Morphology and DNA reveal diverse Antarctic coastal diatom communities

A field survey of 39 habitats at Potter Cove, King George Island, identified a rich and varied community of benthic diatoms in marine, brackish-water and freshwater environments. Researchers combined light and scanning electron microscopy, laboratory cultures and DNA metabarcoding, finding 165 morphological taxa and 238 infrageneric taxa across the combined morphological and molecular records. The study, conducted during the austral summer of 2020, also produced 162 clonal cultures representing 60 taxa, including 54 taxa sequenced for the first time.

Together, these methods exposed diversity that each approach alone could not fully capture. Benthic diatoms are photosynthetic microorganisms that live on sediments, rocks and sea ice in Antarctic coastal zones. They function as primary producers, provide food and organic matter to other organisms, influence elemental fluxes at the sediment-water interface and stabilize sediment surfaces by producing sticky extracellular polymeric substances.

Their assemblages can also serve as bioindicators because they respond rapidly to environmental pressures and occur widely in aquatic systems. Despite their ecological importance, detailed information on Antarctic marine benthic diatom diversity has remained limited, while freshwater Antarctic floras have received considerably more attention. Its combination of glacier fronts, rocky shores and broad areas of soft sediment creates many distinct habitats for attached diatom communities.

The researchers sampled 17 littoral sites, 14 marine sites reached by scuba divers to depths of as much as 20 metres, and eight freshwater sites associated with glacial runoff or drinking-water reservoirs. At each location, they collected a composite sample along an approximately 10-metre transect, scraping biofilm from three or four stones or taking the upper layer from three or four sediment cores. Each composite sample was divided for microscopic examination, culturing and DNA metabarcoding.

For morphological analysis, the team prepared permanent slides and counted at least 400 diatom frustules per environmental sample under light microscopy, while scanning complete slides for rare taxa. The counted samples contained 142 taxa, including 50 identified to genus level and 88 to species level; individual samples contained between two and 52 taxa, with an average of 20. A further 23 taxa were detected during exhaustive slide scans, 11 of which could be assigned unambiguously to species.

These observations produced the study’s total morphological inventory of 165 taxa across environmental samples and cultures. Marine samples contained 116 taxa, freshwater samples 93 and brackish-water samples 21. Community composition differed markedly among environments.

Navicula cf. perminuta accounted for an average 51.8 percent of the counted abundance in marine samples, while Navicula gregaria represented 52.3 percent in brackish water. Freshwater assemblages were distributed among a broader set of taxa, including Nitzschia annewillemsiana, Nitzschia kleinteichiana and Mayamaea sweetloveana. The three analytical approaches agreed on broad patterns in community structure: statistically significant differences were detected among water types and between rock and sediment substrates.

Non-metric multidimensional scaling showed clear separation of marine and freshwater samples, while brackish-water communities were more similar to freshwater communities. PERMANOVA reported significant effects of water type for light microscopy, rbcL and 18S V4, with p = 0.001 in each analysis, and significant effects of substrate for all three inventories, also with p = 0.001. DNA metabarcoding recovered many sequence variants that were absent from the morphological inventory, but also showed where reference data and primer choice limited identification.

The Illumina MiSeq run generated 7,460,203 raw reads for rbcL and 5,623,490 for 18S V4. After processing, quality filtering, chimera removal, contamination control and aggregation of technical replicates, the datasets retained 7,381,429 rbcL reads assigned to 1,041 amplicon sequence variants and 5,570,517 18S V4 reads assigned to 2,251 variants. Of the rbcL variants, 810 belonged to diatoms, as did 1,439 of the 18S V4 variants.

The rbcL data yielded 92 species-level assignments and the 18S V4 data yielded 82, but many variants could be assigned only to genus, particularly in marine samples. The methods shared 34 genera, while 11 were found only by morphology and 23 only by metabarcoding. At the infrageneric level, 33 taxa were detected by all three approaches, 111 only morphologically and 73 only by metabarcoding.

The molecular inventories generally recorded higher richness and Shannon diversity than light microscopy. Average Shannon diversity was 1.46 for microscopy, 1.94 for rbcL and 1.85 for 18S V4. These values do not mean that sequencing directly counted more living cells: several distinct sequence variants can be assigned to the same taxon, and gene copy number varies with cell size and chloroplast number.

Environmental DNA can also persist in sediment, so a detected sequence may represent a resting stage, a dead-cell trace or DNA transported from the water column rather than an active local population. Culturing supplied the link between molecular sequences, physical form and formal taxonomic names. The researchers isolated single cells and maintained them in three culture media at salinities adjusted for marine and brackish samples.

The 162 resulting cultures represented 60 taxa: 33 could be identified to species level, 23 to genus level and four had inconclusive genus affiliations. Only six of the cultured taxa already had sequence records in the international nucleotide databases, making 54 newly sequenced taxa. By pairing cultures with light and electron microscopy, herbarium vouchers and rbcL and 18S V4 barcodes, the project created a regional reference collection.

Its new sequences enabled 47 taxa to be assigned in the environmental metabarcoding dataset that could not have been matched using the previously available public records. Some taxa recovered only through culturing also demonstrated the practical limits of examining preserved valves alone. Lunella sp., for example, has very small, lightly silicified valves without visible ornamentation under light microscopy and may be overlooked or damaged during slide preparation.

Its living cells could be detected in enrichment culture. In contrast, conspicuous microscopic taxa such as a Gyrosigma species and Pteroncola carlinii were underrepresented in the molecular inventories because their barcode references were unavailable. Cocconeis was poorly represented in the rbcL data despite its high morphological diversity, prompting the authors to suggest that the rbcL primer may amplify some marine Cocconeis species inefficiently.

Overall, rbcL assignments more closely matched the composition obtained by microscopy than did the 18S V4 assignments. The resulting slides, cultures, voucher specimens and sequence data constitute what the authors describe as the most extensive biodiversity dataset yet assembled for marine benthic diatoms in Western Antarctica. Its immediate use is as a baseline: it documents communities across a single summer sampling campaign, identifies taxa requiring formal taxonomic study and provides curated links between names, specimens and DNA barcodes.

Repeated sampling with these resources could help evaluate future changes in Antarctic coastal communities, but the present study did not track temporal change and does not establish a climate-driven trend. Its broader methodological finding is that morphological identification, culturing and metabarcoding provide complementary evidence. Microscopy remains essential for observing physical abundance and fine structure, cultures anchor sequences to vouchers, and metabarcoding can reveal rare, delicate or cryptic diversity that conventional counts miss.

Subject of Research: Benthic diatom diversity across marine, brackish and freshwater habitats in Potter Cove, West Antarctica

Article Title: Exploring benthic diatom diversity in the West Antarctic Peninsula: insights from a morphological and molecular approach

Article References: Schimani, K., Abarca, N., Skibbe, O., Mohamad, H., Jahn, R., Kusber, W.-H., Campana, G. L., & Zimmermann, J. (2023). Exploring benthic diatom diversity in the West Antarctic Peninsula: insights from a morphological and molecular approach. Metabarcoding and Metagenomics, 7, Article e110194. https://doi.org/10.3897/mbmg.7.110194

Image Credits: AI Generated

DOI: 10.3897/mbmg.7.110194

Keywords: Antarctic diatoms, DNA metabarcoding, benthic biodiversity, Potter Cove, King George Island, West Antarctic Peninsula, light microscopy, diatom cultures, barcode reference library, microbial ecology, Exploring, benthic