Klebsiella pneumoniae SnebYK Mediates Resistance Against Heterodera glycines and Promotes Soybean Growth

Wheat Rhizosphere-Derived Bacteria Protect Soybean from Soilborne Diseases

Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean 'Williams 82'. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Antagonistic activity and mechanism of Bacillus subtilis CG-6 suppression of root rot and growth promotion in Alfalfa

Root rot is a common disease, that severely affects the yield and quality of alfalfa. Biocontrol is widely used to control plant diseases caused by pathogenic fungi, however, biocontrol strains for alfalfa root rot are very limited. In this study, a Bacillus subtilis CG-6 strain with a significant biocontrol effect on alfalfa root rot was isolated. CG-6 secretes antibacterial enzymes and siderophore, phosphate solubilization and indoleacetic acid (IAA). The inhibition rate of strain CG-6 against Fusarium oxysporum was 87.33%, and it showed broad-spectrum antifungal activity. Inoculation with CG-6 significantly reduced the incidence of alfalfa root rot, the control effect of greenhouse cultivation reached 58.12%, and CG-6 treatment significantly increased alfalfa plant height, root length, fresh weight, and dry weight. The treatment with CG-6 significantly increased the levels of antioxidant enzymes (catalase, peroxidase, superoxide dismutase, and lipoxygenase) in alfalfa leaves by 15.52%-34.03%. Defensive enzymes (chitinase and β-1,3-glucanase) increased by 24.37% and 28.08%, respectively. The expression levels of regulatory enzyme genes (MsCAT, MsPOD, MsCu, Zn-SOD1, MsCu, Zn-SOD2, MsCu, Zn-SOD3, and MsLOX2) and systemic resistance genes (MsPR1, MsPDF1.2, and MsVSP2) increased by 0.50-2.85 fold, which were higher than those in the pathogen treatment group. Therefore, CG-6 could be used as a potential strain to develop biopesticides against alfalfa root rot.

Biocontrol Efficacy and Induced Resistance of Paenibacillus polymyxa J2-4 Against Meloidogyne incognita Infection in Cucumber

Meloidogyne incognita is one of the most destructive agricultural pathogens around the world, resulting in severe damage to yield and quality in agricultural production. Biological control promises to be a great potential alternative to chemical agents against M. incognita. Paenibacillus polymyxa J2-4, isolated from ginger plants injured by M. incognita, has shown excellent biocontrol efficacy against M. incognita in cucumber. In vitro experiments with the strain J2-4 resulted in a correct mortality rate of 88.79% (24 h) and 98.57% (48 h) for second-stage juveniles (J2s) of M. incognita. Strain J2-4 significantly suppressed nematode infection on potted plants, with a 65.94% reduction in galls and a 51.64% reduction in eggs compared with the control. The split-root assay demonstrated that strain J2-4 not only reduced J2s' invasion but also inhibited nematode development through the dependence on salicylic acid and jasmonic acid signaling of strain J2-4 induction of plant resistance in local and systemic roots of cucumbers. Genomic analysis of strain J2-4 indicated biosynthetic gene clusters encoding polymyxin, fusaricidin B, paenilan, and tridecaptin. In addition, genetic analysis showed that none of the genes encoding virulence factors were detected in the genome of J2-4 compared with the pathogenic Bacillus species. Taking all the data together, we conclude that P. polymyxa J2-4 has potential as a biological control agent against M. incognita on cucumbers and can be considered biologically safe when used in agriculture.

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials

BACKGROUND

As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.

RESULTS

WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.

CONCLUSION

All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation

Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.

Biocontrol potential of Pseudomonas rhodesiae GC-7 against the root-knot nematode Meloidogyne graminicola through both antagonistic effects and induced plant resistance

Plant-parasitic nematodes (PPNs) cause serious damage to agricultural production worldwide. Currently, because of a lack of effective and environmental-friendly chemical nematicides, the use of microbial nematicides has been proposed as an eco-friendly management strategy to control PPNs. A nematicidal bacterium GC-7 was originally isolated from the rice rhizosphere, and was identified as Pseudomonas rhodesiae. Treatment with the fermentation supernatant of GC-7 in vitro showed a highly lethal effect on second-stage juveniles of Meloidogyne graminicola, with the mortality rate increasing to 95.82% at 24 h and egg hatching significantly inhibited, with a hatch inhibition rate of 60.65% at 96 h. The bacterium significantly reduced the level of damage caused by M. graminicola infestations to rice (Oryza sativa) in greenhouse and field experiments. Under greenhouse conditions, the GC-7 culture efficiently reduced the gall index and nematode population in rice roots and soils, as well as inhibited nematode development compared to the control. Under field conditions, application of the GC-7 consistently showed a high biocontrol efficacy against M. graminicola (with a control efficiency of 58.85%) and promoted plant growth. In addition, the inoculation of GC-7 in M. graminicola-infested rice plant fields significantly suppressed final nematode populations in soil under natural conditions. Furthermore, activities of plant defense-related enzymes, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase were remarkably increased in plant roots treated with GC-7 compared with roots that were challenge to M. graminicola. Moreover, quantitative real-time PCR analysis showed that GC-7 significantly enhanced the expression of defense genes (PR1a, WRKY45, JaMYB, AOS2, ERF1, and ACS1) related to salicylic acid, jasmonic acid, and ethylene signaling pathways in rice roots after inoculation with GC-7 at different levels. The results indicated that GC-7 could be an effective biological component in the integrated management of M. graminicola infecting rice.

Systemic Resistance Induction of Potato and Tobacco Plants against Potato Virus Y by Klebsiella oxytoca

Simple Summary

Klebsiella oxytoca, as a type of plant growth-promoting rhizobacteria (PGPR), was studied with regards to promoting plant growth and inducing plant systemic resistance against Potato Virus Y (PVY). The results of greenhouse experiments with tobacco and potato plants demonstrated that treatments with the Klebsiella oxytoca and biochar significantly enhanced the growth, while clearly lowering the disease severity and concentration of PVY. An RT-PCR analysis of the defense genes in the tobacco and potato treated with the Klebsiella oxytoca and biochar revealed an association with enhancing the systemic resistance of tobacco and potato to PVY. Klebsiella oxytoca and biochar may be considered valuable options to control PVY in potato and other Solanaceae crops.

Abstract

Potato Virus Y (PVY) is a serious potato disease that may significantly decrease potato production. To suppress potato virus infection, several measures have been undertaken. The utilization of plant growth-promoting rhizobacteria is one of these methods. Biochar soil treatment is believed to provide plants with a number of advantages, including increased plant growth and the development of systemic resistance to a variety of plant diseases. The goal of this research was to see whether adding biochar and Klebsiella oxytoca to the soil might cause PVY resistance and enhance the involved mechanisms in PVY resistance. Potato and tobacco seedlings treated with Klebsiella oxytoca and biochar exhibited the same impact of significant symptom reduction, with complete negative ELISA findings, supporting the antiviral activity of K. oxytoca and biochar. Furthermore, owing to the connection between the ISR implicated substrates, significant amounts of polyphenol oxidase, catalase, and superoxide dismutase were observed in treated plants, with the same behavior as defense genes expression levels. It may be a step forward in the development of biochar and K. oxytoca as potential environmentally friendly disease control strategies against PVY.

Biological Control Efficacy and Action Mechanism of Klebsiella pneumoniae JCK-2201 Producing Meso-2,3-Butanediol Against Tomato Bacterial Wilt

Bacterial wilt caused by Ralstonia solanacearum is a fatal disease that affects the production of tomatoes and many other crops worldwide. As an effective strategy to manage bacterial wilt, biological control agents using plant growth-promoting rhizobacteria (PGPR) are being developed. In this study, we screened 2,3-butanediol (BDO)-producing PGPR to control tomato bacterial wilt and investigated the action mechanism of the disease control agent. Of the 943 strains isolated from soil, Klebsiella pneumoniae strain JCK-2201 produced the highest concentration of 2,3-BDO. The culture broth of K. pneumoniae JCK-2201 did not show any direct activity on R. solanacearum in vitro, but a 100-fold dilution effectively controlled tomato bacterial wilt with a control value of 77% in vivo. Fermentation utilizing K. pneumoniae JCK-2201 was optimized to produce 48 g/L of meso-2,3-BDO, which is 50% of the sucrose conversion efficiency. In addition, the control efficacy and mechanism of meso-2,3-BDO produced by JCK-2201 in tomato bacterial wilt were determined by comparative analysis with Bacillus licheniformis DSM13 producing meso-2,3-BDO and B. licheniformis DSM13 ΔalsS that did not produce 2,3-BDO, as the step of converting pyruvate to α-acetolactate was omitted. Tomato seedlings treated with the K. pneumoniae JCK-2201 (500-fold dilution) and B. licheniformis DSM13 (100-fold dilution) culture broth produced meso-2,3-BDO that significantly reduced R. solanacearum-induced disease severity with control values of 55% and 63%, respectively. The formulated meso-2,3-BDO 9% soluble concentrate (SL; 1,000-fold dilution) showed 87% control against tomato bacterial wilt in the field condition. Klebsiella pneumoniae JCK-2201 and B. licheniformis DSM13 treatment induced the expression of plant defense marker genes, such as LePR1, LePR2, LePR5, LePR3, and PI-II, in the salicylic acid and jasmonic acid signaling pathways at 4 days after inoculation. These results show that 2,3-BDO-producing bacteria and 2,3-BDO are potential biological control agents that act through induction of resistance for controlling tomato bacterial wilt.

Validation and Evaluation of Plant Growth Promoting Potential of Rhizobacteria Towards Paddy Plants

This study aimed to characterize, validate, and evaluate the plant growth potential of bacterial isolates (E-2, T-2, and T-1) to determine their suitability for application as biofertilizers and/or plant-biostimulants. The plant growth-promoting potential of bacteria (E-2, T-2, and T-1) has been validated in a hydroponic study on paddy plants by inoculating bacterial isolates and monitoring the phenotypic and plant growth responses. The applicability of bacteria was tested based on their tolerance to salinity, susceptibility to antibiotics, and identification based on 16S rDNA sequencing. The isolates E-2, T-2, and T-1 improved plant growth variably and significantly (P < 0.05 at 95% confidence interval) when inoculated into the plant growth matrix, ensuring nutrient availability to the plants grown under a nutrient (nitrate or phosphate) deprived growth matrix. Isolates E-2, T-2, and T-1 grew at salt (NaCl) concentrations of 7%, 6%, and 6%, respectively, and were tolerant to saline conditions. Although these three isolates exhibited resistance to certain antibiotics, they were susceptible to a large number of readily available antibiotics. Isolates E-2, T-2, and T-1 were identified as Klebsiella sp. strain BAB-6433, Citrobacter freundii strain R2A5, and Citrobacter sp. DY1981 respectively, and all of these may be assigned to Risk-Group-2 and hence are safe in view of their susceptibility to readily available antibiotics. Hence, these isolates are promising for extensive evaluation as bioinoculants to ecologically improve soil quality, fertility, crop growth, and yield.

Catmint (Nepeta nuda L.) Phylogenetics and Metabolic Responses in Variable Growth Conditions

Nepeta nuda (catmint; Lamiaceae) is a perennial medicinal plant with a wide geographic distribution in Europe and Asia. This study first characterized the taxonomic position of N. nuda using DNA barcoding technology. Since medicinal plants are rich in secondary metabolites contributing to their adaptive immune response, we explored the N. nuda metabolic adjustment operating under variable environments. Through comparative analysis of wild-grown and in vitro cultivated plants, we assessed the change in phenolic and iridoid compounds, and the associated immune activities. The wild-grown plants from different Bulgarian locations contained variable amounts of phenolic compounds manifested by a general increase in flowers, as compared to leaves, while a strong reduction was observed in the in vitro plants. A similar trend was noted for the antioxidant and anti-herpesvirus activity of the extracts. The antimicrobial potential, however, was very similar, regardless the growth conditions. Analysis of the N. nuda extracts led to identification of 63 compounds including phenolic acids and derivatives, flavonoids, and iridoids. Quantification of the content of 21 target compounds indicated their general reduction in the extracts from in vitro plants, and only the ferulic acid (FA) was specifically increased. Cultivation of in vitro plants under different light quality and intensity indicated that these variable light conditions altered the content of bioactive compounds, such as aesculin, FA, rosmarinic acid, cirsimaritin, naringenin, rutin, isoquercetin, epideoxyloganic acid, chlorogenic acid. Thus, this study generated novel information on the regulation of N. nuda productivity using light and other cultivation conditions, which could be exploited for biotechnological purposes.

Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

Metabolic properties, gene functions, and biosafety analysis reveal the action of three rhizospheric plant growth-promoting bacteria of Jujuncao (Pennisetum giganteum)

This study aimed to identify the specific genes associated with plant growth promotion and cadmium tolerance in three bacteria strains associated with Pennisetum giganteum as well as to determine their biosafety levels in their potential use as biofertilizers for promoting plant growth and phytoremediation activities. The plant growth-promoting (PGP) abilities of Enterobacter cloacae strain RCB980 (A3), Klebsiella pneumonia strain kpa (A4), and Klebsiella sp. strain XT-2 (A7) were determined by a growth promotion trial and through testing for PGP traits such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase enzyme production, phosphorus solubilization, siderophore synthesis, and indole-3 acetic acid (IAA) production. The genes that potentially contribute to the beneficial activities of these three strains were identified through an analysis of their genomes. To establish the biosafety of the candidate PGPB, a pathological study was undertaken whereby 20 Kunming mice were injected intraperitoneally to study and analyze the effects of the strains on growth and lung paraffin sections of the mice. The strains had no obvious toxicity effect on the tested mice and were therefore not considered as highly virulent strains. These strains are thus considered non-toxic, safe, and highly recommended for use in environmental remediation strategies and agricultural production.

Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions

Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.

Variation in Peperomia pellucida growth and secondary metabolism after rhizobacteria inoculation

Peperomia pellucida L. Kunth is a herb well-known for its secondary metabolites (SM) with biological potential. In this study, the variations in the SM of P. pellucida during association with rhizobacteria were evaluated. Plants were inoculated with Enterobacter asburiae and Klebsiella variicola, which were identified by sequencing of the 16S rRNA gene. The data were evaluated at 7, 21, and 30-day post inoculation (dpi). Plant-bacteria symbiosis improved plant growth and weight. Total phenolic content and phenylalanine ammonia lyase enzyme activity had a significant increase mainly at 30 dpi. P. pellucida was mainly composed of phenylpropanoids (37.30-52.28%) and sesquiterpene hydrocarbons (39.28-49.42%). The phenylpropanoid derivative 2,4,5-trimethoxy-styrene (ArC2), the sesquiterpene hydrocarbon ishwarane, and the phenylpropanoid dillapiole were the major compounds. Principal component analysis (PCA) of the classes and compounds ≥ 2.0% indicated that plants colonized by E. asburiae had a reduction in the content of sesquiterpene hydrocarbons and an increase in phenylpropanoids and derivatives. Plants treated with this bacterium also had an increase in the content of 2,4,5-trimethoxystyrene at 30 dpi. Plants inoculated with K. variicola had significant increases only in the content of the classes monoterpene hydrocarbons and 'other compounds' (hydrocarbons, esters, ketones, etc.). These data suggest that the production of plant secondary metabolites can be modified depending on the type of rhizobacteria inoculated.

Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis

Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5'-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index-3.47), and protease activity (proteolytic index-2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03020-2.

Evaluation of Scopoletin from Penicillium janthinellum Snef1650 for the Control of Heterodera glycines in Soybean

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is responsible for causing a major soybean disease globally. The fungal strain Penicillium janthinellum Snef1650 was evaluated against H. glycines. However, the effective determinants of the P. janthinellum strain are unknown. By performing pot experiments, a functioning compound was isolated from P. janthinellum Snef1650 through organic solvent extraction, semi-preparative HPLC, Sephadex LH-20 column chromatography, and silica gel column chromatography, and the isolated compound was identified to be scopoletin through 1H NMR, 13C NMR, and HPLC–MS. The pot experiments indicated that the treatment of soybean seeds with scopoletin drastically reduced the SCN population. The field experiments performed in 2017 and 2018 revealed that scopoletin decreased over 43.7% juveniles in the roots and over 61.55% cysts in the soil. Scopoletin treatment also promoted soybean growth and improved its yield, with an increase in plot yield by >5.33%. Scopoletin obtained from P. janthinellum Snef1650 could be used as an anti-H. glycines biocontrol agent.

Co-composting of cotton residues with olive mill wastewater: process monitoring and evaluation of the diversity of culturable microbial populations

With the aim to recommend an integrated alternative for the combined treatment of olive mill wastewater (OMW) and cotton residues (CR), and the production of high value and environmentally friendly products, two compost piles were set up. The first pile (control, pile 1) consisted of ginned CR, whereas the second (pile 2) was made of CR with the addition of OMW. A series of physicochemical parameters and the culturable microbial diversity in both piles were assessed. Co-composting (pile 2) displayed higher temperatures during the whole process, a prolonged second thermophilic phase and temperature values higher than 40 °C even after the thermophilic stage. Comparing the physicochemical parameters of the pile 2 with those of the pile 1, it was deduced that pH in the former was more acidic during the onset of the process; the EC values were higher throughout the process, while the levels of ammonium and nitrate nitrogen, as well as the NH₄⁺/NO₃^- ratios, were lower at most of the sampling dates. By evaluating the abovementioned results, it was estimated that the co-composting process headed sooner toward stability and maturity, Isolated microorganisms from both piles were identified as members of the genera Brevibacillus, Serratia, Klebsiella, and Aspergillus, whereas active thermotolerant diazotrophs were detected in both piles at the 2nd thermophilic phase emerging a promising prospect upon further evaluation for enhancing the end-product quality. Our findings indicate that co-composting is an interesting approach for the exploitation of large quantities of agro-industrial residues with a final product suitable for improving soil fertility and health.

Genomic appraisal of Klebsiella PGPB isolated from soil to enhance the growth of barley

BACKGROUND

PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions.

OBJECTIVE

To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition.

METHODS

We evaluated the activity of three Klebsiella spp. in two different conditions, specific nitrogen-deficient MS media and greenhouse experiment. Applying comparative genomics, genes encoding for PGP traits were identified from the whole-genome sequencing of the three strains. With the help of the RAST tool kit and functional annotation, a total number of genes encoding for cell wall capsule, nitrogen metabolism, sulfur genes and many other functional groups were identified. With the help of blast circular genome, similarity between GC content, pseudogene and tRNA was represented. The percentage of gene similarity of SSN1 was generated against BLAST with M5a1 and SGM81. Other methods like synteny alignment and orthologous gene clusters were applied to understand the homologous present in three strains.

RESULTS

SSN1 was actively producing the maximum amount of ammonia 10.97 ± 0.29 µmol/mL compared to the other two strains. K. oxytoca M5a1 was considered negative for all PGP traits except ammonia production. The activity of SSN1 was showing a consistent pattern both the conditions whereas M5a1 was only active in vitro condition. Gene encoding for allantoin metabolism allD, allC, allB, allA, allE, allR, allH were identified in SSN1 and M5a1 but was absent in SGM81. The highest COG was shared between SGM81 and SSN1 predicting a maximum number of similar genes. The nif gene cluster was 98 % identical to the M5a1 strain.

CONCLUSIONS

Comparatively, SSN1 expressed the additional gene for various PGP traits which suggest higher efficiency of strain in nitrogen deficiency stress.

Efficacy of Bacillus megaterium strain Sneb207 against soybean cyst nematode (Heterodera glycines) in soybean

BACKGROUND

The soybean cyst nematode (SCN, Heterodera glycines) is the most devastating and yield-limiting pest in soybean worldwide. With the increasing awareness of environmental protection, biological control becomes more and more urgent. The Bacillus megaterium Sneb207 has previously shown the ability to inhibit the movement of SCN, but little is known about its effect on nematode control in agricultural settings. The aim of this study was to evaluate the efficiency of Sneb207 against SCN and investigate the ability of Sneb207 to induce systemic resistance to H. glycines in soybean.

RESULTS

The stability and efficiency of SCN control by Sneb207 was assessed in two field experiments. Compared to non-treated control, Sneb207 significantly reduced the number of cysts, SCN juveniles, and eggs, while it promoted soybean growth. Furthermore, results of two pot experiments showed that the number of initial infections of second-stage juveniles were 231.75 and 131.3 after Sneb207 treatment, respectively, lower than control (274.75 and 215.33). Sneb207 reduced the total number of juveniles and females, and lengthened SCN development time. Moreover, through the split-root system and real-time quantitative PCR experiments, we found that Sneb207 induced systemic resistance and enhanced the gene expression of GmACS9b, GmEDS1, GmPAD4, GmSAMT1, and GmNPR1-1 involved in the salicylic acid, jasmonic acid and ethylene pathways at different levels.

CONCLUSION

Our results demonstrate that B. megaterium Sneb207 inhibits the invasion, the development, and reproduction of SCN by inducing systemic resistance. The overall outcomes of the present study support B. megaterium Sneb207 as a potential biocontrol agent for H. glycines.

iTRAQ-Based Proteomic Analysis Reveals the Role of the Biological Control Agent, Sinorhizobium fredii Strain Sneb183, in Enhancing Soybean Resistance Against the Soybean Cyst Nematode

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, poses a serious threat to soybean production worldwide. Biological control agents have become eco-friendly candidates to control pathogens. Our previous study indicated that the biocontrol agent, Sinorhizobium fredii strain Sneb183, may induce soybean resistance to SCN. To study the mechanisms underlying induced disease resistance in the plant by Sneb183, an iTRAQ (isobaric tag for relative and absolute quantitation)-based proteomics approach was used to identify proteomic changes in SCN-infected soybean roots derived from seeds coated with the Sneb183 fermentation broth or water. Among a total of 456 identified differentially expressed proteins, 212 and 244 proteins were upregulated and downregulated, respectively, in Sneb183 treated samples in comparison to control samples. Some identified differentially expressed proteins are likely to be involved in the biosynthesis of phenylpropanoid, flavone, flavanol, and isoflavonoid and have a role in disease resistance and adaptation to environmental stresses. We used quantitative real-time PCR (qRT-PCR) to analyze key genes, including GmPAL (phenylalanine ammonia-lyase), GmCHR (chalcone reductase), GmCHS (chalcone synthase), and GmIFS (isoflavone synthase), that are involved in isoflavonoid biosynthesis in Sneb183-treated and control samples. The results showed that these targeted genes have higher expression levels in Sneb183-treated than in control samples. High performance liquid chromatography (HPLC) analysis further showed that the contents of daidzein in Sneb183-treated samples were 7.24 times higher than those in control samples. These results suggested that the Sinorhizobium fredii strain Sneb183 may have a role in inducing isoflavonoid biosynthesis, thereby resulting in enhanced resistance to SCN infection in soybean.

Isolation and identification of induced systemic resistance determinants from Bacillus simplex Sneb545 against Heterodera glycines

Heterodera glycines is one of the most destructive pathogens of soybean. Soybean seeds coated with Bacillus simplex Sneb545 have shown resistance to H. glycines as a result of induced systemic resistance (ISR) in the plants. In this study, we aimed to identify the resistance-inducing determinants from this B. simplex strain. Combining the ISR bioassay, six ISR-active compounds were isolated from a culture of B. simplex Sneb545 using organic solvent gradient extraction, silica gel column chromatography, Sephadex LH-20 column chromatography, and semi-preparative high-performance liquid chromatography (HPLC), and all systems were based on activity tracking. The compounds were determined as cyclic(Pro-Tyr), cyclic(Val-Pro), cyclic(Leu-Pro), uracil, phenylalanine, and tryptophan using 1H NMR and 13C NMR. In plants from seeds coated with Bacillus simplex Sneb545, these six ISR-active compounds delayed the development of H. glycines in soybean roots. Moreover, cyclic(Pro-Tyr), cyclic(Val-Pro), and tryptophan reduced the number of nematodes in soybean roots. The expression levels of defense-related genes with cyclic(Val-Pro), tryptophan and uracil treatment soybean analysed using Quantitative real-time PCR (qRT-PCR). The results indicate cyclic(Val-Pro), tryptophan and uracil induced the expression of defense-related genes involved in the SA- and JA-pathways to against H. glycines. Our research results provide new agents for the control of H. glycines.

Biocontrol potential of Microbacterium maritypicum Sneb159 against Heterodera glycines

BACKGROUND

The soybean cyst nematode Heterodera glycines (Ichinohe) is the most devastating pathogen affecting soybean production worldwide. Biocontrol agents have become eco-friendly candidates to control pathogens. The aim of this study was to discover novel biocontrol agents against H. glycines.

RESULTS

Microbacterium maritypicum Sneb159, screened from 804 strains, effectively reduced the number of females in field experiments conducted in 2014 and 2015. The stability and efficiency of H. glycines control by Sneb159 was further assessed in growth chamber and field experiments. Sneb159 decreased H. glycines population densities, especially the number of females by 43.9%-67.7%. To confirm Sneb159 induced plant resistance, a split-root assay was conducted. Sneb159 induced local and systemic resistance to suppress the penetration and development of H. glycines, and enhanced the gene expression of PR2, PR3b, and JAZ1, involved in the salicylic acid and jasmonic acid pathways.

CONCLUSION

This is the first report of M. maritypicum Sneb159 suppressing H. glycines infection. This effect may be the result of Sneb159-induced resistance. Our study indicates that M. maritypicum Sneb159 is a promising biocontrol agent against H. glycines. © 2019 Society of Chemical Industry.

Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery-Relevant Compounds

Advances in engineering biology have expanded the list of renewable compounds that can be produced at scale via biological routes from plant biomass. In most cases, these chemical products have not been evaluated for effects on biological systems, defined in the present study as bioactivity, that may be relevant to their manufacture. For sustainable chemical and fuel production, the industry needs to transition from fossil to renewable carbon sources, resulting in unprecedented expansion in the production and environmental distribution of chemicals used in biomanufacturing. Further, although some chemicals have been assessed for mammalian toxicity, environmental and agricultural hazards are largely unknown. We assessed 6 compounds that are representative of the emerging biofuel and bioproduct manufacturing process for their effect on model plants (Arabidopsis thaliana, Sorghum bicolor) and show that several alter plant seedling physiology at submillimolar concentrations. However, these responses change in the presence of individual bacterial species from the A. thaliana root microbiome. We identified 2 individual microbes that change the effect of chemical treatment on root architecture and a pooled microbial community with different effects relative to its constituents individually. The present study indicates that screening industrial chemicals for bioactivity on model organisms in the presence of their microbiomes is important for biologically and ecologically relevant risk analyses. Environ Toxicol Chem 2019;38:1911-1922. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.