Published date: Jun 07 2022

Journal Title: KnE Life Sciences

Issue title: The First Asian PGPR Indonesian Chapter International e-Conference 2021

Pages: 170–179

DOI: 10.18502/kls.v7i3.11118

Etty PratiwiIndonesian Soil Research Institute, Bogor, Indonesia

Alina AkhdiyaIndonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development, Indonesia

Taruna D. SatwikaDepartment of Biology, Jenderal Soedirman University, Indonesia

Methane is a major greenhouse gas that contributes to climate change. Methanogen and methanotrophic group microbes play a role in methane emissions in lowland rice fields. Methane is produced by methanogenic bacteria that decompose organic matter in anaerobic conditions. These bacteria will be active if the soil is inundated for an extended period of time. Some of this methane will be oxidized by methanotrophic bacteria in the rhizosphere. The researchers aimed to isolate, screen, and characterize methane-utilizing bacteria in lowland rice sediment from several Indonesian provinces. 27 methane- utilizing bacteria were isolated from rice field sediments in Lampung, West Java, and East Nusa Tenggara Province. Six of them had the potential to reduce methane emissions by more than half. A pmoA-like gene could be found in all of the selected isolates. The bacterial isolates were identified as Mycobacterium senegalense, Bacillus marisflavi, Bacillus methylotrophicus, Flavobacterium tirrenicum, Providencia stuartii, and Rhizobium rhizoryzae after characterization and identification with the Biolog OmniLog® ID system. These were all capable of nitrogen fixation, phosphorus solubilization, and IAA production. These isolates have the potential to be used as biofertilizers and methane mitigation agents.

Keywords: biofertilizers, greenhouse gas, lowland rice, methane-utilizing bacteria

[1] Schimel J. Rice, microbes and methane. Nature. 2000;403(6768):375–377. https://doi.org/10.1038/35000325

[2] Wassmann R, Schütz H, Papen H, et al. Quantification of methane emissions from Chinese rice fields (Zhejiang Province) as influenced by fertilizer treatment. Biogeochemistry. 1993;20(2):83–101. https://doi.org/10.1007/BF00004136

[3] Ueki A, Ono K, Tsuchiya A, Ueki K. Survival of methanogens in air-dried paddy field soil and their heat tolerance. Water Science and Technology. 1997;36(6–7):517–522. https://doi.org/10.1016/S0273-1223(97)00563-5

[4] Jhala YK, Vyas RV, Shelat HN, Patel HK, Patel HK, Patel KT. Isolation and characterization of methane utilizing bacteria from wetland paddy ecosystem. World Journal of Microbiology and Biotechnology. 2014;30(6):1845–1860. https://doi.org/10.1007/s11274-014-1606-3

[5] Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiological Reviews. 1996;60(2):439–471. https://doi.org/10.1128/mmbr.60.2.439-471.1996

[6] Whittenbury R, Phillips KC, Wilkinson JF. Enrichment, isolation and some properties of methane-utilizing bacteria. Journal of General Microbiology. 1970 May;61(2):205- 18. doi: 10.1099/00221287-61-2-205.

[7] Kumaraswamy S, Rath AK, Ramakrishnan B, Sethunathan N. Wetland rice soils as sources and sinks of methane: A review and prospects for research. Biology and Fertility Soils. 2000;31(6):449–461. https://doi.org/10.1007/s003740000214

[8] David AJ, Bourne G, McDonald IR. Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Applied and Environmental Microbiology. 2001;67(9):3802–9. https://doi.org/10.1128/AEM.67.9.3802– 3809.2001

[9] Pindi PK, Raja R, Shanker AS. Novel approaches of genomic DNA isolation for identification of cultivable bacteria. Jundishapur Journal of Microbiology. 2013;6(10):1-4. https://doi.org/10.5812/jjm.8339

[10] Barber LE, Tjepkema JD, Russell SA, Evans HJ. Acetylene reduction (nitrogen fixation) associated with corn inoculated with Spirillum. Applied and Environmental Microbiology. 1976;32(1):108–113. https://doi.org/10.1128/aem.32.1.108-113.1976

[11] Onyia CE, Anyawu CU, Ikegbunam MN. Ability of fungi, isolated from nsukka peppers and garden-egg plant rhizospheres, to solubilize phosphate and tolerate cadmium. Advance in Microbiology. 2015;5(7):500–506. https://doi.org/10.4236/aim.2015.57051

[12] Glickmann E, Dessaux Y. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Applied and Environmental Microbiology. 1995;61(2):793–796. https://doi.org/10.1128/aem.61.2.793-796.1995

[13] BIOLOG, Inc. Microbial identification: State-of-the-science performance with unmatched power & versatility [Brochure]. 2011. Available from: https://www.biolog.com/wp-content/uploads/2020/04/00A-024-rBMicroSystemsBrochure-2-1.pdf. Hayward, CA 94545 USA.

[14] Alori ET, Glick BR, Babalola OO. Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Frontiers in Microbiology. 2017;8( Jun):1– 8. https://doi.org/10.3389/fmicb.2017.00971

[15] Carrillo AE, Li CY, Bashan Y. Increased acidification in the rhizosphere of cactus seedlings induced by Azospirillum brasilense. Naturwissenschaften. 2002;89(9):428–432. https://doi.org/10.1007/s00114-002-0347-6

[16] Klingler JM, Stowe RP, Obenhuber DC, Groves TP, Mishra SK, Pierson DL. Evaluation of the biolog automated microbial identification system. Applied and Environmental Microbiology. 1992;58(6):2089–2092. https://doi.org/10.1128/aem.58.6.2089- 2092.1992

[17] De Paolis MR, Lippi D. Use of metabolic and molecular methods for the identification of a Bacillus strain isolated from paper affected by foxing. Microbiol.ogical Research. 2008;163(2):121–131. https://doi.org/10.1016/j.micres.2007.06.002

[18] Rupaedah B, Anas I, Santosa DA, Sumaryono W, Budi W. Role of rhizobacteria and arbuscular mycorrhizae on enhancing nutrient absorption efficiency of sweet sorghum (Sorghum bicolor L. Moench) (In Bahasa). Jurnal Ilmu Tanah dan Lingkungan. 2014;16(2):45–52.

[19] Gowtham HG, Singh SB, Niranjana SR. Evaluation of plant growth promoting ability of Providencia spp. collected from north eastern region of India in Crucifers Hittanahallikoppal Gajendramurthy Gowtham, Sudarsha. International Journal of Agricultural Science and Research. 2015;5(3):321–328.

[20] Madhaiyan M, Poonguzhali S, Kwon SW, Sa TM. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil. International Journal of Systematic and Evolutionary Microbiology. 2010;60(10):2490–2495. https://doi.org/10.1099/ijs.0.015487-0

[21] Zhang XX, Tang X, Sheirdil RA, Sun L, Ma XT. Rhizobium rhizoryzae sp. nov., isolated from rice roots. International Journal of Systematic and Evolutionary Microbiology. 2014;64(4):1373–1377. https://doi.org/10.1099/ijs.0.056325-0