Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.

Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms.

Diazotrophic bacteria can reduce N2 into plant-available ammonium (NH4 +), promoting plant growth and reducing nitrogen (N) fertilizer requirements. However, there are few systematic studies on the effects of diazotrophic bacteria on biological N2 fixation (BNF) contribution rate and host plant N uptake and metabolism. In this study, the interactions of the diazotrophic Paenibacillus beijingensis BJ-18 with wheat, maize, and cucumber were investigated when it was inoculated to these plant seedlings grown in both low N and high N soils, with un-inoculated plants as controls. This study showed that GFP-tagged P. beijingensis BJ-18 colonized inside and outside seedlings, forming rhizospheric and endophytic colonies in roots, stems, and leaves. The numbers of this bacterium in the inoculated plants depended on soil N levels. Under low N, inoculation significantly increased shoot dry weight (wheat 86.1%, maize 46.6%, and cucumber 103.6%) and root dry weight (wheat 46.0%, maize 47.5%, and cucumber 20.3%). The 15N-isotope-enrichment experiment indicated that plant seedlings derived 12.9-36.4% N from BNF. The transcript levels of nifH in the inoculated plants were 0.75-1.61 folds higher in low N soil than those in high N soil. Inoculation enhanced NH4 + and nitrate (NO3 -) uptake from soil especially under low N. The total N in the inoculated plants were increased by 49.1-92.3% under low N and by 13-15.5% under high N. Inoculation enhanced activities of glutamine synthetase (GS) and nitrate reductase (NR) in plants, especially under low N. The expression levels of N uptake and N metabolism genes: AMT (ammonium transporter), NRT (nitrate transporter), NiR (nitrite reductase), NR, GS and GOGAT (glutamate synthase) in the inoculated plants grown under low N were up-regulated 1.5-91.9 folds, but they were not obviously changed under high N. Taken together, P. beijingensis BJ-18 was an effective, endophytic and diazotrophic bacterium. This bacterium contributed to plants with fixed N2, promoted plant growth and N uptake, and enhanced gene expression and enzyme activities involved in N uptake and assimilation in plants. However, these positive effects on plants were regulated by soil N status. This study might provide insight into the interactions of plants with beneficial associative and endophytic diazotrophic bacteria.

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Diazotrophic Paenibacillus beijingensis BJ-18 Provides Nitrogen for Plant and Promotes Plant Growth, Nitrogen Uptake and Metabolism.

Integrated eco-strategies towards sustainable carbon and nitrogen cycling in agriculture.

Phosphate (P) availability often limits biological nitrogen fixation (BNF) by diazotrophic bacteria. In soil, only 0.1% of the total P is available for plant uptake. P solubilizing bacteria can convert insoluble P to plant-available soluble P (ionic P and low molecular-weight organic P). However, limited information is available about the effects of synergistic application of diazotrophic bacteria and P solubilizing bacteria on the nitrogenase activity of rhizosphere and nifH expression of endosphere. In this study, we investigated the effects of co-inoculation with a diazotrophic bacterium (Paenibacillus beijingensis BJ-18) and a P-solubilizing bacterium (Paenibacillus sp. B1) on wheat growth, plant and soil total N, plant total P, soil available P, soil nitrogenase activity and the relative expression of nifH in plant tissues. Co-inoculation significantly increased plant biomass (length, fresh and dry weight) and plant N content (root: 27%, shoot: 30%) and P content (root: 63%, shoot: 30%). Co-inoculation also significantly increased soil total N (12%), available P (9%) and nitrogenase activity (69%) compared to P. beijingensis BJ-18 inoculation alone. Quantitative real-time PCR analysis showed co-inoculation doubled expression of nifH genes in shoots and roots. Soil nitrogenase activity and nifH expression within plant tissues correlated with P content of soil and plant tissues, which suggests solubilization of P by Paenibacillus sp. B1 increased N fixation in soils and the endosphere. In conclusion, P solubilizing bacteria generally improved soil available P and plant P uptake, and considerably stimulated BNF in the rhizosphere and endosphere of wheat seedlings.

Phosphate solubilizing bacteria stimulate wheat rhizosphere and endosphere biological nitrogen fixation by improving phosphorus content

The bacterial communities inhabiting the rhizosphere play an important role in plant development and health. Here we studied the effect of inoculation with Pseudomonas fluorescens LBUM677, a plant growth promoting rhizobacterium that promotes seed oil accumulation, on the rhizosphere microbiome of three oilseed crops (Brassica napus, Buglossoides arvensis, and Glycine max) over time. Next-Generation high-throughput sequencing targeting the V4 region of 16S rDNA was used to characterize the microbial communities associated with the three different crops, inoculated or not with LBUM677, over a time period of up to 90 days post-inoculation. A total of 1,627,231 amplicon sequence variants were obtained and were taxonomically grouped into 39 different phyla. LBUM677 inoculation and sampling date were found to significantly influence the rhizosphere microbiome of the three oil-producing crops under study. Specifically, inoculation with LBUM677 and sampling date, but not the plant species, were found to significantly alter the alpha- and the beta-diversity of the rhizosphere microbial communities. Differential abundance analyses found that 29 taxonomical bacterial groups were significantly more abundant in the LBUM677 treatments while 30 were significantly more abundant in the control treatments. Predicted functions of the microorganisms were also enriched, including 47 enzymatic pathways in LBUM677 treatments. These non-targeted effects on rhizosphere bacterial communities are discussed in the context of oilseed crops.

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Inoculation With the Plant-Growth-Promoting Rhizobacterium Pseudomonas fluorescens LBUM677 Impacts the Rhizosphere Microbiome of Three Oilseed Crops

Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere.

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption.

https://www.mdpi.com/2076-2607/8/1/101/pdf

Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species.

A novel Gram-stain-positive, yellow, short-rod-shaped or coccoid bacterial strain, W204T, was isolated from a soil sample collected from Jiadengyu national forest park in China and characterized using a polyphasic approach. The cell-wall peptidoglycan contained ornithine as the diagnostic diamino acid. 16S rRNA gene sequence analysis indicated that strain W204T was closely related to Ornithinimicrobium flavum CPCC 203535T (97.4 %, similarity), Serinicoccus profundi CGMCC 4.5582T (96.9 %), Serinicoccus sediminis GP-T3-3T (96.8 %), Serinicoccus hydrothermalis JLT9T (96.7 %), Ornithinimicrobium cerasi CPCC 203383T (96.6 %) and Ornithinimicrobium kibberense K22-20T (96.6 %). However, the digital DNA-DNA genome hybridization value between strain W204T and the closest related strain O. flavum CPCC 203535T was 21.90 %. Complete genome analyses revealed that the size of the genome was 3.54 Mb and the genomic DNA G+C content was 70.79 mol%. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. The phenotypic, chemotaxonomic and phylogenetic data suggested that strain W204T should be classified as representative of a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium pratense sp. nov. is proposed. The type strain is W204T (=GDMCC 1.1391T=KCTC 49237T).

Ornithinimicrobium pratense sp. nov., isolated from meadow soil.

The invention discovers a gene with a hydroxylase function discovered from deinococcus radiodurans. The invention constructs a recombinant vector containing the gene, and the recombinant vector is expressed in prokaryotic host cell Escherichia coli. An experiment proves that after the gene is expressed in the prokaryotic host cell, carotenoid can be catalyzed to perform hydroxylation reaction. The gene can be used in the catalytic synthesis of the microorganisms.

Application of hydroxylase gene Dr2473 to catalytic synthesis of microorganisms

The invention provides a gene dicX5 with a function of degrading herbicides. A recombinant vector containing the gene is constructed and is expressed in the escherichia coli of a prokaryotic host cell. Experiments prove that the gene has a function of degrading herbicides after being expressed in the prokaryotic host cell and can be used in cultivation of herbicide-resistant genetically modified crops and biological repairing of polluted soil.

Ke Xiubin

Papers

Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere.

Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species.

Ornithinimicrobium pratense sp. nov., isolated from meadow soil.

Application of hydroxylase gene Dr2473 to catalytic synthesis of microorganisms

DicX5 gene and degradation function thereof on herbicides