Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum)
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Abstract. Juwanda M, Sakhidin, Saparso, Kharisun. 2020. Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum). Biodiversitas 21: 2832-2839. Sulfur is one of the primary elements required by plants for growth and development. Sulfur-oxidizing bacteria (SOB) can oxidize sulfur to sulfate, which is directly taken up by plant roots. This study aims to evaluate the soil properties and SOB diversity in various shallot planting patterns, i.e. PP1 (shallot-dry season-shallot-shallot), PP2 (shallot-dry season-shallot-rice), and PP3 (shallot-pulses-shallot-rice). Soil samples were collected from the rhizosphere of the shallot plant and analyzed for the soil properties based on the standard methods. Bacteria isolation was cultured on Starkey broth and Starkey agar. Bacteria isolate was identified based on the 16S rRNA gene sequence and compared to the GenBank database. The results showed that shallot planting patterns influence soil properties and SOB diversity. The highest content of sulfate (41.31 ppm), organic C (0.957 %), organic matter (1.650%), C/N ratio (9.57), and SOB diversity was obtained in PP3 planting pattern. Three bacterial strains have been successfully isolated i.e. A-3245D, B-3246F, and C-3247C with their closest related to Burkholderia cepacia, Klebsiella variicola, and Klebsiella aerogenes, respectively. The highest diversity and population density of SOB was in the PP3 planting patterns, i.e Burkholderia cepacia (7.45 x 105 CFU/mL); Klebsiella variicola (1.79 x 107 CFU/mL; Klebsiella aerogenes: 3.9 x 106 CFU/mL). K. variicola can be found in three planting patterns of shallot.
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References
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Behera BC, Singh SK, Patra M, Mishra RR, Sethi BK, Dutta SK, Thatoi HN. 2016. Partial purification and characterisation of sulfur oxidase from Micrococcus sp. and Klebsiella sp. isolated from mangrove soils of Mahanadi River Delta, Odisha, India. Univers J Microbiol Res 4: 66-78.
Congreves KA, Hooker DC, Hayes A, Verhallen EA, Van Eerd LL. 2017. Interaction of long-term nitrogen fertilizer application, crop rotation, and tillage system on soil carbon and nitrogen dynamics. Plant Soil 410 (1-2): 113-127.
Diriba-Shiferaw G, Nigussie-Dechassa R, Woldetsadik K, Tabor G, Sharma JJ. 2015. Effect of nitrogen, phosphorus, and sulfur fertilizers on growth yield, and economic returns of garlic (Allium sativum L.). Sci Technol Arts Res J 4: 10-22.
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Fageria NK. 2009. The Use of Nutrients in Crop Plants. CRC Press Taylor and Francis Group, USA.
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Gaofei, Li Z, Fan F, Chu G, Hou Z, Liang Y. 2010. Soil biological activity and their seasonal variations in response to long-term application of organic and inorganic fertilizers. Plant Soil 326: 31-44.
Gevenez de Souza LF, Filho ABC, Alberto de Túlio1 F, Nowaki RHD. 2015. Effect of sulfur dose on the productivity and quality of onions. Aust J Crop Sci 9(8): 728-733.
Glab T, Cigalaska BS, Labuz B. 2013. Effect of crop rotation on the root system morphology and productivity of triticale (×Triticosecale Wittm). J Agric Sci 152: 642-654.
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Hilman Y, Sopha, Lukman L. 2014. Nitrogen effect on production, nutrients uptake and nitrogen-use efficiency of shallot (Allium cepa var aggregatum). AAB Bioflux 6(2): 128-133.
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Manogaran M, Ahmad SA, Yasid NA, Yakasai HM, Shukor MY. 2018. Characterisation of the simultaneous molybdenum reduction and glyphosate degradation by Burkholderia vietnamiensis AQ5-12 and Burkholderia sp. AQ5-13. 3 Biotech 8(2): 117.
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Moradi Y, Moradi-Sardareh H, Ghasemi H, Mohamadi N, Moradi MN, Hosseini-Zijoud SM. 2013. Medicinal properties of persian shallot. Eur J Exp Biol 3(1): 371-379.
Pandey AK, Gaind S, Ali A, Nain L. 2009. Effect of bioaugmentation and nitrogen supplementation on composting of paddy straw. Biodegradation 20(3): 293-306.
Pivovarova TA, Bulaev AG, Roshchupko PV, Belyi AV, Kondrat’eva TF. 2012. Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities. Prikl Biokhim Mikrobiol 48(6): 640-5.
Pradhan R, Pattnaik AK, Tripathy P, Mallikarjunarao K, Sahoo BB, Lenka J. 2015. Influence of sulfur fertilization on nutrient uptake of onion (Allium cepa L.). J Crop Weed 11: 134-138.
Prenafeta-Boldú FX, Rojo N, Gallastegui G, Guivernau M, Viñas M, Elías A. 2014. Role of Thiobacillus thioparus in the biodegradation of carbon disulphide in a biofilter packed with a recycled organic pelletized material. Biodegradation 25(4): 557-568.
Puspitasari DH, Pramono, Oedjiono. 2014. Identifikasi bakteri pengoksidasi besi dan sulfur berdasarkan gen 16S rRNA dari lahan tambang timah di Belitung. Scripta Biologica 1(1) : 8-14.
Rieddel, WE, Pikul JL, Jaradat, Shumacher TE. 2009. Crop rotation and nitrogen input effects on soil fertility, maize mineral nutrition, yield, and seed composition. Agron J 101(4): 870-879.
Ryu HW, Moon HS, Lee EY, Cho KS, Choi H, 2003. Leaching characteristics of heavy metals from sewage sludge by Acidithiobacillus thiooxidans MET. J Environ Qual 32(3): 751-759.
Sabagh H, Khoramivafa M, Honarmand S, Al Agha AB. 2014. Effect of Thiobacillus bacteria, sulfur and manure on the nutrient and pH of soil in garlic (Allium sativum). Int J Biosci 5(4): 186-193.
Satapute P, Kaliwal B. 2016. Biodegradation of propiconazole by newly isolated Burkholderia sp. strain BBK_9. 3 Biotech 6(1):110.
Schaeffer A, Nannipieri P, Kästner M, Schmidt B, Botterweck J. 2015. From humic substances to soil organic matter–microbial contributions. In honour of Konrad Haider and James P. Martin for their outstanding research contribution to soil science. J Soil Sediment 15(9): 1865-1881.
Sriramachandrasekharan MV. 2012. Sulfur use efficiency of radish as affected by sulfur source and rate in typic ustifluvent soil. Commun Biometry Crop Sci 7(1): 35-40.
Stevenson FJ. 1994. Humus Chemistry Genesis, Composition, Reactions, 2nd ed. Wiley, NewYork.
Tambone F, Genevini P, Adani F. 2007. The effect of short-term compost aplication on soil chemical propertis and on nutritional status of maize plant. Compost Sci Util 15(3): 176-183.
Ullah I, Jilani G, Khan KS, Akhtar MS, Rasheed M. 2014. Sulfur oxidizing bacteria from sulfur rich ecologies exhibit high capability of phosphorous solubilization. Int J Agric Biol 16(3): 550-556.
Velivelli SL, Sessitsch A, Prestwich BD. 2014. The role of microbial inoculants in integrated crop management systems. Potato Res 57(3-4): 291-309.
Vidyalakshmi R, Sridar R. 2007. Isolation and characterization of sulfur oxidizing bacteria. Journal of Culture Collections 5(1): 73-77.
Behera BC, Patra M, Dutta SK, Thatoi HN. 2014. Isolation and characterization of Sulfur oxidizing bacteria from mangrove soil of Mahanadi river delta and their Sulfur oxidizing ability. J Appl Environ Microbiol 2: 1-5.
Behera BC, Singh SK, Patra M, Mishra RR, Sethi BK, Dutta SK, Thatoi HN. 2016. Partial purification and characterisation of sulfur oxidase from Micrococcus sp. and Klebsiella sp. isolated from mangrove soils of Mahanadi River Delta, Odisha, India. Univers J Microbiol Res 4: 66-78.
Congreves KA, Hooker DC, Hayes A, Verhallen EA, Van Eerd LL. 2017. Interaction of long-term nitrogen fertilizer application, crop rotation, and tillage system on soil carbon and nitrogen dynamics. Plant Soil 410 (1-2): 113-127.
Diriba-Shiferaw G, Nigussie-Dechassa R, Woldetsadik K, Tabor G, Sharma JJ. 2015. Effect of nitrogen, phosphorus, and sulfur fertilizers on growth yield, and economic returns of garlic (Allium sativum L.). Sci Technol Arts Res J 4: 10-22.
Central Bureau of Statistics (BPS). 2018. Brebes Dalam Data 2017. Bureau of Statistics of Brebes regency. Indonesia.
Endalew W, Getahun A, Demissew A, Ambaye T. 2014. Storage performance of naturally ventilated structure for onion bulbs. Agric Eng Int: CIGR Journal 16(3): 97–101.
Balai Penelitian Tanah (Balittanah). 2009. Analisis Kimia Tanah, Tanaman, Air dan Pupuk. Departemen Pertanian, Bogor.
Fageria NK. 2009. The Use of Nutrients in Crop Plants. CRC Press Taylor and Francis Group, USA.
Farhan M, Khan AU, Wahid A, Ali AS, Ahmad F. 2013. Potential of indogeneous Klebsiella sp. for chlorpyrifos biodegradation. Pakistan J Sci 65(1): 133-137.
Gaofei, Li Z, Fan F, Chu G, Hou Z, Liang Y. 2010. Soil biological activity and their seasonal variations in response to long-term application of organic and inorganic fertilizers. Plant Soil 326: 31-44.
Gevenez de Souza LF, Filho ABC, Alberto de Túlio1 F, Nowaki RHD. 2015. Effect of sulfur dose on the productivity and quality of onions. Aust J Crop Sci 9(8): 728-733.
Glab T, Cigalaska BS, Labuz B. 2013. Effect of crop rotation on the root system morphology and productivity of triticale (×Triticosecale Wittm). J Agric Sci 152: 642-654.
Hartini E. 2011. Kadar Plumbum (Pb) dalam umbi bawang merah di Kecamatan Kersana Kabupaten Brebes. VISIKES: Jurnal Kesehatan Masyarakat 10(1): 69–75.
Hilman Y, Sopha, Lukman L. 2014. Nitrogen effect on production, nutrients uptake and nitrogen-use efficiency of shallot (Allium cepa var aggregatum). AAB Bioflux 6(2): 128-133.
Jaggi RC, Sharma RK. 2010. Sulphur management in onion (Allium cepa) cultivation in hills of Himachal Pradesh. J Environ Biol 31(3): 391-3
Juwanda M. 2011. Growth, Results and Efficiency Nitrogen of Fertilization to Shallot in Giving Doses of Nitrogen Fertilizer and Cow Manure. [Thesis]. Pascasarjana Program, Jenderal Soedirman University. [Indonesia].
Khambalkar P, Sridar R. 2015. Isolation and characterization of nitrogen fixing Burkholderia sp. Int J Agric Environ Biotechnol 8(3): 681-689.
Kumar M, Lakshmi CV, Khanna S. 2008. Microbial biodiversity and in situ bioremediation of endosulphan contaminated soil. Indian J Microbiol 48(1): 128-133.
Lasmini SA, Kusuma Z, Santoso M, Abadi AL. 2015. Application of organic and inorganic fertilizer improving the quantity and quality of shallot yield on dry land. International Journal of Scientific & Technology Research 4(4): 243-246.
Lin L, Wei C, Chen M, Wang H, Li Y, Li Y, An Q. 2015. Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E. Stand Genomic Sci 10(1): 2-7.
Li Z, Zhao B, Wang Q, Cao X, Zhang J. 2015. Differences in chemical composition of soil organic carbon resulting from long-term fertilization strategies. PloS One 10(4): e0124359.
Liu Y, Qian C, Daulet SM. 2015. Effect of dongshengbao liquid organic fertilizer on soil improvement of continuous cropping cucumbar. Agricultural Science and Technology 16(10): 2252-2255.
Losák T, Hlušek J, Krá?mar S, Varga L. 2008. The effect of nitrogen and sulfur fertilization on yield and quality of kohlrabi (Brassica oleracea, L.). Rev Bras Cienc Solo 32(2) : 697-703.
Manogaran M, Ahmad SA, Yasid NA, Yakasai HM, Shukor MY. 2018. Characterisation of the simultaneous molybdenum reduction and glyphosate degradation by Burkholderia vietnamiensis AQ5-12 and Burkholderia sp. AQ5-13. 3 Biotech 8(2): 117.
Mason J, Kelly DP. 1988. Thiosulphate oxidation by obligately heterotrophic bacteria. Microb Ecol 15(2): 123-134.
Moradi Y, Moradi-Sardareh H, Ghasemi H, Mohamadi N, Moradi MN, Hosseini-Zijoud SM. 2013. Medicinal properties of persian shallot. Eur J Exp Biol 3(1): 371-379.
Pandey AK, Gaind S, Ali A, Nain L. 2009. Effect of bioaugmentation and nitrogen supplementation on composting of paddy straw. Biodegradation 20(3): 293-306.
Pivovarova TA, Bulaev AG, Roshchupko PV, Belyi AV, Kondrat’eva TF. 2012. Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities. Prikl Biokhim Mikrobiol 48(6): 640-5.
Pradhan R, Pattnaik AK, Tripathy P, Mallikarjunarao K, Sahoo BB, Lenka J. 2015. Influence of sulfur fertilization on nutrient uptake of onion (Allium cepa L.). J Crop Weed 11: 134-138.
Prenafeta-Boldú FX, Rojo N, Gallastegui G, Guivernau M, Viñas M, Elías A. 2014. Role of Thiobacillus thioparus in the biodegradation of carbon disulphide in a biofilter packed with a recycled organic pelletized material. Biodegradation 25(4): 557-568.
Puspitasari DH, Pramono, Oedjiono. 2014. Identifikasi bakteri pengoksidasi besi dan sulfur berdasarkan gen 16S rRNA dari lahan tambang timah di Belitung. Scripta Biologica 1(1) : 8-14.
Rieddel, WE, Pikul JL, Jaradat, Shumacher TE. 2009. Crop rotation and nitrogen input effects on soil fertility, maize mineral nutrition, yield, and seed composition. Agron J 101(4): 870-879.
Ryu HW, Moon HS, Lee EY, Cho KS, Choi H, 2003. Leaching characteristics of heavy metals from sewage sludge by Acidithiobacillus thiooxidans MET. J Environ Qual 32(3): 751-759.
Sabagh H, Khoramivafa M, Honarmand S, Al Agha AB. 2014. Effect of Thiobacillus bacteria, sulfur and manure on the nutrient and pH of soil in garlic (Allium sativum). Int J Biosci 5(4): 186-193.
Satapute P, Kaliwal B. 2016. Biodegradation of propiconazole by newly isolated Burkholderia sp. strain BBK_9. 3 Biotech 6(1):110.
Schaeffer A, Nannipieri P, Kästner M, Schmidt B, Botterweck J. 2015. From humic substances to soil organic matter–microbial contributions. In honour of Konrad Haider and James P. Martin for their outstanding research contribution to soil science. J Soil Sediment 15(9): 1865-1881.
Sriramachandrasekharan MV. 2012. Sulfur use efficiency of radish as affected by sulfur source and rate in typic ustifluvent soil. Commun Biometry Crop Sci 7(1): 35-40.
Stevenson FJ. 1994. Humus Chemistry Genesis, Composition, Reactions, 2nd ed. Wiley, NewYork.
Tambone F, Genevini P, Adani F. 2007. The effect of short-term compost aplication on soil chemical propertis and on nutritional status of maize plant. Compost Sci Util 15(3): 176-183.
Ullah I, Jilani G, Khan KS, Akhtar MS, Rasheed M. 2014. Sulfur oxidizing bacteria from sulfur rich ecologies exhibit high capability of phosphorous solubilization. Int J Agric Biol 16(3): 550-556.
Velivelli SL, Sessitsch A, Prestwich BD. 2014. The role of microbial inoculants in integrated crop management systems. Potato Res 57(3-4): 291-309.
Vidyalakshmi R, Sridar R. 2007. Isolation and characterization of sulfur oxidizing bacteria. Journal of Culture Collections 5(1): 73-77.