Environmental Biotechnology Diagnostics

Environmental biotechnology diagnostics encompass a suite of molecular and cellular tools designed to detect biological and chemical markers in natural and engineered systems. Core methods include environmental DNA (eDNA) metabarcoding, which retrieves genetic material shed by organisms into water, soil or air and applies high-throughput sequencing and bioinformatics to profile community composition. Complementary approaches employ biosensors—living or cell-free constructs engineered to produce optical, electrochemical or colourimetric signals upon binding specific pollutants or microbial targets. Together, these strategies enable non-invasive, high-resolution surveys of biodiversity, early warning of invasive or pathogenic species, and monitoring of antibiotic-resistance genes, with applications ranging from riverine ecosystem assessment to water-safety screening and public-health surveillance.

Research from Nature Portfolio

Intensive spatio-temporal sampling of river networks has demonstrated that eDNA metabarcoding can resolve entire animal communities across tens of kilometres and multiple seasons. By integrating systematic sampling with measurements of flow, pH, temperature and rainfall, researchers showed that beta diversity in rivers is driven predominantly by species turnover rather than downstream transport of DNA, and that eDNA faithfully records seasonal migrations of fish such as salmon and eels. In parallel, deep-sequencing studies have revealed that human DNA sequences are routinely co-captured in eDNA surveys—a phenomenon termed human genetic bycatch—highlighting both novel possibilities for environmental surveillance and the urgent need for ethical frameworks addressing privacy and consent in large-scale eDNA monitoring.

Research from all publishers

Quantitative PCR analyses of wastewater treatment plants in northern China have uncovered persistent loads of clinically important carbapenemase genes throughout all treatment stages, including chlorination, and substantial carriage in dewatered sludge. These findings underscore treatment plants as reservoirs and dissemination routes for antibiotic resistance. In another development, an online Pest Alert Tool has been introduced for screening eDNA metabarcoding datasets to flag marine non-indigenous and pathogenic species. By filtering sequence identity and length and offering linked phylogenetic validation, this application streamlines environmental biosecurity and rapid identification of taxa of concern. Meanwhile, soil eDNA metabarcoding along a desert transect in Northwest China detected hundreds of plant species, including ephemeral taxa overlooked by traditional surveys, and linked diversity patterns to temperature gradients and anthropogenic land use, illustrating the power of eDNA to reveal hidden biodiversity in remote landscapes.

Environmental Biotechnology Diagnostics publication trend

The graph below shows the total number of articles in environmental biotechnology diagnostics across all publications each year (not limited to Nature Index journals).

Technical terms

environmental DNA (eDNA): Genetic material released by organisms into substrates such as water, soil or air, used to infer species presence.

metabarcoding: Simultaneous amplification and sequencing of a standardised genetic marker from mixed DNA samples to identify multiple taxa.

high-throughput sequencing (HTS): Automated platforms generating millions of DNA reads in parallel for large-scale genetic analyses.

biosensor: A biological or biomimetic device that produces a measurable signal in response to a target analyte, including living cells or cell-free systems.

antibiotic resistance gene (ARG): A DNA segment encoding a mechanism enabling bacteria to survive antibiotic exposure.

beta diversity: A measure of variation in species composition between different spatial or temporal samples.

human genetic bycatch: The unintended recovery of human DNA sequences during environmental DNA surveys.

References

1. An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding. Nature Communications (2024).
2. Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA. Nature Ecology & Evolution (2023).
3. Prevalence and Fate of Carbapenemase Genes in a Wastewater Treatment Plant in Northern China. PLOS ONE (2016).
4. Pest Alert Tool-a web-based application for flagging species of concern in metabarcoding datasets.. Nucleic Acids Research (2023).