Pedro Beschoren da Costa

Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil.

In this work, a total of 311 putative nitrogen-fixing bacilli were isolated from seven distinct wheat production zones of the Rio Grande do Sul State, Brazil. Strains belonging to several species were grouped into 40 different nifH-RFLP-PCR profiles. The genus Paenibacillus was the most prominent group in both the rhizosphere (77.8%) and soil (79%). Paenibacillus borealis was the most frequently identified species, followed by Paenibacillus graminis. The remainder of the isolated bacteria belonged to the genus Bacillus sp. Indolic compound production (indole 3-acetic acid (IAA), indolepyruvic acid (IPyA) and indoleacetamide (IAM)) was detected in 33.6% and 26% of the isolates from the rhizosphere and soil, respectively. Among the 311 isolates, nine were able to solubilize phosphate and 48 were able to produce siderophores. The isolates SBR5, CSR16 and EsR7, identified by the 16S rRNA gene sequence as strains of Paenibacillus sp., were chosen for in vivo experiments in a greenhouse and proved to be very efficient in promoting a significant increase in the shoot and dry matter of wheat plants. Those strains could be useful in formulation of new inoculants, improving the cropping systems into which they can be most profitably applied.

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.

Paenibacillus riograndensis sp. nov., a nitrogen- fixing species isolated from the rhizosphere of Triticum aestivum

A bacterial strain designated SBR5(T) was isolated from the rhizosphere of Triticum aestivum. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genus Paenibacillus, being most closely related to Paenibacillus graminis RSA19(T) (98.1 % similarity). The isolate was a Gram-reaction-variable, motile, facultatively anaerobic bacterium, with spores in a terminal position in cells. Starch was utilized and dihydroxyacetone and catalase were produced. Strain SBR5(T) displayed plant-growth-promoting rhizobacteria characteristics: the ability to fix nitrogen and to produce siderophores and indole-3-acetic acid. The DNA G+C content was 55.1 mol%. Chemotaxonomic analysis of the isolated strain revealed that MK-7 was the predominant menaquinone, while the major fatty acid was anteiso-C(15 : 0). DNA-DNA hybridization values between strain SBR5(T) and P. graminis RSA19(T), Paenibacillus odorifer TOD45(T) and Paenibacillus borealis KK19(T) were 43, 35 and 28 %, respectively. These DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain SBR5(T) should be considered as the nitrogen-fixing type strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus riograndensis sp. nov. is proposed. The type strain is SBR5(T) (=CCGB 1313(T) =CECT 7330(T)).

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.

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.

Comparison among bacterial communities present in arenized and adjacent areas subjected to different soil management regimes

AimsThe aims of this work were to characterize the soil bacterial communities in an arenized area in southern Brazil subjected to different management regimes through cultivation-dependent and cultivation-independent methods and to evaluate the potential of selected plant growth-promoting (PGP) bacteria to improve the growth of native Lupinus albescens plants.MethodsBulk soil samples from an arenized site and rhizospheric soil and roots of L. albescens grown in this arenized site as well as samples from soils of the same region outside of the arenized area and rhizospheric soil and roots of L. albescens grown in non-arenized sites were evaluated. Phosphate solubilization, indolic compound and siderophore production abilities of the isolates were screened and compared. Some isolates were selected for in vivo plant growth promotion in greenhouse experiment.ResultsThe samples from the arenized area presented less microbial biomass and less diverse bacterial communities compared with those from non-arenized areas. The PGP characteristics produced by the bacterial isolates showed differences among arenized and non arenized areas. A growth chamber experiment with L. albescens showed that phosphate-insoluble conditions coupled with bacterial inoculation resulted in the best PGP effect.ConclusionsCulture-dependent and culture-independent methods showed converging results regarding diversity indices and the rhizospheric environments increased bacterial diversity and biomass when compared to bulk soils. The PGP traits analyzed in this work were affected by environmental conditions.

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.

Cultivable bacteria isolated from apple trees cultivated under different crop systems: Diversity and antagonistic activity against Colletotrichum gloeosporioides

This study evaluated the diversity of cultivable plant growth-promoting (PGP) bacteria associated with apple trees cultivated under different crop management systems and their antagonistic ability against Colletotrichum gloeosporioides. Samples of roots and rhizospheric soil from apple trees cultivated in organic and conventional orchards in southern Brazil were collected, together with soil samples from an area never used for agriculture (native field). Bacteria were identified at the genus level by PCR-RFLP and partial sequencing of the 16S rRNA, and were evaluated for some PGP abilities. The most abundant bacterial genera identified were Enterobacter (27.7%), Pseudomonas (18.7%), Burkholderia (13.7%), and Rahnella (12.3%). Sixty-nine isolates presented some antagonist activity against C. gloeosporioides. In a greenhouse experiment, five days after exposure to C. gloeosporioides, an average of 30% of the leaf area of plants inoculated with isolate 89 (identified as Burkholderia sp.) were infected, whereas 60 to 73% of the leaf area of untreated plants was affected by fungal attack. Our results allowed us to infer how anthropogenic activity is affecting the bacterial communities in soil associated with apple tree crop systems, and to obtain an isolate that was able to delay the emergence of an important disease for this culture.

Functional abilities of cultivable plant growth promoting bacteria associated with wheat (Triticum aestivum L.) crops

Abstract In the pursuit of sustainable agriculture, bioinoculants usage as providers of a crops needs is a method to limit environmental damage. In this study, a collection of cultivable putative plant growth promoting (PGP) bacteria associated with wheat crops was obtained and this bacterial sample was characterized in relation to the functional diversity of certain PGP features. The isolates were obtained through classical cultivation methods, identified by partial 16S rRNA gene sequencing and characterized for PGP traits of interest. Functional diversity characterization was performed using Categorical Principal Component Analysis (CatPCA) and Multiple Correspondence Analysis (MCA). The most abundant genera found among the 346 isolates were Pseudomonas, Burkholderia, and Enterobacter. Occurrence of PGP traits was affected by genus, niche, and sampling site. A large number of genera grouped together with the ability to produce indolic compounds; phosphate solubilization and siderophores production formed a second group related to fewer genera, in which the genus Burkholderia has a great importance. The results obtained may help future studies aiming prospection of putative plant growth promoting bacteria regarding the desired organism and PGP trait.