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Organik ve kimyasal gübre ile kullanılmak üzere mikroorganizma izolasyon ve karakterizasyonu

Year 2024, Volume: 17 Issue: 1, 91 - 98, 15.04.2024
https://doi.org/10.46309/biodicon.2023.1226337

Abstract

Isolation and characterization of microorganisms for use with manure and chemical fertilizers
Levent Değirmenci1, Özge Kaygusuz İzgördü2, Cihan Darcan3
ORCID: 0000-0001-6608-0398; 0000-0002-3652-4266; 0000-0003-0205-3774
1 Corresponding author: Department of Chemical Engineering, Bilecik Şeyh Edebali University, 11210, Bilecik/Turkey Tel: +90 228 2141548, e-mail: levent.degirmenci@bilecik.edu.tr
2 Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11210, Bilecik, Turkey 3 3Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, 11210, Bilecik, Turkey

Abstract
A microbial consortium with the ability to utilize nitrogen of certain chemical fertilizers were established via a series of tests. Results indicated four strains, 3 of which were identified as Bacillus cereus sp and an Alcaligenes faecalis sp. which was the only non-Bacillus member of the consortium. The members of the consortium showed no antagonistic activity against each other implying their successful utilization as components of a commercial fertilizer.
Keywords: IAA, siderophore, Bacillus spp., nitrogen fixation, ammonia/nitrite oxidation

Organik ve kimyasal gübre olarak kullanım potansiyeline sahip mikroorganizmarın İzolasyon ve karakterizasyonu

Özet
Farklı kimyasal gübrelerin içeriğinde yer alan azotu bitkinin kullanımına sunabilen mikroorganizma karışımı bir dizi testler sonucunda elde edilmiştir. Sonuçların değerlendirilmesiyle mikroorganizma karışımına üç Bacillus Cereus sp. suşu ile karışımın Bacillus sp. olmayan tek üyesi Alcaligenes faecalis sp. seçilmiştir. Mikroorganizma karışımında yer alan suşların birbirlerine karşı antagonistik etki göstermediği dolayısıyla karışımın mikrobiyal gübre olarak ticarileştirilmesinin mümkün olduğu da elde edilen sonuçlar arasındadır.
Anahtar Kelimeler: IAA, siderophore, Bacillus spp. azot fiksasyonu, amonyum/nitrit oksidasyonu
1. Introduction
Chemical fertilizer is gaining an increasing attention and its harmful effects on environment possesses a serious threat [2]. Heavy metal accumulation is another problem during utilization of chemical fertilizers [2].The variation of soil pH, another problem encountered due to excessive fertilizer utilization, has negative impact on phosphorus uptake [3]. Plant growth promoting bacteria when added to soil, operate via certain mechanisms facilitating acquisition of already existing resources in soil [4]. Siderophore producing bacteria also acts as biocontrol agent capable of decreasing phytopathogen population in the flora [4–7].
Certain procedures were developed and/or modified in the present study to obtain a microbial consortium which would act as an enhancer during plant growth.
2. Materials and Method

2.1. Semi-selective isolation procedure as starting-point

Semi-selective isolation procedures were conducted according to [12].
2.2. Standard tests applied to determine the potential of isolates as PGPB.

Nitrogen fixation ability, IAA production, phosphate solubility siderophore production were conducted according to [13-18].
2.3. Specified tests to determine nitrogen evaluation potential of PGP isolates

Nitrogen evaluation potential was determined according to [19].
2.4. Biochemical tests conducted to determine Bacillus sp. in accordance with MALDI-TOF MS analyses evaluated for validation.

Biochemical tests were evaluated based on positive results for both caseinase activity and starch hydrolysis [20-22].
MALDI-TOF MS analyses applied for selected strains and an isolate with positive activity towards siderophore production.
3. Results
IAA production, Nitrogen fixation performance, Ammonifier selection, phosphate solubility, siderophore production ability, urea degradation, ammonium oxidation and nitrite oxidation abilities of strains were evaluated to establish a microbial consortium.
4. Conclusion and discussion
• Media selection could serve as a selection criterion to assemble a certain group of microorganisms.
• Tests conducted for isolates could be diversified to establish a consortium with modified properties.
• Test procedures could be modified to facilitate establishment of microbial consortium.
• Strains with different properties could serve as members of consortium which was the case in our study.
• Identification in species level was possible to a certain extent. MALDI-TOF MS analysis presented a brief idea on strains and similar results would have been obtained in the case of applying its costlier alternatives. Hence a relatively simpler procedure is concluded to be better for initial investigation.
• Evaluation of results led to investigation of certain prospects including determination of physicotolerant activity of strains and management of Fusarium wilt disease as the topics of future investigations.

References

  • [1] Karim, A. Z. (2013). Impact of a growing population in agricultural resource management: exploring the global situation with a micro-level example. Asian Social Science, 9(15), 14.
  • [2] Savci, S. (2012). An agricultural pollutant: chemical fertilizer. International Journal of Environmental Science and Development, 3(1), 73.
  • [3] Aygün, Y. Z., & Mert, M. (2021). The effect of phosphorus doses on cotton growth under full and deficit irrigation conditions. Biyolojik Çeşitlilik ve Koruma, 14(3), 464-469.
  • [4] Glick, B. R. (2012). Plant growth-promoting bacteria: mechanisms and applications. Scientifica, 2012.
  • [5] Felestrino, É. B., Santiago, I. F., Freitas, L. D. S., Rosa, L. H., Ribeiro, S. P., & Moreira, L. M. (2017). Plant growth promoting bacteria associated with Langsdorffia hypogaea-rhizosphere-host biological interface: a neglected model of bacterial prospection. Frontiers in microbiology, 8, 172.
  • [6] Bashan, Y., & Holguin, G. (2002). Plant growth-promoting bacteria: a potential tool for arid mangrove reforestation. Trees, 16(2-3), 159-166.
  • [7] Elsheikh, E. A., & Elzidany, A. A. (1997). Effects of Rhizobium inoculation, organic and chemical fertilizers on yield and physical properties of faba bean seeds. Plant Foods for Human Nutrition, 51, 137-144.
  • [8] Miliute, I., Buzaite, O., Gelvonauskiene, D., Sasnauskas, A., Stanys, V., & Baniulis, D. (2016). Plant growth promoting and antagonistic properties of endophytic bacteria isolated from domestic apple. Zemdirbyste-Agriculture, 103(1).
  • [9] Meng, L., Li, W., Zhang, S., Wu, C., Jiang, W., & Sha, C. (2016). Effect of different extra carbon sources on nitrogen loss control and the change of bacterial populations in sewage sludge composting. Ecological Engineering, 94, 238-243.
  • [10] Woźniak, M., Gałązka, A., Tyśkiewicz, R., & Jaroszuk-Ściseł, J. (2019). Endophytic bacteria potentially promote plant growth by synthesizing different metabolites and their phenotypic/physiological profiles in the Biolog GEN III MicroPlateTM Test. International Journal of Molecular Sciences, 20(21), 5283.
  • [11] Hussein, K. A., & Joo, J. H. (2015). Isolation and characterization of rhizomicrobial isolates for phosphate solubilization and indole acetic acid production. Journal of the Korean Society for Applied Biological Chemistry, 58, 847-855.
  • [12] Prijambada, D. I., Widada, J., Kabirun, S., Widianto, D. (2009). Secretion of Organic Acids by Phosphate Solubilizing Bacteria Isolated from Oxisols. Journal of Tropical Soils., 14(3), 245-251.
  • [13] Qing-Ping, H., & Jian-Guo, X. (2011). A simple double-layered chrome azurol S agar (SD-CASA) plate assay to optimize the production of siderophores by a potential biocontrol agent Bacillus. African Journal of Microbiology Research, 5(25), 4321-4327.
  • [14] Elbanna, K., El-Shahawy, R. M., & Atalla, K. M. (2012). A new simple method for the enumeration of nitrifying bacteria in different environments. Plant, Soil and Environment, 58(1), 49-53.
  • [15] Mehmet, A. Ş. A. N. (2007). Development of New Culture Medium for Various Microorganisms. Journal of Agricultural Sciences, 13(01), 75-79.
  • [16] El-Banna, T. E., Abd-Aziz, A. A., Abou-Dobara, M. I., & Ibrahim, R. I. (2007). Production and immobilization of alpha-amylase from Bacillus subtilis. Pakistan Journal of Biological Sciences: PJBS, 10(12), 2039-2047.
  • [17] Li, H., Wei, Z., Song, C., Chen, X., Zhang, R., & Liu, Y. (2022). Functional keystone drive nitrogen conversion during different animal manures composting. Bioresource Technology, 361, 127721.
  • [18] Wu, Y., Li, H., & Li, Y. (2021). Biomineralization induced by cells of Sporosarcina pasteurii: Mechanisms, applications and challenges. Microorganisms, 9(11), 2396.
  • [19] Amoo, A. E., & Babalola, O. O. (2017). Ammonia-oxidizing microorganisms: key players in the promotion of plant growth. Journal of soil science and plant nutrition, 17(4), 935-947.
  • [20] Sönmez, B., Özbahçe, A., Akgül, S., & Keçeci, M. (2018). Türkiye topraklarının bazı verımlilik ve organik karbon (TOK) içeriğinin coğrafi veritabanının oluşturulması (in Turkish). Tarım ve orman bakanlığı, tarımsal araştırmalar ve politikalar genel müdürlüğü proje sonuç raporu TAGEM. Tarım ve Orman Bakanlığı, Tarımsal Araştırmalar ve Politikalar Genel Müdürlüğü Proje Sonuç Raporu TAGEM, 13.
  • [21] Hasan, M. M., Hasan, M. M., Teixeira da Silva, J. A., & Li, X. (2016). Regulation of phosphorus uptake and utilization: transitioning from current knowledge to practical strategies. Cellular & molecular biology letters, 21, 1-19.
  • [22] Merry, R., Espina, M. J., Lorenz, A. J., & Stupar, R. M. (2022). Development of a controlled-environment assay to induce iron deficiency chlorosis in soybean by adjusting calcium carbonates, pH, and nodulation. Plant Methods, 18(1), 36.
  • [23] Lechner, S., Mayr, R., Francis, K. P., Prüß, B. M., Kaplan, T., Wießner-Gunkel, E. L. K. E., ... & Scherer, S. (1998). Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. International journal of systematic and evolutionary microbiology, 48(4), 1373-1382.
  • [24] Antil, S., Kumar, R., Pathak, D. V., Kumar, A., Panwar, A., & Kumari, A. (2022). Plant growth-promoting rhizobacteria-Bacillus cereus KMT-5 and B. megaterium KMT-8 effectively suppressed Meloidogyne javanica infection. Applied Soil Ecology, 174, 104419.
  • [25] Saranya, K., Sundaramanickam, A., Manupoori, S., & Kanth, S. V. (2022). Screening of multi-faceted phosphate-solubilising bacterium from seagrass meadow and their plant growth promotion under saline stress condition. Microbiological Research, 261, 127080.

Isolation and Characterization of Microorganisms for Use with Manure and Chemical Fertilizers

Year 2024, Volume: 17 Issue: 1, 91 - 98, 15.04.2024
https://doi.org/10.46309/biodicon.2023.1226337

Abstract

Isolation and Characterization of Microorganisms for Use with Manure and Chemical Fertilizers
Levent Değirmenci1, Özge Kaygusuz İzgördü2, Cihan Darcan3
ORCID: 0000-0001-6608-0398; 0000-0002-3652-4266; 0000-0003-0205-3774
1 Corresponding author: Department of Chemical Engineering, Bilecik Şeyh Edebali University, 11210, Bilecik/Turkey Tel: +90 228 2141548, e-mail: levent.degirmenci@bilecik.edu.tr
2 Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11210, Bilecik, Turkey 3 3Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, 11210, Bilecik, Turkey

Abstract
A microbial consortium with the ability to utilize nitrogen of certain chemical fertilizers were established via a series of tests. Results indicated four strains, 3 of which were identified as Bacillus cereus sp and an Alcaligenes faecalis sp. which was the only non-Bacillus member of the consortium. The members of the consortium showed no antagonistic activity against each other implying their successful utilization as components of a commercial fertilizer.
Keywords: IAA, siderophore, Bacillus spp., nitrogen fixation, ammonia/nitrite oxidation, MALDI-TOF MS

Organik ve Kimyasal Gübre ,le Kullanılmak Üzere Mikroorganizma İzolasyon ve Karakterizasyonu

Özet
Farklı kimyasal gübrelerin içeriğinde yer alan azotu bitkinin kullanımına sunabilen mikroorganizma karışımı bir dizi testler sonucunda elde edilmiştir. Sonuçların değerlendirilmesiyle mikroorganizma karışımına üç Bacillus Cereus sp. suşu ile karışımın Bacillus sp. olmayan tek üyesi Alcaligenes faecalis sp. seçilmiştir. Mikroorganizma karışımında yer alan suşların birbirlerine karşı antagonistik etki göstermediği dolayısıyla karışımın mikrobiyal gübre olarak ticarileştirilmesinin mümkün olduğu da elde edilen sonuçlar arasındadır.
Anahtar Kelimeler: IAA, siderophore, Bacillus spp. azot fiksasyonu, amonyum/nitrit oksidasyonu, MALDI-TOF MS
1. Introduction
Chemical fertilizer is gaining an increasing attention and its harmful effects on environment possesses a serious threat [2]. Heavy metal accumulation is another problem during utilization of chemical fertilizers [2].The variation of soil pH, another problem encountered due to excessive fertilizer utilization, has negative impact on phosphorus uptake [3]. Plant growth promoting bacteria when added to soil, operate via certain mechanisms facilitating acquisition of already existing resources in soil [4]. Siderophore producing bacteria also acts as biocontrol agent capable of decreasing phytopathogen population in the flora [4–7].
Certain procedures were developed and/or modified in the present study to obtain a microbial consortium which would act as an enhancer during plant growth.
2. Materials and Method

2.1. Semi-selective isolation procedure as starting-point

Semi-selective isolation procedures were conducted according to [12].
2.2. Standard tests applied to determine the potential of isolates as PGPB.

Nitrogen fixation ability, IAA production, phosphate solubility siderophore production were conducted according to [13-18].
2.3. Specified tests to determine nitrogen evaluation potential of PGP isolates

Nitrogen evaluation potential was determined according to [19].
2.4. Biochemical tests conducted to determine Bacillus sp. in accordance with MALDI-TOF MS analyses evaluated for validation.

Biochemical tests were evaluated based on positive results for both caseinase activity and starch hydrolysis [20-22].
MALDI-TOF MS analyses applied for selected strains and an isolate with positive activity towards siderophore production.
3. Results
IAA production, Nitrogen fixation performance, Ammonifier selection, phosphate solubility, siderophore production ability, urea degradation, ammonium oxidation and nitrite oxidation abilities of strains were evaluated to establish a microbial consortium.
4. Conclusion and discussion
• Media selection could serve as a selection criterion to assemble a certain group of microorganisms.
• Tests conducted for isolates could be diversified to establish a consortium with modified properties.
• Test procedures could be modified to facilitate establishment of microbial consortium.
• Strains with different properties could serve as members of consortium which was the case in our study.
• Identification in species level was possible to a certain extent. MALDI-TOF MS analysis presented a brief idea on strains and similar results would have been obtained in the case of applying its costlier alternatives. Hence a relatively simpler procedure is concluded to be better for initial investigation.
• Evaluation of results led to investigation of certain prospects including determination of physicotolerant activity of strains and management of Fusarium wilt disease as the topics of future investigations.

References

  • [1] Karim, A. Z. (2013). Impact of a growing population in agricultural resource management: exploring the global situation with a micro-level example. Asian Social Science, 9(15), 14.
  • [2] Savci, S. (2012). An agricultural pollutant: chemical fertilizer. International Journal of Environmental Science and Development, 3(1), 73.
  • [3] Aygün, Y. Z., & Mert, M. (2021). The effect of phosphorus doses on cotton growth under full and deficit irrigation conditions. Biyolojik Çeşitlilik ve Koruma, 14(3), 464-469.
  • [4] Glick, B. R. (2012). Plant growth-promoting bacteria: mechanisms and applications. Scientifica, 2012.
  • [5] Felestrino, É. B., Santiago, I. F., Freitas, L. D. S., Rosa, L. H., Ribeiro, S. P., & Moreira, L. M. (2017). Plant growth promoting bacteria associated with Langsdorffia hypogaea-rhizosphere-host biological interface: a neglected model of bacterial prospection. Frontiers in microbiology, 8, 172.
  • [6] Bashan, Y., & Holguin, G. (2002). Plant growth-promoting bacteria: a potential tool for arid mangrove reforestation. Trees, 16(2-3), 159-166.
  • [7] Elsheikh, E. A., & Elzidany, A. A. (1997). Effects of Rhizobium inoculation, organic and chemical fertilizers on yield and physical properties of faba bean seeds. Plant Foods for Human Nutrition, 51, 137-144.
  • [8] Miliute, I., Buzaite, O., Gelvonauskiene, D., Sasnauskas, A., Stanys, V., & Baniulis, D. (2016). Plant growth promoting and antagonistic properties of endophytic bacteria isolated from domestic apple. Zemdirbyste-Agriculture, 103(1).
  • [9] Meng, L., Li, W., Zhang, S., Wu, C., Jiang, W., & Sha, C. (2016). Effect of different extra carbon sources on nitrogen loss control and the change of bacterial populations in sewage sludge composting. Ecological Engineering, 94, 238-243.
  • [10] Woźniak, M., Gałązka, A., Tyśkiewicz, R., & Jaroszuk-Ściseł, J. (2019). Endophytic bacteria potentially promote plant growth by synthesizing different metabolites and their phenotypic/physiological profiles in the Biolog GEN III MicroPlateTM Test. International Journal of Molecular Sciences, 20(21), 5283.
  • [11] Hussein, K. A., & Joo, J. H. (2015). Isolation and characterization of rhizomicrobial isolates for phosphate solubilization and indole acetic acid production. Journal of the Korean Society for Applied Biological Chemistry, 58, 847-855.
  • [12] Prijambada, D. I., Widada, J., Kabirun, S., Widianto, D. (2009). Secretion of Organic Acids by Phosphate Solubilizing Bacteria Isolated from Oxisols. Journal of Tropical Soils., 14(3), 245-251.
  • [13] Qing-Ping, H., & Jian-Guo, X. (2011). A simple double-layered chrome azurol S agar (SD-CASA) plate assay to optimize the production of siderophores by a potential biocontrol agent Bacillus. African Journal of Microbiology Research, 5(25), 4321-4327.
  • [14] Elbanna, K., El-Shahawy, R. M., & Atalla, K. M. (2012). A new simple method for the enumeration of nitrifying bacteria in different environments. Plant, Soil and Environment, 58(1), 49-53.
  • [15] Mehmet, A. Ş. A. N. (2007). Development of New Culture Medium for Various Microorganisms. Journal of Agricultural Sciences, 13(01), 75-79.
  • [16] El-Banna, T. E., Abd-Aziz, A. A., Abou-Dobara, M. I., & Ibrahim, R. I. (2007). Production and immobilization of alpha-amylase from Bacillus subtilis. Pakistan Journal of Biological Sciences: PJBS, 10(12), 2039-2047.
  • [17] Li, H., Wei, Z., Song, C., Chen, X., Zhang, R., & Liu, Y. (2022). Functional keystone drive nitrogen conversion during different animal manures composting. Bioresource Technology, 361, 127721.
  • [18] Wu, Y., Li, H., & Li, Y. (2021). Biomineralization induced by cells of Sporosarcina pasteurii: Mechanisms, applications and challenges. Microorganisms, 9(11), 2396.
  • [19] Amoo, A. E., & Babalola, O. O. (2017). Ammonia-oxidizing microorganisms: key players in the promotion of plant growth. Journal of soil science and plant nutrition, 17(4), 935-947.
  • [20] Sönmez, B., Özbahçe, A., Akgül, S., & Keçeci, M. (2018). Türkiye topraklarının bazı verımlilik ve organik karbon (TOK) içeriğinin coğrafi veritabanının oluşturulması (in Turkish). Tarım ve orman bakanlığı, tarımsal araştırmalar ve politikalar genel müdürlüğü proje sonuç raporu TAGEM. Tarım ve Orman Bakanlığı, Tarımsal Araştırmalar ve Politikalar Genel Müdürlüğü Proje Sonuç Raporu TAGEM, 13.
  • [21] Hasan, M. M., Hasan, M. M., Teixeira da Silva, J. A., & Li, X. (2016). Regulation of phosphorus uptake and utilization: transitioning from current knowledge to practical strategies. Cellular & molecular biology letters, 21, 1-19.
  • [22] Merry, R., Espina, M. J., Lorenz, A. J., & Stupar, R. M. (2022). Development of a controlled-environment assay to induce iron deficiency chlorosis in soybean by adjusting calcium carbonates, pH, and nodulation. Plant Methods, 18(1), 36.
  • [23] Lechner, S., Mayr, R., Francis, K. P., Prüß, B. M., Kaplan, T., Wießner-Gunkel, E. L. K. E., ... & Scherer, S. (1998). Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. International journal of systematic and evolutionary microbiology, 48(4), 1373-1382.
  • [24] Antil, S., Kumar, R., Pathak, D. V., Kumar, A., Panwar, A., & Kumari, A. (2022). Plant growth-promoting rhizobacteria-Bacillus cereus KMT-5 and B. megaterium KMT-8 effectively suppressed Meloidogyne javanica infection. Applied Soil Ecology, 174, 104419.
  • [25] Saranya, K., Sundaramanickam, A., Manupoori, S., & Kanth, S. V. (2022). Screening of multi-faceted phosphate-solubilising bacterium from seagrass meadow and their plant growth promotion under saline stress condition. Microbiological Research, 261, 127080.
There are 25 citations in total.

Details

Primary Language English
Subjects Structural Biology, Plant and Fungus Systematics and Taxonomy, Food Technology
Journal Section Research Articles
Authors

Levent Değirmenci 0000-0001-6608-0398

Özge Kaygusuz İzgördü 0000-0002-3652-4266

Cihan Darcan 0000-0003-0205-3774

Early Pub Date January 18, 2024
Publication Date April 15, 2024
Submission Date December 29, 2022
Acceptance Date December 27, 2023
Published in Issue Year 2024 Volume: 17 Issue: 1

Cite

APA Değirmenci, L., Kaygusuz İzgördü, Ö., & Darcan, C. (2024). Isolation and Characterization of Microorganisms for Use with Manure and Chemical Fertilizers. Biological Diversity and Conservation, 17(1), 91-98. https://doi.org/10.46309/biodicon.2023.1226337

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