Easy extraction of Ganoderma boninense liquid sample using portable on‐chip device

Adella Josephin; Yudan Whulanza; Siti Fauziyah Rahman; Kenny Lischer; Muhammad Imam Surya; Irfan Martiansyah; Wiguna Rahman; Uda Hashim

doi:10.22146/ijbiotech.83645

Easy extraction of Ganoderma boninense liquid sample using portable on‐chip device

https://doi.org/10.22146/ijbiotech.83645

Adella Josephin⁽¹⁾, Yudan Whulanza^(2*), Siti Fauziyah Rahman⁽³⁾, Kenny Lischer⁽⁴⁾, Muhammad Imam Surya⁽⁵⁾, Irfan Martiansyah⁽⁶⁾, Wiguna Rahman⁽⁷⁾, Uda Hashim⁽⁸⁾

(1) Department of Electrical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia; Research Center of Biomedical Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia
(2) Department of Mechanical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia; Research Center of Biomedical Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia
(3) Department of Electrical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia; Research Center of Biomedical Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia
(4) Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia; Research Center of Biomedical Engineering, Universitas Indonesia, Depok 16424, West Java, Indonesia
(5) Research Center for Applied Botany, National Research and Innovation Agency, Cibinong, Bogor 16911, West Java, Indonesia
(6) Research Center for Applied Botany, National Research and Innovation Agency, Cibinong, Bogor 16911, West Java, Indonesia
(7) Research Center for Applied Botany, National Research and Innovation Agency, Cibinong, Bogor 16911, West Java, Indonesia
(8) Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Seriab 01000 Kangar, Perlis, Malaysia
(*) Corresponding Author

Abstract

Detecting Ganoderma boninense in Indonesia is crucial for effectively controlling and mitigating the spread of basal stem disease in oil palm fields. While there is ongoing development of tolerant plants, no such plant has been successfully created yet. Consequently, researchers are actively studying detection methods for Ganoderma boninense. One established and highly accurate approach is the use of polymerase chain reaction (PCR) techniques for molecular detection. However, this method requires time‐consuming sample preparation, which can pose challenges in plantation settings. To address this problem, a portable lab‐on‐chip device has been introduced. This technology enables easy and automatic DNA retrieval from liquid samples by absorbing lysed DNA using magnetic beads. An efficient mechanism for manipulating the magnetic bead within the semiconductor has been successfully implemented. The extraction process typically takes around 15 minutes using a modified methodology on the chip device approach. The chip facilitates the retrieval of two samples with a capacity of 120 µL for each sample. The PCR method was utilized to validate the equivalence of the lab‐on‐chip device extraction to the standard extraction method. This represents a promising alternative for expedited and simplified detection of Ganoderma boninense in field conditions.

Keywords

Ganoderma boninense; Infected oil palms; Lab‐on‐chip; Molecular detection; Polymerase chain reaction

Full Text:

PDF

References

Abubakar A, Ishak MY, Bakar AA, Uddin MK. 2022. Ganoderma boninense basal stem rot induced by climate change and its effect on oil palm. Environ. Sustain. 5(3):289–303. doi:10.1007/s42398-022-00244-7.

Ayoib A, Hashim U, Gopinath SC. 2020. Automated, high-throughput DNA extraction protocol for disposable label free, microfluidics integrating DNA biosensor for oil palm pathogen, Ganoderma boninense. Process Biochem. 92:447–456. doi:10.1016/j.procbio.2020.02.003.

Barcelos E, De Almeida Rios S, Cunha RN, Lopes R, Motoike SY, Babiychuk E, Skirycz A, Kushnir S. 2015. Oil palm natural diversity and the potential for yield improvement. Front. Plant Sci. 6:190. doi:10.3389/fpls.2015.00190.

Bentivoglio D, Finco A, Bucci G. 2018. Factors affecting the Indonesian palm oil market in food and fuel industry: Evidence from a time series analysis. Int. J. Energy Econ. Policy 8(5):49–57.

Budiani A, Nugroho IB, Sari DA, Palupi I, Putranto RA. 2019. CRISPR/Cas9-mediated knockout of an oil palm defense-related gene to the pathogenic fungus Ganoderma boninense. Indones. J. Biotechnol. 24(2):101–105. doi:10.22146/ijbiotech.52170.

Dislich C, Keyel AC, Salecker J, Kisel Y, Meyer KM, Auliya M, Barnes AD, Corre MD, Darras K, Faust H, Hess B, Klasen S, Knohl A, Kreft H, Meijide A, Nurdiansyah F, Otten F, Pe’er G, Steinebach S, Tarigan S, Tölle MH, Tscharntke T, Wiegand K. 2017. A review of the ecosystem functions in oil palm plantations, using forests as a reference system. Biol. Rev. 92(3):1539–1569. doi:10.1111/brv.12295.

Durand-Gasselin T, Asmady H, Flori A, Jacquemard JC, Hayun Z, Breton F, De Franqueville H. 2005. Possible sources of genetic resistance in oil palm (Elaeis guineensis Jacq.) to basal stem rot caused by Ganoderma boninense - Prospects for future breeding. In: Mycopathologia, volume 159. p. 93–100. doi:10.1007/s11046-004-4429-1.

Elkins K. 2013. DNA Extraction. Academic Press. p. 39– 52. doi:10.1016/B978-0-12-394585-3.00004-3.

Fathana H. 2018. Palm oil politics in Malaysia and Indonesia: Competition or collaboration? J. Southeast Asian Stud. 23(2):47–64. doi:10.22452/jati.vol23no2.3.

Fowotade SA, Yusof NA, Abdullah J, Sulaiman Y, Abd Rahman SF. 2019. Enhanced electrochemical sensing of secondary metabolites in oil palms for early detection of Ganoderma boninense based on novel nanoparticle-chitosan functionalized multiwalled carbon nanotube platform. Sens. Bio-Sensing Res. 23:100274. doi:10.1016/j.sbsr.2019.100274.

Godswill NN, Frank NEG, Walter AN, Edson MYJ, Kingsley TM, Arondel V, Martin BJ, Emmanuel Y. 2016. Chapter 10 - Oil Palm. San Diego: Academic Press. p. 217–273. doi:10.1016/B978-0-12-801309- 0.00010-0.

Green MR, Sambrook J. 2017. Isolation of highmolecular-weight DNA using organic solvents. Cold Spring Harb. Protoc. 2017(4):pdb.prot093450. doi:10.1101/pdb.prot093450.

Hushiarian R, Yusof NA, Dutse SW. 2013. Detection and control of Ganoderma boninense: Strategies and perspectives. Springerplus 2(1):555. doi:10.1186/2193- 1801-2-555.

Idris AS, Ahmad Kushairi D, Ismail S, Ariffin D. 2004. Selection for partial resistance in oil palm progenies to Ganoderma basal stem rot. J. Oil Palm Res. 16:12–18.

Kartika E, Lizawati L, Hamzah H. 2010. Isolasi, karakterisasi dan pemurnian cendawan mikoriza arbuskular dari tanah bekas tambang batu bara [Isolation, identification and purification of arbuscular mycorrhiza fungi (AMF) from coal post mining soil]. In: Seminar Nasional MKTI. p. 3–257.

Liew WL, Kassim MA, Muda K, Loh SK, Affam AC. 2015. Conventional methods and emerging wastewater polishing technologies for palm oil mill effluent treatment: A review. J. Environ. Manage. 149:22– 235. doi:10.1016/j.jenvman.2014.10.016.

Lischer K, Avila F, Sahlan M, Whulanza Y. 2021. Assessment of cost-efficient thermocycler prototype for polymerase chain reaction and loop-mediated isothermal amplification. Int. J. Technol. 12(6):1207–1216. doi:10.14716/IJTECH.V12I6.5207.

Minarsih H, Widiastuti H, Santoso D. 2018. Deteksi Ganoderma secara molekuler pada kebun kelapa sawit yang diberi perlakuan biofungisida Ganor [Molecular detection of Ganoderma on oil palm plantation treated with Ganor biofungicide]. E-Journal Menara Perkeb. 86(1):21–28. doi:10.22302/iribb.jur.mp.v1i1.289.

Mohd Hilmi Tan MIS, Jamlos MF, Omar AF, Kamarudin K, Jamlos MA. 2023. Ganoderma boninense classification based on near-infrared spectral data using machine learning techniques. Chemom. Intell. Lab. Syst. 232:104718. doi:10.1016/j.chemolab.2022.104718.

Moncalvo JM, Wang Hsi-Hua, Hseu Ruey-Shyang. 1995. Phylogenetic relationships in Ganoderma inferred from the internal transcribed spacers and 25S ribosomal DNA sequences. Mycologia 87(2):223. doi:10.2307/3760908.

Nadhif MH, Whulanza Y, Istiyanto J, Bachtiar BM. 2017. Delivery of Amphotericin B to Candida albicans by using biomachined lab-on-A-chip. J. Biomimetics, Biomater. Biomed. Eng. 30:24–30. doi:10.4028/www.scientific.net/JBBBE.30.24.

Naher L, Yusuf U, Tan S, Ismail A. 2013. Ecological status of Ganoderma and basal stem rot disease of oil palms (Elaeis guineensis Jacq). Aust. J. Crop Sci. 7:1723– 1727.

Nathani RC, Irwansyah R, Nurhayati RW, Whulanza Y. 2022. Analysis of droplet size control for stem cells encapsulation using lab-on-a-chip. In: AIP Conf. Proc., volume 2537. p. 040006. doi:10.1063/5.0097945.

Nusaibah SA, Latiffah Z, Hassaan AR. 2011. ITS-PCRRFLP analysis of Ganoderma sp. infecting industrial crops. Pertanika J. Trop. Agric. Sci. 34(1):83–91.

Ommelna BG, Jennifer AN, Chong KP. 2012. The potential of chitosan in suppressing Ganoderma boninense infection in oil-palm seedlings. J. Sustain. Sci. Manag. 7(2):186–192.

Park SY, Jang SH, Oh SO, Kim JA, Hur JS. 2014. An easy, rapid, and cost-effective method for DNA extraction from various lichen taxa and specimens suitable for analysis of fungal and algal strains. Mycobiology 42(4):311. doi:10.5941/MYCO.2014.42.4.311.

Paterson RR. 2007. Ganoderma disease of oil palm-A white rot perspective necessary for integrated control. Crop Prot. 26(9):1369–1376. doi:10.1016/j.cropro.2006.11.009.

Paterson RR, Sariah M, Lima N. 2013. How will climate change affect oil palm fungal diseases? Crop Prot. 46:113–120. doi:10.1016/j.cropro.2012.12.023.

Paterson RRM. 2019. Ganoderma boninense disease of oil palm to significantly reduce production after 2050 in Sumatra if projected climate change occurs. Microorganisms 7(1):24. doi:10.3390/microorganisms7010024.

Priwiratama H, Susanto A. 2014. Utilization of fungi for the biological control of insect pests and Ganoderma disease in the Indonesian oil palm industry. J. Agric. Sci. Technol. A 4:103–111.

Rees RW, Flood J, Hasan Y, Potter U, Cooper RM. 2009. Basal stem rot of oil palm (Elaeis guineensis); Mode of root infection and lower stem invasion by Ganoderma boninense. Plant Pathol. 58(5):982–989. doi:10.1111/j.1365-3059.2009.02100.x.

Siddiqui Y, Surendran A, Paterson RRM, Ali A, Ahmad K. 2021. Current strategies and perspectives in detection and control of basal stem rot of oil palm. Saudi J. Biol. Sci. 28(5):2840–2849. doi:10.1016/j.sjbs.2021.02.016.

Siegel CS, Stevenson FO, Zimmer EA. 2017. Evaluation and comparison of FTA card and CTAB DNA extraction methods for nonagricultural taxa. Appl. Plant Sci. 5(2):apps.1600109. doi:10.3732/apps.1600109.

Soh AC. 2012. Breeding and Genetics of the Oil Palm. AOCS Press. p. 31–58. doi:10.1016/B978-0- 9818936-9-3.50005-8.

Tahir S, Putri W, Wardani A, Sunaryanto R. 2023. Fermentation medium optimization of Streptomyces sp. as an antifungal agent against the Ganoderma boninensis pathogen in oil palm. Indones. J. Biotechnol. 28:216. doi:10.22146/ijbiotech.82396.

USDA. 2012. MALAYSIA : Stagnating Palm Oil Yields Impede Growth. October 2012. United States Dep. Agric. - Foreign Agric. Serv. URL https://ipad.fas.u sda.gov/highlights/2012/12/Malaysia/.

Utomo C, Niepold F. 2000. Development of diagnostic methods for detecting Ganoderma-infected oil palms. J. Phytopathol. 148(9-10):507–514. doi:10.1046/j.1439-0434.2000.00478.x.

Whulanza Y, Aditya R, Arvialido R, Utomo MS, Bachtiar BM. 2017. Ease fabrication of PCR modular chip for portable DNA detection kit. In: AIP Conf. Proc., volume 1817. p. 040006. doi:10.1063/1.4976791.

Whulanza Y, Antory AD, Warjito, Rahman SF, Gozan M, Utomo MS, Kassegne S. 2022a. Integrated electrochemical dopamine sensing with finger priming pump on a chip. Int. J. Technol. 13(8):1735–1744. doi:10.14716/ijtech.v13i8.6140.

Whulanza Y, Arafat YB, Rahman SF, Utomo MS, Kassegne S. 2022b. On-chip testing of a carbon-based platform for electro-adsorption of glutamate. Heliyon 8(5):e09445. doi:10.1016/j.heliyon.2022.e09445.

Whulanza Y, Widyaratih DS, Istiyanto J, Kiswanto G. 2014. Realization and testing of lab-on-chip for human lung replication. ARPN J. Eng. Appl. Sci. 9(11):2064–2067.

Zakaria L. 2023. Basal stem rot of oil palm: The pathogen, disease incidence, and control methods. Plant Dis. 107(3):603–615. doi:10.1094/PDIS-02-22-0358-FE.

DOI: https://doi.org/10.22146/ijbiotech.83645