Biodiversity Monitoring with Acoustics and eDNA

Updated 2026-11-02 · 4 min read · By the akar.earth specialist team

How bioacoustics and eDNA monitoring work for land and blue carbon projects in Indonesia, what they can prove, survey design steps and pitfalls.

Bioacoustics and eDNA are two survey methods that detect species without needing to see them. Acoustic recorders capture calls of birds, primates, frogs, insects and bats over weeks; eDNA samples of water or soil reveal genetic traces of many species at once. Used together with habitat data, they give land and blue carbon projects repeatable evidence of biodiversity condition and change.

Traditional biodiversity surveys rely on experts walking transects, which is slow, costly and hard to repeat consistently. In Indonesia’s dense forests, peat swamps and mangroves, many species are heard far more often than they are seen. That makes passive methods a good fit for projects that need monitoring over decades.

What each method does well

Step-by-step: designing a monitoring programme

1. Define what you need to show. Species presence for HCV, a trend for a biodiversity credit, or evidence of no net harm for a carbon project’s co-benefits.
2. Choose target groups. Pick indicator species that respond to the change your project creates, such as forest-dependent birds or gibbons for restoration.
3. Design the sampling. Place recorders or sample points by habitat stratum, with control or reference sites outside the project. Reuse the stratification from carbon plots where possible (see plot sampling design).
4. Set the schedule. Record across seasons; repeat at the same points and times each year.
5. Standardise protocols. Recorder settings, mounting height and duration; eDNA filter volumes, preservation and chain of custody.
6. Process and validate. Use automated classifiers for acoustic data, but have experts check a sample. For eDNA, use accredited labs and report which detections match to species level.
7. Analyse trends with uncertainty. Occupancy models handle imperfect detection better than raw species counts.
8. Store raw data. Keep audio files and sequence data, so results can be re-analysed as tools improve.

Linking biodiversity data to carbon and credit methods

Biodiversity credit methods increasingly accept or require field-based species evidence alongside habitat metrics. Carbon projects seeking CCB or similar co-benefit labels can use the same data. Collecting acoustic and eDNA data at existing carbon plot locations keeps logistics simple and lets you relate biodiversity to canopy structure and biomass measured for DMRV.

Indonesia specifics

• Call libraries: recordings of Indonesian birds and primates exist, but coverage is uneven for eastern Indonesia. Local expert input is essential.
• Reference DNA databases: many endemic species in Sulawesi, Maluku and Papua lack reference sequences.
• Permits: research and sample export may need permits from national authorities; check before shipping samples to overseas labs.
• Community roles: local people can deploy recorders, collect samples and contribute species knowledge, which also supports benefit sharing.
• Climate: heat and humidity damage equipment and samples. Plan for waterproofing, batteries and cold chains.

Costs and practicalities

Costs depend on scale, number of sites, lab fees and analysis. Acoustic recorders are reusable, so costs fall in later years. eDNA costs scale with samples and sequencing. Budget for expert validation, not just equipment. Avoid the temptation to cut sites once the first year’s results are in, because trend detection depends on consistent coverage.

Combining methods

Neither method covers everything. A practical design for an Indonesian restoration or REDD+ project often combines:

• acoustic recorders at a subset of carbon plots and reference sites, covering birds, primates, frogs and insects,
• eDNA sampling in streams, rivers or mangrove channels draining the project area, covering fish, amphibians and some mammals,
• camera traps for large mammals that rarely call, such as sun bears, deer and wild pigs,
• habitat condition data from field plots and satellite imagery.

Together these give a richer picture than any single tool and let you cross-check results. Start with the methods that answer your main question, then add others as budget allows.

Common mistakes

• Running one survey and calling it monitoring.
• Moving recorder locations between years.
• Reporting acoustic index values without checking what drives them, such as rain or insects.
• Treating eDNA non-detection as proof of absence.
• Collecting data that no one has budget to analyse.

Our biodiversity valuation service designs monitoring to match credit and disclosure needs. See the biodiversity hub and HCV and HCSA assessments for related topics.