eDNA in water vs soil: which sample type do you need?

The most common early question about eDNA is 'what do I actually collect?' The answer depends almost entirely on which species you want to see. Water, soil, and swabs each excel at a different slice of the biosphere.

Water: the aquatic community

A liter of pond, stream, lake, or wetland water is a moving library of the vertebrates and invertebrates that live in or visit it. Fish shed constantly through mucus, gill exchange, and feces. Amphibians add larval and adult DNA. Waterfowl leave feather and fecal traces. Aquatic insects contribute at every life stage.

Water samples are also the standard for detecting invasive aquatic species — Asian carp, quagga mussels, chytrid fungus — long before visual confirmation.

Soil: the terrestrial community

Soil integrates everything that walked, burrowed, rooted, or fell there. Mammal urine and feces, insect exoskeletons, fungal hyphae, plant roots, and reptile shed skin all contribute. A single core can yield mammals, birds, insects, plants, and fungi from the same sample.

For a homeowner asking 'what actually lives on my land,' soil is usually the highest-yield choice.

Swabs: targeted contact surfaces

Swabs of flowers pick up pollinators — bees, hoverflies, moths, beetles — that recently visited. Swabs of tree bark or nest cavities pick up whatever mammal or bird used the site. Swabs of a burrow entrance target its occupant.

Swabs are less about breadth and more about answering a specific question: which pollinators use this patch of flowers, or which mammal is denning in this cavity.

Quick chooser

Rules of thumb:

Fish, amphibians, aquatic invertebrates → water
Mammals, ground beetles, plants, fungi, reptiles → soil
Pollinators on a specific plant → flower swab
Cavity-nesting or denning wildlife → cavity swab
Full biodiversity of a small property → soil + water where available

Frequently asked questions

Will a soil sample pick up fish?

Rarely, unless the soil was recently underwater. Fish DNA belongs in water samples.

Do I need multiple samples?

For a property inventory, yes. Different microhabitats yield different species. One sample is a snapshot; several samples across the property is a survey.