Characterisation of Plant Growth Promoting Actinobacteria from Sungai Wain Protected Forest, East Kalimantan
Keywords:
Actinobacteria, IAA production, Nitrogen fixation, Phosphate solubilization, PGPR
Abstract
The excessive use of chemical-based fertilisers, herbicides, and pesticides in Indonesian agriculture has resulted in negative environmental impacts. As a sustainable alternative, the application of biofertilisers remains uncommon despite their proven ecological benefits. A group of microorganisms known as Plant Growth Promoting Rhizobacteria (PGPR) that plays a crucial role in enhancing plant growth. Among them, actinobacteria are gram-positive bacteria that involved in ecological processes such as organic matter decomposition, nutrient cycle, plant growth promotion and plant pathogen’s suppression. This study aims to investigate the potency of actinobacteria isolated from Sungai Wain Protected Forest, East Kalimantan as plant growth-promoting agents. A total of 96 actinobacteria isolates were revived from glycerol stock and subjected to primary screening through qualitative assays to assess phosphate solubilisation activity, nitrogen fixation, and Indole-3-Acetic Acid (IAA) production. Twenty-eight isolates demonstrated positive result among three PGP traits were subsequently selected for secondary screening, involving quantitative determination of IAA production and phosphate solubilisation through colorimetric assay. K22S-63 was identified as the most promising candidate, exhibiting the highest IAA production and phosphate solubilisation values of 43.80 and 41.51 µg mL-1, respectively. Molecular analysis was performed by amplifying PGPR-associated genes using PCR. The targeted genes included iaaM, phoD, PKS, and NRPS. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that K22S-63 shared 99.65 % similarity with Peterkaempfera griseoplana. These findings suggested that K22S-63 holds potential as bioinoculants with promising capabilities as plant growth promoter and biocontrol agents.
References
Agricultural Research and Development Agency, 2015. Sumber Daya Lahan Pertanian Indonesia: Luas, Penyebaran, dan Potensi Ketersediaan. Jakarta: IAARD Press, pp.9–10.
Backus, E.J., Tresner, H.D. & Campbell, T.H., 1957. The nucleocidin and alazopeptin producing organisms: Two new species of Streptomyces. Antibiotics and Chemotherapy, 7(10), pp.532–541.
Baig, K., Zahir, S., Arshad, M. & Cheema, M., 2010. Comparative efficacy of qualitative and quantitative methods for rock phosphate solubilization with phosphate solubilizing rhizobacteria. Journal of Soil and Environment, 29(1), pp.82–86.
Baldani, J.I., Reis, V.M. & Videira, S.S., 2014. The art of isolating nitrogen-fixing bacteria from non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists. Plant and Soil, 384, pp.413–431. doi: 10.1007/s11104-014-2186-6
Beatriz, G. et al., 2024. Comparative study between Salkowski reagent and chromatographic method for auxins quantification from bacterial production. Frontiers in Plant Science, 15, p.1378079. doi: 10.3389/fpls.2024.1378079
Boeck, L.D., Christy, K. & Shah, R., 1971. Production of anticapsin by Streptomyces griseoplanus. Applied Microbiology, 21(6), p.1075. doi: 10.1128/am.21.6.1075-1079.1971
Caulier, S. et al., 2019. Overview of the antimicrobial compounds produced by Bacillus group. Frontiers in Microbiology, 10, p.302. doi.org/10.3389/fmicb.2019.00302
Coelho, M. et al., 2009. Molecular detection and quantification of nifH gene sequences in the rhizosphere of Sorghum bicolor sown with two levels of nitrogen fertilizer. Applied Soil Ecology, 42(1), pp.48–53. doi.org/10.1016/j.apsoil.2009.01.010
Etesami, H. & Glick, B.R., 2024. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural resilience. Microbiological Research, 281, p.127602. doi: 10.1016/j.micres.2024.127602
FAO and ITPS, 2015. Status of the World’s Soil Resources (SWSR) – Main Report. Rome: Food and Agriculture Organization of the United Nations.
Farrag, A. et al., 2022. A new trial for bioformation of antimicrobial agent controlling multi-drug resistance. Azhar Journal of Pharmaceutical Sciences, 62, pp.71–97. doi: 10.21608/ajps.2020.118377
Fatmawati, U. et al., 2019. Screening and characterization of Actinobacteria isolated from soybean rhizosphere for promoting plant growth. Biodiversitas, 20(10), pp.2970–2977. doi.org/10.13057/biodiv/d201027
Fraser, T. et al., 2015. Soil bacterial phoD gene abundance and expression in response to applied phosphorus. Soil Biology and Biochemistry, 88, pp.137–147. doi.org/10.1016/j.soilbio.2015.04.014
Gaby, D.H. & Buckley, J.C., 2012. A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS ONE, 7(7), p.e42149. doi.org/10.1371/journal.pone.0042149
Khamna, S., Yokota, A. & Lumyong, S., 2009. Actinomycetes isolated from medicinal plant rhizosphere soils: Diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World Journal of Microbiology and Biotechnology, 25, pp.649–655. doi: 10.1007/s11274-008-9933-x
Long, J. et al., 2021. Environmental factors influencing phyllosphere bacterial communities in Giant Pandas’ staple food bamboos. Frontiers in Microbiology, 12, p.748141. doi.org/10.3389/fmicb.2021.748141
Madhaiyan, M. et al., 2022. Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. International Journal of Systematic and Evolutionary Microbiology, 72. doi:10.1099/ijsem.0.005570
Mahyarudin, Rusmana, I. & Lestari, Y., 2015. Metagenomic of Actinomycetes based on 16S rRNA and nifH genes in soil and roots of four Indonesian rice cultivars using PCR-DGGE. HAYATI Journal of Biosciences, 22, pp.113–121. doi.org/10.1016/j.hjb.2015.10.001
Nautiyal, C.S., 1999. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiology Letters, 170, pp.265–270. doi: 10.1111/j.1574-6968.1999.tb13383.x
Nouioui, I. et al., 2019. Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. International Journal of Systematic and Evolutionary Microbiology, 69(4), pp.1047–1056. doi.org/10.1099/ijsem.0.003267
Nurkanto, A. & Agustam, A., 2015. Molecular identification and morpho-physiological characterization of Actinomycetes with antimicrobial properties. Jurnal Biologi Indonesia, 11(2), pp.195–203.
Olanrewaju, O.S. et al., 2021. Genome mining of three plant growth-promoting Bacillus species from maize rhizosphere. Applied Biochemistry and Biotechnology, 193, pp.3949–3969. doi: 10.1007/s12010-021-03660-3
Passari, A.K. et al., 2016. Detection of biosynthetic gene and phytohormone production by endophytic Actinobacteria associated with Solanum lycopersicum and their plant-growth-promoting effect. Research in Microbiology, 167(8), pp.692–705. doi.org/10.1016/j.resmic.2016.07.001
Ragot, S. et al., 2017. Soil phoD and phoX alkaline phosphatase respond to multiple factors. FEMS Microbiology Ecology, 93(1), pp.1–13. doi: 10.1093/femsec/fiw212
Rahman, A. et al., 2010. Salkowski’s reagent test as a primary screening index for functionalities of rhizobacteria isolated from wild dipterocarp saplings. Bioscience, Biotechnology, and Biochemistry, 74(11), pp.2202–2208. doi: 10.1271/bbb.100360
Saif, K.M.S., 2014. Phosphate Solubilizing Microorganisms. Switzerland: Springer International Publishing, pp.137–157.
Sakurai, M. et al., 2008. Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter. Journal of Soil Science and Plant Nutrition, 54(1), pp.62–71. doi.org/10.1111/j.1747-0765.2007.00210.x
Sharma, A. et al., 2013. Biological control and its importance in agriculture. International Journal of Biotechnology and Bioengineering Research, 4, pp.175–180.
Sharma, S.B. et al., 2013. Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency. SpringerPlus, 2, p.587. doi.org/10.1186/2193-1801-2-587.
Silva, G.C. et al., 2022. The potential use of Actinomycetes as microbial inoculants and biopesticides in agriculture. Frontiers in Soil Science, 2, p.833181. doi.org/10.3389/fsoil.2022.833181
Suliasih & Widawati, S., 2020. Isolation of indole acetic acid (IAA) producing Bacillus siamensis from peat and optimization of the culture conditions for maximum IAA production. IOP Conference Series: Earth and Environmental Science, 572, p.012025. doi: 10.1088/1755-1315/572/1/012025
Tang, J. et al., 2023. Biosynthetic pathways and functions of indole-3-acetic acid in microorganisms. Microorganisms, 11, p.2077. doi.org/10.3390/microorganisms 11082077
Vijayabharathi, R. et al., 2014. Biological activity of entomopathogenic actinomycetes against lepidopteran insects (Noctuidae: Lepidoptera). Canadian Journal of Plant Science, 94, pp.759–769. doi: 10.4141/CJPS2013-298
Weyens, N. et al., 2019. Phytoremediation: Plant-endophyte partnerships take the challenge. Current Opinion in Biotechnology, 20(2), pp.248–254. doi: 10.1016/j.copbio.2009.02.012
Widawati, S., 2012. The use of plant growth promoting rhizobacteria (Pseudomonas fluorescens and Serratia marcescens) for paddy growth. Seminar Nasional Biodiversitas. doi: 10.13057/psnmbi/m010109
Xu, N. et al., 2016. Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. European Journal of Soil Biology, 74, pp.1–8. doi.org/10.1016/j.ejsobi.2016.02.004
Zakhia, F. et al., 2006. Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microbial Ecology, 51, pp.375–393. doi: 10.1007/s00248-006-9025-0
Backus, E.J., Tresner, H.D. & Campbell, T.H., 1957. The nucleocidin and alazopeptin producing organisms: Two new species of Streptomyces. Antibiotics and Chemotherapy, 7(10), pp.532–541.
Baig, K., Zahir, S., Arshad, M. & Cheema, M., 2010. Comparative efficacy of qualitative and quantitative methods for rock phosphate solubilization with phosphate solubilizing rhizobacteria. Journal of Soil and Environment, 29(1), pp.82–86.
Baldani, J.I., Reis, V.M. & Videira, S.S., 2014. The art of isolating nitrogen-fixing bacteria from non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists. Plant and Soil, 384, pp.413–431. doi: 10.1007/s11104-014-2186-6
Beatriz, G. et al., 2024. Comparative study between Salkowski reagent and chromatographic method for auxins quantification from bacterial production. Frontiers in Plant Science, 15, p.1378079. doi: 10.3389/fpls.2024.1378079
Boeck, L.D., Christy, K. & Shah, R., 1971. Production of anticapsin by Streptomyces griseoplanus. Applied Microbiology, 21(6), p.1075. doi: 10.1128/am.21.6.1075-1079.1971
Caulier, S. et al., 2019. Overview of the antimicrobial compounds produced by Bacillus group. Frontiers in Microbiology, 10, p.302. doi.org/10.3389/fmicb.2019.00302
Coelho, M. et al., 2009. Molecular detection and quantification of nifH gene sequences in the rhizosphere of Sorghum bicolor sown with two levels of nitrogen fertilizer. Applied Soil Ecology, 42(1), pp.48–53. doi.org/10.1016/j.apsoil.2009.01.010
Etesami, H. & Glick, B.R., 2024. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural resilience. Microbiological Research, 281, p.127602. doi: 10.1016/j.micres.2024.127602
FAO and ITPS, 2015. Status of the World’s Soil Resources (SWSR) – Main Report. Rome: Food and Agriculture Organization of the United Nations.
Farrag, A. et al., 2022. A new trial for bioformation of antimicrobial agent controlling multi-drug resistance. Azhar Journal of Pharmaceutical Sciences, 62, pp.71–97. doi: 10.21608/ajps.2020.118377
Fatmawati, U. et al., 2019. Screening and characterization of Actinobacteria isolated from soybean rhizosphere for promoting plant growth. Biodiversitas, 20(10), pp.2970–2977. doi.org/10.13057/biodiv/d201027
Fraser, T. et al., 2015. Soil bacterial phoD gene abundance and expression in response to applied phosphorus. Soil Biology and Biochemistry, 88, pp.137–147. doi.org/10.1016/j.soilbio.2015.04.014
Gaby, D.H. & Buckley, J.C., 2012. A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS ONE, 7(7), p.e42149. doi.org/10.1371/journal.pone.0042149
Khamna, S., Yokota, A. & Lumyong, S., 2009. Actinomycetes isolated from medicinal plant rhizosphere soils: Diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World Journal of Microbiology and Biotechnology, 25, pp.649–655. doi: 10.1007/s11274-008-9933-x
Long, J. et al., 2021. Environmental factors influencing phyllosphere bacterial communities in Giant Pandas’ staple food bamboos. Frontiers in Microbiology, 12, p.748141. doi.org/10.3389/fmicb.2021.748141
Madhaiyan, M. et al., 2022. Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. International Journal of Systematic and Evolutionary Microbiology, 72. doi:10.1099/ijsem.0.005570
Mahyarudin, Rusmana, I. & Lestari, Y., 2015. Metagenomic of Actinomycetes based on 16S rRNA and nifH genes in soil and roots of four Indonesian rice cultivars using PCR-DGGE. HAYATI Journal of Biosciences, 22, pp.113–121. doi.org/10.1016/j.hjb.2015.10.001
Nautiyal, C.S., 1999. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiology Letters, 170, pp.265–270. doi: 10.1111/j.1574-6968.1999.tb13383.x
Nouioui, I. et al., 2019. Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. International Journal of Systematic and Evolutionary Microbiology, 69(4), pp.1047–1056. doi.org/10.1099/ijsem.0.003267
Nurkanto, A. & Agustam, A., 2015. Molecular identification and morpho-physiological characterization of Actinomycetes with antimicrobial properties. Jurnal Biologi Indonesia, 11(2), pp.195–203.
Olanrewaju, O.S. et al., 2021. Genome mining of three plant growth-promoting Bacillus species from maize rhizosphere. Applied Biochemistry and Biotechnology, 193, pp.3949–3969. doi: 10.1007/s12010-021-03660-3
Passari, A.K. et al., 2016. Detection of biosynthetic gene and phytohormone production by endophytic Actinobacteria associated with Solanum lycopersicum and their plant-growth-promoting effect. Research in Microbiology, 167(8), pp.692–705. doi.org/10.1016/j.resmic.2016.07.001
Ragot, S. et al., 2017. Soil phoD and phoX alkaline phosphatase respond to multiple factors. FEMS Microbiology Ecology, 93(1), pp.1–13. doi: 10.1093/femsec/fiw212
Rahman, A. et al., 2010. Salkowski’s reagent test as a primary screening index for functionalities of rhizobacteria isolated from wild dipterocarp saplings. Bioscience, Biotechnology, and Biochemistry, 74(11), pp.2202–2208. doi: 10.1271/bbb.100360
Saif, K.M.S., 2014. Phosphate Solubilizing Microorganisms. Switzerland: Springer International Publishing, pp.137–157.
Sakurai, M. et al., 2008. Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter. Journal of Soil Science and Plant Nutrition, 54(1), pp.62–71. doi.org/10.1111/j.1747-0765.2007.00210.x
Sharma, A. et al., 2013. Biological control and its importance in agriculture. International Journal of Biotechnology and Bioengineering Research, 4, pp.175–180.
Sharma, S.B. et al., 2013. Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency. SpringerPlus, 2, p.587. doi.org/10.1186/2193-1801-2-587.
Silva, G.C. et al., 2022. The potential use of Actinomycetes as microbial inoculants and biopesticides in agriculture. Frontiers in Soil Science, 2, p.833181. doi.org/10.3389/fsoil.2022.833181
Suliasih & Widawati, S., 2020. Isolation of indole acetic acid (IAA) producing Bacillus siamensis from peat and optimization of the culture conditions for maximum IAA production. IOP Conference Series: Earth and Environmental Science, 572, p.012025. doi: 10.1088/1755-1315/572/1/012025
Tang, J. et al., 2023. Biosynthetic pathways and functions of indole-3-acetic acid in microorganisms. Microorganisms, 11, p.2077. doi.org/10.3390/microorganisms 11082077
Vijayabharathi, R. et al., 2014. Biological activity of entomopathogenic actinomycetes against lepidopteran insects (Noctuidae: Lepidoptera). Canadian Journal of Plant Science, 94, pp.759–769. doi: 10.4141/CJPS2013-298
Weyens, N. et al., 2019. Phytoremediation: Plant-endophyte partnerships take the challenge. Current Opinion in Biotechnology, 20(2), pp.248–254. doi: 10.1016/j.copbio.2009.02.012
Widawati, S., 2012. The use of plant growth promoting rhizobacteria (Pseudomonas fluorescens and Serratia marcescens) for paddy growth. Seminar Nasional Biodiversitas. doi: 10.13057/psnmbi/m010109
Xu, N. et al., 2016. Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. European Journal of Soil Biology, 74, pp.1–8. doi.org/10.1016/j.ejsobi.2016.02.004
Zakhia, F. et al., 2006. Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microbial Ecology, 51, pp.375–393. doi: 10.1007/s00248-006-9025-0
Published
2025-10-20
How to Cite
Haris, I. S., Dewi, T. K., Widawati, S., Ratnakomala, S. and Retnaningrum, E. (2025) “Characterisation of Plant Growth Promoting Actinobacteria from Sungai Wain Protected Forest, East Kalimantan ”, Journal of Tropical Biodiversity and Biotechnology, 10(4), p. jtbb20679. doi: 10.22146/jtbb.20679.
Section
Research Articles
