaining the health and other ecologically relevant functions of cotton plants. However, little is known about the community structures and diversity of endophytic bacteria in cotton plants. In our study, we used the Illumina amplicon sequencing technology to study the endophytic bacteria found in cotton root tissue in Xinjiang, China. A total of 60.84 × 10⁶ effective sequences of the 16S rRNA gene in the V5-V6 variable region revealed a large number of operational taxonomic units (OTUs), namely 81-338 OTUs, at a cut-off level of 3% and a sequencing depth of 50 000 sequences. Among the 23 classes identified, Gammaproteobacteria was the dominant group, followed by Alphaproteobacteria, Actinobacteria, and Bacillus. The diversity of endogenous bacteria differed at different growth periods, with the most OTUs detected in seedlings (654), followed by the budding stage (381), flowering stage (350), and flocking stage (351). A total of 217 OTUs were common to all four stages. Pantoea tags were more common to the Shihezi region, whereas Erwinia labels were more common to the Hami region. These results suggest that the dynamics of endophytic bacterial communities are affected by plant growth stage. This highlights the relevance of microbial diversity studies in improving our understanding of endophyte communities.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

The Effect of Auxin and Auxin-Producing Bacteria on the Growth, Essential Oil Yield, and Composition in Medicinal and Aromatic Plants

Aromatic plants had been used since ancient times for their preservative and medicinal properties, and to impart aroma and flavor to food. Also their secondary metabolites are economically important as drugs, flavor and fragrances, pharmaceuticals, agrochemicals, dye, and pigments, pesticides, cosmetics, food additives, other industrially biochemical, and also play a major role in the adaptation of plants to their environment. Indole acetıc acid-producing rhizobacteria inoculations increase in stomatal density and level of secondary metabolite and have a synergistic effect on monoterpene biosynthesis. Bacterial inoculation significantly affected and increased the chemical composition of essential oil, citronellol, and geraniol content in rose-scented geranium; essential oil composition and total phenolic content in marigold; density, number, and size of glandular trichomes in sweet wormwood and peppermint essential oil components such as geranyl acetate, limonene, and β-pinene in coriander; oil yield and content in calendula; yield of the herb in hyssop; oxygenated compounds, essential oil content and yield, anethol and changing the chemical composition in fennel; growth, number of glandular trichomes and essential oil yield, root branching and length, and total amount of essential oil, production of monoterpenes such as pulegone, menthol, menthone, menthofuran, and terpineol content, biosynthesis of secondary metabolites in peppermint; growth and essential oil yield in marjoram; glandular hair abundance, essential oil yield, and monoterpene biosynthesis in basil; phellandrene, limonene, borneol, and campor in rosemary; carvacrol, thymol, linalool, and borneol in oregano; and α-thujene, α-pinene, α-terpinene, p-simen, β-pinene, and γ-terpinene contents and essential oil yield in summer savory. Inoculation with IAA-producing bacteria medicinal roots increased the valerenic acid in valerian, essential oil and quality in vetiver, curcumin content in turmeric alkaloid and ginsenoside content in ginseng, and inulin content in Jerusalem artichoke.

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

Preliminary data on antibacterial activity of Echinacea purpurea-associated bacterial communities against Burkholderia cepacia complex strains, opportunistic pathogens of Cystic Fibrosis patients

Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A source of such natural compounds is represented by medicinal plants and, in particular, by bacterial communities associated with these plants able to produce molecules with antimicrobial activity. In this work, a panel of 151 (endophytic) bacteria isolated from three different compartments (rhizospheric soil, roots, and stem/leaves) of the medicinal plant Echinacea purpurea were tested (using the cross-streak method) for their ability to inhibit the growth of 10 Bcc strains. Data obtained revealed that bacteria isolated from the roots of E. purpurea are the most active in the inhibition of Bcc strains, followed by bacteria isolated from the rhizospheric soil, and endophytes from stem/leaf compartment. At the same time, Bcc strains of environmental origin showed a higher resistance toward inhibition than the Bcc strains with clinical (i.e. CF patients) origin. Differences in the inhibition activity of E. purpurea-associated bacteria are mainly linked to the environment -the plant compartment- rather than to their taxonomical position.

VIT-CMJ2: Endophyte of Agaricus bisporus in Production of Bioactive Compounds

BACKGROUND

Agaricus bisporus is an edible basidiomycete fungus. Both the body and the mycelium contain compounds comprising a wide range of antimicrobial molecules, contributing in improvement of immunity and tumor-retardation.

OBJECTIVES

The presence of endophytes capable of producing bioactive compounds was investigated in Agaricus bisporus.

MATERIALS AND METHODS

Endophytes from Agaricus bisporus was isolated on LB agar. The obtained isolates were characterized morphologically and biochemically. Further 16S rRNA sequencing was implemented for molecular analysis of isolates. The isolate was mass produced and the bioactive compounds were extracted using ethyl acetate, chloroform and hexane. Agar well diffusion method was carried out to seek the potential of any antimicrobial activity of the crude bioactive compounds against known pathogens. GC-MS and FT-IR analysis were performed for the identification of bioactive compounds.

RESULTS

VIT-CMJ2 was identified as Enterobacter sp. as revealed by 16S rRNA sequencing. Chloroform extract of VIT-CMJ2 showed a maximum zone of inhibition of 19 mm against Salmonella typhi followed by hexane and ethyl acetate extracts. The GC-MS analysis revealed the presence of several bioactive compounds having effective antimicrobial activity like butyl ester, Behenicalcohol, S , S-dioxide derivatives and some others which were later confirmed by FT-IR spectral stretches.

CONCLUSIONS

The present study shows the insight on the way endophytes interact with Agaricus bisporus; thereby improving the nutritional profile.