Jan 31, 2025
Soil Collection Protocol
- Nuttapon Pombubpa1,2,
- Ariya Chindamporn3,2,
- Nattapol Kraisitudomsook4,2,
- Neil Andrew Robert Gow5,2,
- Syahriar Nur Maulana Malik Ibrahim1,2,
- Fikran Aranda Fahrudin6,2
- 1Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- 2Southeast Asia Antifungal Resistance Monitoring Initiative (SEA-ARMi), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- 3Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- 4Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi 70150, Thailand;
- 5Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom;
- 6Program of Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
Protocol Citation: Nuttapon Pombubpa, Ariya Chindamporn, Nattapol Kraisitudomsook, Neil Andrew Robert Gow, Syahriar Nur Maulana Malik Ibrahim, Fikran Aranda Fahrudin 2025. Soil Collection Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.6qpvr929pvmk/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 22, 2025
Last Modified: January 31, 2025
Protocol Integer ID: 118858
Keywords: accurate responses to fungal threat, resistant fungi, extracting fungal genomic dna, fungal genomic dna, antifungal resistance, antifungal resistance to major drug class, fungal pathogen, several pathogenic fungi, fungal threat, agricultural biosecurity, strategies against fungal infection, including fungi, fungal infection, including fusarium group, leveraging genomic technology, fusarium group, specific resistance gene, comprehensive genome database, diverse microorganism, genomic technology, agricultural soil, prevalent in thailand, eumycetoma agent, collecting soil sample, network of mycologist, genomic dna, sustainable agriculture across sea, significant human infection, soil sample, soil
Funders Acknowledgements:
FAILSAFE Awarded projects - Seed Grant
Grant ID: FAILSAFE FR1-23
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Abstract
Soil harbors diverse microorganisms, including fungi that play crucial environmental roles but can also harm plants, animals, and humans through infections or spore exposure. In 2022, the WHO released several pathogenic fungi, including Fusarium group, Mucorales and Eumycetoma agents, which are prevalent in Thailand's agricultural soils and have caused significant human infections. Despite this, the genetic mechanisms behind their infections and antifungal resistance remain poorly understood, particularly in Southeast Asia. Antifungal resistance to major drug classes, such as azoles, echinocandins, and polyenes, is increasing, driven by specific resistance genes. To address these challenges, we propose establishing a Southeast Asian (SEA) network of mycologists to study fungal pathogens, focusing on collecting soil samples, extracting fungal genomic DNA, and creating a comprehensive genome database. This initiative will improve detection and management of drug-resistant fungi, enhance clinical treatments, and strengthen agricultural biosecurity. By leveraging genomic technologies and fostering international collaboration, the project aims to develop targeted strategies against fungal infections and resistance, benefiting public health, food security, and sustainable agriculture across SEA. Establishing a fungal biobank and expert network will support long-term efforts to combat antifungal resistance, providing critical resources for swift and accurate responses to fungal threats.
Materials
1. Dry ice
2. Ethanol 70%
3. Soil tester (pH, temperature and moisture)
4. Sterile centrifuge tube (50 mL)
5. Shovel or Cylinder crop
6. Sterile plastic ziplock bag
7. Tape measure
8. Cooler box
Troubleshooting
Soil sampling collection
Choose Sampling Location: Select a location close to an agricultural area for soil sampling. Ensure the area is representative of the study conditions.
Measure Soil Condition: Use a soil tester to measure and record parameters such as pH, moisture content, and temperature.
Collect Soil Sample: Dig ±10 cm below the soil surface using a shovel or a cylinder crop. Transfer the soil sample into a 40 mL centrifuge tube. Ensure the sample is compacted enough to avoid air gaps but not overpacked.
Replicate Sampling: Move to a new position ±20 m from the initial sampling site to collect the second replicate and third replication.
Store Samples: Place all soil samples into an ice box.
Ensure that at least the e-DNA extraction and isolation processes are performed within the same week or, at the latest, within a month.
Protocol references
Brooks, J. (2016). Soil sampling for microbial analyses. Manual of Environmental Microbiology, 2.6. 3-1-2.6. 3-11.