eDNA Water Filtration for Biodiversity Surveys

Physical filtration of water samples through membrane filters to capture environmental DNA (cellular, extracellular, and free DNA) from target organisms. Foundational sample-collection technique for eDNA metabarcoding, invasive-species surveillance, threatened-species monitoring, and any environmental biodiversity survey. Uses a vacuum manifold or syringe-based filtration. Works with any filter membrane; 0.45 µm cellulose nitrate or GF/F glass-fibre standard. Written for a novice audience.

sample_prep

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Version History

Version 0.1.1 Viewing Latest

Effective: 2026-04-20

Catalog fix (vacuum pump t#43, filter apparatus t#44) bundled. All `procedure N` references converted to Markdown hyperlinks pointing at https://librebiotech.org/?action=show&id=N — enables in-app click-through to referenced sibling procedures. Text content otherwise preserved.

Version 0.1.0

Effective: 2026-04-20

Initial release. Physical filtration technique; procedural facts are field-standard and uncopyrightable. Supports future eDNA content arc (Season 2). Fresh original prose. Catalog gap: vacuum pump + filter apparatus equipment types not yet in LibreBiotech catalog; to be added.

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Procedure Details

Safety & Hazards

Contamination prevention is paramount. eDNA can be picked up on boots, gloves, equipment — a single contaminated sample can skew an entire biodiversity dataset. Dedicated eDNA-only equipment; bleach decontamination between sites; field negative controls (sterile water filtered identically).
Water handling. Treat source water as potentially hazardous (environmental pathogens possible). Gloves; eye protection at minimum; consult local field-safety protocols for unfamiliar water bodies.
Vacuum pump electrical safety. Keep water and electrical outlets separated; use ground-fault protection.
Filter handling. Filters with captured material should be treated as biologically active material — avoid skin contact; store/dispose per biohazard protocols.
Field safety beyond lab scope. Swiftly moving water, boats, wildlife hazards, weather — defer to local field practice.

Preparation Notes

Pre-trip prep:

Sterile sample bottles. 1 L HDPE plastic bottles, autoclaved. Label before field departure.
Filter assortment. Membrane filters in sterile pouches:
- 0.45 µm cellulose nitrate (standard for general eDNA)
- 0.22 µm cellulose nitrate (retains smaller particles; slower filtration)
- GF/F glass-fibre (good for large-particle water; faster filtration)
Filter apparatus. Either: (a) disposable syringe-filter units (Sterivex-GP or similar), or (b) reusable vacuum manifold + funnel + membrane sandwich.
Vacuum pump. Hand-operated diaphragm pump for field use; electric pump for lab filtration. Hand pumps work surprisingly well for 1 L samples in 10–15 minutes.
Preservation buffer. Longmire buffer (100 mM Tris-HCl pH 8.0 + 100 mM EDTA + 10 mM NaCl + 0.5% SDS). Pre-fill 1.5 mL tubes with 800 µL Longmire; filters go directly in on collection.
Ice bucket / dry ice / thermos. For in-transit cold storage of filters until freezer access.
Field documentation. GPS unit, notebook, pen; record every sample's location, time, weather, water temperature, turbidity.

Mental model. Water at your field site contains eDNA from every organism that's recently been in/near the water: fish mucus cells, amphibian skin cells, bacterial cells, algal spores, and free DNA from cell lysis. Filtering captures this material on the membrane; subsequent DNA extraction (procedure 80) and PCR amplification (procedure 72) produces taxonomic calls.

Sample volumes:

1 L per sample is standard for most biodiversity surveys.
2 L for oligotrophic / low-biomass water (clear ocean, alpine lakes).
250 mL for turbid / high-biomass water (eutrophic ponds, wastewater).

Timing

Per sample on-site (~15 min): collect water, filter, transfer filter to preservation buffer.
Batch efficient: 8–10 samples in an afternoon field trip per collector.
Storage transit: filters in Longmire stable on ice for 24 h; at −20°C indefinitely.

Equipment (Catalog) 5

Filter apparatus Liquid handling
Specs: Reusable or Sterivex cartridge; 0.22–0.45 µm membrane compatible
Nalgene bottle-top filtration unit, Sterivex-GP (disposable cartridge, field-sealable), or generic vacuum manifold
Micropipette Liquid handling
Specs: P1000, P200 for preservation-buffer aliquots
Used lab-side for preservation-buffer prep, not field
Vacuum pump Liquid handling
Specs: Diaphragm pump; electric lab or hand-operated field variant
Welch/Rocker (lab) or generic hand-operated (field-deployable, no mains power required)
Biosafety cabinet Safety
Specs: Class II Type A2 or equivalent
Lab-side only — for preservation-buffer preparation and filter unpacking
Freezer (−20 °C) Storage
Specs: Standard lab freezer
For long-term preservation of filters

Materials (Catalog) 1

Buffer Reagent
Qty: 800 µL per filter tube
100 mM Tris-HCl pH 8.0 + 100 mM EDTA + 10 mM NaCl + 0.5% SDS; stable room temp for months

Protocol Parameters Captured per-assay on each run; exported as ISA-Tab Parameter Value columns

Name	Type	Required	Default	Unit	Description
`sample_volume_mL`	number	—	`1000`	milliliter (UO:0000098)	Water volume per sample. 1 L standard; 2 L for low-biomass water; 250 mL for high-biomass / turbid water.
`filter_pore_size_um`	number	—	`0.45`	—	Filter membrane pore size. 0.45 µm standard; 0.22 µm for smaller organisms (bacteria); GF/F (~0.7 µm) for turbid water.
`filter_material`	text	—	`cellulose_nitrate`	—	Filter material. 'cellulose_nitrate' (general eDNA); 'GF/F' (glass fibre, for high-particle water); 'polycarbonate' (flat surface, image-friendly).
`longmire_volume_ul`	number	—	`800`	microliter (UO:0000101)	Longmire preservation buffer per filter tube. 800 µL for 1.5 mL tube; 5 mL for 15 mL conical (Sterivex filters).
`field_negative_ratio`	number	—	`1`	—	Number of field negatives per site per day. 1 minimum; 2 recommended for high-contamination-risk sites.

Procedure Steps (Version 0.1.1)

Pre-label sample bottles with: site ID, date, time slot, collector initials. Label one bottle per sample plus one field negative.

At the field site, collect a water sample. Standard: ~20 cm below surface, away from banks, facing upstream if flowing water. Fill bottle to ~1 L (mark the fill line to verify in the field).

For the field negative: pour 1 L of sterile lab water (brought from the lab) into a labelled sample bottle at the same site. Handle identically to the real samples.

Immediately set up the filtration apparatus. For syringe-filter format: draw sample water into a 60 mL syringe; screw on a Sterivex-GP (or equivalent) sterile filter cartridge. For vacuum-manifold format: mount a sterile membrane filter between two halves of the funnel/base; connect to vacuum pump.

Filter the entire 1 L sample through the filter. For syringe: refill and push repeatedly until the whole sample has passed through. For vacuum: apply suction, allowing water to pass through; refill funnel as needed.

Note the filtration time and any filter resistance. If filtration stops before 1 L has passed, record the actual volume filtered. Clogged filters often indicate high biomass samples — note this.

For syringe-filter format: unscrew the Sterivex cartridge. Dry the outer surface with a clean wipe. Use a blunt-tipped tool to transfer the Sterivex directly into a 15 mL conical tube pre-filled with 5 mL Longmire buffer.

For vacuum-manifold format: using sterile forceps, carefully lift the filter from the base, keeping it oriented with captured-material side up. Fold the filter in half, then in half again (material inside). Transfer directly into a 1.5 mL tube pre-filled with 800 µL Longmire buffer.

Cap the tube. Invert gently 3 times to ensure the filter is submerged in preservation buffer. Do NOT vortex — shears DNA prematurely.

Label the preservation tube with the sample identifier. Store on ice during the remainder of the field day; transfer to −20°C within 24 hours.

Decontaminate all non-disposable equipment between samples: bleach-wipe the filtration apparatus; change gloves; rinse sample bottles with sterile water before reuse (or use single-use bottles for critical projects).

Record the collection event in LibreBiotech when back at the lab: Process record for the collection trip; one Sample record per filter, with annotations for GPS coordinates, filter pore size, filtration time, observed turbidity, water temperature, and cross-reference to the field negative collected at the same site.

Completion Notes

Expected outcome. Filter membranes preserved in Longmire buffer, ready for DNA extraction (procedure 80). Each filter represents ~1 L of filtered water from a specific site/time.

Field negative controls (critical).

Field negative: 1 L of sterile laboratory water filtered identically at the same site. Catches contamination during field handling.
Bottle blank: 1 L of sterile water poured into a sample bottle, carried through the trip, and filtered in the lab. Catches bottle-contamination sources.
Minimum one field negative per site, per day.

QC gate. Every downstream eDNA workflow run should verify field negatives don't amplify target sequences. Positive amplification in a field negative invalidates that site's sample set.

Downstream. DNA extraction via procedure 80; qPCR or metabarcoding via procedure 72 + target-specific primers; species call via procedure 76.

Troubleshooting.

Symptom	Likely cause	Fix
Filtration becomes very slow / stops	Filter clogged by sediment / biomass	Pre-filter through coarser (1.0 µm) membrane first; reduce sample volume
Contamination in field negatives	Cross-contamination during collection	Use gloves changed between sites; bleach-wipe bottle exteriors; dedicated eDNA-only equipment
Weak signal in downstream PCR	Low biomass; inhibitors in preservation	Increase sample volume to 2 L; use different filter membrane (switch cellulose ↔ GF/F)
Filters curl / damage in preservation	Too-stiff filter handling with forceps	Use smooth-tipped forceps; handle filter by edge only
Preservation buffer frozen before filtration	Dry ice transit too cold	Store on wet ice only during transport until filtration; freeze after filter added

References

Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008). Species detection using environmental DNA from water samples. Biol Lett 4(4):423–5. (Foundational eDNA from water). DOI paper
Deiner K, Walser JC, Mächler E, Altermatt F (2015). Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183:53–63. (Filtration method comparison). DOI paper
Thomsen PF, Willerslev E (2015). Environmental DNA — an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18. (Review). DOI paper
LibreBiotech procedure 80 — eDNA Extraction from Filter Membranes (downstream). Link protocol