Utilizing metagenomics and metabarcoding for assessing the diversity and abundance of entomopathogenic fungi in soil ecosystems
Keywords:
entomopathogenic fungi, metabarcoding, metagenomics, ITS, diversity assessmentAbstract
Entomopathogenic fungi play a crucial role in natural pest control and have received significant attention in the field of biological control. The application of metabarcoding and metagenomic techniques has revolutionized the study of microbial communities in various ecosystems by identifying and characterizing many microorganisms at once. These methods improve soil fungal community assessments for entomopathogenic fungi. These studies require fungal DNA extraction from complex environmental samples like soil. These methods improve soil fungal community assessments for entomopathogenic fungi. These studies require fungal DNA extraction from complex environmental samples like soil. Bead-beating, chemical extraction, and commercial kits extract fungal DNA while minimizing environmental DNA contamination. Shotgun sequencing for metagenomics can sequence all genetic material in a sample without targeting specific genes. This method shows the microbial community, including entomopathogenic fungi. Metagenomic data can reveal the soil microbiome's functional potential and interactions. Shotgun sequencing and ITS barcoding for fungal metabarcoding are popular. The ITS region of the fungal genome is variable, making it a good marker for species identification. Researchers can assess soil entomopathogenic fungi diversity and abundance by amplifying and sequencing the ITS region. In this review, the utility of these approaches for the identification and characterization of entomopathogenic fungi in soil samples was assessed. This review focused on the extraction of soil DNA, shotgun sequencing for metagenomics, and the use of Internal Transcribed Spacer (ITS) as a barcode for fungal metabarcoding. Insights into the potential applications and future directions in the study of entomopathogenic fungi were given. These insights were provided by highlighting the benefits and limitations of these methodologies.
References
Asensio L, Carbonell T, Lopez-Jimenez J, Lopez-Llorca L. Entomopathogenic Fungi in Soils from Alicante Province [Spain]. Span J Agric Res. 2003;3(1):37. https://doi org/10.5424/jar/2003013-33
Budiarti L, Nuryanti N. Entomopathogenic Fungus from Rice Rhizosphere Soil in Politeknik Negeri Lampung Land IOP Conf Ser: Earth Environ Sci. 2022;1(1012):012059. https://doi.org/10.1088/1755-1315/1012/1/012059.
Buyers F, Saltykova A, Denayer S, Verhaegen B, Vanneste K, Roosens N. A Practical Method to Implement Strain-level Metagenomics-based Foodborne Outbreak Investigation and Source Tracking In Routine Microorganisms. 2020;8(8):1191. https://doiorg/10.3390/microorganisms8081191.
Chandler J, Liu R, Bennett S. Rna Shotgun Metagenomic Sequencing of Northern California (USA) Mosquitoes Uncovers Viruses, Bacteria, and Fungi Front Microbiol, 2015, 06. https://doi org/10.3389/fmicb201500185.
Curd E, Gold Z, Kandlikar G, Gomer J, Ogden M, O'Connell T. Anacapa Toolkit: An Environmental Dna Toolkit For Processing Multilocus Metabarcode Datasets Methods in Ecology and Evolution. 2019;9(10):1469-1475. https://doi org/10.1111/2041-210x 13214
Dara S. Non-entomopathogenic Roles of Entomopathogenic Fungi in Promoting Plant Health and Growth Insects. 2019;9(10):277. https://doi.org/10.3390/insects10090277.
Feinstein L, Sul W, Blackwood C. Assessment of Bias Associated with Incomplete Extraction Of Microbial Dna From Soil Appl Environ Microbiol. 2009;16(75):5428-5433. https://doi org/10.1128/aem00120-09.
Gielen R, Põldmaa K, Tammaru T. In Search of Ecological Determinants of Fungal Infections: A Semi‐field Experiment with Folivorous Moths Ecology and Evolution, 2022, 5(12). https://doi org/10.1002/ece3 8926.
Gupta V, Bakshi U, Chang D, Lee A, Davis J, Chandrasekaran S, et al. Taxibgc: A Taxonomy-guided Approach For Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters And Secondary Metabolite Production Potential In Metagenomes Msystems, 2022, 6(7). https://doi.org/10.1128/systems 00925-22
Hallouti N, Zahidi N, Bouharroud N, Mousadik N, Aoumar N, Boubaker N. Diversity of Entomopathogenic Fungi in Argane Forest Soil and Their Potential to Manage Mediterranean Fruit Fly (Ceratitis Capitata). Journal of Pharmacy and Pharmacology, 2017, 10(5). https://doi.org/10.17265/2328-2150/201710007.
Hanora A, Amin M, Azab M, Shabayek S, Atwa K. The Vaginal Microbiota During Pregnancy Records of Pharmaceutical and Biomedical Sciences. 2023;2(7):80-92. https://doi org/10 21608/rpbs 2023 196524 1213
Hesketh H, Roy H, Eilenberg J, Pell J, Ails R. Challenges in Modelling Complexity of Fungal Entomopathogens in Semi-natural Populations of Insects Bio Control. 2009;1(55):55-73 https://doi org/10 1007/s10526-009-9249-2.
Hoang M, Rinyi L, Myer W. Long-read Sequencing in Fungal Identification Microbiology Australia. 2022;1(43):14-18. https://doi org/10 1071/ma22006
Kang D, Frula J, Egn R, Wan Z. Metabat, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Peerj. 2015;3:e1165. https://doi org/10 7717/peerj 1165
Lobo J, Shokalla S, Hajiabaei M, Cota F. DNA barcoding for High-throughput Monitoring of Estuarine Macrobenthic Communities Scientific Reports, 2017, 1(7). https://doi org/10 1038/s41598-017-15823-6.
Łopusiewicz Ł, Mazurkiewicz-Zapałowicz K, Koniuszek M, Tkaczuk C, Bartkowiak A. The Influence of Tin Ions on Growth and Enzymatic Activity of Entomopathogenic Fungi Acta Mycol, 2019, 2(54). https://doi org/10 5586/am 1127.
Mahmoudi N, Slater G, Fulthorpe R. Comparison of Commercial Dna Extraction Kits for Isolation and Purification of Bacterial and Eukaryotic Dna from Pah-contaminated Soils Can J Microbiol. 2011;8(57):623-628. https://doi org/10 1139/w11-049.
Majchrowska-Safaryan A, Tkazuk C, Symnowicz B. Effects of the Application of A Mineral-and-organic Fertiliser Produced from Brown Coal on the Occurrence and Infectious Potential of Entomopathogenic Fungi in Soil Journal of Ecological Engineering. 2017;3(18):140-148. https://doi org/10 12911/22998993/70184.
Moreira C, Celetino D, Sobrnho T, Cardoo I, Ellio S. Agroforestry Coffee Soils Increase the Insect‐suppressive Potential Offered by Entomopathogenic Fungi Over Full‐sun Soils: A Case Proposing A "Bait Survival Technique" Ecol Evol. 2019;18(9):10777-10787. https://doi org/10 1002/ece3 5598.
Nayfach S, Pollard K. Toward Accurate and Quantitative Comparative Metagenomics Cell. 2016;5(166):1103-1116. https://doi org/10 1016/j cell 2016 08 007.
Pasolli E, Truong D, Malik F, Waldron L, Segata. Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights Plos Computational Biology. 2016;7(12):e1004977 https://doi org/10 1371/journal pcbi 1004977.
Ramos Y, Taibo A, Vega A, Lemes C, Castañeda-Ruiz R, Portal O. Abundance of Beauveria Spp and Metarhizium Spp in Maize and Banana Agroecosystems in Central Cuba Agron Colomb. 2022;1(40):141-146. https://doi org/10 15446/agron colomb v40n1 100886.
Safitri A, Herlinda S, Setiawan A. Entomopathogenic Fungi of Soils of Freshwater Swamps, Tidal Lowlands, Peatlands, and Highlands of South Sumatra, Indonesia Biodiversitas. 2018;6(19):2365-2373 https://doi org/10 13057/biodiv/d190647.
Sánchez-Peña S, Lara Medina R. Occurrence of Entomopathogenic Fungi from Agricultural and Natural Ecosystems in Saltillo, México, and their Virulence towards Thrips and Whiteflies Journal of Insect Science. 2011;1(11):1-10. https://doi org/10 1673/031 011 0101.
Särkinen T, Staats M, Richardson J, Cowan R, Bakker F. How to Open the Treasure Chest? Optimising Dna Extraction from Herbarium Specimens. PLoS ONE. 2012;8(7):e43808. https://doi org/10 1371/journal pone 0043808.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, et al. Critical Assessment of Metagenome Interpretation–a Benchmark of Metagenomics Software Nature Chemical Biology. 2017;11(14):1063-1071. https://doi org/10 1038/nmeth 4458.
Sevim A, Demir Höfte, Humber R, Demirbag Z. Isolation and Characterization of Entomopathogenic Fungi from Hazelnut-growing Region of Turkey BioControl. 2009;2(55):279-297. https://doi org/10 1007/s10526-009-9235-8.
Shay J, Haniford L, Cooper A, Carrillo Blais B, Lau C. Exploiting a Targeted Resistome Sequencing Approach in Assessing Antimicrobial Resistance in Retail Foods Environmental Microbiome, 2003, 1(18). https://doi org/10 1186/s40793-023-00482-0.
Sun X, Hu Y, Wan J, Fag C, Li J, Han & Suzuki S. Efficient and Stable Metabarcoding Sequencing Data Using a Dnbseq-g400 Sequencer Validated by Comprehensive Community Analyses Gigabyte, 2021, 1-15. https://doi org/10 46471/gigabyte 16.
Suwandi S. Exploring Entomopathogenic Fungi from South Sumatra (Indonesia) Soil and Their Pathogenicity Against a New Invasive Maize Pest, Spodoptera Frugiperda Biodiversitas, 2020, 7(21). https://doi org/10 13057/biodiv/d210711.
Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou N, Wijesundera R. Global Diversity and Geography of Soil Fungi Science, 2014, 6213(346). https://doi org/10 1126/science 1256688.
Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I. Shotgun Metagenomes and Multiple Primer Pair-barcode Combinations of Amplicons Reveal Biases in Metabarcoding Analyses of Fungi Mycokeys. 2015;10:1-43. https://doi org/10 3897/mycokeys 10 4852.
Vega F, Goettel M, Backwell M, Handler D, Jakson M, Kellr S. Fungal Entomopathogens: New Insights on their Ecology Fungal Ecology. 2009;4(2):149-159. https://doi org/10 1016/j funeco 2009 05 001.
Yfun Ecoo S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M. Environmental Dna Metabarcoding Reveals Local Fish Communities in a Species-rich Coastal Sea Scientific Reports, 2017, 1(7). https://doi org/10 1038/srep40368.
Yeates C, Gillings M, Dvison A, Altvilla N, Val D. Methods for Microbial Dna Extraction from Soil for Pcr Amplification Biol Proced Online. 1998;1(1):40-47. https://doi org/10 1251/bpo6.
