Metabarcoding Applications in Phytoplankton Diversity

Metabarcoding has emerged as a transformative tool for assessing phytoplankton diversity across freshwater and marine systems. By coupling high-throughput sequencing of taxonomic markers with robust bioinformatic pipelines, researchers can bypass the limitations of traditional microscopy and rapidly characterise community composition at fine taxonomic resolution. This approach has revealed previously undetected pico- and nano-phytoplankton, uncovered cryptic lineages and highlighted the ecological roles of mixotrophic flagellates. Quantitative applications have matured through the development of gene copy-number correction factors, enabling more accurate estimations of relative biomass and cell abundance. Concurrently, hybrid strategies that integrate morphological counts with molecular readouts are yielding complementary insights into both taxonomic richness and ecosystem function. Metabarcoding surveys now inform on seasonal succession, spatial gradients and biogeographical patterns, underpinning monitoring programmes for water quality, bloom dynamics and carbon cycling. As reference databases expand and analytical standards coalesce, metabarcoding is poised to become a routine component of global phytoplankton observation networks, offering unprecedented resolution of taxa that drive primary productivity and biogeochemical fluxes in aquatic environments.

Research from Nature Portfolio

Recent studies have applied DNA metabarcoding across ocean basins to compare diversity patterns of diatoms and haptophytes, revealing that diatom communities tend to be dominated by a few rapidly growing genera, whereas haptophytes exhibit rich genus-level diversity and potential for mixotrophy. Basin-scale analyses demonstrated how distinct ecological strategies underlie contrasting biogeographical distributions, linking nutrient uptake kinetics to community assembly. These findings establish a global framework for interpreting phytoplankton diversity in relation to ecological traits and oceanographic gradients.

Research from all publishers

In estuarine environments, metabarcoding of the Elbe estuary highlighted the prevalence of centric diatoms but also revealed that microscopy underestimates flagellates and picophytoplankton with mixotrophic capabilities. Seasonal and spatial patterns of key taxa were shown to align with environmental forcing, while quantitative biases arising from gene copy variation were emphasised. A separate study introduced a gene-copy-number correction factor for major protist groups, substantially improving estimates of cell abundance and biomass in coastal plankton samples, and pointing to remaining challenges for diatoms due to high biovolume plasticity. In freshwater systems, the combined use of morphological and metabarcoding methods across multiple lakes enhanced detection of rare and cryptic taxa, with metabarcoding uncovering over three times more operational taxonomic units than microscopy alone. Such integrative approaches have demonstrated that the strengths of each method can be harnessed to deliver more comprehensive assessments of community structure and environmental change.

Metabarcoding Applications in Phytoplankton Diversity publication trend

The graph below shows the total number of articles in metabarcoding applications in phytoplankton diversity across all publications each year (not limited to Nature Index journals).

Technical terms

Metabarcoding: High-throughput sequencing of taxonomic marker genes to profile entire communities from environmental samples.

Operational taxonomic unit (OTU): A cluster of closely related sequences used as a proxy for species or taxonomic groups.

18S rRNA gene: A widely used molecular marker for eukaryotic diversity surveys due to its conserved and variable regions.

Gene copy-number bias: Variation in the number of marker gene copies per genome that can distort relative abundance estimates.

Mixotrophy: A nutritional mode combining photosynthesis and heterotrophic feeding within a single organism.

Amplicon: A DNA fragment generated by PCR amplification of a targeted genomic region for sequencing.

References

1. Metabarcoding reveals potentially mixotrophic flagellates and picophytoplankton as key groups of phytoplankton in the Elbe estuary. Environmental Research (2024).
2. Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean. Scientific Reports (2018).
3. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics (2022).
4. Combining morphological and metabarcoding approaches reveals the freshwater eukaryotic phytoplankton community. Environmental Sciences Europe (2020).