Sample collection for DNA extraction

Collecting a good sample is the first—and most important—step in any microbiome analysis. Even the best laboratory methods cannot recover information that was lost before the sample reached us. This guide walks through collection and shipping procedures for the two main sample categories we encounter in wastewater treatment work: high-biomass environments and low-biomass environments. Read the section that applies to your sample type, and don't hesitate to reach out if you have questions before you collect.

High-biomass samples

High-biomass samples include mixed liquor from activated sludge basins, return activated sludge (RAS), waste activated sludge (WAS), and solids from anaerobic digesters. These samples are rich in microbial cells and DNA, which makes them straightforward to work with—but they still need to be stabilized quickly to prevent community composition from shifting after collection.

Using the Aster Bio sample preservation kit

We offer a test kit that takes the guesswork out of preserving high-biomass samples. The kit includes small vials pre-loaded with a safe, cost-effective preservative, along with a sterile transfer pipet. The workflow is simple:

1. Use the supplied sterile transfer pipet to add your sample to the preservative vial.
2. Label the vial clearly with your site name, sample location, and collection date.
3. Shake the vial to mix the sample with the preservative.
4. Place the sealed, labeled vial in a padded envelope or small box and ship it to the lab.

No ice or ice chest is required. Preserved samples may be shipped at room temperature and are stable for weeks to months. Ground shipping is acceptable.

Alcohol preservation—alternative for international clients

For clients outside the United States who wish to use our analytical services, an alternative preservation method is available. You may mix your high-biomass sample with an equal volume of a common alcohol such as 40% ethanol or 91% isopropanol.

The goal is to achieve a final alcohol concentration of approximately 20% v/v after mixing. For example, combining one part sample with one part 40% ethanol will yield a mixture of roughly 20% ethanol by volume—well within the range needed to stabilize the sample for international shipping.

Note: Check local and international shipping regulations for your country before using alcohol-preserved samples. Contact us if you are unsure whether this option applies to your situation.

Low-biomass samples

Low-biomass samples—such as water from cooling towers, heat exchanger loops, lagoons, ponds, or other environments that appear clear or lightly turbid—present a different challenge. The microbial cell density may be low enough that a small volume simply won't contain enough DNA for reliable analysis. To compensate, we ask for larger volumes and use filtration to concentrate the biomass in the lab.

Volume requirements

Please supply at least 1 liter of sample water. If your site uses multiple monitoring points or you are uncertain about biomass levels, sending 2–4 liters is a reasonable precaution. Plastic bottles are preferred over glass—they are lighter, less fragile during shipping, and easier to label securely.

Choosing and preparing your bottles

A convenient and inexpensive bottle source is standard drinking water bottles (e.g., 1-liter or 1.5-liter PET bottles). Before use, observe one important rule:

Do not drink from the bottle before using it for sample collection. Mouth contact introduces human DNA and oral microbiota that can contaminate results.

Once you have a clean, unused bottle, follow these steps:

1. Rinse the bottle three times with the sample water. Fill, cap, shake, and discard. This removes any residual taste additives or contaminants from the bottle interior.
2. Fill the rinsed bottle with at least 1 liter of sample water and cap it securely.
3. Label the bottle with your site name, sample location, and collection date and time.
4. Ship the bottle to the lab using standard next-day morning delivery (see Shipping below).

Shipping unpreserved water samples

Unpreserved water samples should be shipped overnight and are not compatible with long-term room-temperature storage. No ice is required when using standard next-day delivery—the bottles will arrive cool enough for processing if shipped promptly after collection.

Important: Do not select Priority First AM or any guaranteed early-morning delivery service. These services attempt delivery before 9:00 AM, when lab staff may not yet be present to receive and sign for the package. Standard next-day morning delivery is the correct choice.

Cationic polymer interference with DNA recovery

Cationic polymers are widely used in wastewater treatment as conditioning and flocculation aids. They carry a strong positive charge that binds tightly to negatively charged cell surfaces and extracellular DNA. When present in a sample at sufficient concentration, these polymers can co-precipitate with nucleic acids during extraction, yielding low DNA concentrations, poor PCR amplification efficiency, or results that do not accurately represent the true microbial community.

This is not a rare edge case. Polymer carryover is one of the more common causes of extraction failure or skewed community profiles in wastewater microbiome work, and it is almost always preventable with a brief heads-up before the sample ships.

Situations where polymer interference is likely

Anaerobic digesters fed thickened or conditioned sludge

Gravity belt thickeners, rotary drum thickeners, and dissolved-air flotation thickeners routinely dose cationic polymer to improve solids capture before the thickened sludge is pumped to the digester. If your digester is fed thickened sludge as a substrate—rather than raw primary or waste activated sludge directly—the polymer will travel into the digester with the feed. Digester contents sampled from these systems can carry enough residual polymer to significantly inhibit DNA extraction.

Please let us know if your digester receives thickened sludge as a feed stream. This allows us to apply an appropriate washing or dilution step during extraction to reduce polymer carryover before the lysis step.

Aeration basins preceded by dissolved-air or dissolved-nitrogen flotation

Dissolved-air flotation (DAF) and dissolved-nitrogen flotation (DNF) units are common in petrochemical refinery wastewater treatment, where they are used to remove free and emulsified oils and suspended solids before biological treatment. These flotation units almost always require cationic polymer addition to function effectively—the polymer destabilizes the oil-in-water emulsion and allows fine solids to attach to rising air or nitrogen bubbles.

Mixed liquor sampled from an aeration basin that receives DAF or DNF effluent as its primary influent can carry measurable residual polymer. The biological floc in these systems also tends to have a higher-than-normal positive surface charge due to polymer adsorption, which can complicate cell lysis and nucleic acid binding during extraction.

If your facility uses a DAF or DNF unit upstream of the aeration basin you're sampling, please note this when you submit your sample. Knowing the source of the influent helps us interpret both the extraction yield and any unusual community composition results.

When in doubt, tell us. A brief note on your sample submission form—“polymer dosed upstream” or “DAF effluent to aeration basin”—gives us the context we need to adjust our protocol and flag any results that warrant a re-extraction.

Quick reference summary

Questions?

Every site is a little different. If you have a sample type not covered here, or if you're unsure which protocol applies to your situation, contact us before collecting. We would rather spend a few minutes on the phone than have you collect a sample that won't yield usable data.

Contact Environmental Genomics