Environmental research and conservation

Portable, affordable nanopore sequencing technology delivers unique opportunities for environmental research and has been used extensively to analyse environmental DNA (eDNA) and microbiome samples to support biodiversity assessment, ecosystem biomonitoring, pathogen identification, and animal conservation. Long nanopore sequencing reads provide enhanced species identification, while real-time data analysis delivers immediate access to results, whether in the field or in the lab.

[There is a] need for decentralised labs with democratic access to ruggedise field technology, and herein lies nanopore technologies greatest advantage

Mrinalini Erkenswick Watsa, San Diego Wildlife Alliance, USA

Technology comparison

Oxford Nanopore sequencing

Traditional short-read technologies

Sequence at sample source or lab

  • Powerful, portable devices — starting at just $1,999, including sequencing reagents
  • Get faster access to results — no more sample shipping delays
  • Minimise potential for sample degradation — reveal the true biology

Constrained to the lab

Traditional sequencing technologies are typically bulky, cumbersome to ship, and require substantial site infrastructure, making them difficult to deploy in mobile settings or remote locations — where much of the world’s biodiversity is located.

Real-time data streaming

  • Analyse data as it is generated for rapid insights
  • Stop sequencing when sufficient data obtained — wash and reuse flow cell
  • Use intuitive EPI2ME workflows for real-time microbiome analysis

Fixed run time with bulk data delivery

Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.

Unrestricted read length (>4 Mb shown)

  • Get enhanced phylogenetic and taxonomic resolution through metabarcoding with full-length reads of informative loci (e.g. entire 16S and CO1 genes)
  • Assemble complete genomes and plasmids from metagenomic samples — resolving similar species and complex genomic regions

Read length typically 50–300 bp

Short sequencing reads may not span complex genomic regions, reducing the contiguity of metagenome assemblies. Metabarcoding of specific regions of interest with short reads has been reported to provide limited phylogenetic resolution.

Streamlined workflows

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency. Base modifications (e.g. methylation) are not detected as standard, with extra preparation steps and additional sequencing runs required.

White papers

Addressing the challenges of metagenomics

Microbial communities can have a profound effect on their environment, for example breaking down pollutants or generating useful by-products. In the same manner, environmental pressures, such as climate change, can impact the constitution of microbial communities. As a result, metagenomic analysis, which interrogates the genetic material of all microorganisms in a given community, not only provides significant insights into the structure and function of microbial communities but can also act as an environmental monitoring system. This White paper explores the challenges of metagenomics, with real-world examples of how they are now being addressed through the use of nanopore sequencing technology.

Get more environmental sequencing content, including eDNA, metabarcoding, and metagenomics publications, posters, and videos, in our Resource centre, or visit our Portable sequencing page.


Supporting rapid sequencing of critically endangered species, anywhere, by anyone

ORG.one is a pilot-stage project designed to support faster, more localised sequencing of critically endangered species, by enabling biologists to rapidly sequence those species close to the sample’s origin, using the latest ultra-long read approaches.

Data-rich, de novo whole-genome assemblies will be enabled through the provision of consumable support that can be used with Oxford Nanopore sequencers, on the condition that the data generated will be openly shared with the scientific community.

ORG.one supports the sequencing of species from the IUCN Red List, specifically the critically endangered and extinct in the wild categories (more than 8000 species)

Case study

Cataloguing biodiversity to improve economic resilience

During the COVID-19 pandemic in 2020, tourism in the Galapagos islands plummeted with devastating effect on the population. At London Calling 2023, Jaime A. Chaves shares how his team used nanopore technology to create new employment opportunities to improve economic resilience whilst protecting the archipelago’s ecosystem.

The best example of how nanopore technologies … is democratising science

Jaime A. Chaves, San Francisco State University, USA

Case study

ORG.one: a new program to promote sequencing biodiversity

As part of the ORG.one initiative to support faster, more localised sequencing of critically endangered species, Tomas Marques-Bonet and his team (Institute of Evolutionary Biology, Spain) sequenced nine species (covering birds, mammals, and amphibians) to develop improved genome assemblies to support conservation efforts. Watch the talk to find out how nanopore sequencing is being used to assemble high-quality genomes for all the species within approximately two months, generating read N50s of 20-40 kb, with contig N50s of 30-50 Mb. The data generated is online and open access to encourage further scientific and community support for this vital initiative.

We are in the sixth mass extinction of species, and this time it is because of us... We need to take action from [the] economy perspective, from ecology perspective, from social perspective, and genetics and genomics as well

Tomas Marques-Bonet, Institute of Evolutionary Biology, Spain

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Scalable sequencing for environmental research and conservation

From portable yet powerful Flongle and MinION devices to the flexible, high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific environmental sample sequencing requirements.

Recommended for environmental genomics


Paired with a contemporary laptop, the MinION Mk1B is a portable and affordable sequencing device. Perform real-time sequencing at sample source for the fastest access to results. Ideal for in-field or lab-based analysis of eDNA, metabarcoding, and metagenomics.


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