Isolation and Identification of Plant Growth-Promo
Isolation and Identification of Plant Growth-Promo
Isolation and Identification of Plant Growth-Promo
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ABSTRACT
Soil salinity is one of the limiting factors of agricultural production in arid and
semi-arid areas that reduces yields and optimal crop production. Awareness of
Keywords rhizosphere bacterial diversity and use of salinity-resistant bacteria is considered as
a critical strategy to increase plant growth in these areas. This study aimed to
Phosphate, determine the population diversity of sugarcane rhizosphere bacteria in saline and
Inceptisol, non-saline soil and survey some growth-promoting properties. For this purpose,
Potassium, random sampling from the rhizosphere of sugarcane was performed. Bacteria were
Nitrogen, Auxin, isolated by culturing serial on nutrient agar medium and were identified based on
Enterobacter biochemical assays. The ability of isolates to fix nitrogen, dissolute phosphate and
cloacae.
potassium and auxin production was investigated. Finally, the best growth-
Article Info promoting isolates were identified based on 16S rRNA sequences. Generally, 40
bacteria were isolated from saline and non-saline soil that these strains were mainly
Accepted:
28 September 2016 from Bacillus, Paenibacillus and Pseudomonas. Salinity had the highest effect on
Available Online: bacterial community structure with the higher diversity of microorganisms in saline
10 October 2016 soils. Four strains were selected as growth-promoting strains which based on
biochemical and phylogenetic analysis were identified asEnterobacter cloacae
R13, Enterobacter cloacae R33, Paenibacillus lactis and Pseudomonas sp.
Introduction
Salinity challenge is one of the major 2010). In Iran over 32 million hectares of
problems that reduce productivity of fertile soils are affected by salinity that covers
lands. Salinity affects not only plant nearly 30 percent of the entire country (34
production but also the biodiversity million hectares) and 55% of arable lands
(Fernandez et al., 2010). High levels of (Paziraand Homaee, 2010). Sugarcane
salinity (more than 4 dS/m) are created culture in Khuzestan has a significant role in
usually due to salts in irrigation water and providing sugar. Nowadays, this industry
fertilizers, low rainfall, high temperature, developed in the region and produces more
inappropriate management practices and than half of the country's sugar. Salinity of
long-term drop irrigation (Yao et al., soil under sugarcane cultivation due
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Int.J.Curr.Microbiol.App.Sci (2016) 5(10): 1072-1083
irrigation practices and application of adhered to the roots. Soil properties such as
chemical fertilizer is now being a serious soil texture parameters (Hydrometery), pH
issue. Some of the microorganisms, in saturated mud, the electrical conductivity
particularly valuable bacteria can develop of saturated extract (ECe), Soil organic
plant performance under stress condition matter (the K2Cr2O7-H2SO4 oxidation–
and, improve yield (Evelin et al., 2010; reduction titration method), soil respiration
Sahoo and Dhal, 2009). Their abundance (Anderson, 1982) and microbial biomass
and activities are controlled by various carbon by fumigation-extraction method
physical and chemical factors. Measuring were measured (Jenkinson and Powlson,
biodiversity of microbial communities for 1976).
the immediate application and fundamental
understanding of microbial communities are To isolate bacteria, 10g of soil was serially
important. Plant growth promoting diluted to 10-8. About 50µl of 10-3 to 10-8
rhizobacteria (PGPR) employed to promote dilutions were spread on nutrient agar
plant growth by supplying nutrients such as medium and incubated at 28°C for 72 h. The
nitrogen through biological nitrogen appeared colonies on the medium were
fixation, phosphate and potassium through purified based on appearance and color.
solubilization of their insoluble forms, Purified bacteria were examined by
induce phytohormones production and plant morphological characteristics such as shape,
resistance to microbial pathogens and margin, color and pigment occurrence,
siderophore production aiding plant nutrition elevation, texture and size of colony, after
by chelation (Ogboand Okonkwo, 2010). that, the bacteria were identified by standard
Our knowledge about microbial diversity biochemical tests on the basis of the
and microorganisms’ activity in the Bergey’s manual of bacterial classification
rhizosphere of sugarcane is very important (Harrigan and McCance, 1976). Microbial
in understanding the plants function and this diversity was assayed by Shannon index
knowledge is necessary to adjust the effect (H'). The higher Shannon index reflects the
of management and conservation strategies. higher diversity (Swingland, 2001).
There is no information about associated
bacteria with sugarcane growing in the fields Shannon's index ⟹ ,
of Iran, therefore this study was conducted
to isolate and characterize potential
beneficial bacteria that may be present in
rhizosphere of sugarcane in saline and non- Evenness index ⟹Evenness= H/Hmax(Hmax=
saline soil. ln N)
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KCl and 2% Agar and set to pH 6.8-7. From Results and Discussion
overnight culture of isolates, 10µl were
cultured on PVK medium in plates and Some chemical and physical properties of
incubated for 7 days at 30°C. Appearance of the soil are presented in Table 1. The soil
clear zone around the colony was regarded texture of both samples with EC= 1.5 and
as their ability of the phosphate solubility. 4.7 dS/m was clay loam and soil pH for
The phosphorus solubility index (SI) was saline and non-saline soils were 9.02 and
calculated from the ratio of colony to halo 8.86, respectively. Microbial biomass
zone diameter. The solubility of phosphorus carbon in non- saline soil was higher than
in liquid medium was also determined in saline soil. Decreased microbial biomass
Pikovskaya's broth medium using the carbon by increasing soil salinity has been
standard curve and determining the reported (Yuan et al., 2007).The low
absorption intensity at 880 nm (Ramani, respiration rate in saline soil is in agreement
2011). Nitrogen-fixation ability investigated with other studies (Yuan et al., 2007;
according to Döbereiner (Döbereiner, 1972) Wichern et al., 2006; Rietz and Haynes,
and the dissolution of potassium was also 2003)and can be explained salt induced low
performed on Aleksandrov agar medium osmotic potential which reduces water
containing vermiculite powder (Aleksandrov availability to microbes and may draw water
et al., 1967). Auxin production was out of the cells.
discovered according to Bric et al., (Bric et
al., 1991). Isolation and Identification of Bacteria
and by Paenibacillus and Enterobacter in specific roles in the rhizosphere saline soil
saline soil. Numbers of bacterial species to induce plant toleration against salinity.
associated with sugarcane rhizosphere have
been isolated which belonging to Growth Promoting Properties of Isolates
Azospirillum, Alcaligens, Arthrobacter,
Acinetobacter, Bacillus, Burkholderia, Generally, 87.5% of the isolates were able to
Enterobacter, Erwinia, Flavobacterium, grow in Deubernier medium and because of
Pseudomonas, Rhizobium, and Serratia nitrogen fixation, color change of medium
(Nakade Dhanraj, 2013). Diversity and from dark green to yellow was
evenness of isolated bacteria in both saline happened(Table 4). Of these, 45.9 percent of
and non-saline soils was calculated using isolates were from non-saline soil and
Shannon’s index. Diversity (Shannon’s 41.5% from saline soil. Emtiazi et al.,
Index) and evenness of isolated bacteria (2007) identified Paenibacillus as nitrogen-
from saline soil was as H= 1.63 and fixing bacterium. The different genuses of
E=0.840, respectively, and these was H= Paenibacillus have nitrogen fixation ability
1.04 and E=0.753 for non-saline soil. (Xieand Du, 2014).
Diversity and evenness of isolated bacteria
from sugarcane rhizosphere in saline soil Various reports have shown Pseudomonas
were higher than non-saline soil that as diazotrophicus bacteria in the rhizosphere
indicates high severity of salt stress of different plants such as rice (Mirza et al.,
increases diversity in the bacterial 2006), sugarcane (Ramesh kumar et al.,
communities (Table3). This might be 2012; Ashraf et al., 2011) and legumes
attributed to proliferation of halophylic (Ahmad et al., 2008). Khanet al.(2008)
bacteria in soil. Yang et al., (Yang et al., isolated and identified Bacillus and
2016)determined higher diversity of bacteria Enterobacter as nitrogen-fixing bacteria
in the rhizosphere soil at high salinity than from the rhizosphere of rice in Bangladesh.
low. In this study, Enterobacter, Nitrogen-fixing enterobacteria have been
Corynebacterium, Micrococcus and isolated from sugarcane plants cultivated in
Pediococcus were only found in saline soil. other countries (Loiret et al., 2004; Magnani
Pediococci commonly grow with plant et al., 2010; Mehnaz et al., 2010; Mirza et
associated lactic acid bacteria in various al., 2001; Taulé et al., 2010).
types of forage crops. Pediococci have
potential of fermenting xylose and Some isolates with following codes of E1-1
arabinose, they can be used as good (10), E1-2 (10) and E1-3 (10) isolated from
candidates for efficient lignocellulosic saline soil and E1-9 (12) isolated from non-
feedstock bioconversions (Boguta et al., saline soil had the ability to produce auxin,
2014). In industry, Corynebacterium species which first 3 isolates were related to
are used for economic production of Enterobacter and the other was
glutamic acid (Hermann, 2003). Paenibacillus. Change in the color intensity
due to auxin production in the presence of
The production of amino acids by (10) E1-1 and (10) E1-3, both were isolated
rhizobacteria may play an important role in from saline soil, was greater than other
the growth of plants and might also have a isolates. Earlier research reported that auxin
direct application in agricultural producing Enterobacter sp. strain 35
technologies. More research is required to isolated from sugarcane successfully
determine whether those bacteria have colonized and promoted growth of Brassica
oleracea (Zakria et al., 2008).The
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production of auxin and various other ratio of halo to colony diameter (0.8) was in
indolic and phenolic compounds by second place and Bacillus [E1-2] with a halo
Paenibacillus. Polymyxa RP, RS and NRS diameter ratio (0.75) in third place.
isolates has been reported (Lebuhn et al., According to the study of Mehnazet al.,
1997). (2010)on isolation of sugarcane rhizosphere
bacteria in Punjab, 32 isolates, including
Potassium is one of the essential nutrients Enterobacter, Klebsiella and Pseudomonas
for plant growth and development. Most of were detected that, 17 isolates had
the potassium in soil exists in various phosphate dissolution ability. Phosphate
insoluble minerals (Goldstein, 1994). solubilizing microorganisms by production
Microorganisms play an important role to of phosphatase enzymes and organic acids,
release potassium from minerals and supply increase plants availability to the soluble
soluble K for plant. Test results of potassium phosphorus (Khan et al., 2009).
dissolution by our isolates have been
provided in Table 5. Isolates 10(E1-2) from The quantity of phosphate solubilizing by
saline soil had higher ratio of halo to colony isolates in liquid medium have been
diameter. provided in Table 7.Based on these results,
the highest phosphate solubilization ability
Most of the KSB obtained from the plant was respectively belong to Bacillus [12(K2)]
rhizosphere are Bacillus sp. and from non-saline soil, Pseudomonas[E1-2-2]
Pseudomonas sp (Archana et al., 2013; isolated from non-saline soil and Bacillus
Gopal et al., 2005; Liu et al., 2001; [2.6(K6)] from saline soil. Pearson
Sugumaran and Janarthanam, 2007; Zhou et correlation coefficient between phosphate
al., 2006). Zhang and Kong (Zhang and dissolution and pH of the medium (-0.73)
Kong, 2014) found 2 strains belonged to showed a significant negative correlation
Enterobacter cloacae as potassium (p<0.01) between these two parameters.
solubilizing from mica. Potassium Since the phosphate dissolution reaction
solubilizing bacteria have been isolated from occurs in rhizosphere so the probability of
rice crops, corn crops, and coconut tree finding solubilizing bacteria in this area is
(Gopal et al., 2005), tobacco (Zhang and higher (Mehta and Nautiyal, 2001).The pH
Kong, 2014). However, there are relatively reduction of the medium suggests the release
few studies on potassium solubilizing of organic acids by the P-solubilizing
bacteria in the sugarcane rhizosphere. microorganisms (Nautiyal et al., 2001,
Ghevariya and Deasi (2014) show Rashid et al., 2004).
Pseudomonas sp. of potassium
solubilization from mica. Figure 1 shows PCR amplification product
of extracted DNA from selected bacteria in
The results of phosphate dissolution by terms of growth-promoting properties, 1,500
isolates have been provided in Table 6. bp product represents correct genome
Based on these results, Pseudomonas (E1-2- amplification. Results of the sequencing of
2) with high ratio of halo to colony diameter the amplified fragment of each bacterium
(2.4) showed the greatest ability of insoluble were edited using Bio edit software and
phosphate dissolution in solid medium. Then were identified by Blast.
Enterobacter cloacae [10(E1-2)] with the
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Number Pi ln Pi* Pi
non-Saline non-Saline non-Saline
Saline soil Saline soil Saline soil
soil soil soil
Paenibacillus 3 6 0.157 0.285 -0.290 -0.356
Bacillus 8 12 0.421 0.571 -0.364 -0.319
Pseudomonas 2 2 0.105 0.095 -0.236 -0.223
Enterobacter 3 - 0.157 - -0.290 -
Pediococcus 1 - 0.052 - -0.153 -
Corynebacterium 1 - 0.052 - -0.153 -
Micrococcus 1 - 0.052 - -0.153 -
Arthrobacter - 1 - 0.047 - -0.143
K2HPO4 Vermiculite
Bacteria code
Halo Colony Halo/Colony Halo Colony Halo/Colony
10(E1-2) 7 3 2.3 - - -
E1-2-2 7 5 1.4 10 5 2
10(E1-3) - - - 9 5 1.8
12(K1) 3 5 0.6 - - -
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Table.6 Halo and colony diameter (mm) of isolates solubilizing phosphate in PVK agar medium
and pH and quantity of phosphate solubilizing in broth PVK medium
Bacteria Phosphate
Halo Colony Halo/Colony pH
code solubilizing(mg/L)
10(E1-2) 8 10 0.8 10.10 5.37
10(E1-5) 2 10 0.2 7.07 5.06
10(E1-4) 4 10 0.4 10.73 4.55
E1-2-2 12 5 2.4 13.64 4.1
10(E1-1) 4 8 0.5 10.42 5.41
1(S7) 4 10 0.4 7.06 4.84
10(E2-3) 2 8 0.25 2.95 5.26
10(E3-2) 4 10 0.4 10.42 4.82
12(E1-9) 4 8 0.5 6.68 5.7
2.6(K6) 2 10 0.2 13.53 4.8
E1-2 6 8 0.75 4.89 5.45
1(a1)E 2 10 0.2 11.19 4.48
10(E1-3) 8 10 0.8 12.13 4.2
12(K2) 6 8 0.75 14.15 4.7
K2 3 7 0.43 12.59 4.42
1(d9)E 5 9 0.55 7.77 4.84
1 2 3 4
5
1500bp
According to the results of comparing the In conclusion, during recent years, a great
sequences of 16S rRNA, growth-promoting attention has been paid to saline soils due to
strains had 98 percent similarity with the reducing arable land, and of the
Enterobacter cloacae R13 [10(E1-1)], increasing demand for agricultural
Paenibacillus lactis [12(E1-9)], and production of areas influenced by secondary
Pseudomonas sp [E1-2-2], Enterobacter salinization processes. Actually salt-affected
cloacae R33 [10(E1-3)], which were soils may have a biotechnological potential
deposited in Gene Bank under accession No: in their microbial communities, which
KX262855, KX262856, KX262854, represent a reserve for future exploitation in
KX262856, respectively. biotechnological applications. A survey of
available literature, suggests that
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Int.J.Curr.Microbiol.App.Sci (2016) 5(10): 1072-1083
microbiology of saline soil and exploitation properties (methods of soil an 2), 831-
of microorganisms from these soil has not 871.
been dealt extensively. As mentioned in the Archana, D., Nandish, M., Savalagi,V.,
introduction, very few studies have Alagawadi, A., 2013.
considered in addressing the diversity of Characterization of potassium
PGPR, in relation to salinity. According to solubilizing bacteria (KSB) from
our results salinity had the strongest effect rhizosphere soil. BIOINFOLET-A
on bacterial community structure. On Quarterly J. Life Sci., 248-257.
completing this investigation, I am Ashraf, M.A., Rasool, M., Mirza, M.S.
impressed with the wide diversity of 2011. Nitrogen fixation and indole
microorganisms present in saline soils. Our acetic acid production potential of
study revealed a high plasticity of bacterial bacteria isolated from rhizosphere of
phyla that evidently possess genera and sugarcane (Saccharum officinarum
species adaptable to salinity conditions with L.). Adv. Biol. Res., 5(6): 348-355.
plant growth promoting properties. There is Boguta, A.M., Bringel, F., Martinussen, J.,
scope for use of nitrogen fixer and Jensen, P.R. 2014. Screening of lactic
phosphate and potassium solubilizing acid bacteria for their potential as
bacteria as potential biofertilizers for microbial cell factories for
reclamation saline soils of local area because bioconversion of lignocellulosic
isolates belongs to the same soil. From 40 feedstocks. Microbial cell factories
isolates on two saline and non- saline soils 4 13(1): 1.
isolates having good plant growth promotion Bric, J.M., Bostock, R.M., Silverstone, S.E.
were chosen and will be suggested to 1991. Rapid in situ assay for
produce for sugarcane cultivation in the indoleacetic acid production by
future. bacteria immobilized on a
nitrocellulose membrane. Appl.
Acknowledgments Environ. Microbiol., 57(2): 535-538.
Döbereiner, J., Day, L., Dart, P. 1972.
The authors thank the Shahid Chamran Nitrogenase activity and oxygen
University of Ahvaz for support this project. sensitivity of the Paspalum notatum-
Azotobacter paspali association.
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