Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.
Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct observation, capturing a snapshot of whole communities at local or global scales.
NGS has also expanded the ability to sequence the genomes of specific taxa at higher resolution and lower cost. This allows us to characterize them and understand their response to environmental variables across ecosystems.
In this article, we will cover the history of NGS technologies to understand how they made possible the latest discoveries in environmental microbiology, ecosystem monitoring, and conservation genomics.
How NGS transformed environmental DNA sequencing
Environmental DNA, or eDNA, refers to genetic material collected from environmental samples such as water, soil, or air, rather than directly from organisms. What this means is that you can characterize a whole community with a single sample, making eDNA sequencing a very scalable, non-invasive, and informative approach.
High-throughput is essential here to obtain enough information on low-abundance DNA from many organisms, and compare communities across ecosystems. NGS expanded this eDNA research, and it all started with environmental microbiology, to later involve macroorganisms.
From Sanger sequencing of clones to high‑throughput eDNA
The first attempts to understand the uncultured majority of environmental microbes required weeks of manual work. It involved extracting environmental DNA, cloning it into plasmids, and sequencing genes for taxonomical identification with Sanger sequencing.
This could produce hundreds of sequences per sample at most, hardly reaching more than 1Gbp of data for a whole library.
The first wave of NGS and how it enabled metabarcoding at scale
With the release of 454 pyrosequencing and later of Illumina platforms, thousands to millions of reads could be produced from a single eDNA sample. As these were short‑read technologies, sequencing efforts focused on conserved marker regions, such as hypervariable regions of the 16S rRNA gene in bacteria, the ITS region of the rRNA gene cluster in fungi.
This targeted strategy became known as amplicon sequencing. When applied to complex environmental samples to obtain a broad picture of the community, amplicon sequencing is usually referred to as metabarcoding and is now dominated by Illumina short‑read instruments.
The first metabarcoding studies, focused on microbial communities, were published in the early 2000s. But researchers soon detected short DNA fragments from macroorganisms in environmental samples too, including aquatic samples. Monitoring whole ecosystems and individual species at the macroorganism level was then possible with eDNA as well.
However, metabarcoding only offers information on taxonomy classification, and the field quickly moved into functionality.
Metagenomics and long reads for genome‑resolved ecology
When sequencing costs started to drop and computational models improved, it was possible to obtain enough short reads from eDNA samples to reconstruct whole genomes, known as metagenome-assembled genomes (MAGs).
MAGs are built on shotgun metagenomics, which initially served to explore function, sequencing random DNA regions rather than targeted amplicons. This approach moved the field of eDNA from taxonomy to metabolic potential and ecological roles, especially in microbial contexts.
For macroorganisms, shotgun sequencing also made an impact, but mainly in individual whole-genome sequencing approaches, aimed at studying population genomics and genotype-environment associations.
Both amplicon sequencing and shotgun pose their own challenges. Amplicon sequencing is PCR-biased and can distort abundance metrics, while shotgun sequencing produces fragmented genomes, especially in highly similar microbial strains, and poorly resolves repetitive regions.
Long-read sequencing and improved genome reconstruction
Long-read platforms are trying to overcome the difficulties of short-read technologies. With ONT and PaCBio platforms, reads reach 10 kb to >1 Mb, allowing reconstruction of repetitive regions and providing less fragmented MAGs with improved taxonomic identification. Still, their higher cost and error rates slow down their adoption.
While PacBio HiFi achieves high read accuracy, costs are high, and throughput is lower than with ONT. This is a rapidly evolving field, with recent articles working on assemblers that could make ONT compete with PacBio’s HiFi accuracy.
These technological advances translate into improved methods, which are at the base of the latest discoveries across soil microbiology, ecosystem monitoring, and conservation strategies.
Mapping hidden microbial diversity in soils
Soil is among the most diverse ecosystems on Earth, and it's dominated by microorganisms. NGS now allows researchers to map this diversity and explore how climate, soil properties, and agricultural management affect these communities. This is crucial to understand and maintain soil health and agricultural productivity.
Large-scale projects, such as the Earth Microbiome Project (EMP), have significantly contributed to these efforts. The EMP provided standardized methods to obtain genomic and metabolomic data from many ecosystems, including soils, and link them to environmental gradients.
Together, the EMP and other studies have pointed to pH as the strongest predictor of community composition, along with other climatic and edaphic variables like soil carbon, temperature, and humidity.
Agricultural practices play a role in soil microbiome too. A recent paper showed that pesticide presence in soils across Europe explained a large fraction of the variation in soil microbial communities, raising awareness of how agricultural inputs can affect soil biodiversity and soil health.
Using soil microbial diversity to improve crops
Soil microbial diversity is also an extensive resource for making agriculture more sustainable, with multiomics helping to move from description to application. In a recent study, 175 rapeseed varieties were analyzed by combining plant genomics, root transcriptomics, ionomics, and rhizosphere metagenomics.
Using GWAS and TWAS, researchers found that the association of the bacterial genus Sphingopyxis with plant roots was strongly regulated by plant gene expression. They then isolated these bacteria and demonstrated, through inoculation experiments and rapeseed mutant lines, that Sphingopyxis enhances nitrogen acquisition and promotes auxin-mediated root development.
Beyond microbes: NGS in biodiversity monitoring and conservation strategies
Conservation strategies rely on accurate data about which species are where and how communities are changing. NGS now enables high‑throughput eDNA surveys across the tree of life, making biodiversity monitoring faster, less biased, and more scalable.
Beyond eDNA, sequencing individual genomes has become routine. This allows tracking specific threatened taxa across environments and understanding how they adaptively respond to climate change and other global pressures.
Ecosystem monitoring in days
Biodiversity monitoring with eDNA has been primarily done in aquatic ecosystems, where a single water sample can capture DNA from an entire trophic network.
But in terrestrial ecosystems, collecting multiple samples is needed, which is why airborne eDNA, obtained from aerosol stations, offers a promising alternative.
With this technique, a recent paper successfully identified 2739 genera across the tree of life and along a 34-year time frame, using archived filters from a Swedish boreal radionuclide station.
Does eDNA reflect real biodiversity patterns?
An important question when working with eDNA is whether it reflects real biodiversity patterns. Read counts don’t necessarily reflect absolute abundance, as other factors such as organism size (e.g., amount of pollen released) also contribute.
However, the authors from the previous paper provide optimistic results. They compared the distribution of eight bird species using eDNA and traditional surveys, finding that conventional data explained 60% of the variation.
Airborne eDNA also captured long-term ecosystem trends. The authors observed a decline in diversity over 34 years and a sharp increase in pine-associated eDNA. This pattern matches historical data, where primary forests were halved and largely replaced by pines in the same period of time.
Climate‑aware conservation with coral genomics
As oceans warm, many species face extinction if they cannot adapt to increasing temperatures. But populations also show genetic adaptations to heat. Linking these adaptive traits with data on past heatwaves can help us predict which regions are more vulnerable to future climate scenarios.
This approach is known as genotype-environment associations (GEA), and a recent paper explored how it works in corals. Researchers obtained 595 samples from five Acropora species and used whole genome sequencing and RAD-seq to identify genetic variants enriched in heat-resistant populations.
Then, they mapped these variants to specific genomic regions, identified genes, and validated their function with transcriptomic data and Gene Ontology enrichment analyses. It turned out that these regions were enriched in heat-responsive genes such as HSP70.
Rethinking conservation priorities for reefs
The study’s data were integrated into a model that predicts the frequency of heat-tolerant genotypes across reefs based on marine heatwave data. With this model, the authors found that climate refugia, regions expected to escape major climate impacts, were strongly depleted in heat-adapted genotypes.
In contrast, reefs that have already experienced heatwaves harbor more adaptive traits, and conservation efforts should also focus on protecting these areas to maintain the genetic diversity that can make coral reefs more resilient to future warming.
These are just some examples of how NGS allows tracking individual species and whole communities at large spatial and temporal scales. Further improvements in sequencing technologies and the integration of other omics will broaden the picture of how ecosystems work, and how we can support them.
About the author: Nuria M. Wentzien got her Ph.D. from the University of Granada in 2023. After finishing her Ph.D., she discovered that science communication brings together her two favorite worlds: science and writing. Her career reflects her passion for learning and exploring new topics, from a Bachelor's degree in Biochemistry (with a strong focus on human sciences) to a Ph.D. in sustainable agriculture. She brings this same curiosity to every project, making readers feel as inspired by science as she does. Now dedicated to helping life-science companies communicate rigorous science in an engaging way, she is the co-founder of Helixa Communications.