Elsevier

European Journal of Soil Biology

Volume 50, May–June 2012, Pages 144-150
European Journal of Soil Biology

Original article
Characterization of plant growth-promoting traits of bacteria isolated from the rhizosphere of grapevine grown in alkaline and acidic soils

https://doi.org/10.1016/j.ejsobi.2012.01.007Get rights and content

Abstract

The purpose of this study was to investigate the diversity of cultivable N2-fixing, P-solubilising and siderophores-producing bacteria originated from acidic and alkaline rhizospheric soil of native grapevine grown at three locations. Ninety–five dominant, morphologically distinct rhizobacteria were purified, which belonged to 27 genera and 44 species. Gram-negative bacteria were dominating in the grapevine environment. Bacillus spp. and Pseudomonas spp. were common at both the acidic and alkaline soils. Among different groups, Gammaproteobacteria, Firmicutes and Actinobacteria comprised the largest groups contributing to about 42.1, 33.7 and 9.5% of the total N2-fixing isolates, respectively. The cultivated bacterial community from rhizosphere of native grapevine represented 27 different known bacterial genera represented by Pseudomonas, Bacillus, Brevibacillus, Stenotrophomonas, and Paenibacillus as as the predominant genera. Of the 95 nitrogen fixing isolates, 12 were able to fixe nitrogen and solubilize phosphates, 12 were able to fixe nitrogen and produce siderophores, only five isolates were able to fix nitrogen, produce siderophores and solubilize phosphates at the same time. In addition, the majority of the isolates were able to grow under high NaCl concentration. Our result showed that different geographical locations, soil pH, and vegetation type in the investigated sites resulted in the different bacterial population and bacterial type.

Highlights

► We isolated and identified rhizobacteria from acidic and alkaline soil wild grape. ► We evaluated their N2-fixing, P-solubilising, siderophores-producing and other traits. ► rhizosphere wild grape surveyed first time as P-solubilizers, N2-fixers and others. ► 95 isolates fix N, 12 fixe N and solubilize P, 12 fixe N and produce siderophores. ► Some of isolates may be represent new nitrogen-fixing and P-solubilizing species.

Introduction

Microorganisms colonizing the rhizosphere can affect plant growth both positively and negatively, the term plant growth promoting rhizobacteria (PGPR) often describes beneficial rhizobacteria that stimulate plant growth. PGPR in turn having a great impact on root biology, influence plant growth, nutrition and development are important for long-term sustainability. Plant-associated N2-fixing and P-solubilizing bacteria are regarded as a possible alternative for inorganic nitrogen fertilizers, and PGPR strains have previously been attracted the attention of agriculturists as soil inoculums to improve the plant growth and yield [1], [10], [13], [23], [35]. Apart from fixing N2, PGPR can influence plant growth directly by the synthesis of phytohormones, antibiotics, vitamins, enzymes and/or fungicidal compounds, inhibition of plant ethylene synthesis, improvement of nutrient uptake, enhanced stress resistance, production of siderophores, solubilization of inorganic phosphate, and mineralization of organic phosphate [19], [27].

The thin layer of soil surrounding crop roots and the volume of soil occupied by roots is known as the rhizosphere. The rhizosphere is well known to host a variety of PGPR and the majority of plant-associated bacteria derive from the soil environment [17]. One strategy that may contribute to the establishment of pre-selected beneficial organisms in the root zone of soils is through early establishment of selected communities of bacteria in the rhizosphere. In the last few years, the number of PGPR that have been identified has seen a great increase, mainly because the role of the rhizosphere as an ecosystem has gained importance in the functioning of the biosphere and also because mechanisms of action of PGPR have been deeply studied. Rhizosphere soil is influenced by plant roots which select for specifically adapted microbial communities [2], [4]. Several studies have demonstrated that the bacterial diversity in rhizospheres can be influenced by a number of different factors, i.e., the plant species, varietal differences within a species, plant age, plant genotype, agricultural management, or soil properties [7], [12], [18], [30], [39]. An important factor to be considered when screening new isolates is their activity in the range of environments in which they would be expected to be used; in particular different plants and soil types. Previous isolations of N2-fixing bacteria have revealed a broad diversity of diazotrophs to inhabit the crop rhizosphere [7], [11]. Nevertheless, many rhizospheric, N2-fixing and P-solubilizing bacterial species remain unknown and more studies are needed to reveal the high biodiversity of these bacteria.

Isolating of native strains adapted to the environment and their study may contribute to the formulation of inoculants to be used in region crops. Native isolates may be preferred in the selection of bacteria for inoculation, as they are adapted in the environment and can be more competitive than the foreign bacteria. The advantage of using natural soil isolates is the easier adaptation and succession when inoculated into the plant rhizosphere [13]. On the other hand, characterization and identification of these bacteria are necessary for wide ecological studies of the plant rhizosphere. Some endophytic bacteria colonize upper grapevine organs, especially berries, flowers, fruits and seeds on grapevine [16] and inoculation of Vitis vinifera explants with PGPR strain increased grapevine growth and physiological activity at low temperature [1]. Though much information is available on the activity of soil microorganisms and nitrogen fixation and phosphate solubilization for annual crops, information about the characteristics of composition and diversity of the bacterial community in perennial crops soil ecosystems is scarce. The diversity of PGPR species in grapevine soils remains unknown, especially of those strains that can fix nitrogen and solubilise phosphate besides having several plant growth promoting and biocontrol properties. Also, there is not sufficient knowledge on rhizosphere microbiology of the wild or cultured grape regions. For this reason it is important to study native strains isolated in the wild or cultured grape-growing regions where they may be used as berries and/or grapevine inoculants. The study was focused on rhizosphere bacteria as these represent an important group of soil microorganisms interacting with plant nutrition and health. The purpose of the present work was to isolate and identify PGPR of rhizosphere soils of native wild grapevines at three different region locations in Turkey and evaluation of their N2-fixing, P-solubilising, siderophores-producing status and other plant growth traits.

Section snippets

Soil samples and isolation of bacteria

We conducted a survey of PGPR, naturally colonizing a mild and continental climate and mostly acidic and alkaline rhizospheric soil of native grape; in the mild climate with high precipitation and acidic environmental area of the Storm (Fırtına) Valley in the Black Sea Region, a hard, grey and limestone alkaline soil of Akdamar Island in the Eastern Anatolia and Mediterranean climate of the Kemalpaşa in the Aegean Region have never been studied before. These regions have very widespread and

Results

The number of cultivable N2-fixing bacteria expressed as colony-forming units (CFU) ranged between 4.0 ± 0.4 × 105 and 4.2 ± 0.9 × 107 CFU g−1 dry soils in the sampled the rhizosphere of wild grape-growing zones of various agro climatic regions in Turkey. Morphological, biochemical and physiological tests showed that 95 rhizobacterial isolates obtained from the wild grape rhizosphere have several common characteristics (Table 2). For example, 44.2 and 27.4% of them were oxidase and sucrose

Discussion

The taxonomic identities of 27 genera and 44 species from approximately 95 rhizospheric root-associated bacteria isolated from rhizospheric soil samples of grape, grown at 3 sites were determined. Identification of the bacterial isolates was more successful in the grapevine rhizosphere samples expressing an overall identification of about 74.2% of the total isolates. Characterization of the isolates on the basis of their FAME profiles revealed the presence of both Gram-positive and

References (47)

  • P. Marschner et al.

    Soil and plant specific effects on bacterial community composition in the rhizosphere

    Soil Biol. Biochem.

    (2001)
  • P.K. Mishra et al.

    Bioassociative effect of cold tolerant Pseudomonas spp. and Rhizobium leguminosarum-PR1 on iron acquisition, nutrient uptake and growth of lentil (Lens culinaris L.)

    Eur. J. Soil Biol.

    (2011)
  • M. Park et al.

    Isolation and characterization of diazotrophic growth promoting bacteria from rhizosphere of agricultural crops of Korea

    Microbiol. Res.

    (2005)
  • E. Perez et al.

    Isolation and characterization of mineral phosphate-solubilizing bacteria naturally colonizing a limonitic crust in the south-eastern Venezuelan region

    Soil Biol. Biochem.

    (2007)
  • P. Piromyou et al.

    Effect of plant growth promoting rhizobacteria (PGPR) inoculation on microbial community structure in rhizosphere of forage corn cultivated in Thailand

    Eur. J. Soil Biol.

    (2011)
  • N. Rau et al.

    Evaluation of functional diversity in rhizobacterial taxa of a wild grass (Saccharum ravennae) colonizing abandoned fly ash dumps in Delhi urban ecosystem

    Soil Biol. Biochem.

    (2009)
  • A. Rusznyák et al.

    Cultivable bacterial composition and BIOLOG catabolic diversity of biofilm communities developed on Phragmites australis

    Aquat. Bot.

    (2008)
  • B. Schwyn et al.

    Universal chemical assay for the detection and determination of siderophores

    Analyt. Biochem.

    (1987)
  • H.-J. Son et al.

    Solubilization of insoluble inorganic phosphates by a novel salt- and pH-tolerant Pantoea agglomerans R-42 isolated from soybean rhizosphere

    Bioresour. Technol.

    (2006)
  • E. Ait Barka et al.

    Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN

    Appl. Environ. Microbiol.

    (2006)
  • R. Aravind et al.

    Endophytic bacterial flora in root and stem tissues of black pepper (Piper nigrum L.) genotype: isolation, identification and evaluation against Phytophthora capsici

    Lett. Appl. Microbiol.

    (2009)
  • H.P. Bais et al.

    The role of root exudates in rhizosphere interactions with plants and other organisms

    Ann. Rev. Plant Biol.

    (2006)
  • A.A. Belimov et al.

    Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling

    New Phytol.

    (2009)
  • Cited by (55)

    • Genomic and molecular evolutionary dynamics of transcriptional response regulator genes in bacterial species of the Harveyi clade of Vibrio

      2021, Gene
      Citation Excerpt :

      Hence, the differences in evolutionary dynamics of the TRRs in the species of the Harveyi clade could be linked to their environmental spread. Studies about the environmental distribution of Vibrios suggest that species of the third cluster of the clade exhibit a high specialization for marine environments (Payne, 1960; Pujalte et al., 1993; Yoshizawa et al., 2009, 2010), while the species of the first and second clusters have been extended beyond the marine environment, occurring predominantly in aquaculture hatcheries, freshwater (Mishra et al., 2010; Sarkar et al., 1985), dry soils (Okafo et al., 2003; Li et al., 2003; Karagöz et al., 2012), and the digestive tract of humans (Austin, 2010). Therefore, the reduction of TRR genes in the species of the first cluster could be the product of their specialization for marine environments, in contrast to the expansion of TRR observed in the others species of the clade could be due to the possible interaction with diverse bacterial communities given their wide environmental spread.

    • Drainage class and soil phosphorus availability shape microbial communities in Irish grasslands

      2021, European Journal of Soil Biology
      Citation Excerpt :

      Nevertheless, well-drained soils with low-P status (WLP) showed higher relative abundance of Firmicutes and the genus Xanthobacter (16 S rRNA gene based), and a distinct community structure of the phoD gene was identified between WLP and PHP soils. Several members of the Firmicutes are known plant growth promoting bacteria, with some of them identified as phosphorus solubilizing bacteria, such as Bacillus [44]. Members of this clade have been identified to possess alkaline phosphatase pathways [45] that include the marker gene phoD.

    • Pectin drives microbial phosphorus solubilization in soil: Evidence from isolation-based and community-scale approaches

      2020, European Journal of Soil Biology
      Citation Excerpt :

      As SIMPER analysis suggests, Bacillales members were responsible to the transition in overall community structure. They are phylogenetically close to previously-reported PSB isolates, many of which belong to the order Bacillales, and they could be the drivers of phosphorus solubilization observed here [13,40,41]. Members of this clade are also reported to be the dominant PSB in agricultural soils [42].

    View all citing articles on Scopus
    View full text