Rocheli de Souza

The effect of plant growth-promoting rhizobacteria on the growth of rice (Oryza sativa L.) cropped in southern Brazilian fields

Background and AimsSeveral strains of rhizobacteria may be found in the rhizospheric soil, on the root surface or in association with rice plants. These bacteria are able to colonize plant root systems and promote plant growth and crop yield through a variety of mechanisms. The objectives of this study were to isolate, identify, and characterize putative plant growth-promoting rhizobacteria (PGPR) associated with rice cropped in different areas of southern Brazil.MethodsBacterial strains were selectively isolated based on their growth on three selective semi-solid nitrogen-free media. Bacteria were identified at the genus level by PCR-RFLP 16S rRNA gene analysis and partial sequencing methodologies. Bacterial isolates were evaluated for their ability to produce indolic compounds and siderophores and to solubilize phosphate. In vitro biological nitrogen fixation and the ability to produce 1-aminocyclopropane-1-carboxylate deaminase were evaluated for each bacterial isolate used in the inoculation experiments.ResultsIn total, 336 bacterial strains were isolated representing 31 different bacterial genera. Strains belonging to the genera Agrobacterium, Burkholderia, Enterobacter, and Pseudomonas were the most prominent isolates. Siderophore and indolic compounds producers were widely found among isolates, but 101 isolates were able to solubilize phosphate. Under gnotobiotic conditions, eight isolates were able to stimulate the growth of rice plants. Five of these eight isolates were also field tested in rice plants subjected to different nitrogen fertilization rates.ConclusionsThe results showed that the condition of half-fertilization plus separate inoculation with the isolates AC32 (Herbaspirillum sp.), AG15 (Burkholderia sp.), CA21 (Pseudacidovorax sp.), and UR51 (Azospirillum sp.) achieved rice growth similar to those achieved by full-fertilization without inoculation, thus highlighting the potential of these strains for formulating new bioinoculants for rice crops.

The effects of different fertilization conditions on bacterial plant growth promoting traits: guidelines for directed bacterial prospection and testing

AimsIn this work, the effects of fertilization on diazotroph diversity and plant growth promoting traits were analyzed. An interaction model was then suggested and tested in field.MethodsOne hundred and ninety bacterial strains were isolated from rhizospheric soil and roots of rice cropped in three different fertilization conditions. Phosphate solubilization, indolic compound (IC) and siderophore production, and nitrogen fixation abilities of the isolates were screened and compared. Some isolates were selected for in vivo plant growth promotion in greenhouse and field experiments.ResultsWe found that fertilization had a limited effect on diversity but had a major effect on phosphate solubilization and IC production abilities. We demonstrated that plants select bacteria that present good phosphate solubilization ability for intimate root association in lieu of good IC production under nutrient-poor conditions and select good IC producers in lieu of good phosphate solubilizers under nutrient-moderate conditions. In nutrient-rich conditions, this selection preference seems to be deactivated. In the field trial, good phosphate solubilizers only contributed effectively to plant growth at nutrient-poor conditions and good IC producers only contributed to plant growth at nutrient-moderate conditions.ConclusionsFertilization affects the PGP traits of the diazotrophic community. These findings may be used for directed PGPR prospection and anticipated PGPR candidate selection.

Ecological role of bacterial inoculants and their potential impact on soil microbial diversity

BackgroundMicrobial inoculants are an alternative method of increasing crop productivity that can reduce the use of chemical fertilizers, which is one of the more controversial agricultural practices that affect the environment. Beneficial bacteria, collectively known as plant growth-promoting bacteria (PGPB), enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms. Bacterial inoculation efficiency is associated with the beneficial features of the inoculated bacterium, as well as with the complex network of interactions occurring in the soil.ScopeBeneficial bacteria have previously been examined for interactions with different plant hosts, soil types, and agricultural practices, but there is limited information concerning the potential effects of the release of microorganisms on soil functionality. Despite the plant growth promotion characteristics, the survival, abundance, and persistence of inoculant in soil or plant roots are characteristics that could potentially lead to its invasiveness. Inoculants can also interfere with soil health and microbial and faunal community composition.ConclusionThis review presents an overview of plant-PGPB interactions and their impacts on microbial communities, hypothesizing about the potential of these interactions to promote positive disturbances in soil, mainly in poor environments. The inoculation of free-living bacteria seems to cause a short-term impact to agricultural soils, while rhizobia-based inoculants or bacterial inoculations performed under stress conditions are long-term processes. However, there is great variability amongst results concerning the effects of bacterial inoculation into different plant and soil conditions.

A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates

Plant growth-promoting bacteria can greatly assist sustainable farming by improving plant health and biomass while reducing fertilizer use. The plant-microorganism-environment interaction is an open and complex system, and despite the active research in the area, patterns in root ecology are elusive. Here, we simultaneously analyzed the plant growth-promoting bacteria datasets from seven independent studies that shared a methodology for bioprospection and phenotype screening. The soil richness of the isolates origin was classified by a Principal Component Analysis. A Categorical Principal Component Analysis was used to classify the soil richness according to isolates indolic compound production, siderophores production and phosphate solubilization abilities, and bacterial genera composition. Multiple patterns and relationships were found and verified with nonparametric hypothesis testing. Including niche colonization in the analysis, we proposed a model to explain the expression of bacterial plant growth-promoting traits according to the soil nutritional status. Our model shows that plants favor interaction with growth hormone producers under rich nutrient conditions but favor nutrient solubilizers under poor conditions. We also performed several comparisons among the different genera, highlighting interesting ecological interactions and limitations. Our model could be used to direct plant growth-promoting bacteria bioprospection and metagenomic sampling.

Characterization of plant growth-promoting bacteria associated with rice cropped in iron-stressed soils

Plant growth-promoting rhizobacteria (PGPR) are able to promote plant growth using a wide variety of mechanisms as well as provide bioprotection against biotic and abiotic stresses. The objectives of this study were to isolate and characterize putative PGPR associated with rice cultivars with a distinct tolerance to iron toxicity grown in two areas: one area with a well-established history of iron toxicity and another without iron toxicity. Bacterial strains were selectively isolated based on their growth in selective media and were identified by partial sequencing of their 16S rRNA genes. Bacterial isolates were evaluated for their ability to produce indolic compounds, siderophores, and ACC deaminase and to solubilize tricalcium phosphates. In vitro biological nitrogen fixation was evaluated for the bacterial isolates used in the inoculation experiments. A total of 329 bacterial strains were isolated. The composition of the bacterial genera and the occurrence of different plant growth-promoting (PGP) traits were significantly affected by the iron conditions and by the cultivar. Strains belonging to the Burkholderia and Enterobacter genera were the most abundant of all the Gram-negative isolates, and those belonging to the Paenibacillus and Bacillus genera were the most abundant of the Gram-positive isolates. A large number of putative PGPR belonging to different bacterial genera presented several PGP traits. Strains belonging to the Burkholderia, Chryseobacterium, and Ochrobactrum genera contributed to plant growth as well as to enhanced nutrient uptake of the rice plants in in vivo experiments. Growth and nutrient uptake of plants inoculated with isolate FeS53 (Paenibacillus sp.) in the presence of an iron excess were similar to those of plants submitted to the control iron condition, indicating that this bacterium can mitigate the effects caused by iron stress.

Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5 T

Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated from a wheat field in the south of Brazil, has a great potential for agricultural applications due to its plant growth promotion effects. Here we present the draft genome sequence of P. riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the diazotrophic lifestyle and plant growth promotion, such as nitrogen fixation, antibiotic resistance, nitrate utilization, and iron uptake.

Screening of plant growth promoting bacteria associated with barley plants (Hordeum vulgare L.) cultivated in South Brazil

The occurrence of associations between bacteria and plant roots may be beneficial, neutral or detrimental. Plant growth promoting (PGP) bacteria form a heterogeneous group of beneficial microorganisms that can be found in the rhizosphere, the root surfaces or in association with host plant. The aim of this study was to isolate and characterize PGP bacteria associated to barley plants (Hordeum vulgare L.) aiming a future application as agricultural inoculant. One hundred and sixty bacterial strains were isolated from roots or rhizospheric soil of barley based on their growth in nitrogen-free selective media. They were evaluated for their ability to produce indolic compounds (ICs) and siderophores, and to solubilize tricalcium phosphate inin vitro assays. Most of them (74%) were able to synthesize ICs in the presence of the precursor L-tryptophan, while 57% of the isolates produced siderophores in Fe-limited liquid medium, and 17% were able to solubilize tricalcium phosphate. Thirty-two isolates possessing different PGP characteristics were identified by partial sequencing of their 16S rRNA gene. Strains belonging to Cedecea andMicrobacterium genera promoted the growth of barley plants in insoluble phosphate conditions, indicating that these bacteria could be used as bioinoculants contributing to decrease the amount of fertilizers applied in barley crops.

Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification

Species from the genus Paenibacillus are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify Paenibacillus strains. For this purpose, Paenibacillus riograndensis SBR5T, Paenibacillus sonchi X19-5T, and their close relatives were compared through phenotypic, genotypic, and genomic approaches. With respect to P. sonchi X19-5T, P. riograndensis SBR5T, Paenibacillus sp. CAR114, and Paenibacillus sp. CAS34 presented ANI (average nucleotide identity) values ranging from 95.61 to 96.32%, gANI (whole-genome average nucleotide identity) values ranging from 96.78 to 97.31%, and dDDH (digital DNA–DNA hybridization) values ranging from 68.2 to 73.2%. Phylogenetic analyses of 16S rRNA, gyrB, recA, recN, and rpoB genes and concatenated proteins supported the monophyletic origin of these Paenibacillus strains. Therefore, we propose to assign Paenibacillus sp. CAR114 and Paenibacillus sp. CAS34 to P. sonchi species, and reclassify P. riograndensis SBR5T as a later heterotypic synonym of P. sonchi (type strain X19-5T), with the creation of three novel genomovars, P. sonchi genomovar Sonchi (type strain X19-5T), P. sonchi genomovar Riograndensis (type strain SBR5T), P. sonchi genomovar Oryzarum (type strain CAS34T = DSM 102041T; = BR10511T).

Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields

ABSTRACT Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.

Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils

ABSTRACT Pseudomonas sp. FeS53a was isolated from the roots of rice plants cultivated in one area with a well-established history of iron toxicity. The FeS53a genome sequence provides the genetic basis for understanding its lifestyle and survival in association with rice in conditions of iron toxicity.