Enhanced cercosporin production by co-culturing Cercospora sp. JNU001 with leaf-spot-disease-related endophytic bacteria

BACKGROUND

Owing to the excellent properties of photosensitization, cercosporin, one of naturally occurring perylenequinonoid pigments, has been widely used in photodynamic therapy, or as an antimicrobial agent and an organophotocatalyst. However, because of low efficiency of total chemical synthesis and low yield of current microbial fermentation, the limited production restricts its broad applications. Thus, the strategies to improve the production of cercosporin were highly desired. Besides traditional optimization methods, here we screened leaf-spot-disease-related endophytic bacteria to co-culture with our previous identified Cercospora sp. JNU001 to increase cercosporin production.

RESULTS

Bacillus velezensis B04 and Lysinibacillus sp. B15 isolated from leaves with leaf spot diseases were found to facilitate cercosporin secretion into the broth and then enhance the production of cercosporin. After 4 days of co-culture, Bacillus velezensis B04 allowed to increase the production of cercosporin from 128.2 mg/L to 984.4 mg/L, which was 7.68-fold of the previously reported one. Lysinibacillus sp. B15 could also enhance the production of cercosporin with a yield of 626.3 mg/L, which was 4.89-fold higher than the starting condition. More importantly, we found that bacteria B04 and B15 employed two different mechanisms to improve the production of cercosporin, in which B04 facilitated cercosporin secretion into the broth by loosening and damaging the hyphae surface of Cercospora sp. JNU001 while B15 could adsorb cercosporin to improve its secretion.

CONCLUSIONS

We here established a novel and effective co-culture method to improve the production of cercosporin by increasing its secretion ability from Cercospora sp. JNU001, allowing to develop more potential applications of cercosporin.

LC-MS/MS-based profiling of bioactive metabolites of endophytic bacteria from Cannabis sativa and their anti-Phytophthora activity

Protection of crop plants from phytopathogens through endophytic bacteria is a newly emerged area of biocontrol. In this study, endophytic bacteria were isolated from the rhizosphere of Cannabis sativa. Based on initial antimicrobial screening, three (03) bacteria Serratia marcescens MOSEL-w2, Enterobacter cloacae MOSEL-w7, and Paenibacillus MOSEL-w13 were selected. Antimicrobial assays of these selected bacteria against Phytophthora parasitica revealed that E. cloacae MOSEL-w7 and Paenibacillus sp. MOSEL-w13 possessed strong activity against P. parasitica. All these bacterial extracts showed strong inhibition against P. parasitica at different concentrations (4-400 µg mL^-1). P. parasitica hyphae treated with ethyl acetate extract of E. cloacae MOSEL-w7 resulted in severe growth abnormalities compared to control. The extracts were further evaluated for in vivo detached-leaf assay against P. parasitica on the wild type tobacco. Application of 1% ethyl acetate bacterial extract of S. marcescens MOSEL-w2, E. cloacae MOSEL-w7, and Paenibacillus sp. MOSEL-w13 reduced P. parasitica induced lesion sizes and lesion frequencies by 60-80%. HPLC based fractions of each extract also showed bioactivity against P. parasitica. A total of 24 compounds were found in the S. marcescens MOSEL-w2, 15 compounds in E. cloacae MOSEL-w7 and 20 compounds found in Paenibacillus sp. MOSEL-w13. LC-MS/MS analyses showed different bioactive compounds in the bacterial extracts such as Cotinine (alkylpyrrolidine), L-tryptophan, L-lysine, L-Dopa, and L-ornithine. These results suggest that S. marcescens MOSEL-w2, E. cloacae MOSEL-w7, and Paenibacillus MOSEL-w13 are a source of bioactive metabolites and could be used in combination with other biocontrol agents, with other modes of action for controlling diseases caused by Phytophthora in crops. They could be a clue for the broad-spectrum biopesticides for agriculturally significant crops.

Roseomonas hellenica sp. nov., isolated from roots of wild-growing Alkanna tinctoria

Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523^T and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523^T and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523^T and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523^T and LMG 31524. Since the strains LMG 31523^T and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523^T (=CECT 30032^T).

Application of bio-fertilizers for enhancing growth and yield of common bean plants grown under water stress conditions

This study was planned to enhance the growth and productivity of common bean plants (Phaseolus vulgaris L.) grown under different water stress level by using different microorganisms as bio-fertilizer agents. Water stress is a international problem that effects on morphological, functional and chemical processes of plants occasioning in altering growth, yield and water relations of economic plants like common bean plants. The interaction effect between water stress (WW as recommended irrigation after 6 days, WS1 after 12 days and WS2 after 18 days) and inoculation with different microorganisms [AMF (Glomus mosseae) and endophytic bacteria, (Bacillus amyloliquefaciens)] used alone or in mixed was examined on the development and productivity of common bean plants. Mutual application of AMF and endophytic bacteria significantly increased the average values of most of growth, water relations (photosynthetic rate, transpiration rate and stomatal conductance) and yield parameters of common bean plants grown at WS1 and WS2 comparing with non-colonized plants. In this connection, colonization with AMF and endophytic bacteria with WS1 are the greater pods number, pod length, pods weight, 100 seeds weight, Yield by ton /Fed and water-use efficiency (WUE) by ton/ m³ than other treatments. Common bean yielded seeds had significantly increased nutrients content (nitrogen, potassium, phosphorus, magnesium and calcium), vitamin B₁, Folic acid, crude protein and crude fibers at AMF + endophytic bacteria under second water stress (WS1) when compared to other treatments.

Antifungal potential against Sclerotinia sclerotiorum (Lib.) de Bary and plant growth promoting abilities of Bacillus isolates from canola (Brassica napus L.) roots

Endophytic bacteria show important abilities in promoting plant growth and suppressing phytopathogens, being largely explored in agriculture as biofertilizers or biocontrol agents. Bacteria from canola roots were isolated and screened for different plant growth promotion (PGP) traits and biocontrol of Sclerotinia sclerotiorum. Thirty isolates belonging to Bacillus, Paenibacillus, Lysinibacillus, and Microbacterium genera were obtained. Several isolates produced auxin, siderophores, hydrolytic enzymes, fixed nitrogen and solubilized phosphate. Five isolates presented antifungal activity against S. sclerotiorum by the dual culture assay and four of them also inhibited fungal growth by volatile organic compounds production. All antagonistic isolates belonged to the Bacillus genus, and had their genomes sequenced for the search of biosynthetic gene clusters (BGC) related to antimicrobial metabolites. These isolates were identified as Bacillus safensis (3), Bacillus pumilus (1), and Bacillus megaterium (1), using the genomic metrics ANI and dDDH. Most strains showed several common BGCs, including bacteriocin, polyketide synthase (PKS), and non-ribosomal peptide synthetase (NRPS), related to pumilacidin, bacillibactin, bacilysin, and other antimicrobial compounds. Pumilacidin-related mass peaks were detected in acid precipitation extracts through MALDI-TOF analysis. The genomic features demonstrated the potential of these isolates in the suppression of plant pathogens; however, some aspects of plant-bacterial interactions remain to be elucidated.

The cypsela (achene) of Echinacea purpurea as a diffusion unit of a community of microorganisms

Echinacea purpurea is a plant cultivated worldwide for its pharmaceutical properties, mainly related to the stimulation of the immune system in the treatment of respiratory infections. The cypselas (fruits) of E. purpurea were examined in order to investigate the presence, localization and potential function(s) of endophytic microorganisms. Electron and confocal microscopy observations showed that three different components of microorganisms were associated to cypselas of E. purpurea: (i) one endocellular bacterial component in the cotyledons, enclosed within the host membrane; (ii) another more generic bacterial component adhering to the external side of the perianth; and (iii) a fungal component inside the porous layer of the perianth, the woody and porous modified residual of the flower, in the form of numerous hyphae able to cross the wall between adjacent cells. Isolated bacteria were affiliated to the genera Paenibacillus, Pantoea, and Sanguibacter. Plate tests showed a general resistance to six different antibiotics and also to an antimicrobial-producing Rheinheimera sp. test strain. Finally, microbiome-deprived E. purpurea seeds showed a reduced ability to germinate, suggesting an active role of the microbiome in the plant vitality. Our results suggest that the endophytic bacterial community of E. purpurea, previously found in roots and stem/leaves, might be already carried at the seed stage, hosted by the cotyledons. A further microbial fungal component is transported together with the seed in the perianth of the cypsela, whose remarkable structure may be considered as an adaptation for fungal transportation, and could influence the capability of the seed to germinate in the soil.Key Points• The fruit of Echinacea purpurea contains fungi not causing any damage to the plant.• The seed cotyledons contain endocellular bacteria.• Seed/fruit deprived of the microbiome showed a reduced ability to germinate.

Evaluation of seed associated endophytic bacteria from tolerant chilli cv. Firingi Jolokia for their biocontrol potential against bacterial wilt disease

In this study, the seed endosphere of a bacterial wilt tolerant chilli cv. Firingi Jolokia was explored in order to find effective agents for bacterial wilt disease biocontrol. A total of 32 endophytic bacteria were isolated from freshly collected seeds and six isolates were selected based on R. solanacearum inhibition assay. These isolates were identified as Bacillus subtilis (KJ-2), Bacillus velezensis (KJ-4), Leuconostoc mesenteroides (KP-1), Lactococcus lactis (LB-3), Bacillus amyloliquefaciens (WK-2), and Bacillus subtilis (WK-3) by 16S rRNA gene sequencing. In the in planta R. solanacearum inhibition assay carried out by seedling root bacterization method, Bacillus subtilis (KJ-2) exhibited highest biocontrol efficacy of 86.6 % on 7^th day post R. solanacearum inoculation and a minimum biocontrol efficacy of 52.9 % was noted for Leuconostoc mesenteroides (KP-1). GC-HRMS analysis detected several known antimicrobial compounds in the extract of the culture supernatant of Bacillus subtilis (KJ-2); which may contribute to inhibition of R. solanacearum. In the growth promotion assay conducted using these isolates, only two of them namely Bacillus subtilis (KJ-2) and Bacillus amyloliquefaciens (WK-2) showed growth promotion in true leafed tomato plants. All the selected seed endophytic isolates were able to control bacterial wilt of tomato at the seedling stage and Bacillus subtilis (KJ-2) was found to be most effective in controlling the disease. The results of the present study highlighted that seed endosphere of bacterial wilt tolerant cultivar is a rich source of R. solanacearum antagonizing bacterial isolates.

Root-Associated Endophytic Bacterial Community Composition of Asparagus officinalis of Three Different Varieties

Asparagus (Asparagus officinalis L) is an economically important crop, rich in nutrients, and is also conducive to solving ecological and environmental problems. Plants may acquire benefits from root-associated endophytic bacteria. However, the composition of the endophytic bacterial community associated with the roots of asparagus is poorly elucidated. In this study, the nine root samples of asparagus from three different varieties including Asparagus officinalis var. Grande (GLD), A. officinalis var. Jinglvlu3 (JL3) and A. officinalis var. Jingzilu2 (JZL) were investigated by high-throughput sequencing technology of the 16S rDNA V5-V7 hypervariable region of endophytic bacteria. A total of 16 phyla, 29 classes, 90 orders, 171 families, and 312 genera were identified. Endophytic bacteria diversity and bacteria structure was different among the three varieties and was influenced by rhizosphere soil properties and varieties. In the GLD variety, the main phyla were Proteobacteria, Actinobacteria, and Firmicutes. The main phylum in JL3 and JZL varieties was Proteobacteria. The observations showed that GLD had the highest diversity of endophytes as indicated by the Shannon index (GLD > JZL > JL3). The order of the endophytes richness was GLD > JL3 > JZL. The PCA and PCoA analysis revealed the microbial communities were different between three different asparagus varieties, and the microbial composition of GLD and JZL was more similar. This report provides an important reference for the study of endophytic microorganisms of asparagus.

Supplementary information

The online version contains supplementary material available at (10.1007/s12088-021-00926-6) contains supplementary material, which is available to authorized users.

Impacts and tolerance responses of Coprinus comatus and Pleurotus cornucopiae on cadmium contaminated soil

Large amounts of cadmium (Cd) have been discharged into soil with the rapid development of industry. In this study, we revealed the impacts of Coprinus comatus (C. comatus) and Pleurotus cornucopiae (P. cornucopiae) on soil and the tolerance responses of macrofungi in the presence of Cd by the analysis of soil biochemical properties and macrofungi growth indexes. Results showed that with the cultivation of C. comatus and P. cornucopiae, the HOAc-extractable Cd in soil individually reduced by 9.53% and 11.35%, the activities of soil urease, acid phosphatase, dehydrogenase, and Fluorescein diacetate (FDA) hydrolysis increased by 18.11-101.45%, 8.39-18.24%, 9.37-55.50% and 28.94-41.92%, respectively. Meanwhile, different soil bacterial communities were observed with various macrofungi cultivations. Also, Cd accumulation significantly enhanced the macrofungi antioxidant enzyme activities, which increased by 24.10-45.43%, 30.11-61.53% and 7.03-26.81% for catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities in the macrofungi, respectively. Moreover, the enhanced macrofungi endophytic bacterial diversities with Cd existence was firstly observed in the present experiment. These findings revealed the possible Cd resistance mechanisms in macrofungi, suggesting C. comatus and P. cornucopiae were promising ameliorators for Cd contaminated soil.

Exploration of microbiome of medicinally important plants as biocontrol agents against Phytophthora parasitica

In a preliminary plant-based microbiome study, diverse bacterial taxa were identified from different medicinal plants using 16S rRNA gene sequencing. Based on initial antimicrobial screening, eight (8) bacterial endophytes in six (6) different genera, Streptomyces, Pseudomonas, Enterobacter, Bacillus, Arthrobacter, and Delftia, from four important medicinal plants Dodonaea viscosa, Fagonia indica, Caralluma tuberculata, and Calendula arvensis were selected for further analyses. Antimicrobial assays revealed that Pseudomonas taiwanensis MOSEL-RD23 has strong anti-Phytophthora activity. Volatiles produced by P. taiwanensis MOSEL-RD23and Bacillus flexus MOSEL-MIC5 inhibited the growth of Phytophthora parasitica by more than 80%. Ethyl acetate extracts of Streptomyces alboniger MOSEL-RD3, P. taiwanensis MOSEL-RD23, Enterobacter hormaechei MOSEL-FLS1, and Bacillus tequilensis MOSEL-FLS3, and Delftia lacustris MB322 displayed high potency against P. parasitica. All these bacterial extracts showed strong inhibition of more than 80% inhibition in vitro against P. parasitica at different concentrations (4-400 µg/mL). Bacterial extracts showing strong antimicrobial activity were selected for bioactivity-driven fractionation and showed anti-Phytophthoral activity in multiple fractions and different peaks observed in UV-Vis spectroscopy. In the detached-leaf assay against P. parasitica on tobacco, 1% ethyl acetate bacterial extract of S. alboniger MOSEL-RD3, P. taiwanensis MOSEL-RD23, E. hormaechei MOSEL-FLS1, B. tequilensis MOSEL-FLS3, and D. lacustris MB322 reduced lesion sizes and lesion frequencies caused by P. parasitica by 68 to 81%. Overall, P. taiwanensis MOSEL-RD23 showed positive activities for all the assays. Analyzing the potential of bacterial endophytes as biological control agents can potentially lead to the formulation of broad-spectrum biopesticides for the sustainable production of crops.

Volatile organic compounds profile synthesized and released by endophytes of tomato (Solanum lycopersici L.) and their antagonistic role

The endophytic microbiome uses mechanisms such as the secretion of diffusible antibiotic molecules, synthesis and release of volatile organic compounds, and/or toxins to protect plants. The aim of this research was to study the volatile organic compounds (VOCs) profile as well as the diffusible secondary metabolites produced and released by endophytic bacteria isolated from tomato plants that in in-vitro assays prevented growth of pathogenic fungi. Bacteria belonging to seven genera (Acinetobacter, Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, and Stenotrophomonas) were isolated from different tissues of tomato plants with and without symptoms of Gray leaf spot, a disease provoked by Stemphylium lycopersici. In vitro, antagonistic assays were performed and the effect of volatile and soluble compounds released by endophytic bacteria on the growth of pathogenic fungi was determined. The VOCs synthesized by the endophytes were extracted, identified and quantified. These isolates representatives of seven bacterial genera inhibited the growth of three fungal pathogens of tomato S. lycopersici, Alternaria alternata and Corynespora cassiicola, which was related to the synthesis of soluble compounds as well as VOCs. Endophytes synthesize and release different VOCs, probably due to the different type of interaction that each bacterium establishes with the fungus, presenting a range of fungal growth inhibition.

Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus

Background

Plants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear.

Methods

We analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants.

Results

Our results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations.

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest

Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant-epiphytic and plant-endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.

Bioprospecting of a novel endophytic Bacillus velezensis FZ06 from leaves of Camellia assamica: Production of three groups of lipopeptides and the inhibition against food spoilage microorganisms

Food contamination caused by microorganisms has become a threat to consumers' health. Exploring antagonistic endophytes from plants of food raw-material and applying bioactive metabolites to inhibit the contamination has been an alternative and safer solution. In this study, we isolated and screened potential antagonistic endophytes from fresh Camellia assamica leaves, which were widely used in tea beverage production. We focused on a strain that showed visible inhibitory activity to Gram-positive bacteria, Gram-negative bacteria, and fungi. It was identified as a member of Bacillus velezensis and named FZ06. The results of genome analysis showed the strain FZ06 had 167 single-copy specific genes, much higher than those of most related strains. Also, 11 potential gene clusters of antimicrobial metabolites were found. Three groups of lipopeptides (surfactin, iturin, and fengycin) were identified by UPLC-MS/MS in purified antimicrobial methanol fraction of strain FZ06. The results of minimum inhibitory concentration (MIC) test proved the lipopeptide extract showed significant inhibitory effect on food spoilage bacteria (MIC 512-2048 μg/mL) and toxigenic fungi (MIC 128-256 μg/mL). In conclusion, this study suggests that the endophytic B. velezensis FZ06 and its lipopeptide extract hold great potential applications in the inhibition of food spoilage bacteria and toxic fungi in food industry.

Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea mays L. var. DKB 177)

Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.25 %, 30 min), resulting in a reduction of the cultivable-dependent fraction of seed-borne bacteria population, but not significantly detected by real-time PCR, microscopy, and biochemical analysis of the roots on germinated seeds. 16S rRNA sequencing revealed that bacteriome of non-germinated seeds and roots of 5-d germinated seeds exhibited similar diversity and did not differ in the structure concerning seed-disinfection. On the other hand, the relative abundance reduction of the genera f_Enterobacteriaceae_922761 (unassigned genus), Azospirillum, and Acinetobacter in disinfected-seed prior germination seems to display changes in prominence of several new taxa in the roots of germinated seeds. Interestingly, this bacteriome community rebuilt negatively affected the germination speed and growth of maize plantlets. Additionally, bacteriome re-shape increased the maize var. DKB 177 susceptible to the seed-borne plant pathogen Penicillium sp. Such changes in the natural seed-borne composition removed the natural barrier, increasing susceptibility to pathogens, impairing disinfected seeds to germinate, and develop. We conclude that bacteria borne in seeds modulate the relative abundance of taxa colonizing emerged roots, promote germination, seedling growth, and protect the maize against fungal pathogens.

Comprehensive assessment of growth parameters for screening endophytic bacterial strains in Solanum lycopersicum (Tomato)

Conventional agricultural practices demand application of pesticides for better yield, yet their uncontrolled use for longer duration exhibit deleterious effects on the soil health and subsequent plant productivity. These circumstances have displayed alarming effects on food security in the modern world. Therefore, biological solutions to the crisis can be practiced in consideration to their environmental benefits. Bacterial endophytes are ubiquitous in the phytosystem and beneficial for the plant growth and productivity. The present study aimed to obtain endophytic bacterial strains that can be developed as effective plant growth promoters. For this purpose twelve strains of bacterial endophytes were isolated from different plant sources and their putative plant growth promoting attributes were analyzed by morphological and biochemical studies. Subsequently these isolates were inoculated in the Solanum lycopersicum (Tomato) and the factors like germination percentage, seedling length, biomass production, and leaf variables were analyzed. However, the vigour index was considered as the prime parameter for determining plant growth. In essence, RR2 and RR4 strains were observed as effective growth promoter, hence in future they can be utilized as effective biofertilizers.

Isolation and characterization of Pb-resistant plant growth promoting endophytic bacteria and their role in Pb accumulation by fast-growing trees

Lead (Pb) contamination is one of the major environmental problems on a global scale. Bacterial endophytes have been accepted as a promising technique to assist phytoremediation. In this study, three Pb-tolerant endophytic bacteria were isolated from the roots of Pityrogramma calomelanos. Based on partial 16S rRNA gene sequencing analysis, all isolates were similar to Pseudomonas and tolerated Pb concentration up to 1850mg/L, producing siderophores and solubilized phosphate. Among them, Pc isolate closely related to Pseudomonas psychrophila showed the highest water-soluble Pb in solution (Pb solubilization) and in contaminated soil. This isolate was chosen to study the effects on Pb accumulation in the roots of Acacia mangium and Eucalyptus camaldulensis by a hydroponic experiment. The results showed that, in the Hoagland nutrient solution with no Pb spiking, the roots showed no significant difference (p > 0.05), and the concentration of Pb ranged from 10 to 89 mg/kg. In the nutrient solution in the presence of 30 mg/L Pb, there were no significant changes in Pb contents in roots. However, A. mangium showed an increase in Pb concentration in the roots (6829 ± 697 mg/kg), compared to non-inoculation (6242 ± 272 mg/kg). E. camaldulensis inoculation showed a decrease in Pb content (3763 ± 592 mg/kg), compared to non-inoculation (4233 ± 264 mg/kg). These results suggest that the Pc isolate closely related to P. psychrophila was effective in promoting the phytoremediation potential of A. mangium, but it was not useful for E. camaldulensis.

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.

Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year

BACKGROUND

The dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites.

RESULTS

In this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1-3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1-3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium.

CONCLUSIONS

This study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.

Effect of different stimuli on twitching behavior of endophytic bacteria isolated from Loranthus sp. Jacq

Bacteria need to adopt to different behavioral tuning depending on the dynamic eco-physiological conditions they are exposed to. One of these adaptive strategies is the use of motility. Here we report the twitching motility response of four endophytic isolates of Bacillus sp. when exposed to different eco-physiological stimuli like different nutrient sources, and mechanical and chemical antagonists on solid surfaces. These endophytic bacteria were isolated from different parts of a hemiparasite Loranthus sp. Jacq. (Loranthaceae) growing on economically important mango trees. The results show that the twitching motility of these bacteria was more when exposed to organic acids, metals salts (among nutrients) and mechanical shearing (stress) than the other factors. Their motility is not affected by surface lubrication or EPS production, but instead is influenced by shear-sensitive structures and affinity to metal ions. Further molecular studies are needed to elucidate the basis of this twitching behaviour on solid surfaces.

Isolation and characterization of plant growth-promoting endophytic bacteria Bacillus stratosphericus LW-03 from Lilium wardii

In the present study, a new strain of Bacillus stratosphericus LW-03 was isolated from the bulbs of Lilium wardii. The isolated endophytic strain LW-03 exhibited excellent antifungal activity against common plant pathogens, such as Fusarium oxysporum, Botryosphaeria dothidea, Botrytis cinerea, and Fusarium fujikuroi. The growth inhibition percentage of Botryosphaeria dothidea was 74.56 ± 2.35%, which was the highest, followed by Botrytis cinerea, Fusarium fujikuroi, and Fusarium oxysporum were 71.91 ± 2.87%, 69.54 ± 2.73%, and 65.13 ± 1.91%, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several of which were putatively identified as antimicrobial agents, such as 4-hydroxy-2-nonenylquinoline N-oxide, sphingosine ceramides like cer(d18:0/16:0(2OH)), cer(d18:0/16:0), and cer(d18:1/0:0), di-peptides, tri-peptide, cyclopeptides [cyclo(D-Trp-L-Pro)], [cyclo (Pro-Phe)], dehydroabietylamine, oxazepam, 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine like compound (PC(0:0/20:4), phosphatidylethanolamine (PE(18:1/0:0)), 3-Hydroxyoctadecanoic acid, 7.alpha.,27-Dihydroxycholesterol, N-Acetyl-d-mannosamine, p-Hydroxyphenyllactic acid, Phytomonic acid, and 2-undecenyl-quinoloin-4 (1H). The LW-03 strain exhibits multiple plant growth-promoting traits, including the production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation activity. The beneficial effects of the endophytic strain LW-03 on the growth of two lily varieties were further evaluated under greenhouse conditions. Our results revealed plant growth-promoting activity in inoculated plants relative to non-inoculated control plants. The broad-spectrum antifungal activity and multiple plant growth-promoting properties of Bacillus stratosphericus LW-03 make it an important player in the development of biological fertilizers and sustainable agricultural biological control strategies.

The Endophytic Bacteria Bacillus velezensis Lle-9, Isolated from Lilium leucanthum, Harbors Antifungal Activity and Plant Growth-Promoting Effects

Bacillus velezensis is an important plant growth-promoting rhizobacterium with immense potential in agriculture development. In the present study, Bacillus velezensis Lle-9 was isolated from the bulbs of Lilium leucanthum. The isolated strain showed antifungal activities against plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea and Fusarium fujikuroi. The highest percentage of growth inhibition i.e., 68.56±2.35% was observed against Fusarium oxysporum followed by 63.12 ± 2.83%, 61.67 ± 3.39% and 55.82 ± 2.76% against Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several were identified as antimicrobial agents such as diketopiperazines, cyclo-peptides, linear peptides, latrunculin A, 5α-hydroxy-6-ketocholesterol, (R)-S-lactoylglutathione, triamterene, rubiadin, moxifloxacin, 9-hydroxy-5Z,7E,11Z,14Zeicosatetraenoic acid, D-erythro-C18-Sphingosine, citrinin, and 2- arachidonoyllysophosphatidylcholine. The presence of these antimicrobial compounds in the bacterial culture might have contributed to the antifungal activities of the isolated B. velezensis Lle- 9. The strain showed plant growth-promoting traits such as production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation and phosphate solubilization. IAA production was accelerated with application of exogenous tryptophan concentrations in the medium. Further, the lily plants upon inoculation with Lle-9 exhibited improved vegetative growth, more flowering shoots and longer roots than control plants under greenhouse condition. The isolated B. velezensis strain Lle-9 possessed broad-spectrum antifungal activities and multiple plant growth-promoting traits and thus may play an important role in promoting sustainable agriculture. This strain could be developed and applied in field experiments in order to promote plant growth and control disease pathogens.

Burkholderia Phytofirmans PsJN Stimulate Growth and Yield of Quinoa under Salinity Stress

One of the major challenges in agriculture is to ensure sufficient and healthy food availability for the increasing world population in near future. This requires maintaining sustainable cultivation of crop plants under varying environmental stresses. Among these stresses, salinity is the second most abundant threat worldwide after drought. One of the promising strategies to mitigate salinity stress is to cultivate halotolerant crops such as quinoa. Under high salinity, performance can be improved by plant growth promoting bacteria (PGPB). Among PGPB, endophytic bacteria are considered better in stimulating plant growth compared to rhizosphere bacteria because of their ability to colonize both in plant rhizosphere and plant interior. Therefore, in the current study, a pot experiment was conducted in a controlled greenhouse to investigate the effects of endophytic bacteria i.e., Burkholderia phytofirmans PsJN on improving growth, physiology and yield of quinoa under salinity stress. At six leaves stage, plants were irrigated with saline water having either 0 (control) or 400 mM NaCl. The results indicated that plants inoculated with PsJN mitigated the negative effects of salinity on quinoa resulting in increased shoot biomass, grain weight and grain yield by 12%, 18% and 41% respectively, over un-inoculated control. Moreover, inoculation with PsJN improved osmotic adjustment and ion homeostasis ability. In addition, leaves were also characterized for five key reactive oxygen species (ROS) scavenging enzyme in response to PsJN treatment. This showed higher activity of catalase (CAT) and dehydroascobate reductase (DHAR) in PsJN-treated plants. These findings suggest that inoculation of quinoa seeds with Burkholderia phytofirmans PsJN could be used for stimulating growth and yield of quinoa in highly salt-affected soils.

Antagonistic activity of olive endophytic bacteria and of Bacillus spp. strains against Xylella fastidiosa

Strains of Xylella fastidiosa subsp. pauca characterized by a specific genotype, the so called sequence type "ST53", have been associated with a severe disease named Olive Quick Decline Syndrome (OQDS). Despite the relevant research efforts devoted to control the disease caused by X. fastidiosa, so far there are no therapeutic means able to cure the infected host plants. As such, the aim of this study was the identification of antagonistic bacteria potentially deployable as bio-control agents against X. fastidiosa. To this end, two approaches were used, i.e. the evaluation of the antagonistic activity of: i) endophytic bacteria isolated from olive trees located in an infected area but showing mild or no symptoms, and ii) Bacillus strains, as they are already known as bio-control agents. Characterization of endophytic bacterial isolates revealed that the majority belonged to different species of the genera Sphingomonas, Methylobacterium, Micrococcus and Curtobacterium. However, when they were tested in vitro against X. fastidiosa ST53 none of them showed antagonistic activity. On the contrary, when strains belonging to different species of the genus Bacillus were included in these tests, remarkable antagonistic activities were recorded. Some B. velezensis strains also produced culture filtrates with inhibitory activity against X. fastidiosa ST53. Taking also into account that two of these B. velezensis strains (namely strains D747 and QST713) are already registered and commercially available as bio-control agents, our results pave the way for further studies aimed at the development of a sustainable bio-control strategy of the OQDS.

Midgut microbiota diversity of potato tuber moth associated with potato tissue consumed

Background

The potato tuber moth (PTM), Phthorimaea operculella (Zeller), is a worldwide pest that feeds on both the leaves and tubers of potato plants. PTM larvae can digest leaves, or tubers, resulting in serious damage to potato plants in the field and potato tubers in storage. To understand how midgut bacterial diversity is influenced by the consumption of these two tissue types, the symbiotic bacteria in the potato-feeding PTM midgut and the endophytic bacteria of potato tissues were analyzed.

Results

At the genus level, the bacterial community composition in the PTM midgut was influenced by the tissues consumed, owing to their different nutrient contents. Escherichia_Shigella and Enterobacter were the most dominant genera in the midgut of leaf-feeding and tuber-feeding PTMs, respectively. Interestingly, even though only present in low abundance in leaves and tubers, Escherichia_Shigella were dominantly distributed only in the midgut of leaf-feeding PTMs, indicating that specific accumulation of these genera have occurred by feeding on leaves. Moreover, Enterobacter, the most dominant genus in the midgut of tuber-feeding PTMs, was undetectable in all potato tissues, indicating it is gut-specific origin and tuber feeding-specific accumulation. Both Escherichia_Shigella and Enterobacter abundances were positively correlated with the dominant contents of potato leaves and tubers, respectively.

Conclusions

Enrichment of specific PTM midgut bacterial communities was related to different nutrient levels in different tissues consumed by the insect, which in turn influenced host utilization. We provide evidence that a portion of the intestinal microbes of PTMs may be derived from potato endophytic bacteria and improve the understanding of the relationship between potato endophytic bacteria and the gut microbiota of PTMs, which may offer support for integrated management of this worldwide pest.