Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability

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.

1 An experimental multispecies screening of leaf decomposition rates was undertaken in order to identify and quantify general patterns in leaf decomposition rates in functional plant types and taxa. Functional species groups were characterized using whole-plant and whole-leaf features relevant to the functioning of plants in their natural environments. 2 The experiment included fresh leaf litters of 125 British vascular plant species, covering a wide range of life-forms, leaf habits and taxa. Preweighed litter samples were enclosed in two types of litter bags and exposed to natural weather conditions and soil-borne decomposers by burying them simultaneously in an experimental outdoor leaf-mould layer. 3 Relative litter dry weight losses showed largely similar patterns among species between both litter bag types, between 8 and 20-week burial periods in winter and between winter and summer burial. 4 Life-form, deciduous vs. evergreen habit, autumn coloration of leaf litter, family and evolutionary advancement sensu Sporne could each explain part of the variability in litter dry weight loss among species. The correlation with litter specific leaf area appeared confounded with taxonomy. 5 Some of these easy-to-assess predictors of species' relative leaf decomposition rates may prove useful for modelling soil decomposition rates under vegetations differing in species composition.

An experimental comparison of leaf decomposition rates in a wide range of temperate plant species and types.

Biology of Frankia strains, actinomycete symbionts of actinorhizal plants.

In order to develop a rapid and specific detection test for bacteria in soil, we improved a method based on the polymerase chain reaction (PCR). Each step of the protocol, including direct lysis of cells, DNA purification, and PCR amplification, was optimized. To increase the efficiency of lysis, a step particularly critical for some microorganisms which resist classical techniques, we used small soil samples (100 mg) and various lytic treatments, including sonication, microwave heating, and thermal shocks. Purification of nucleic acids was achieved by passage through up to three Elutip d columns. Finally, PCR amplifications were optimized via biphasic protocols using booster conditions, lower denaturation temperatures, and addition of formamide. Two microorganisms were used as models: Agrobacterium tumefaciens, which is naturally absent from the soil used and was inoculated to calibrate the validity of the protocol, and Frankia spp., an actinomycete indigenous to the soil used. Specific primers were characterized either in the plasmid-borne vir genes for A. tumefaciens or in the variable regions of the 16S ribosomal gene for Frankia spp. Specific detection of the inoculated A. tumefaciens strain was routinely obtained when inocula ranged from 10(7) to 10(3) cells. Moreover, the strong correlation we observed between the size of the inocula and the results of the PCR reactions permitted assessment of the validity of the protocol in enumerating the number of microbial cells present in a soil sample. This allowed us to estimate the indigenous population of Frankia spp. at 0.2 x 10(5) genomes (i.e., amplifiable target sequences) per g of soil. Images

Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction.

An enzyme recently described for Strepiomyces sp. protoplast formation was used to digest Frankia sp. cell walls. This new enzyme, achromopeptidase, allowed the use of an in situ method to detect large plasmids. Plasmids ranging in size from 7 to 190 kilobases were detected in some Frankia strains.

An improved method for lysis of Frankia with acharomopeptidase allows detection of new plasmids

After the initial screening of more than 200 Frankia strains, the plasmid DNA observed in eight Frankiae was analyzed. In situ lysis was performed to obtain an estimate of their copy number and molecular weight. Four plasmid classes were distinguished, 7–9, 18–20, 30–35 and 50–55 kb. Twelve plasmids were thus analysed with restriction enzymes to determine their plasmid restriction patterns.

Restriction enzyme digestion patterns of Frankia plasmids

A set of oligonucleotides has been developed to study the competitivity of two Frankia strains in the nodulation of the roots of two host plant species: Alnus glutinosa and Alnus incana. Two 20 mer-oligonucleotides, complementary to highly conserved sequences inside the nifH gene, were used as primers for the polymerase chain reaction (PCR) system in order to amplify microsymbiont DNA extracted from actinorhizae. PCR products were analyzed using two strain-specific 15-mer oligonucleotides identified in the amplified region. Hybridization data indicate that strain ACoN24d is more competitive than train ArI3 in the nodulation of both hosts.

Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specific oligonucleotide probes.

Repeated attempts at isolating the Frankia endophyte of Coriaria spp. have not yielded infective microbial cultures that could fulfil Koch's postulates. In order to circumvent the critical isolation step, nodule endophytes of Coriaria were characterized directly by means of specific amplification of nodule DNA (PCR) followed by sequencing of part of the 16S rDNA gene. Three closely related sequences were obtained from nodules originating from France, Mexico and New Zealand, containing unique sequences different from all other Frankia strains characterized so far. The sequences obtained were closest (with 5 or 6 substitutions) to those of Frankia alni and those of Casuarina-infective Frankia strains, respectively. Two nucleotides unique to the Coriaria endophyte sequences were used to define specific primers, resulting in a hybridization test that could discriminate between Frankia DNAs originating from Coriaria nodules and those recovered from all cultured Frankia strains tested. The endophytes of Coriaria thus appear to form a distinct Frankia lineage.

The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia.

Among the Frankia strains capable of establishing a nitrogen-fixing symbiosis with actinorrhizal plants, in planta sporangial formation is not universal and has led to the distinction between spore-positive (Sp+) and spore-negative (Sp-) nodules. Numerous Frankia strains have been isolated in pure culture from Sp+ nodules of different host plants, but, although they were able to reinfect their respective host plant, none of them was able to differentiate endophytic sporangia under laboratory conditions. The first step of this study was to demonstrate, at the molecular level, the existence of specific Sp+ strain genotypes differing from Sp- strain genotypes in a single alder stand. In a second step, by way of PCR amplification and sequencing of the PCR products, we have characterized oligonucleotide primers specific for the genus Frankia and for each of the two types of Frankia microsymbionts able, or not, to differentiate sporangia inside natural green alder nodules. These primers applied in PCRs with DNA extracted from nodules confirmed the morphological identification and revealed the presence of nodules colonized by both types of actinomycetes. Finally, a preliminary PCR study was conducted with DNA extracted directly from soil samples which permitted checking the rhizosphere of Sp+ and Sp- nodules for the presence of the corresponding strains.

A. Moiroud

Papers

An improved method for lysis of Frankia with acharomopeptidase allows detection of new plasmids

Restriction enzyme digestion patterns of Frankia plasmids

Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specific oligonucleotide probes.

The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia.

Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand.