基礎講座 電気泳動(Electrophoresis)

Plant growth-promoting rhizobacteria (PGPR) are the rhizosphere bacteria that can enhance plant growth by a wide variety of mechanisms like phosphate solubilization, siderophore production, biological nitrogen fixation, rhizosphere engineering, production of 1-Aminocyclopropane-1-carboxylate deaminase (ACC), quorum sensing (QS) signal interference and inhibition of biofilm formation, phytohormone production, exhibiting antifungal activity, production of volatile organic compounds (VOCs), induction of systemic resistance, promoting beneficial plant-microbe symbioses, interference with pathogen toxin production etc. The potentiality of PGPR in agriculture is steadily increased as it offers an attractive way to replace the use of chemical fertilizers, pesticides and other supplements. Growth promoting substances are likely to be produced in large quantities by these rhizosphere microorganisms that influence indirectly on the overall morphology of the plants. Recent progress in our understanding on the diversity of PGPR in the rhizosphere along with their colonization ability and mechanism of action should facilitate their application as a reliable component in the management of sustainable agricultural system. The progress to date in using the rhizosphere bacteria in a variety of applications related to agricultural improvement along with their mechanism of action with special reference to plant growth-promoting traits are summarized and discussed in this review.

Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture

Increasing energy demands are not only exploiting the fossil resources but, also depleting natural environment. Biofuels from lignocellulosic biomass is a renewable, ecofriendly, sustainable and could be a promising alternative to fossil fuels. However, pretreatment is an essential step to disarray the layers of lignocellulose prior to enzymatic hydrolysis. Among various pretreatments of lignocellulose, the biological pretreatment using microorganisms such as bacteria and fungi are gaining popularity due to its financial and environmental benefits. Careful selection of the suitable microbial consortium for efficient pretreatment of biomass is a critical step. The co-culture of bacteria and/or fungi in consolidated bioprocessing (CBP) is highly beneficial in the breakdown of complex biopolymers due to their high enzyme activity. Our selection of highly promising bacterial and/or fungal consortium has the ability to produce various extracellular enzymes including cellulase, hemicellulase, and lignases. It can be used in CBP for efficient biological pretreatment of lignocellulosic biomass following production of biofuels and bioproducts.

Biological Pretreatment of Lignocellulosic Biomass for Biofuels and Bioproducts: An Overview

Vermicomposting is a non-thermophilic, boioxidative process that involves earthworms and associated microbes. This biological organic waste decomposition process yields the biofertilizer namely the vermicompost. Vermicompost is a finely divided, peat like material with high porosity, good aeration, drainage, water holding capacity, microbial activity, excellent nutrient status and buffering capacity thereby resulting the required physiochemical characters congenial for soil fertility and plant growth. Vermicompost enhances soil biodiversity by promoting the beneficial microbes which inturn enhances plant growth directly by production of plant growth-regulating hormones and enzymes and indirectly by controlling plant pathogens, nematodes and other pests, thereby enhancing plant health and minimizing the yield loss. Due to its innate biological, biochemical and physiochemical properties, vermicompost may be used to promote sustainable agriculture and also for the safe management of agricultural, industrial, domestic and hospital wastes which may otherwise pose serious threat to life and environment.

https://link.springer.com/content/pdf/10.1186%2F2193-1801-1-26.pdf

Microbial diversity of vermicompost bacteria that exhibit useful agricultural traits and waste management potential

Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.

MOESM3 of Current knowledge and perspectives of Paenibacillus: a review

Molecular and functional characterization of bacteria isolated from straw and goat manure based vermicompost

Secondary metabolites are low molecular weight compounds, less than 2.5 KDa produced during the idiophase of bacterial growth. Bacteria belonging to Pseudomonas, Bacillus and Streptomyces are prolific producers of secondary metabolites that include a wide array of naturally produced compounds viz., peptides, polypeptides, cyclic lipopeptides, polyketides, pyrroles, phenazines, phloroglucinols, lantibiotics, bacteriocins, lactones, macrolactone, anthracyclines, alkaloids, quinones, polyenes, pyrone, quinolones, isoquinoline, aminoglycosides, macrolides, bithiazoles, isocoumarins, aminosugars, phospholipids, siderophores and volatiles. These metabolites exhibit remarkable antimicrobial, plant growth regulatory, plant enzyme inhibitory, herbicidal, insecticidal and anti-parasitic properties. All these biological properties paved way for the use of these secondary metabolites as biocontrol agents in agriculture. Use of microbial antagonists and their secondary metabolites in agriculture in the place of agrochemicals could alleviate pollution hazard.

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Secondary Metabolite Production by Bacterial Antagonists

Plant pathogens cause persistent and significant yield losses in economically important crop plants. Incessant use of chemicals to control pathogens causes health problems and environmental pollution. Biological control agents are eco friendly and, therefore, have emerged as promising alternatives. Fluorescent pseudomonads, the ubiquitous soil bacteria, form a large group of plant growth-promoting rhizobacteria with plant growth-promoting and disease-suppressing attributes. They possess an array of innate beneficial traits such as successful root colonization, production of phytohormones, vitamins, lytic enzymes, antibiotics, and induction of systemic resistance in plants, thereby resulting in biological control of plant pathogens and enhancing plant growth and yield. Knowledge on the mechanisms that mediate beneficial attributes is important for the selection of potent biocontrol strains and for registration, patenting, recognition, and quality checking, which are essential not only for understanding their ecological role as biocontrol agents, but also for their biotechnological applications.

Mechanisms of Fluorescent Pseudomonads That Mediate Biological Control of Phytopathogens and Plant Growth Promotion of Crop Plants

Antagonistic fluorescent pseudomonads isolated from rice rhizospheric soil were characterized using biochemical, taxonomical and molecular tools. Production of cyclopropane fatty acid (CFA) was correlated with their antagonistic potential. Strains were grouped into 18 different genotypes on the basis of amplified ribosomal DNA restriction analysis (ARDRA) and repetitive (rep)-PCR based genotypic fingerprinting analyses. High phylogenetic resolution among antagonistic fluorescent pseudomonad strains was obtained based on the DNA gyrase B subunit (gyrB) and RNA polymerase sigma factor 70 (rpoD) gene sequence analyses. Combined gyrB and rpoD sequence analysis resulted in the accurate estimation of molecular phylogeny and provided a significant correlation between the genetic distances among strains. Present study demonstrated the genetic and functional relationship of fluorescent pseudomonads. The knowledge on genetic and functional potential of fluorescent pseudomonads associated with rice rhizosphere is useful to understand their ecological role and for their utilization in sustainable agriculture.

Assessment of genetic and functional relationship of antagonistic fluorescent pseudomonads of rice rhizosphere by repetitive sequence, protein coding sequence and functional gene analyses

Jayakumar Pathma

Papers

Microbial diversity of vermicompost bacteria that exhibit useful agricultural traits and waste management potential

Molecular and functional characterization of bacteria isolated from straw and goat manure based vermicompost

Secondary Metabolite Production by Bacterial Antagonists

Mechanisms of Fluorescent Pseudomonads That Mediate Biological Control of Phytopathogens and Plant Growth Promotion of Crop Plants

Assessment of genetic and functional relationship of antagonistic fluorescent pseudomonads of rice rhizosphere by repetitive sequence, protein coding sequence and functional gene analyses