Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance

Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina

BACKGROUND

Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.

RESULTS

Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.

CONCLUSION

The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.

Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli

The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.

Improvement of Euglena gracilis Paramylon Production through a Cocultivation Strategy with the Indole-3-Acetic Acid-Producing Bacterium Vibrio natriegens

We investigated the putative effects on the growth and paramylon production of Euglena gracilis of cocultivation with Vibrio natriegensE. gracilis heterotrophically cocultivated with V. natriegens displayed significant increases in biomass productivity and paramylon content. In addition, the effects of the bacterial inoculum density and the timing of inoculation on the growth of E. gracilis were examined, to determine the optimal conditions for cocultivation. With the optimal deployment of V. natriegens, biomass productivity and paramylon content were increased by more than 20% and 35%, respectively, compared to those in axenic E. gracilis cultures. Interestingly, indole-3-acetic acid biosynthesized by V. natriegens was responsible for these enhancements of E. gracilis The morphology of cocultured E. gracilis cells was assessed. Paramylon granules extracted from the cocultivation were significantly larger than those from axenic culture. Our study showed that screening for appropriate bacteria and subsequent cocultivation with E. gracilis represented an effective way to enhance biomass and metabolite production.IMPORTANCEEuglena gracilis has attracted special interest due to its ability to excessively accumulate paramylon. Paramylon is a linear β-1,3-glucan polysaccharide that is the principal polymer for energy storage in E. gracilis The polysaccharide features high bioactive functionality in the immune system. This study explored a new method to enhance the production of paramylon by E. gracilis, through cocultivation with the indole-3-acetic acid-producing bacterium Vibrio natriegens The enhanced production was achieved indirectly with the phytohormone-producing bacteria, instead of direct application of the hormone. The knowledge obtained in this study furthers the understanding of the effects of V. natriegens on the growth and physiology of E. gracilis.

Nitrosative stress-mediated inhibition of OsDHODH1 gene expression suggests roots growth reduction in rice (Oryza sativa L.)

This study monitored the transcriptional response of OsDHODH1 under nitrosative stress conditions relative to the transcripts accumulations for the core mitochondrial cytochrome c oxidase1 (CcOX1) subunit, nuclear CcOX subunits 5b and 5c, two rice nitrate reductases (OsNIA1 and OsNIA2), and nitric oxide excess 1 (OsNOE1) genes. Our findings reveal that short-term exposure of rice seedlings to 1 mM SNP (Nitric oxide donor) applied exogenously for 1 h resulted in significant down-regulation of OsDHODH1 expression in all rice cultivars. In addition, the transcriptional patterns for the CcOX subunits, which are known to have a high affinity for nitric oxide, showed that the core catalytic subunit (OsCcOX1) and the nuclear subunit (OsCcOX5b) were up-regulated, while the nuclear subunit (OsCcOX5c) gene expression was suppressed. OsGSNOR1 expression was enhanced or decreased concomitant with a decrease or increase in SNO accumulation, particularly at the basal level. Moreover, high OsNIA1 expression was consistent with impaired root development, whereas low transcript accumulation matched a balanced root-growth pattern. This suggests that OsNIA1 expression would prevail over OsNIA2 expression under nitrosative stress response in rice. The level of malondialdehyde (MDA) content increased with the increase in SNP concentration, translating enhanced oxidative damage to the cell. We also observed increased catalase activity in response to 5 mM SNP suggesting that potential cross-talk exist between nitrosative and oxidative stress. These results collectively suggest a possible role of OsDHODH1 and OsCcOX5b role in plant root growth during nitrosative stress responses.

Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism

Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.

A Growth-Promoting Bacteria, Paenibacillus yonginensis DCY84T Enhanced Salt Stress Tolerance by Activating Defense-Related Systems in Panax ginseng

Panax ginseng (C.A. Mayer) is a well-known medicinal plant used in traditional medicine in Korea that experiences serious salinity stress related to weather changes or incorrect fertilizer application. In ginseng, the use of Paenibacillus yonginensis DCY84^T to improve salt stress tolerance has not been thoroughly explored. Therefore, we studied the role of P. yonginensis DCY84^T under short-term and long-term salinity stress conditions in a controlled environment. In vitro testing of DCY84^T revealed high indole acetic acid (IAA) production, siderophore formation, phosphate solubilization and anti-bacterial activity. We determined that 10-min dip in 10¹⁰ CFU/ml DCY84^T was sufficient to protect ginseng against short-term salinity stress (osmotic stress) upon exposure to 300 mM NaCl treatment by enhancing nutrient availability, synthesizing hydrolyzing enzymes and inducing osmolyte production. Upon exposure to salinity stress (oxidative and ionic stress), strain DCY84^T-primed ginseng seedlings were protected by the induction of defense-related systems such as ion transport, ROS scavenging enzymes, proline content, total sugars, and ABA biosynthetic genes, as well as genes involved in root hair formation. Additionally, ginseng primed with DCY84^T and exposed to 300 mM NaCl showed the same metabolite profile as control ginseng plants, suggesting that DCY84^T effectively reduced salt stress. These results indicated that DCY84^T can be widely used as a microbial inoculant to protect ginseng plants against salinity stress conditions.