Environmental Sustainability

, Volume 1, Issue 4, pp 461–469 | Cite as

Rhizobacteria isolated under field first strategy improved chickpea growth and productivity

  • Nitin Baliyan
  • Shrivardhan DheemanEmail author
  • Dinesh Kumar MaheshwariEmail author
  • R. C. Dubey
  • Vineet Kumar Vishnoi
Short Communication


Plant growth promoting rhizobacteria (PGPR) are being used as bioinoculant for enhancing plant growth and productivity. But their failure to survive and influence plant growth is a major hurdle because of rhizospheric rejection and crop-specific nature which can be overcome by field first strategy, as a revision of the existing protocol. The research is aimed to explore the beneficial impacts of rhizobacteria on crop plants at field-scale. The PGPR were, therefore, isolated from the standing healthy plants. The isolates were directly applied in the field using seed bacterization for cultivation of the crop and the evaluation of vegetative parameters. Simultaneously, the isolates were evaluated for plant growth promoting (PGP) traits in the laboratory. Thereafter, selection of field—adapted rhizobacteria was done on the basis of in-field and in vitro plant growth promotion. The potential rhizobacteria were used for yield improvement of chickpea (Cicer arietinum) in a second field trial. In this study, a consortium of two taxonomically distinct rhizobacteria Bacillus altitudinis MRN-16 and Pseudomonas chlororaphis MRN-52 showed promising plant growth promotion during in-field selection; in spite of PGP attributes, Pseudomonas korensis MRN-58 failed to improve crop yield. On the other hand, both the isolates showed effective inhibition of radial mycelial growth of Fusarium oxysporum, causing wilt of chickpea. The consortium of MRN-16 and MRN-52 enhanced the production of chickpea in terms of grain yield (9.86%) and biological yield (3.49%) with harvest index (6.45%). Thus, ‘field-first strategy’ proved more significant scheme for the recruitment of beneficial bacteria with much certainty and suitability in order to achieve growth and yield improvement of chickpea.

Graphical abstract


Rhizobacteria Chickpea Biocontrol Pseudomonas Bacillus 


The failure of plant growth promoting rhizobacteria (PGPR) in the field is a major problem due to their non-survival and insufficient effects on crop plants. Besides, soil pathogens also utilize certain metabolites of beneficial bacteria, which nullify the beneficial effect of PGPR (Schippers et al. 1987). The competition for limited resources between the introduced rhizobacteria and the resident microorganisms, compatibility between the composition of the host plant root exudates and natural complexity of the rhizosphere as a biological system are some of the major factors for PGPR survival in the field (Edge and Wyndham 2002; Strigul and Kravchenko 2006). These unprotected and inoculated bacteria must compete with the often better-adapted native microorganisms and withstand predation by soil fungi. Rhizobacteria at field-scale have to be explored to provide a dependable resource of PGPR that can survive in the soil and become available to crops (Bashan 1998). It is evident that soon after inoculation of bacteria in the rhizosphere, population of most of PGPR declines rapidly (Bashan et al. 2014).

Several rhizobacteria have been found successful in colonization of soil and plant roots to sufficiently high levels for the intended purposes (Maheshwari et al. 2014). Besides, non-survival of PGPR during field application is influenced due to microbial density, homeostasis and niche acquisition (van Veen et al. 1997). The rhizobacteria including Bacillus and Pseudomonas have been known as PGPR that also act as biocontrol agents (BCA) (Kumar et al. 2012). Rhizosphere-competitive nature of Bacillus has been observed effective in improving the yield of chickpea (Cicer arietinum) (Dubey et al. 2014). The rhizobacterial consortia bearing PGP traits have proved useful for plant growth and development over mono-inoculant (Maheshwari et al. 2015). Broadly, two-species and multi-species microbial consortia have widely been applied in growth promotion of several field crops (Pandey and Maheshwari 2007). In the present study, the field-adapted beneficial isolates of rhizobacteria from standing chickpea crop were evaluated for their effects in crop yield improvement. This research provides first-hand information on the suitability of PGPR using field first strategy as a revision of existing schemes of rhizobacterial selection. The field-adapted rhizobacteria having least rhizospheric rejection contribute in the enhancement of crop productivity, in comparison to that of the laboratory selected PGPR. This study explores the benefits of in-field plant growth promotion carried out prior to laboratory tests, as a precise scheme of PGPR selection for introduction in crop cultivation.

Materials and methods

Soil analysis and isolation of rhizobacteria

The farmer’s field (29°24′57.10 N 77°35′08.51 E; 245 MSL) was surveyed and distributed in 24 equal blocks (2 sq. m each). The soil sample from each block was collected from different depths viz., upper (0–10 cm), middle (11–20 cm) and lower (21–30 cm), sieved through 2 mm sieve and composited into three samples during the autumn season at temperature 18–22 °C. The pedology was studied using the standard methods (Van Reeuwijk 1993; Soil Survey Staff 2010). The bacteria were isolated on Luria–Bertani agar (LBA) medium from the rhizospheric soil of the mature healthy chickpea plants from each block and processed for seed bio-priming (Gupta et al. 2002) by using rhizobacterial isolates namely, MRN-2 to MRN-58.

In-field characterization

Seeds of similar shape and size of chickpea (Cicer arietinum) [ver. PUSA-372 (Desi)] were hand-picked and soaked overnight in lukewarm water. All bacterial isolates were grown in LB broth medium separately at 28 ± 1 °C for 12-24 h. The cultures were centrifuged at 7000×g at 4 °C for 15 min. The culture supernatants were discarded and pellets were washed and re-suspended in sterile distilled water (SDW) to get a final bacterial population density of 1 × 108 cells ml−1. The cell suspensions of the bacterial isolates were mixed with 1% carboxymethylcellulose (CMC) solution in a ratio of 1:0.5 separately to form slurry and coated on the surface of seeds as described earlier (Aeron et al. 2012). Seeds of chickpea coated with 1% CMC slurry, seeds without bacterial isolates served as control. All the treatments were sown in 1 sq. m plots (10 × 20 seed to seed and plant to plant) of gross field size 100 sq. m. The treated seeds were sown in five replicates by random block design using lottery method. Plots were irrigated regularly with naturally available water. No chemical fertilizer was added in the field during experiment. The experiment was conducted during crop season (October 2015). All the vegetative parameters except seed germination were measured under field condition up to 30 days after sowing (DAS).

Plant growth promoting characterization

The standard methodology was adopted to reveal the core mechanisms of beneficial attributes in rhizobacteria and consortia of synergistic isolates in the laboratory conditions. The pair-wise synergistic interaction studies were carried out for in vitro inhibition following the method of Pandey and Maheshwari (2007). Further, plant growth promoting (PGP) characters of individual isolates and consortia were evaluated according to standard procedures following Kumar et al. (2012). The ability to fix atmospheric nitrogen was evaluated up to seven successive cultivations on Ashby’s N-free agar medium and secretion of the IAA was evaluated by following Chauhan et al. (2017). To determine the phosphate (P) and potassium (K) solubilization ability, the zone of solubilization (mm) formed around colonies on specific media was calculated using the following formula:
$${\text{Solubilizing}}\,\,{\text{efficiency}}\,\,(\% \,\,{\text{SE}}) = \frac{Z - C}{C} \times 100$$
where Z = Solubilization zone (mm) and C = Colony diameter (mm).

The production of iron-chelating siderophores was estimated following Schwyn and Neilands (1987) and volatile hydrocyanic acid (HCN) production was determined by employing the modified method of Bakker and Schippers (1987). All the bacterial isolates were primarily screened for their antagonistic activity against Fusarium oxysporum [NTCCFRI; procured from National Type Culture Collection, Forest Pathology Division, Forest Research Institute, Dehradun, Uttarakhand (India)] following dual culture method of Skidmore and Dickinson (1976). Chitinase production was performed following the method of Dunne et al. (1997).

Molecular identification of rhizobacteria

The molecular identification and phylogeny determination of three potential rhizobacterial isolates were carried out following Sambrook and Russel (2001). For amplification of 16S rRNA, primers 27F (5′-AGAGTTTGATCMTGGCTC AG-3′) and 1492R (5′-TACGGYTACCTTGTTACGACT T-3′) with 100 ng of the template DNA and 2.5 mM of dNTPs were used. The sequencing of the amplified 16S rRNA gene was performed at Macrogen Inc., Seoul, Republic of Korea. The phylogeny was inferred using MEGA7 (Kumar et al. 2016). The sequences were submitted in gene bank and accession numbers obtained were MG062748, MF039629 and MF039630, respectively.

Field trial and statistical analysis

The rhizobacteria MRN-16 and MRN-52 (isolates showed positive results during in-field and in vitro) as well as and consortia of MRN-16 and MRN-52 along with MRN-58 (showed positive results only in vitro selection) were re-assessed in the final field trials. Treatments of seeds included seed without bacterial inoculation (control), seed inoculated with individual isolates MRN-16 (Bacillus altitudinis), MRN-52 (Pseudomonas chlororaphis), MRN-58 (Pseudomonas korensis) and co-culture of B. altitudinis MRN-16 + P. chlororaphis MRN-52. Field trials were conducted using a randomized block design (RBD) taking five replicates of each treatment. The crop was cultivated as earlier in the field size 5.8 m2; during crop season November 2016 to April 2017. Plots were irrigated regularly with raw water without adding any chemical fertilizers during the course of study. Yield parameters were recorded after harvesting at 120 DAS using the following formulae:
$${\text{Grain}}\,\,{\text{yield}}\,\,({\text{kg}}\,\,{\text{ha}}^{ - 1} ) = \frac{{{\text{Grain}}\,\,{\text{yield}}\,\, ( {\text{kg)}}\,\,{\text{per}}\,\,{\text{subplot}}}}{{{\text{Area}}\,\,{\text{per}}\,\,{\text{sub}}\,\,{\text{plot}}}} \times 1000$$
$${\text{Biological}}\,\,{\text{yield}}\,\,({\text{kg}}\,\,{\text{ha}}^{ - 1} ) = \frac{{{\text{Biological}}\,\,{\text{yield}}\,\, ( {\text{kg)}}\,\,{\text{per}}\,\,{\text{subplot}}}}{{{\text{Area}}\,\,{\text{per}}\,\,{\text{sub}}\,\,{\text{plot}}}} \times 1000$$
$${\text{Harvest}}\,\,{\text{Index}}\,\, ( {\text{H}} . {\text{I}} . )= \frac{{{\text{Grain}}\,\,{\text{yield}}}}{{{\text{Biological}}\,\,{\text{yield}}}}$$

The data were analyzed by one way ANOVA at CD 0.5-5.0 (Gomez and Gomez 1984).


Soil analysis and isolation of rhizobacteria

In the present investigations, the soil texture is Udic Haplustepts (Order: Inceptisol; Sub-order: Ustep; Great-group: Haplustep; Sub-group: Udic) having a distinct color variation on account of various edaphic factors. Soil moisture varied from 18 to 33 ± 4% and water holding capacity (aw) indicating the actual amount of water (moisture) present in the pore spaces, varied between 41 and 60 ± 4 (in %) under natural climatic conditions. The soil pH, biological carbon (%), available phosphorus, potash, and sulfur along with available trace elements such as zinc, iron, manganese, and copper was observed in variable ranges (Table 1). A total of 62 bacterial isolates were obtained from rhizospheric soil of standing healthy chickpea plants based on visual observations by random selection and abbreviated as MRN1-MRN62. To avoid redundancy of similar morphotypes, 23 rhizobacterial isolates were screened for seed bacterization.
Table 1

Chemical analysis of soil sampled from farmer’s field

Soil sample

Primary nutritional elements

Secondary nutritional elements

Available trace elements (ppm)


Biological carbon (%)

Soluble phosphate (kg−1)

Soluble potash (kg−1)







Sample 1











Sample 2











Sample 3











All values are the average mean of three consecutive analyses

In-field characterization

The crop was cultivated to evaluate the overall performance of plant growth and development with rhizobacterial treatments. The emergence of seedling and early vegetative parameters of the chickpea plants revealed that MRN-16 and MRN-52 maximally induced seedling and overall plant growth. Both the isolates MRN-16 and MRN-52 increased root/shoot length and weight (dry/fresh) of chickpea plants in comparison to non-bacterized plants (Supplementary Table 1).

Plant growth promoting characterization

Further, in order to reveal major PGP mechanism of rhizobacteria, 23 isolates with plant growth promotion exhibited diversity in their functional beneficial attributes (Table 2). Isolates MRN-16 and MRN-52 were mutually non-inhibitory during in vitro synergistic interaction (Supplementary Fig. 1). In vitro, three isolates MRN-16, MRN-52 and MRN-58 showed the ability to fix nitrogen and secrete IAA in the range of 78.6–82.5 µg/mL, whereas consortia of MRN-16 and MRN-52 recorded the maximum secretion of IAA 84.3 µg/mL (Fig. 1a). Phosphate solubilization efficiency (PSE) of MRN-16, MRN-52, and MRN-58 were recorded to be 53.5, 59.3 and 61.2% respectively (Fig. 1b). Similarly, potassium (K) was also solubilized by MRN-16, MRN-52, and MRN-58 and was in the range between 47.2 and 49.7% KSE (K solubilization efficiency). The solubilization efficiency for both P and K was much higher (62.7 and 50.3%) by the consortia (MRN-16 and MRN-52) than the individual isolates (Fig. 1c). The three isolates MRN-16, MRN-52, MRN-58 and consortia of MRN-16 and MRN-52 secreted 44.82, 44.85, 44.75 and 45.23% siderophore respectively (Fig. 1d). On the other hand, production of volatile cyanogen (HCN) and diffusible metabolite chitinase was also demonstrated by these bacterial isolates, individually as well as in mix-culture. Isolates MRN-16, MRN-52, MRN-58, and MRN-16 + MRN-52 were very effective in inhibiting the radial mycelial growth up to 68.7, 65.7, 64.6 and 71.8% respectively, besides aborting the germination of F. oxysporum propagules causing wilt disease in chickpea.
Table 2

Plant growth promoting traits in different isolates of plant growth promoting rhizobacteria (PGPR)


Plant growth promoting attributes


P solubilization

K solubilization

Siderophore secretion

HCN production

Presence of chitinase

Antagonistic to F. oxysporum















































































P phosphate, K potassium, HCN hydrocyanic acid

 +  positive; − negative

Fig. 1

Quantitative estimation of plant growth promoting attributes in rhizobacteria a IAA production; b phosphate (mineral) solubilization efficiency; c potassium solubilization efficiency; d siderophore production

Field trial

The consortia of the isolates MRN-16 and MRN-52 were more effective in enhancing the yield parameters in comparison to that of MRN-16, MRN-52, and MRN-58. B. altitudinis MRN-16 and P. chlororaphis MRN-52 induced the growth and yield of chickpea. The combined effect of both the isolates was significant on the vegetative and yield parameters of chickpea, while laboratory selected P. korensis MRN-58 showed plant growth similar to that of non-treated control (Table 3). A significant increase in grain yield and biological yield with 2.5% harvest efficiency showed the promising effect of mix-culture of MRN-16 and MRN-52 in comparison to individual isolates and non-bacterized crop plants (Table 3). The rhizobacterial consortia containing MRN-16 and MRN-52 increased grain yield and biological yield by 9.86 and 3.49% respectively, with 6.45% harvest index (HI) (Table 3; Fig. 2). Thus, the field-first strategy proved significant for the selection of PGPR for growth and yield enhancement of chickpea.
Table 3

Yield parameter of chickpea during reassessment of field applicability at 120 DAS

Rhizobacterial isolates

Biological yield (kg ha−1)

Grain yield (kg ha−1)

Harvest index (%)









MRN-16 + MRN-52












Values are mean of ten sample plant from each treatment

MRN-16, Bacillus altitudinis; MRN-52, Pseudomonas chlororaphis; MRN-58, Pseudomonas korensis

Significance at 0.01 and 0.05 level of analysis of variance (ANOVA). **Significant at 0.01 level of LSD as compared to control; *Significant at 0.05 level of LSD as compared to control; ns = not significant at 0.05 level of LSD as compared to control

Fig. 2

Production parameters of chickpea on field reassessment experimentation. a Grain yield of Cicer arietinum L. under different bacterial treatments; b Harvest index on vertical axis illustrating percentage increase over control. Bar showing SD ± 5%; values are mean of five replicates. *Significantly different from controls


Since last three decades, the selection of PGPR is based on the isolation, laboratory characterization, identification and field applications (Kumar et al. 2014; Kumari et al. 2018). Although, the above strategy is universally accepted but have limitations that PGPR often fail to offer beneficial effects on the crops in natural conditions. For instance, more than two-thirds of the population of PGPR during field application has no significant effect on crop yield (Okon and Labandera-Gonzalez 1994). On the other hand, rhizobacteria also failed to provide desirable results in different crops due to rhizosphere rejection (Jagnow et al. 1991; van Veen et al. 1997). The reality is that the failures to achieve the desired results are intermittently reported, especially by commercial PGPB-based biofertilizer producers. As an alternative, the selection of rhizobacteria at field scale for crop cultivation and production enhancement proved to be more precise scheme.

This study was focused to revise existing echelons of selection of rhizobacteria for crop yield improvement. In field-first strategy, rhizobacterial isolates were applied in-field to assess their PGP traits prior to characterizing in the laboratory; in vitro PGP traits were evaluated later. During in-field selection, B. altitudinis MRN-16 and P. chlororaphis MRN-52 increased plant growth promotion in term of above ground and below ground parameters, significantly. Simultaneously, MRN-16, MRN-52, and MRN-58 evaluated for PGP traits in the laboratory further proved them potential protagonists to synthesize IAA (auxin) constitutively. IAA production has been found in about 80% rhizosphere bacterial population (Mitter et al. 2013). Since, MRN-16, MRN-52, and MRN-58 solubilized phosphate and potassium thus, allow the plants for better uptake of nutrients and assist to induce growth as observed by Meena et al. (2015). In addition, the potentiality of the isolates for nitrogen-fixing ability was recorded for several generations and secretion of iron-chelating siderophore lead to favor the growth of the chickpea crop. Arora et al. (2001) stated the beneficial role of siderophore producing rhizobacteria for plant health and growth promotion. Volatile production of cyanogens by MRN-16, MRN-52 and MRN-58 and presence of lytic enzyme like chitinase conferred their ability to ward off deleterious F. oxysporum. The use of such microbes or their secretions to prevent plant pathogens and insect pests offers an attractive alternative or supplement for the control of plant diseases (Stirling 2014; Agarwal et al. 2017). The action of MRN-16, MRN-52, and MRN-58 in vitro proved quite effective in inhibiting radial mycelia growth and abortion of conidial germination of F. oxysporum. The protective role of bacilli and Pseudomonads against F. oxysporum, F. solani, F. udum, S. sclerotiorum, and R. solani have been demonstrated by earlier workers (Singh et al. 2008; Kumar et al. 2012; Selvakumar et al. 2013; Jain et al. 2015). The use of 16SrRNA sequencing and phylogeny identified MRN-16, MRN-52 and MRN-58 as Bacillus altitudinis, Pseudomonas chlororaphis, Pseudomonas korensis. The sequences were deposited in gene bank under accession numbers MG062748, MF039629 and MF039630, respectively.

In our study, the co-culture of bacteria performed better and exhibited greater PGP influence under natural conditions than individual’s isolates. Both MRN-16 and MRN-52 isolates in combination were grown synergistically in vitro and proved their successful mutual niche selection for site and substrate. It was interesting to observe that, during pair-wise synergistic evaluation isolates MRN-58 showed inhibitory effect against B. altitudinis MRN-16, while remaining neutral with Pseudomonas chlororaphis MRN-52. Thus, a much suitable consortium of isolates MRN-16 and MRN-52 was developed, by avoiding the inhibitory effect with one important isolate. Besides, isolate MRN-58 was not as efficient in imparting PGP effects on crop health and growth promotion. Earlier, the synergistic behavior and better utilization of shared nutritional niche by two different genera was evidenced by Pandey and Maheshwari (2007). Reduction in wilt disease was observed while working on the combined application of Sinorhizobium fredii KCC5 and Pseudomonas fluorescens, thus, improved plant health in one of the field trials (Kumar et al. 2010). Similarly in this study, during re-assessment at field level, a combination of B. altitudinis MRN-16 with P. chlororaphis MRN-52 was more effective in increasing the grain yield, biological yield, and harvest index. The significance of consortia has been discussed earlier as the best to have PGP traits at qualitative and quantitative assessments. It was recorded that consortia raised the production to two times higher than individual isolates for phytohormone production, mineral mobilization and siderophore production, which coincides with field results, where consortia had shown maximum grain yield with significant harvest index. Imran et al. (2015) have reported the enhanced grain yield of chickpea (PUSA-372) under influence of PGPR screened by the conventional approach. Such enhancement in productivity is due to the additive effect of both the bacterial isolates in combined form. Thus, the field adapted isolates were more efficient to raise farm productivity, growth, and yield of chickpea.

This study establishes the field- first strategy as effective and explores successful and effective PGPR isolates. Such an approach has been  recommended so as to recognize the efficiency of beneficial soil bacteria for plant growth and health promotion (Welbaum et al. 2004). Thus, field-first approach proves its merit for the recruitment of beneficial bacteria because the majority of selected bacteria performed well in field conditions.


The field-adaptive bacterial strategy proved more authentic for effective growth and health promotion of chickpea (C. arietinum). Bacillus altitudinis MRN-16 and Pseudomonas chlororaphis MRN-52 were beneficial individually as well as in combination for growth and yield improvement. In vitro chosen PGPR Pseudomonas korensis MRN-58 was less effective in field conditions. Thus, “field-first strategy” of rhizobacterial selection prior to study in the laboratory was reported beneficial to decipher functional attributes. The rhizobacterial consortium involving MRN-16 and MRN-52 performed quite well during two successive years. Thus, the “field-first strategy” provided novel beneficial rhizobacteria for crop yield improvement in comparison to conventional approach.



The authors wish to thank the Head, Department of Botany and Microbiology, Gurukul Kangri Vishwavidyalaya, Haridwar (India) for providing necessary facilities.

Author contributions

NB designed and conceived the experiment. SD assisted during the experiments and prepared the manuscript with the help of VKV. RCD and DKM corrected and finalized the manuscript before to the submission.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

42398_2018_42_MOESM1_ESM.docx (217 kb)
Supplementary material 1 (DOCX 216 kb)


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Copyright information

© Society for Environmental Sustainability 2018

Authors and Affiliations

  1. 1.Department of Botany and MicrobiologyGurukula Kangri VishwavidyalayaHaridwarIndia
  2. 2.Department of MicrobiologySardar Bhagwan Singh UniversityDehradunIndia

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