Genetic and Microscopic Methods Tell the Same Story of Beach Nourishment Damage

Every five years, the tourist beach of Ahrenshoop on Germany’s Baltic Sea coast undergoes a dramatic transformation. Between late October 2021 and mid-February 2022, more than 650,000 cubic metres of sand were pumped from an offshore deposit onto a nearly four-kilometre stretch of shoreline, widening the beach by up to 40 metres and reinforcing the dunes behind it. The operation is a textbook example of sand nourishment, one of the most widely used and cost-effective coastal protection measures in the face of rising seas and intensifying storms. But what happens to the microscopic animals living between the sand grains when a metre-thick layer of new sediment buries their entire world?

A new study has now provided the most detailed answer yet for the non-tidal coasts of the Baltic Sea, and the findings carry a twist that could change how coastal ecosystems are monitored worldwide. Researchers from the Senckenberg research institute and their collaborators monitored meiofauna communities at the beach-water interface of Ahrenshoop before the nourishment and for a full year afterwards, using two fundamentally different approaches: traditional morphological identification and counting of the animals under the microscope, and whole-community metabarcoding, a high-throughput genetic technique that reads DNA from entire samples. Remarkably, both methods told the same story, a consistency that is far from guaranteed in this field.

Meiofauna are the animals of the marine sediment in the size class between 32 and 1000 micrometres. They include nematodes, harpacticoid copepods, flatworms, gastrotrichs, mites, tardigrades, rotifers and segmented worms, among others. They are the most abundant metazoans in the marine benthos and play a crucial role in benthic food webs. Unlike many larger organisms, they have no pelagic larval stages; their entire life cycle is bound to the sediment. Their diminutive size makes them readily transported by currents when wave action resuspends them, and changes in their community composition are widely used as bioindicators of ecosystem disturbance, including anthropogenic impacts.

The study team established six sampling stations along the beach. Five lay within the nourished zone, from the boundary of a nature reserve in the northeast to just north of a breakwater, while an unaffected reference station south of Ahrenshoop served as a control. Sampling took place at four dates: September 2021 before the nourishment, March 2022 directly after its completion, September 2022, and March 2023. At each station, researchers inserted Plexiglass cores vertically into the sediment down to 15 centimetres and sliced them into three five-centimetre layers, preserving the material in ethanol for later analysis.

The genetic approach was ambitious in scale. A total of 198 meiofauna samples and 23 negative controls were filtered, dried, and processed for DNA extraction using a soil kit. The researchers amplified two hypervariable regions of the 18S rDNA gene and sequenced the products on an Illumina MiSeq platform. The sequencing run produced over 1.1 million reads, of which nearly 737,000 were non-chimeric and classified into 3427 amplicon sequence variants. After taxonomic filtering to retain only true marine meiofauna, the meiofauna variants clustered into 843 operational taxonomic units at a three percent genetic distance cut-off. Rigorous quality controls, including bleach washing of all equipment and blank samples introduced during filtering, ensured that no sequences remained in the negative controls.

The morphological approach, though applied to a subset of four stations, counted 27,445 individuals across ten higher taxa. Copepods and nematodes dominated the community overall, together accounting for over half of all individuals counted. The results were stark. Before the nourishment, copepods reached abundances of up to 805 individuals per 10 square centimetres at a single station. Directly after the impact, they were almost absent from the nourished zone, with maximum counts dropping to fewer than 23 individuals in the same area. Copepod nauplii, the larval stages, vanished entirely from the impacted stations. Marine mites of the family Halacaridae and small annelids nearly disappeared, while flatworms increased dramatically, peaking at over 350 individuals per 10 square centimetres.

The metabarcoding data mirrored these patterns with striking fidelity. Before the nourishment, mites and annelids were represented by tens of thousands of reads in the impacted zone; after the impact, both groups were almost absent. Copepoda reads dropped from over 20,000 to fewer than 10,000, while flatworms surged to over 124,000 reads, becoming the dominant group. Statistical analyses confirmed the visual impression. An Analysis of Similarities on the metabarcoding data yielded a highly significant global R value of 0.712, indicating that community composition differed substantially among sampling dates, with the greatest pairwise differences between the pre-impact and post-impact samples. The morphological data produced an equally significant result with a global R of 0.516, and the same pattern of greatest differences immediately after the nourishment.

Recovery was underway but incomplete. By September 2022, six months after the nourishment ended, copepods had re-established themselves in the impacted zone, and annelids were again detected, though their relative abundance did not reach pre-nourishment levels. Mites, however, were never found again during the remainder of the study except for a few reads at one station. By March 2023, one year after the impact, nematode reads were mostly higher than at other dates, and the community had developed towards its pre-impact state, but the composition of the different sampling dates remained distinct throughout the monitoring period and never fully reverted to the original state. The researchers attribute this to the relatively short monitoring period, the substantial quantity of nourished sediment, or a potential mismatch in grain size between the added sand and the original beach material.

The consistency between the two methods is the study’s most consequential finding. In marine meiofauna research, morphological and metabarcoding approaches frequently produce divergent results, with genetic analyses typically revealing higher diversity than microscopy because they can detect juvenile stages, damaged specimens, and species lacking distinctive morphological features. Challenges such as primer inefficiency, variable PCR success, and gaps in publicly available reference barcodes have been identified as key obstacles. The researchers suggest that the low diversity of the studied beach community may have facilitated the alignment of the two methods, since fewer taxa meant fewer opportunities for discrepancy.

The implications extend beyond the Baltic. Sand nourishment is a global phenomenon, from the North Sea coasts of the Netherlands and Germany to the Gold Coast of Australia, and meiofauna are frequently neglected in marine monitoring despite their value as indicator organisms. The study recommends that after initial assessments employing both methods in parallel, metabarcoding alone may be considered for comparable sites and situations, provided that a subset of morphological samples is retained for validation, barcode library construction, and future quantification efforts. Standardised protocols, including the use of ethanol rather than formalin as a preservative, consistent sieve sizes, and uniform extraction methods, are essential to ensure that genetic and microscopic results remain comparable. As climate change accelerates erosion and sea-level rise along the world’s sandy shores, the ability to rapidly and reliably assess the ecological cost of coastal defence has never been more urgent.

Subject of Research: Coastal Ecology and Molecular Biodiversity Monitoring

Article Title: Impact of a coastal protection measure on sandy-beach meiofauna at Ahrenshoop (Baltic Sea, Germany): results from metabarcoding and morphological approaches are similar

Article References: Kapshyna, I., Veit-Köhler, G., Hoffman, L., & Khodami, S. (2024). Impact of a coastal protection measure on sandy-beach meiofauna at Ahrenshoop (Baltic Sea, Germany): results from metabarcoding and morphological approaches are similar. Metabarcoding and Metagenomics, 8, Article e127688. https://doi.org/10.3897/mbmg.8.127688

Image Credits: AI Generated

DOI: 10.3897/mbmg.8.127688

Keywords: meiofauna, sand nourishment, metabarcoding, Baltic Sea, coastal protection, beach ecology, environmental DNA, biodiversity monitoring, Impact, coastal, protection, measure