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Mushtaq et al., The J. Anim. Plant Sci. 29(4):2019

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CHARACTERIZATION OF PLANT GROWTH PROMOTING ACTIVITIES OFBACTERIAL ENDOPHYTES AND THEIR ANTIBACTERIAL POTENTIAL ISOLATED

FROM CITRUS

S. Mushtaq1, M. Shafiq1, T. Ashraf2, M. S. Haider1, M. Ashfaq1* and M. Ali1

1 Institute of Agricultural Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore.2University College of Agriculture University of Sargodha

Corresponding Author e-mail: [email protected]

ABSTRACT

In this study screening of novel bacterial endophytes isolated from the leaves of citrus were performed for plant growthpromoting activities which include Indole Acetic Acid (IAA), Siderophores and phosphate Solubilization. Isolatedbacterial endophytes were also tested for the screening of cell wall hydrolyzing enzymes production such as cellulase,chitinase, protease, pectinase and lipase as well as antibacterial activity. Thirteen genera of different bacteria wereisolated and characterized from twelve different varieties of citrus on the basis of morphological, biochemical andmolecular 16S rRNA. Neighbor joining phylogenetic dandrogram showed that all the isolates have genetic relatednessamong them. According to results 75-80% of the strains were positive for plant growth promoting (PGP) and enzymaticactivities of test strains except few of them. However antibacterial activity were found positive in 68.75% of test cultureswhile five isolates Enterococcus faecalis, Klebsiella pneumonia, Staphylococcus haemolyticus, Bacillus megaterium andBacillus cereus did not show any antibacterial activity against any of the targeted bacterial strains. The data presented inthis article is unique and this type of work on these bacterial species has not been reported from citrus. The findings willbe helpful for the use of these endophytes to enhance the plant growth and yield. On the other hand, the study will beequally beneficial to the scientist and farmers community.

Key words: Antibacterial activity, Siderophores, Indole acetic acid, cell wall degrading enzymes.

INTRODUCTION

Bacterial endophytes isolated from plants haveability to reduce the deleterious effects of certainpathogens. The positive beneficial effects of endophyticbacteria on their host plants happen through similarmechanisms as occurs with rhizobacteria. In depth studyof these mechanisms has been performed by (Gray andsmith, 2005). Different disease causing agents such asbacteria, fungi, viruses, insects, nematode and othermicrobes can be managed by the use of bacterialendophytes as inoculants for infected hosts (Ping andBoland, 2004; Berg and Hallmann, 2006). Hence it’sgenerally believed that some endophytic bacteria trigger aphenomenon known as ISR (Induced systemic resistance)that is apparently similar to Systemic acquired resistance(SAR). Frequently when plants primarily infected by apathogen as response of plant defense activation SARdevelops. As a result of hypersensitive response pathogenbecome limited to a necrotic lesion of brown dead tissue.In comparison ISR is quite different hence the bacteriumdoes not cause any visible sign of infections on hostplants (Santoyo et al., 2016).There are many reports onthe emergence of pathogenic strains of endophytes fromthe rhizosphere of the plants which includesEnterobacter, Burkholderia, Herbasipirillum,Pseudomonas, Ochrobactrum, Ralstonia and

Staphylococcus (Berg et al., 2005). Hence manyfacultative endophytes have been recruited from the largepopulation of bacterial endophytes from soil andrhizosphere adapted to live inside plant tissues mayinclude opportunistic human and animal pathogens.There is a report of association of bacterium from theinterior of alfalfa plant. So this area should be furtherinvestigated to prevent the establishment of risk ofpathogen association with plants endophytic bacterialniche that appear by the use of biotechnologicalapplications.

Endophytic bacteria are those bacteria thatreside inside plant tissues and showed no visible externalsigns of invasion or negative effects on plant growth(Schulz and Boyle, 2006). There are nearly 300,000plants species present on the earth, so each individualplant is host of one or more endophytes out of total, onlyfew of the plant species has been studied completely fortheir biology. As a result there is increase chances to findnew and beneficial endophytes among the diverse hostsin complex ecosystem is considerably possible. Theseendophytes colonize similarly as phyto-pathogensprevails in plants ecosphere and interact with each otherso make it possible their use as biological control agents(Berg et al., 2005). There are several reports thatrepresent the ability of these endophytic microbes as abio control agents to control plant pathogens (Kong et al.,

The Journal of Animal & Plant Sciences, 29(4): 2019, Page: 978-991ISSN: 1018-7081


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2015), insects (Azevedo et al., 2000) and nematodes (Ek-Ramos et al., 2019). The endophytic niche providesprotection from the external environment for thosebacteria that can colonize and establish inside plants.These bacteria generally inhabit in the intercellularspaces and plant parts (Posada and Vega, 2005). Thesemicrobes can be isolated from the wide host range fromboth monocotyledonous and dicotyledonous plants, suchas oak and pear, or to filed crop plants such as sugar beetand maize.

Plant growth promoting traits of bacterialendophytes has been studied to check the PGPR abilitiesof many rhizobacteria. These endophytes differ frombiological control agents as they improve the growth ofplants not necessarily inhibit pathogens. Althoughbacterial endophytes found inside the plant tissues alsopromote plant growth by similar mechanisms. Generallythese mechanism includes indole acetic acid production(Lee et al., 2004), phosphate solubilization activity(Verma et al., 2001; Wakelin et al., 2004), production ofa siderophores (Pandey et al., 2015).These organismsalso supply the essential mineral and vitamins to plants(Pirttila et al., 2004). However a number of otherbeneficial aspects on plant growth has been studied whichconsist of osmotic adjustment, regulation of stomatalopenings, root morphology modification, increase ofmineral and change of nitrogen deposition inside tissues,or metabolism of plant (Compant et al., 2005a, 2005b). Interrestrial plants phosphorous is second most importantnutrient that can limit the growth. Although total amountof phosphorous are maximum in agriculture soils buttheir availability to plants is limited because large amountof phosphorus is present in insoluble form (Azevedo etal., 2016). On the other hand, soluble form of inorganicphosphorous applied as a fertilizer is stopped soon itsapplication (Glick, 2012). Plants root zone soil is rich inphosphate solubilizing bacteria which secretes organicacids and phosphatases converts the soluble form ofphosphorus to available form to plants (Mesa et al.,2017). Now agricultural microbiologists are takingattention in utilization of the P-solubilizing strains forimproving P uptake of crops (Stefan et al., 2013). Mostof the bacterial populations residing in soil are involvedin various biotic activities of the ecosystem to make itdynamic for essential nutrients and sustainable cropproduction. As balanced quantity of nutrients are requiredfor plant growth.

There are various functions and effects of indoleacetic acid (IAA) on the physiology of plants that controlvegetative growth process; disturbed the plant celldivision, extension and differentiation; increase thedevelopment of roots and starts the lateral andadventitious root formation; enhance the nutrients uptakethrough xylem, improve the light responses, gravity andfluorescence; it also alter the biosynthesis of differentmetabolites, photosynthesis, pigment production and

resistance of plant against stress conditions (Spaepen andVander Leyden, 2011). However reaction of plant forIAA depends on plant tissue type. PGPR bacterial hasability to alter the internal pool of IAA while theendogenous level of IAA in plant roots may be optimumfor growth hence more IAA required from soilrhizosphere bacteria may enhance or suppress the plantgrowth as a result promotion or inhibition happensrespectively (Phan et al., 2016). Usually a PGPRbacterium secretes IAA which increases the plant rootaccess to nutrients by increasing the surface area of rootand length. In returns it increase the root exudates fromplant to attracts PGPR and also increases root exudationby loosening plant cell walls which provide nutrients torhizosphere bacteria (Riera et al., 2017).

PGPR produce variety of extracellular andintracellular lytic enzymes such as chitinases, β 1, 3-glucanases, proteases, cellulases, and lipases which havefunction to lyse the cell wall of many plant pathogens.Several strains of bacteria have found to be produced oneor more enzymes and have the ability to control a rangeof pathogenic fungi (ElTarabily, 2006) ; also affect thespore germination and germ-tube elongation of plantpathogenic fungi (Frankowski et al., 2001). On the otherhand, the enzyme producing bacteria has been used insynergism with other biocontrol agents to control plantpathogens. (Chen et al., 2019).The aim of the currentstudy was to isolate and characterize the endophyticbacterial strains from different varieties of citrus through6S rRNA and their screening for the plant growthpromoting trait IAA, siderophores detection, Phosphatesolubilization, cell wall degrading enzymes andantibacterial activities against pathogenic strains ofbacteria.

MATERIALS AND METHODS

Survey and sampling: A comprehensive survey of thecitrus orchards of Sargodha were conducted and 12different varieties of citrus showing symptoms of citrusgreening were collected and proceeded for isolation ofendophytic bacteria from leaves.

Isolation and identification of bacteria: Isolation ofendophytic bacteria from 3-4 cm mid rib portions ofcitrus leaves were performed by surface sterilization ofleaf mid ribs with 1 % sodium hypochlorite solution for3-5 minutes and three consecutive washings with sterilizedistilled water. Homogenized mixture of grinded mid ribportion were prepared with distilled water and inoculatedon Nutrient agar medium plates, and incubated at 28ºCfor 24-48 hours. Further isolated bacterial colonies werepurified on nutrient agar plates and incubated at 28ºC for24-48 hours. Pure cultures of bacterial isolates werecharacterized on the basis of colony morphology andGram staining (Garrity, 2005). Glycerol stocks of all


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isolated and identified bacterial cultures were preparedfor long time preservation and stored at -80ºC.

Molecular characterization of isolates: CTAB (cetyltrimethyl ammonium bromide) method was used forisolation of total genome of DNA (Wilson, 1987).Bacterial culture were grown in 5ml of growth medium(Nutrient agar) for 24 hours and centrifugation at 13000rpm for 2 minutes to make pellet. The pellet wassuspended in 567μL of TAE buffer and 30μL of 10%SDS, 3μL of proteinase k (20 mg/ml) was added andincubated at 37oC for 1 hour. 100μL of 5M NaCl, 80μLof CTAB were mixed and incubated for 10 minutes at65oC followed by addition of 750μL of ChloroformIsoamyl Alcohol (24:1) and centrifuged for 5-10 minutes.400μL of the upper layer was transferred to a neweppendorf tube. The 700μL of Phenol Chloroform wasmixed and centrifuged for 10 minutes and againtransferred supernatant to new tube. On the other hand,20μL of 3M Sodium Acetate and 500μL of AbsoluteEthanol (100%) were added and mixed gently toprecipitate DNA and placed at -20oC for overnight. Nextday the tubes were centrifuged again at 13000 rpm or10000 rpm for 5-10 minutes and the supernatant wasdiscarded. Pallet was washed with 70% ethanol and resuspended in 50μL sterile double distilled water. DNAwas run on 1% [w/v] agarose gels containing ethidiumbromide (0.5 μg/ mL).

Genomic DNA 16 bacterial isolates weresubjected to PCR for further DNA sequencing, using thebacterial primers 27-F(5’AGAGTTTGATCMTGGCTCAG 3’), 1492-R(5’ACCTTGTTACGAC TT 3’) and previously reportedPCR conditions were applied. All PCR products werepurified and directly sequenced Macrogen Korea. Thegene sequences obtained were compared by aligning theresult with the reported sequences in Gene Bank usingthe Basic Local Alignment Search Tool (BLAST) searchprogram at the National Centre for Biotech Information(NCBI), as well as Ribosomal databased project (RDPHierarchy Browser) was used to classify the isolatedbacterial sequences. Sequences were submitted to NCBIGene Bank data base and accession numbers wereobtained.

Phylogenetic analysis: Multiple sequence alignmentswere generated and the 16S rDNA gene sequences werephylogenetically analyzed using MEGA 6.0. (Tamura etal., 2011). A confidence value for the aligned sequencedataset was obtained by performing a bootstrap analysisof 1000 replications. A phylogenetic tree was constructedusing the neighbor joining algorithm to study theevolutionary relationship among organisms.

Characterization of plant growth promotion traitsassay

IAA production assay: Indole-3-acetic acid (IAA)production of the selected bacterial strains was measuredby following the method of (Patten and Glick, 2002) withslight modification. All the strains were replicated thriceand experiment was performed in sterile conditions.About 20 µl aliquots of an overnight grown bacterialculture were used to inoculate 5 ml TSB without and withtryptophan (500 µg ml-1) and incubated at 37oC forovernight. After incubation the cultures were centrifugedfor 30 minutes and 1 ml supernatant was mixed with 4 mlSalkowski’s reagent (Gordon and Weber, 1951). Themixture was incubated for 20 minutes at roomtemperature and then the absorbance was measured at535 nm by using spectrophotometer.

Phosphate solubilization: Phosphate solubilizingactivity of rhizobacteria was determined qualitatively byusing (Nautiyal, 1999) method. Bacterial strains wereevaluated for their ability to solubilize inorganicphosphate. Tri-calcium orthophosphate was used in agarmedium as insoluble inorganic form of phosphate andwas used as a source of indication for phosphatesolubilization property of the bacterial strains. Themedium used to access the phosphate solubilizationproperty of selected bacterial strains was comprised ofagar (15 g), glucose (10 g), NH4Cl (5 g), NaCl (1 g),MgSO4.7H2O (1 g), Ca3 (HPO4) (0.8 g) and yeastextract (0.5 g) per liter while pH of the medium wasadjusted to 7.2. On each plate three bacterial strains werechecked with triplicate and the plates were incubated at30±1 °C for 4 days where as non-inoculated medium withtri calcium phosphate source served as control. A clearhalo formed around some of the colonies after 4 daysindicated that these isolates were positive for phosphatesolubilization.

Siderophores detection: To determine siderophoresproduction for selected bacterial strains isolated fromcitrus leaves method was used. In this assay CASmedium was used which was prepared according to(Schwyn and Neilands, 1987) procedure with somemodifications in the absence of nutrients. The CASmedium (1L) contained Chrome azurol S (CAS) 60.5 mg,hexadecyltrimetyl ammonium bromide (HDTMA) 72.9mg, Piperazine-1,4-bis (2ethanesulfonic acid) (PIPES)30.24 g, and 1 mM FeCl3·6H2O in 10 mM HCl 10 mL.Agarose (0.9%, w/v) was used as gelling agent.Siderophores detection was achieved after 10 ml(standard, 80 mm diameter Petri dishes) overlays of thismedium were applied over those agar plates containingcultivated microorganisms to be tested for siderophoresproduction. After a maximum period of 80 minutes, achange in color was observed in the overlaid mediumexclusively surrounding producer microorganisms, from


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blue to purple or from blue to orange. All theseexperiments were performed at least three times each inthree replicates.

Enzymatic characterization: Different enzymaticactivities of the isolated bacterial strains from citrus leafsamples were conducted and are described below.

Protease activity: In order to determine the proteaseactivity of the selected bacterial isolates from citrus. Theprotease activities of selected bacterial strains weredetermined by using skim milk agar medium. All thestrains were processed in triplicates and strict measureswere taken to avoid any kind of contamination. About500 ml of modified TSB medium was prepared, while inanother flask 1.5% (W/V) of skimmed milk wasdissolved in distilled water (100 ml). Both of these flaskswere properly plugged, labeled and autoclaved at 121 ºCfor 20 minutes. From each of the strains to be tested forprotease activity, a colony was picked with a sterileinoculation loop and was spotted on the media platecontaining skim milk. On each plate five morphologicallydifferent strains were spotted. All the plates were thenplaced in an incubator at 30oC and were regularlychecked after 24, 48 and 72 hours to find out if therewere any protease activity.

Cellulase activity: In order to determine the cellulaseactivity of the selected bacterial strains, all the strainswere processed in triplicates. Cellulase activities of thebacterial strains were analyzed by (Cattelan et al., 1999)method. Carboxy Methyl Cellulose medium (0.2%) wasprepared (1g CMC and 3 g of TSB dissolved in 500 ml ofdistilled water). The CMC medium was properlyplugged, labeled and autoclaved at 121 ºC for 20 minutes.After autoclaving the media was cooled and poured intoplates, five different strains were inoculated onto a singleplate. All the plates were then placed in an incubator at37oC for 48 hours. After 48 hours incubation all theplates were flooded with 0.1% of Congo red dye solution(0.1 g CRD in 100 ml of distilled water), the plates wereshaken carefully in shaker for about 20-30 minutes. Aftershaking the plates were washed with 1 M NaCl solution.Data was recorded by examining yellow halos against redbackground.

Lipase activity: In order to determine the Lipase activityof the selected bacterial strains, all the strains wereprocessed in triplicates. For lipase activity 1% of tween20 was added to TSB medium and was properly plugged,labeled and autoclaved at 121 ºC for 20 minutes. Themedia was cooled and poured into plates; five differentstrains were spotted onto a single plate with sterileinoculation loop. All the plates were then placed in anincubator at 25oC and were regularly checked after 24and 48 hours to find out if there was any proteaseactivity. Data was recorded by examined white typeprecipitation surrounding their colony.

Chitinase activity: Chitinase activity was determined byusing (Renwick et al., 1991) method, in which carbonwas the sole source in a defined medium having colloidalchitin. All the strains were processed in triplicates andstrict measures were taken to avoid any kind ofcontamination. TSA medium (0.5g of MgSO4-7H2O,0.7g of K2HPO4, 0.3 g of KH2PO4, 0.01 g of FeSO4 ·H2O, 0.001 g of ZnSO4, 0.001 g of MnCl2) with 0.6%(w/v) colloidal chitin was used. For colloidal chitin twograms of chitin from crab shell (UniChem) was dissolvedin concentrated HCl (200 ml), by shaking the mixtureovernight at 4oC in shaker. To decrease the viscosity ofmixture it was incubated in water bath at 37oC. Theseisolates were screened to determine chitinase production.Each isolate was inoculated on colloidal chitin agar(CCA) and incubated at 28ºC in the dark until (after 7days incubation) zones of chitin clearing were seenaround colonies. Clear zone diameters are measured(mm) and used to indicate the chitinase activity of eachisolate.

Pectinase activity: The pectinase activity wasdetermined by (Raju and Divakar, 2013) method. After48 hours incubation at 28°C, the plates were flooded withiodine solution (50 mM) and incubated for 15 minutes at37oC. Strains surrounded by clear halos around colonieswere considered positive for pectinase activity.Composition of media used for pectinolytic activity waspectin (0.2%), KH2PO4 (0.3%), MgSO4.7H2O (0.01%),NaCl (0.5%), NH4Cl (0.2%), Na2HPO4 (0.6%).Bacterial isolates were spot inoculated on plates andincubated at 28± 2°C for three days. The medium wasproperly plugged, labeled and autoclaved at 121ºC for 20minutes. From each of the strains to be tested forpectinase activity, single colony was picked with a sterileinoculation loop and was spotted on the media plates.After incubation, plates were observed for pectinaseactivity by flooding plates with iodine solution. Isolatespossessing pectinolytic activity formed clear zonesaround colonies

Antibacterial activity: In order to determine theantibacterial activities by agar well diffusion method(Azoro et al., 2002) of the selected bacterial isolates wasconducted. All the strains were processed in triplicates.Antibacterial activity of test strains were tested againstXanthomonas oryzae, Pseudomonas syringae, Bacilluscompestris, Acidovorax faecalis, Kluyvera sp.,Pseudomonas aeruginosa, Burkholderia pseudomallei,Xanthobacter autotrophicus, Bacillus fortis. The bacterialstrains that were used as test and target strains weregrown in LB broth overnight in a shaking incubator at25oC. About 50 ul (1.5x105 CFU) of these selected targetstrains were spread on solidified LB agar plates with asterile glass spreader. Then 5 sterile filter disks wereplaced on top of solidified media plates, the control diskwas placed in the center while the other four disks were


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placed at equal distance from the center. From each teststrains 10 µl was poured onto separate filter disks, whileonto the center filter disk 10 µl antibiotic solution(kanamycin) was applied at 20 µg/ml and was consideredas positive control. These plates were then incubated at37oC and were observed clear zones after 24-72 hours.After the incubation period, the diameter of inhibitionzones of each well was measured and the values werenoted. Replications were maintained and the averagevalues were calculated for the eventual antimicrobialactivity.

Statistical analyses: Statistical analysis was performedusing one way analysis of variance (ANOVA) followedby least significant difference (LSD) using the Statisticssoftware version 8.1.

RESULTS

Phylogenetic analysis of isolated bacterial strains: Inthis study molecular characterization of the isolatedstrains of endophytic bacteria were performed through16S rDNA universal primer and sequenced. Sequenceswere assembled and blast in NCBI to identify bacteria.Neighbor joining tree was constructed by using Mega 6.0with bootstrap value 1000 (figure 1). All the strains haveshown maximum similarity of 97-100 percent. Accordingto phylogenetic analysis all strains were laid in differentclades along with their type strain and showed geographicrelatedness with each other.

Plant growth promotion traits of selected isolatesfrom citrus: Bacterial strains were isolated from leavesof different varieties of citrus. Morphologically differentgenera of bacterial strains isolated through culturingmethod were selected for the study of plant growthpromoting (PGP) traits. All the tested strains wereidentified through16S rRNA gene sequencing. Totalsixteen bacterial strains were selected for in vitroscreening for PGP traits e.g., siderophores, phosphatesolubilization. The data regarding each activity was givenin (Table 1).

Phosphate solubilization: Phosphate solubilizingactivity of the selected bacterial strains isolated fromleaves of different varieties of citrus were screened onmedia containing Tricalcium phosphate (TCP) assubstrate. Out of sixteen bacterial strains SM-68, SM-57,SM-42, SM-27, SM-82, SM-1, SM-30, SM-58, SM-56,SM-20 and Sm-36 displayed the development of a clearzone around colonies as an indication of phosphatesolubilization activity. Five bacterial strains Sm-34, SM-90, SM-15, SM-37, and SM-76 showed phosphatesolubilization activity with zone diameter (2-3 mm).Three isolates of GM maize rhizosphere (n=3) werepositive for phosphate solubilization, whereas 11 isolates

were positive for phosphate solubilization. While fiveisolate did not show phosphate solubilizing activity.

Siderophores production: Siderophores activities of theselected bacterial strains isolated from different varietiesof citrus leaves were assessed on Chrome azurol S agar(CAS) medium. Total sixteen isolates were used to checkthe siderophores production. SM-34, SM-68, SM-57,SM-90, SM-15, SM-37, SM-1, SM-30, SM-58, SM-56,SM-20 and SM-36 changed the color of CAS mediumfrom blue to orange and were positive for siderophoresproduction. While three isolates showed growth up tosome extent but not changed the color of CAS medium,hence these isolates were negative for siderophoresproduction.

Indole acetic acid (IAA): Indole acetic productions ofthe selected bacterial strains isolated from leaves ofdifferent varieties of citrus were screened. Overnightgrown bacterial culture was used to inoculate 5 ml TSBwithout and with tryptophan (500 µg mL−1) andincubated at 30◦C in rotary shaker for 24 hour. The indoleacetic acid concentration was detected byspectrophotometer. Majority of the bacterial strainsshowed IAA production. The culture with no tryptophan,isolate SM-34 (Bacillus safensis) produced maximumIAA (0.353 µg mL−1) and isolate SM-58(Psychrobacterium pulmonis) produced maximum IAA(0.226 µg mL−1) as compared to other isolates. Whereasthe culture with tryptophan, isolate SM-34 (Bacillussafensis) produced maximum IAA (0.355 µg mL−1) andminimum IAA (0.215 µg mL−1) in isolate SM-27(Enterobacter hermachei) as compared to other isolatesas shown in (figure 2).

Production of cell wall hydrolyzing enzymes byselected isolates of citrus: All the 16 different bacterialisolates were in vitro characterized for production offungal cell wall hydrolyzing enzymes such as cellulase,chitinase, protease, pectinase and lipase (Table 1).

Cellulase activities of the isolated bacterial strains: Allthe 16 bacterial strains were screened for cellulaseenzyme production. After two days of incubation andtreatments of the individual plates with Congo red dyeand NaCl solution, cellulase activity of the strains wereestimated by measuring the yellowish brown halo aroundindividual colonies. The bacterial strains isolated fromdifferent varieties of citrus were screened, 75% showedcellulase positive activity while 25% did not show anyactivity. From the diameter of the zone it was concludedthat 12 strains SM-34, SM-68, SM-90, SM-42, SM-27,SM-37, SM-82, SM-1, SM-30, SM-58, SM-56 and SM-20 showed positive cellulase activities. Four bacterialstrains (25%) not showed cellulase activity.

Chitinase activities of isolated bacterial strains: Theselected bacterial isolates were in vitro screen for


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chitinase activities. The chitinase activity was screenedfor all the 16 bacterial strains on TSA medium, in whichcarbon was the sole source in a defined medium havingcolloidal chitin. These isolates were screened todetermine chitinase production. Each isolate wasinoculated on colloidal chitin agar (CCA) and incubatedat 28ºC in the dark up to 7 days, zones of chitin clearingwere observed around colonies. Results showed that 12out of 16 selected strains namely; SM-68, SM-57, SM-42, SM-15, SM-37, SM-76, SM-82, SM-1, SM-58, SM-56, SM-20, SM-36 were positive for chitinase productionwhich was 75% of the total isolates. While the remaining4 (25%) isolates did not show any chitinase activities.

Protease activities of isolated bacterial strains:Bacterial isolates were in vitro screen for proteaseactivity. The protease activities were screened for all the13 bacterial strains of harvesting stage on their respectivemedium with added skimmed milk. All the bacterialstrains after three days inoculation on medium werescreened for protease activities. Strains producing a clearzone around colony were assumed to have positive forprotease production. Results showed that 14 out of 16selected strains SM- 36, SM-20, SM-56, SM-58, SM-1,SM-82, SM-76, SM-37, SM-15, SM-27, SM-42, SM-57,SM-68, SM-34 (87.5%) were proved to possess theprotease activity. While 2 (12.5%) isolates SM-30 andSM-90 did not show any protease activity.

Pectinase activities of isolated bacterial strains:Selected isolates were in vitro screen for pectinaseactivity results showed that 13 out of 16 bacterial strainsSM-34, SM-68, SM-57, SM-27, SM-37, SM-76, SM-2,SM-1, SM-30, SM-58, SM-56, SM-20, SM-36 showedpectinase activity. While the remaining 3 (18.25%) SM-90, SM-40, SM-15 isolate did not show any pectinaseactivities.

Lipase activities isolated bacterial strains: Bacterialisolates of citrus were in vitro screened for lipase activity.Total 16 strains were evaluated for enzymes production.Lipase activity was determined on TSB medium with 1%tween 20. Strains surrounded by white precipitation wereconsidered positive for lipase production. Results showedthat maximum isolates showed lipase activity. All the13(81.25%) isolate SM-34,SM-68,SM-42,SM-27,SM-15,SM-37,SM-76,SM-82,SM-1,SM-30,SM-56,SM-

20,SM-36 were able to produced lipase enzyme. Whereas3(18.75%) SM-57, SM-90, SM-58 isolates do notproduced lipase enzyme (Table 1).

Antibacterial activities of isolated bacterial strainsfrom different varieties of citrus: All the selectedbacterial strains were assessed for antibacterial activityusing disc diffusion method against various pathogenicbacteria such as Pseudomonas syringae(FCBP-009) ,Xanthomonas oryzae (FCBP-133), Bacillus compestris(FCBP-324), Acidovorax faecalis (FCBP-464), Kluyverasp.(FCBP-642), Xanthomonas compestris (FCBP-003),Burkholderia pseudomallei(FCBP-460), Xanthobacterautotrophicus(FCBP-432), Bacillus fortis (FCBP-162).The results were checked for any antibacterialactivity at intervals of 24 hours, 48 hours and 72 hoursrespectively. According to results out of 16 selectedstrains maximum isolates showed antibacterial potentialagainst selected targeted pathogenic strains. Isolate SM-34 (Bacillus safensis) showed positive results forXanthomonas oryzae, Burkholderia pseudomallei only,while isolate SM-68(Pseudomonas aeruginosa) haspotential to control Xanthomonas compestris. Howeverisolate SM-57 (Pseudomonas sp.) showed good resultsfor Pseudomonas syringae, Acidovorax faecalis,Kluyvera sp., Xanthomonas compestris (Table 2).whereasisolate SM-90 (Staphylococcus scuiri) has maximumpotential to control Pseudomonas syringae andXanthomonas compestris. Isolate SM-42(Brevibacteriumborstelensis) showed antibacterial potential againstXanthomonas oryzae, Bacillus compestris, Acidovoraxfaecalis, Xanthomonas compestris, and Burkholderiapseudomallei. On the other hand Isolate SM-30 (Bacillussubtilis) has potential for Xanthomonas oryzae,pseudomonas syringae, Bacillus fortis, while SM-20(Proteus mirabilis) showed good results forPseudomonas syringae, Xanthomonas compestris,Burkholderia pseudomallei. Isolate SM-58(Psychrobacterium pulmonis) has good potential tocontrol Bacillus compestris and Acidovorax faecalisrespectively. Five isolates SM-76(Enterococcus faecalis),SM-82 (Klebsiella pneumonia), SM-1 (Staphylococcushaemolyticus), SM-56(Bacillus megaterium) and SM-36(Bacillus cereus) did not show any antibacterial activityagainst any of the targeted bacterial strains (figure 3).


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Table 1. Screening of entophytic bacterial isolates of citrus for Plant growth promotion traits and cell wall degrading enzymes production.

Strains Code Bacterial Isolates Citrus Varieties Phosphatesolubilization

Siderophoresdetection

Cell wall degrading enzymesProtease Cellulase Lipase Chitinase Pectinase

SM-34 Bacillus safensis Lemon -ve +ve +ve +ve +ve -ve +veSM-68 Pseudomonas aeruginosa Olinda Valencia +ve +ve +ve +ve +ve +ve +veSM-57 Pseudomonas sp. Dancy +ve +ve +ve -ve -ve +ve +veSM-90 Staphylococcus scuiri Parson brown -ve +ve -ve +ve -ve -ve -veSM-42 Brevibacterium borstelensis Sweet orange +ve -ve +ve +ve +ve +ve -veSM-27 Enterobacter hermachei Grape fruit +ve -ve +ve +ve +ve -ve +veSM-15 Comamonas terrigena Casa grand -ve +ve +ve -ve +ve +ve -veSM-37 Yersinia mollaretti Lemon -ve +ve +ve +ve +ve +ve +veSM-76 Enterococcus faecalis Sour orange -ve -ve +ve -ve +ve +ve +veSM-82 Klebsiella pneumoniae Gada dahi +ve +ve +ve +ve +ve +ve +veSM-1 Staphylococcus haemolyticus Musambi +ve +ve +ve +ve +ve +ve +ve

SM-30 Bacillus subtilis Grape fruit +ve +ve -ve +ve +ve -ve +veSM-58 Psychrobacterium pulmonis Natal +ve +ve +ve +ve -ve +ve +veSM-56 Bacillus megaterium Dancy 4 +ve +ve +ve +ve +ve +ve +veSM-20 Proteus mirabilis Kinnow +ve +ve +ve +ve +ve +ve +veSM-36 Bacillus cereus Lemon +ve +ve +ve -ve +ve +ve +ve

Table 2. Antibacterial activity of isolated strain of citrus against pathogenic strains of bacteria collected from first fungal culture bank of Pakistan (FCBP).

Isolates TargetMicro organisms

Accessionnumbers

16srRNA based

%identity

Test micro organismsXanthomonasoryzae

Pseudomonassyringae

Bacilluscompestris

Acidovoraxfaecalis

Kluyverasp.

xanthomonas compestris

Burkholderiapseudomallei

Xanthobacterautotrophicu

s

Bacillusfortis

SM-34 Bacillus safensis MF801628 99% +ve - ve - ve - ve - ve - ve + ve - ve - veSM-68 Pseudomonas

aeruginosaMF802727 95% - ve - ve - ve - ve - ve + ve - ve - ve - ve

SM-57 Pseudomonas sp. MF973203 89% - ve + ve - ve + ve + ve + ve - ve - ve - veSM-90 Staphylococcus scuiri LT745975 99% - ve + ve - ve - ve - ve + ve - ve - ve - veSM-42 Brevibacterium

borstelensisLT745989 93% + ve - ve + ve + ve - ve + ve + ve - ve - ve

SM-27 Enterobacter hermachei LT745966 97% - ve - ve - ve - ve - ve + ve - ve - ve + veSM-15 Comamonas terrigena LT844635 95% + ve + ve + ve + ve - ve + ve + ve - ve + veSM-37 Yersinia mollaretti LT745988 87% - ve - ve + ve - ve - ve + ve - ve - ve - veSM-76 Enterococcus faecalis LT844634 100% - ve - ve - ve - ve - ve - ve - ve - ve - veSM-82 Klebsiella pneumoniae MF966247 98% - ve - ve - ve - ve - ve - ve - ve - ve - veSM-1 Staphylococcus

haemolyticusMF957708 89% - ve - ve - ve - ve - ve - ve - ve - ve - ve

SM-30 Bacillus subtilis MF977360 99% + ve + ve - ve - ve - ve - ve - ve - ve + veSM-58 Psychrobacterium

pulmonisLT745968 97% - ve - ve + ve + ve - ve - ve - ve - ve - ve

SM-56 Bacillus megaterium MF802485 94% - ve - ve - ve - ve - ve - ve - ve - ve - veSM-20 Proteus mirabilis MF958504 99% - ve + ve - ve - ve - ve + ve + ve - ve - veSM-36 Bacillus cereus MF801630 97% - ve - ve - ve - ve - ve - ve - ve - ve - ve



985

Figure 1. Neighbor joining Phylogenetic tree from analysis of partial 16S rDNA of citrus leaf bacterialendophytes. Level of bootstrap support based on 1000 replication data set are shown greater than 90%the scale bar represents 0.05 substitutions per nucleotide position.


986

Figure 2. Screening of entophytic bacterial isolates of citrus for Indole acetic acid (µg mL−1) Production

Figure 3. Antibacterial potential of test bacterial strains against isolated strains from this study.


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DISCUSSION

The ability of a PGPR to solubilize and makeavailable insoluble forms phosphorus to plants make theirapplication more beneficent and interesting in agriculturesystems. The use of phosphate solubilizing bacteria asinoculants increases the P uptake by plants (Chen et al.,2006; Alori et al., 2017; Nassal et al., 2018). Similarly,the plant beneficial effects of PGPR have mainly beenattributed to the production of phytohormones like IAAand nitrate reduction (Somers et al., 2004; Khan et al.,2017). During the current studies, the improvement inplant growth due to PGPR inoculation may be attributedto their secretion of IAA, capacity of phosphatesolubilization. Among other isolates, bacillus safensisisolated from lemon exhibited higher IAA productionwhile minimum in Enterobacter hermachei while SM-68,SM-57, SM-42, SM-27, SM-82, SM-1, SM-30, SM-58,SM-56, SM-20 and SM-36 were capable of phosphatesolubilization activity.

Siderophores are low-molecular-weightmolecules secreted by microorganisms under ironlimiting conditions (Shah et al., 2018). Previous studieshave shown that PGPR capable of phosphatesolubilization and IAA production also producedsiderophores (Shameer et al., 2018). During presentstudies, the isolates SM-34, SM-68, SM-57, SM-90, SM-15, SM-37,SM-1,SM-30,SM-58, SM-56,SM-20 and SM-36 were capable of producing siderophores. Previousstudies have shown that most of the siderophoresproducing bacteria are Gram-negative among whichPseudomonas and Enterobacter genera are common.Whereas, Bacillus and Rhodococcus genera are theGram-positive bacteria having potential of siderophoresproduction (Tian et al., 2009; Rosales et al., 2017).Siderophores produced by Rhizobacteria scavenge iron inthe rhizosphere starving pathogenic organisms of propernutrition to mount an attack of the crop (Saharan andNehra, 2011). The siderophores produced byRhizobacteria not only act as biocontrol but also help inmitigating abiotic stresses in various crop plants.

The beneficial effects of rhizobacteria on plantsare also due to their inhibitory effects on soil bornepathogens (Van Loon and Glick, 2004; Parewa et al.,2018). Cellulase production and utilization of substratesavailable in the rhizosphere are important for controllingthe rhizosphere competence (Yadav et al., 2017). Duringcurrent studies, the cellulase activity was recorded forrhizobacteria strains SM-34, SM-68, SM-90, SM-42,SM-27, SM-37, SM-82, SM-1, SM-30, SM-58, SM-56and SM-20 isolated from different varieties of citrus wereshowed positive results for cellulose, lipase, protease,pectinase activities etc. The beneficial rhizobacteriainhibit the growth of phytopathogens by the production ofcell wall lytic enzymes like cellulose, chitinase etc.(Kumar et al., 2012). The extracellular cell wall

degrading enzymes are positively correlated withbiocontrol abilities of the producing rhizobacteria (El-Tarabily, 2006; Rizvi et al., 2017).

Identification of chitinase producing bacteriafrom rhizosphere soil is important for the isolation ofbacteria that have antifungal activities. A vast majority ofbacteria and fungi produce chitinase enzymes (Bai et al.,2016) which plays important role in the control of fungaldiseases (Kamil et al., 2007). According to current study,maximum chitinase activity was shown by rhizobacteriabelonging to genera Pseudomonas, Brevibacterium,Comamonas, Yersinia, Enterococcus, Klebsiella,Staphylococcus, Psychrobacterium, Bacillus , Proteuswere positive for chitinase inhibit fungal growth byhydrolyzing chitin which is a major component of thefungal cell wall. Moreover, chitinases are of greatbiotechnological importance for engineering of phyto-pathogenic resistant plants, their use as food andpreservative agents for seeds (Kamil et al., 2007; Islamand Datta, 2015) isolated 400 isolates from rhizosphericsoil in Egypt and tested them for chitinase production.They found that majority of the chitinase producingrhizobacteria belonged to genus Bacillus. Moreover, themembers of the genus Bacillus have been previouslyreported for the production of chitinases (Schallmey etal., 2004; Wahyuni et al., 2016).

Lipases are widely distributed amongmicroorganisms and are of great industrial importance.They not only hydrolyse triglycerides to free fatty acidsand glycerol but are also used in the production of foods,biodiesel, pharmaceuticals, textiles and detergents etc.(Pascoal et al., 2018). Majority of the lipase producingbacteria isolated from citrus strains i.e. SM-34,SM-68,SM-42,SM-27,SM-15,SM-37,SM-76,SM-82,SM-1,SM-30,SM-56,SM-20,SM-36 were positive for lipaseproduction. A large number of bacteria produce lipasewhich has capacity to hydrolyze triglycerides (Javed etal., 2018). The bacteria belonging to generaAchromobacter, Alcaligenes, Arthobacter, Bacillus,Burkholderia, Chromo bacterium and Pseudomonas arereported extensively for the production of extracellularlipases (Gupta et al., 2004; Ismail et al., 2018). Amongthe different genera, the extracellular lipases produced byPseudomonas and Bacillus are widely used inbiotechnological applications (Hasan et al., 2018). It isinferred that bacteria associated with rhizosphere of GMand NON-GM maize can be exploited for commercialscale production of lipases.

On the other hand, microbial proteases may beuseful and play an important role in infection of hosts bydegrading the host’s protective barriers. Microbialproteases have been proposed as virulence factors in theirpathogenesis against nematodes (Huang et al., 2004;Stach et al., 2018). Majority of the protease producingbacteria isolated from citrus belonged to generaKlebsiella, Psychrobacter, Proteus, Enterobacter,


988

Pseudomonas, Brevibacterium, Enterococcus, Yersinia,Comamonas, and Enterobacter. These results are inagreement with previous findings of (Lian et al., 2007;Rahman et al., 2017) who have reported that bacteriabelonging to genus Bacillus are more efficient producerof proteases. Multiple Bacillus sp. can promote crophealth by suppressing plant pathogens and pests throughthe production of antibiotic metabolites or directlythrough the stimulation of plant host defense before theoccurrence of infection (Lian et al., 2007; Rahman et al.,2017). It could be inferred that various Bacillus specieswhich have capacity of protease production mightcontribute to their activity as biocontrol agents (Siddiquiet al., 2005; Rocha et al., 2017; Santos et al., 2018).

Pectinolytic enzymes produced by non-pathogenic bacteria are essential in the decay of deadplant material and thus contribute in the recycling ofcarbon compounds in biosphere. Among the variousbacteria isolated from citrus varieties isolates SM-34,SM-68, SM-57, SM-27, SM-37, SM-76, SM-2, SM-1,SM-30, SM-58, SM-56, SM-20, SM-36 showed highestpectinase activity. The pectinolytic enzymes play crucialrole in root invasion by bacteria and thus play importantrole in plant microbe interaction (Hayat et al., 2010;Vardharajula et al., 2017). Moreover, these pectinaseproducing bacteria isolated from citrus contribute to thenutrient cycling by degrading the pectic compoundspresent in the cell wall of plants and thus contribute to thefertility of soil.

Antimicrobial activity of isolated endophyticbacteria was studied against Gram positive and Gramnegative bacteria. Endophytic bacteria with potentantibacterial activity isolated from roots of Solanum sp.and medicinal plants were reported by (Long et al., 2003;Khunjamayum et al., 2017). Furthermore, B. megateriumand B. licheniformis isolated from P. tenuiflorus leavesexhibited antibacterial activity against E. coli, S. aureusand S. typhi. It has been also reported that bacterialendophytes Bacillus sp., B. licheniformis, Paenibacillussp., B. pumilus, and B. subtilis isolated from medicinalplants produce antibiotics (Madigan et al., 2005;Egamberdieva et al., 2017). Generally, the extract ofendophytic bacteria was significantly effective againstboth Gram-positive and Gram-negative bacteria.Endophytic bacteria produce antibiotics, which can actagainst human pathogenic bacteria, have previously beenreported (Seo et al., 2010; Pina et al., 2018). Thus,endophytes can be a good source for the industrialproduction of antibiotics.

Conclusion: The present findings conclusivelydemonstrate that maximum endophytes have goodpotential for plant growth promoting traits and enzymaticactivities except few of them. Altogether the test bacterialendophytes showed a broad spectrum activity againstmost of the targeted bacterial pathogens. It is concluded

that the endophytic bacteria from citrus leaves havepotential to reduce the bacterial plant pathogens exceptfive isolates Enterococcus faecalis, Klebsiellapneumonia, Staphylococcus haemolyticus, Bacillusmegaterium and Bacillus cereus did not show anyantibacterial activity against any of the targeted bacterialstrains. Detailed investigations on citrus endophyticbacteria are required to attest its antimicrobial potentialand it will leads to the discovery of numerousvaluable antimicrobial compounds that can be helpful indisease management. This study provides baseline for theuse of endophytes against the plant pathogens whichcaused different bacterial diseases and yield loses incrops. Moreover research on other aspects of antibacterialcompounds produced by test bacteria and theircharacterization suggests a better understanding aboutthese biological agents. The bacterial endophytes couldbe more useful for controlling the different diseases offield crops, less costly, time saving, not harmful forhuman health and equally beneficial to the scientific andfarmer’s community for increasing the economy of thecountry.

Acknowledgement: The authors are highly thankful tothe University of the Punjab and Higher EducationCommission (HEC) Islamabad for providing funds tocomplete the research work.

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