A Framework for the Selection of Plant Growth-Promoting Rhizobacteria Based on Bacterial Competence Mechanisms

Abstract

<jats:title>ABSTRACT</jats:title> <jats:p>The use of plant growth-promoting rhizobacteria (PGPR) is increasingly meaningful for the development of more environmentally friendly agricultural practices. However, often the PGPR strains selected in the laboratory fail to confer the expected beneficial effects when evaluated in plant experiments. Insufficient rhizosphere colonization is pointed out as one of the causes. With the aim of minimizing this inconsistency, we propose that besides studying plant growth promotion traits (PGP), the screening strategy should include evaluation of the microbial phenotypes required for colonization and persistence. As a model, we carried out this strategy in three <jats:italic>Rhizobium</jats:italic> sp. strains that showed phosphorus solubilization ability and production of siderophores. All strains displayed colonization phenotypes like surface spreading, resistance to hydrogen peroxide, and formed biofilms. Regarding their ability to persist, biofilm formation was observed to be influenced by pH and the phosphorus nutrient provided in the growth media. Differences in the competence of the strains to use several carbon substrates were also detected. As part of our framework, we compared the phenotypic characteristics of the strains in a quantitative manner. The data analysis was integrated using a multicriteria decision analysis (MCDA). All our results were scored, weighted, and grouped as relevant for PGP, colonization, or persistence. MCDA demonstrated that, when the phenotypes related to PGP and colonization are weighted over those for persistence, strain B02 performs better than the other two <jats:italic>Rhizobium</jats:italic> sp. strains. The use of our framework could assist the selection of more competent strains to be tested in greenhouse and field trials.</jats:p> <jats:p><jats:bold>IMPORTANCE</jats:bold> Numerous plant growth-promoting rhizobacteria (PGPR) have been inoculated into the soil with the aim of improving the supply of nutrients to crop plants and decreasing the requirement of chemical fertilizers. However, sometimes these microbes fail to competitively colonize the plant roots and rhizosphere. Hence, the plant growth promotion effect is not observed. Here, we describe a new screening strategy aiming at the selection of more competent PGPR. We evaluated bacterial phenotypes related to plant growth promotion, colonization, and persistence. Our results demonstrated that despite the fact that our <jats:italic>Rhizobium</jats:italic> sp. strains successfully solubilized phosphorus and produced siderophores, their abilities to spread over surfaces, resist hydrogen peroxide, and form biofilms varied. Additionally, a multicriteria decision analysis was used to analyze the data that originated from bacterial physiological characterizations. This analysis allowed us to innovatively evaluate each strain as a whole and compare the performances of the strains under hypothetical scenarios of bacterial-trait requirements.</jats:p>

Shifts in the rhizobiome during consecutive in planta enrichment for phosphate‐solubilizing bacteria differentially affect maize P status

“…Isolates that looked promising in the laboratory often fail to deliver in pot or field trials (Chauhan et al ., 2015). The major factors that adversely affect bacterial efficiency in the field are (i) the soil physicochemical properties of farmlands, which differ largely from laboratory trials; (ii) the bacterial inability to colonize the plant rhizosphere, resulting in the lack of so‐called rhizosphere competence (Bach et al ., 2016; Amaya‐Gómez et al ., 2020); (iii) and the strict mutual dependencies and competition in the rhizobiome (Benizri et al ., 2001; Schink, 2002; Barea et al ., 2005; Babalola, 2010; de Souza et al ., 2015; Backer et al ., 2018). The rationale behind this current study is that the rhizosphere environment is not included in the in vitro screenings for PSB, while the plant–bacteria interactions are paramount in securing effective plant growth‐promoting traits (Schloss and Handelsman, 2005; Bais et al ., 2006; Lebeis et al ., 2012; Stewart, 2012; Castrillo et al ., 2017).…”

Genomic and Physiological Characterization of Bacilli Isolated From Salt-Pans With Plant Growth Promoting Features

“…Strain performance was compared with those of two promising PGPB, RHFS10, and RHFS18 strains, belonging to the Bacillus genus and isolated from J. sabina rhizosphere of the same collection site ( Castaldi et al, 2021 ) and proposed as biocontrol agents for their antagonistic activity against the phytopathogen M. phaseolina . Most of the new strains displayed root-colonization phenotypes since able to surface spread by swarming and to form biofilms ( Amaya-Gómez et al, 2020 ), while only five were found either positive to both solubilization of phosphate, indoleacetic acid (IAA), and siderophore production. Strains RHF6, RHF15, and RHFB showed a better performance than when compared against the already characterized rhizobacteria strains RHFS10 and RHFS18, confirming that the microenvironments created under or nearby nurse shrubs are a promising source of PGPB ( Rodríguez-Echeverría et al, 2016 ).…”

Absence of 4-Formylaminooxyvinylglycine Production by Pseudomonas fluorescens WH6 Results in Resource Reallocation from Secondary Metabolite Production to Rhizocompetence

“…In addition to gaining understanding of gvg cluster regulation, the impact of FVG production on the transcriptome, and the regulation of FVG production by acidic amino acids, we observed that genes necessary for rhizocompetence phenotypes were positively regulated in the absence (or decrease) of FVG. There are several well-documented competence traits common to rhizosphere-colonizing bacteria [ 51 , 52 , 53 , 54 , 55 ]. Motility in Pf is important for root colonization [ 56 ] and highly motile variants have a competitive advantage [ 57 ].…”