https://www.cell.com/trends/microbiology/pdf/S0966-842X(08)00192-3.pdf

Properties of bacterial endophytes and their proposed role in plant growth.

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

/pdf/rhizosphere-microbiome-assemblage-is-affected-by-plant-4aqfq5isiq.pdf

Rhizosphere microbiome assemblage is affected by plant development.

Plant growth promoting rhizobacteria (PGPR) shows an important role in the sustainable agriculture industry. The increasing demand for crop production with a significant reduction of synthetic chemical fertilizers and pesticides use is a big challenge nowadays. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth through either a direct or indirect mechanism. The mechanisms of PGPR include regulating hormonal and nutritional balance, inducing resistance against plant pathogens, and solubilizing nutrients for easy uptake by plants. In addition, PGPR show synergistic and antagonistic interactions with microorganisms within the rhizosphere and beyond in bulk soil, which indirectly boosts plant growth rate. There are many bacteria species that act as PGPR, described in the literature as successful for improving plant growth. However, there is a gap between the mode of action (mechanism) of the PGPR for plant growth and the role of the PGPR as biofertilizer—thus the importance of nano-encapsulation technology in improving the efficacy of PGPR. Hence, this review bridges the gap mentioned and summarizes the mechanism of PGPR as a biofertilizer for agricultural sustainability.

https://www.mdpi.com/1420-3049/21/5/573/pdf

Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability-A Review.

Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.

/pdf/plant-growth-promoting-bacteria-as-inoculants-in-y66qht4wo9.pdf

Plant growth-promoting bacteria as inoculants in agricultural soils.

Patterns of colonization of Vitis vinifera L. cv. Chardonnay plantlets by a plant growth-promoting bacterium, Burkholderia sp. strain PsJN, were studied under gnotobiotic conditions. Wild-type strain PsJN and genetically engineered derivatives of this strain tagged with gfp (PsJN::gfp2x) or gusA (PsJN::gusA11) genes were used to enumerate and visualize tissue colonization. The rhizospheres of 4- to 5-week-old plantlets with five developed leaves were inoculated with bacterial suspensions. Epiphytic and endophytic colonization patterns were then monitored by dilution plating assays and microscopic observation of organ sections. Bacteria were chronologically detected first on root surfaces, then in root internal tissues, and finally in the fifth internode and the tissues of the fifth leaf. Analysis of the PsJN colonization patterns showed that this strain colonizes grapevine root surfaces, as well as cell walls and the whole surface of some rhizodermal cells. Cells were also abundant at lateral root emergence sites and root tips. Furthermore, cell wall-degrading endoglucanase and endopolygalacturonase secreted by PsJN explained how the bacterium gains entry into root internal tissues. Host defense reactions were observed in the exodermis and in several cortical cell layers. Bacteria were not observed on stem and leaf surfaces but were found in xylem vessels of the fifth internode and the fifth leaf of plantlets. Moreover, bacteria were more abundant in the fifth leaf than in the fifth internode and were found in substomatal chambers. Thus, it seems that Burkholderia sp. strain PsJN induces a local host defense reaction and systemically spreads to aerial parts through the transpiration stream.

Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN.

Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum, Ideonella, Enterobacter, and Azospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and 15N2 gas incorporation assays. Therefore, we conclude that Herbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis.

Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species

https://cyberleninka.org/article/n/1198741.pdf

Beneficial effect of plant growth promoting bacteria isolated from the roots of potato plant

Bacterial population in grassland soil (sampled in 1992) was studied in terms of component colony-forming curves (cCFCs) to be compared with that in soil sampled in 1987. The simulated colony-forming curve (CFC) pattern was essentially similar to that of the former study; that is, four cCFCs were observed during 163h of incubation time. Bacterial isolates were picked up from colonies appearing along each cCFC and clustered according to their morphological and physiological characteristics (biotypes). The histograms of the frequency distribution of tr value for the isolates corresponding to cCFC groups I, II and III showed a similar pattern as previously. The trend of appearing of oligotrophic bacteria among the isolates of cCFCs groups was also similar to that of the former study although the percent of oligotrophic bacteria differed; that is, oligotrophic bacteria were not found among isolates of cCFCs groups I and II, appeared at 30% in cCFC group III and increased to 68% in cCFC group IV; as the oligotrophic bacteria increased, the sensitivity to 1% NaCl also increased. The bacterial population of the grassland soil is considered to be comprised of at least four component groups (cCFC groups) through yearly variations, although the biotype composition of the respective groups varies either widely or narrowly.

Comparative Study of Bacterial Populations in a Grassland Soil in 1987 and 1992

Potency of Certain Cyanobacterial Strains on Wheat Grown in Sandy and Alluvial Soils

The community structure of nitrogen-fixing endophytic bacteria associated with roots of three varieties, Oryza sativa cv. Sprice and cv. Koshihikari and line NERICA 5 (an interspecific hybrid between O. sativa and O. glaberrima) was analyzed using culture-independent molecular techniques. A segment of nifH gene was amplified from crude rice root DNA, cloned to construct nifH library and sequenced. About 25 clone sequences from each rice root were recovered and their amino acid sequences were compared with those published in DNA Data Bank of Japan (DDBJ). Majority of nifH sequences (79%) of the clones recovered from cv. Sprice were similar to those of unknown and known nitrogen-fixing anaerobes forming cluster (cluster C) distantly related to other nitrogen-fixing bacteria. Moreover, no clone sequences belonging to β- and γ-subdivisions of Proteobacteria (cluster B) were recovered, revealing limited nifH diversity for cv. Sprice root associated community. Although the clone sequences recovered from both cv. Koshihikari and NERICA 5 were belonging to same clusters and dominated mainly by genera belonging to β- and γ-subdivisions of Proteobacteria (cluster B), the composition and occupancy of each cluster were relatively different. However, the clones recovered from line NERICA 5 roots were more enriched with sequences belonging to α-subdivision of Proteobacteria (cluster A) than those of vs. Koshihikari and Sprice. This variability may reveal the impact of plant genotype on community structure of root-associated diazotrophes.

Phylogenetic analysis of nifH gene sequences from nitrogen-fixing endophytic bacteria associated with the roots of three rice varieties

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