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Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils

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Abstract

The purpose of this study was to investigate the diversity of cultivable phosphate solubilising (PSB) and total bacteria originated from 384 rhizospheric acidic soils samples of tea plants grown at 32 locations. Over 900 rhizoplane bacteria were randomly selected from agar-solidified trypticase soy broth, and identified using fatty acid methyl ester (FAME) profiles. Based on FAME profiles, 53 bacterial genera were identified with a similarity index >0.3, but 60.3% of the identified isolates belonged to five genera: Bacillus (34.6%), Pseudomonas (8.9%), Stenotrophomonas (6.1%), Paenibacillus (5.9%) and Arthrobacter (4.8%). The bacilli group comprised many different species, with the most abundant being B. cereus, B. megaterium and B. sphaericus. The main identified Pseudomonads included P. fluorescens, P. putida, and P. alcaligenes. About 30.4% of the bacterial isolates could not be classified to genus since their similarity indices were <0.3 indicating no close matches. Most of the total and P-solubilizing bacteria isolated were Gram positive (61.3 and 52.3%), and Gram negative constituted only 38.7 and 47.7%. Out of the 214 PSB from a pool of 506 bacterial isolates recovered on the selective media from the rhizosphere of tea, 74 of them were characterized by carbon sources using BIOLOGM GN2 and GP2 plates. Bacillus, Pseudomonas, Paenibacillus and Stenotrophomonas genera were the most prominent P-solubilizing groups in the rhizosphere and soil populations analyzed. B. cereus, P. fluorescens, S. maltophilia, B. megaterium, P. putida, B. sphaericus and Paenibacillus polymyxa were the most frequent P-solubilizing species in the acidic tea rhizosohere soils. Selected Gram-positive PSB appeared to favour carbohydrates, and Gram-negative bacteria appeared to favour carboxylic acids, amino acids and carbohydrates as carbon sources. Selected phosphate solubilizing acid tolerant strains showed high variability in utilizing various carbon sources.

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References

  • Alisi C, Lasinio GJ, Dalmastri C, Sprocati A, Tabacchioni S, Bevivino A, Chiarini L (2005) Metabolic profiling of Burkholderia cenocepacia, Burkholderia ambifaria, and Burkholderia pyrrocinia isolates from maize rhizosphere. Microb Ecol 50:385–395

    Article  CAS  PubMed  Google Scholar 

  • Altındal E, Balta F (2002) Comparison of rooting capabilities of Turkish tea clones. Turk J Agric For 26:195–201

    Google Scholar 

  • Aravind R, Kumar A, Eapen SJ, Ramana KV (2009) 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 48:58–64

    Article  CAS  PubMed  Google Scholar 

  • Asghar HN, Zahir ZA, Arshad M, Khaliq A (2002) Relationship between in vitro production of auxins by rhizobacteria and their growth-promoting activities in Brassica juncea L. Biol Fertil Soils 35:231–237

    Article  CAS  Google Scholar 

  • Ash C, Priest FG, Collins MD (1993) Molecular identification of rDNA group 3 bacilli (Ash, Farrow Wallbanks and Collins) using a PCR probe test. Antonie Van Leeuwenhoek 64:253–260

    Article  CAS  PubMed  Google Scholar 

  • Baudoin E, Benizri E, Guckert A (2003) Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere. Soil Biol Biochem 35:1183–1192

    Article  CAS  Google Scholar 

  • Beneduzi A, Peres D, Vargas LK, Bodanese-Zanettini MH, Passaglia LMP (2008) Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil. Appl Soil Ecol 39:311–320

    Article  Google Scholar 

  • Borsodi AK, Makk J, Rusznyák A, Vajna B, Taba G, Márialigeti K (2007) Phenotypic characterization and molecular taxonomic studies on Bacillus and related isolates from Phragmites australis periphyton. Aquat Bot 86:243–252

    Article  CAS  Google Scholar 

  • Caesar-TonThat TC, Caesar AJ, Gaskin JF, Sainju UM, Busscher WJ (2007) Taxonomic diversity of predominant culturable bacteria associated with microaggregates from two different agroecosystems and their ability to aggregate soil in vitro. Appl Soil Ecol 36:10–21

    Article  Google Scholar 

  • Çakmakçi R, Dönmez F, Aydin A, Sahin F (2006) Growth promotion of plants by plant growth-promoting rhizobacteria under greenhouse and two different field soil conditions. Soil Biol Biochem 38:1482–1487

    Article  Google Scholar 

  • Çakmakçı R, Dönmez MF, Erdogan Ü (2007a) The effect of plant growth promoting rhizobacteria on barley seedling growth, nutrient uptake, some soil properties, and bacterial counts. Turk J Agric For 31:189–199

    Google Scholar 

  • Çakmakçı R, Erat M, Erdoğan Ü, Dönmez F (2007b) The influence of plant growth-promoting rhizobacteria on growth and enzyme activities in wheat and spinach plants. J Plant Nutr Soil Sci 170:288–295

    Article  Google Scholar 

  • Canbolat MY, Bilen S, Çakmakçı R, Sahin F, Aydin A (2006) Effect of plant growth-promoting bacteria and soil compaction on barley seedling growth, nutrient uptake, soil properties and rhizosphere microflora. Biol Fertil Soils 42:350–357

    Article  CAS  Google Scholar 

  • Chen YP, Rekha PD, Arun AB, Shen FT, Lai W-A, Young CC (2006) Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities. Appl Soil Ecol 34:33–41

    Article  Google Scholar 

  • Chowdhury SP, Schmid M, Hartmann A, Tripathi AK (2007) Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India. Microb Ecol 54:82–90

    Article  PubMed  Google Scholar 

  • Chun S-C, Schneider RW, Chung I-M (2003) Determination of carbon source utilization of Bacillus and Pythium species by Biolog® Microplate assay. J Microbiol 41:252–258

    CAS  Google Scholar 

  • Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56:236–249

    Article  CAS  PubMed  Google Scholar 

  • de Freitas JR, Banerjee MR, Germida JJ (1997) Phosphate-solubilizing rhizobacteria enhance the growth and yield but not phosphorus uptake of canola (Brassica napus L.). Biol Fertil Soils 24:358–364

    Article  Google Scholar 

  • Dey R, Pal KK, Bhatt DM, Chauhan SM (2004) Growth promotion and yield enhancement of peanut (Arachis hypogaea L.) by application of plant growth-promoting rhizobacteria. Microbiol Res 159:371–394

    Article  CAS  PubMed  Google Scholar 

  • Dias ACF, Costa FEC, Andreote FD, Lacava PT, Teixeira MA, Assumpcao LC, Araujo WL, Azevedo JL, Melo IS (2009) Isolation of micropropagated strawberry endophytic bacteria and assessment of their potential for plant growth promotion. World J Microbiol Biotechnol 25:189–195

    Article  CAS  Google Scholar 

  • Donate-Correa J, León-Barrios M, Pérez-Galdona R (2004) Screening for plant growth-promoting rhizobacteria in Chamaecytisus proliferus (tagasaste), a forage tree-shrub legume endemic to the Canary Islands. Plant Soil 266:261–272

    Article  CAS  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 103:626–631

    Article  CAS  PubMed  Google Scholar 

  • Forbes BA, Sahm DF, Weissfeld AS (1998) Bailey and Scott’s diagnostic microbiology, 11th edn. Mosby Inc, St. Louis, p 1068

    Google Scholar 

  • Garbeva P, van Veen JA, van Elsas JD (2003) Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE. Microb Ecol 45:302–316

    Article  CAS  PubMed  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterisation of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source-utilization. Appl Environ Microbiol 57:2351–2359

    PubMed  Google Scholar 

  • Germida JJ, Siciliano SD (2001) Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol Fertil Soils 33:410–415

    Article  Google Scholar 

  • Germida JJ, Siciliano SD, de Freitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50

    Article  CAS  Google Scholar 

  • Hariprasad P, Niranjana SR (2009) Isolation and characterization of phosphate solubilizing rhizobacteria to improve plant health of tomato. Plant Soil 316:13–24

    Article  CAS  Google Scholar 

  • Hoberg E, Marschner P, Lieberei R (2005) Organic acid exudation and pH changes by Gordonia sp. and Pseudomonas fluorescens grown with P adsorbed to goethite. Microbiol Res 160:177–187

    Article  CAS  PubMed  Google Scholar 

  • Idris A, Labuschagne N, Korsten L (2009) Efficacy of rhizobacteria for growth promotion in sorghum under greenhouse conditions and selected modes of action studies. J Agric Sci 147:17–30

    Article  CAS  Google Scholar 

  • Johnson SE, Loeppert RH (2006) Role of organic acids in phosphate mobilization from iron oxide. Soil Sci Soc Am J 70:222–234

    Article  CAS  Google Scholar 

  • Kozdrój J (2008) Microbial community in the rhizosphere of young maize seedlings is susceptible to the impact of introduced pseudomonads as indicated by FAME analysis. J Gen Appl Microbiol 54:205–210

    Article  PubMed  Google Scholar 

  • Larkin RP (2003) Characterization of soil microbial communities under different potato cropping systems by microbial population dynamics, substrate utilization, and fatty acid profiles. Soil Biol Biochem 35:1451–1456

    Article  CAS  Google Scholar 

  • Macphail MK, Garland JL (1996) Patterns of potential C source utilization by rhizosphere communities. Soil Biol Biochem 28:223–230

    Article  Google Scholar 

  • Mantelin S, Touraine B (2004) Plant growth-promoting bacteria and nitrate availability: impacts on root development and nitrate uptake. J Exp Bot 55:27–34

    Article  CAS  PubMed  Google Scholar 

  • Mehta S, Nautiyal CS (2001) An efficient method for qualitative screening of phosphate-solubilizing bacteria. Curr Microbiol 43:51–56

    Article  CAS  PubMed  Google Scholar 

  • Misko A, Germida J (2002) Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola. FEMS Microbiol Ecol 42:399–407

    Article  CAS  PubMed  Google Scholar 

  • Naik PR, Raman G, Narayanan KB, Sakthivel N (2008) Assessment of genetic and functional diversity of phosphate solubilizing fluorescent pseudomonads isolated from rhizospheric soil. BMC Microbiol 8:230

    Article  PubMed  Google Scholar 

  • Oka N, Hartel PG, Finlay-Moore O, Gagliardi J, Zuberer DA, Fuhrmann JJ, Angle JS, Skipper HD (2000) Misidentification of soil bacteria by fatty acid methyl ester (FAME) and BIOLOG analyses. Biol Fertil Soils 32:256–258

    Article  CAS  Google Scholar 

  • Pal SS (1998) Interactions of an acid tolerant strain of phosphate solubilizing bacteria with a few acid tolerant crops. Plant Soil 198:169–177

    Article  CAS  Google Scholar 

  • Park M, Kim C, Yang J, Lee H, Shin W, Kim S, Sa T (2005) Isolation and characterization of diazotrophic growth promoting bacteria from rhizosphere of agricultural crops of Korea. Microbiol Res 160:127–133

    Article  CAS  PubMed  Google Scholar 

  • Perez E, Sulbaran M, Ball MM, Yarzabal LA (2007) Isolation and characterization of mineral phosphate-solubilizing bacteria naturally colonizing a limonitic crust in the south-eastern Venezuelan region. Soil Biol Biochem 39:2905–2914

    Article  CAS  Google Scholar 

  • Pikovskaya RE (1948) Mobilization of phosphates in soil in connection with vital activities of some microbial species. Microbiologia 17:362–370

    CAS  Google Scholar 

  • Poonguzhali S, Madhaiyan M, Sa T (2006) Cultivation-dependent characterization of rhizobacterial communities from field grown Chinese cabbage Brassica campestris ssp pekinensis and screening of traits for potential plant growth promotion. Plant Soil 286:167–180

    Article  CAS  Google Scholar 

  • Rau N, Mishra V, Sharma M, Das MK, Ahaluwalia K, Sharma RS (2009) 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 41:813–821

    Article  CAS  Google Scholar 

  • Rengel Z, Marschner P (2005) Nutrient availability and management in the rhizosphere: exploiting genotypic differences. New Phytol 168:305–312

    Article  CAS  PubMed  Google Scholar 

  • Richardson AE (2001) Prospects for using soil microorganisms to improve the acquisition of phosphorus by plants. Aust J Plant Physiol 28:897–906

    Google Scholar 

  • Rivas R, Mateos PF, Martinez-Molina E, Velázquez E (2005) Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55:405–408

    Article  CAS  PubMed  Google Scholar 

  • Rusznyák A, Vladár P, Molnár P, Reskóné MN, Kiss G, Márialigeti K, Andrea K, Borsodi AK (2008) Cultivable bacterial composition and BIOLOG catabolic diversity of biofilm communities developed on Phragmites australis. Aquat Bot 88:211–218

    Article  Google Scholar 

  • Sahin F, Çakmakçi R, Kantar F (2004) Sugar beet and barley yields in relation to inoculation with N2-fixing and phosphate solubilizing bacteria. Plant Soil 265:123–129

    Article  CAS  Google Scholar 

  • Schutter M, Dick R (2001) Shifts in substrate utilization potential and structure of soil microbial communities in response to carbon substrates. Soil Biol Biochem 33:1481–1491

    Article  CAS  Google Scholar 

  • Son H-J, Park G-T, Cha M-S, Heo M-S (2006) Solubilization of insoluble inorganic phosphates by a novel salt- and pH-tolerant Pantoea agglomerans R-42 isolated from soybean rhizosphere. Bioresour Technol 97:204–210

    Article  CAS  PubMed  Google Scholar 

  • Suckstorff I, Berg G (2003) Evidence for dose-dependent effects on plant growth by Stenotrophomonas strains from different origins. J Appl Microbiol 95:656–663

    Article  CAS  PubMed  Google Scholar 

  • Thakuria D, Talukdar NC, Goswami C, Hazarika S, Boro RC, Khan MR (2004) Characterization and screening of bacteria from rhizosphere of rice grown in acidic soils of Assam. Curr Sci 86:978–985

    Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586

    Article  CAS  Google Scholar 

  • Xue D, Yao HY, Ge DY, Huang CY (2008) Soil microbial community structure in diverse land use systems: a comparative study using Biolog, DGGE, and PLFA analyses. Pedosphere 18:653–663

    Article  CAS  Google Scholar 

  • Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101–1108

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported financially by a grant (TOVAG; 107 O 360) from the Scientific and Technological Research Council of Turkey (TUBİTAK)

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Authors and Affiliations

  1. Faculty of Agriculture, Department of Agronomy, Atatürk University, 25240, Erzurum, Turkey

    Ramazan Çakmakçı

  2. Faculty of Agriculture, Department of Plant Protection, Atatürk University, 25240, Erzurum, Turkey

    Mesude Figen Dönmez

  3. Technical Vocational School İspir, Atatürk University, 25900, Erzurum, Turkey

    Yaşar Ertürk

  4. Erzurum Vocational Training School, Atatürk University, 25240, Erzurum, Turkey

    Mustafa Erat

  5. The General Directorate of Tea Processing Plants, Atatürk Tea Garden Cultures Research Instıtute, Rize, Turkey

    Ayhan Haznedar & Remzi Sekban

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  1. Ramazan Çakmakçı
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  2. Mesude Figen Dönmez
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  3. Yaşar Ertürk
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Correspondence to Ramazan Çakmakçı.

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Responsible Editor: Petra Marschner.

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Çakmakçı, R., Dönmez, M.F., Ertürk, Y. et al. Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils. Plant Soil 332, 299–318 (2010). https://doi.org/10.1007/s11104-010-0295-4

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