Biology subjects

Janse, M.

Publications and source records attributed to Janse, M..

3 recordsLinked to original sources

bioRxiv2023

Biocalcification in porcelaneous foraminifera

Living organisms control the formation of mineral skeletons and other structures through biomineralization. Major phylogenetic groups usually consistently follow a single biomineralization pathway. Foraminifera, which are very efficient marine calcifiers, making a substantial contribution to global carbonate production and global carbon sequestration, are regarded as an exception. This phylum has been commonly thought to follow two contrasting models of either in situ "mineralization of extracellular matrix" attributed to hyaline rotaliid shells, or "mineralization within intracellular vesicles" attributed to porcelaneous miliolid shells. Our previous results on rotaliids along with those on miliolids in this paper question such a wide divergence of biomineralization pathways within the same phylum of Foraminifera. We found that both groups produced calcareous shells via the intravesicular formation of unstable mineral precursors (Mg-rich amorphous calcium carbonates) supplied by endocytosed seawater and deposited at the site of new wall formation within the organic matrix. Precipitation of high-Mg calcitic mesocrystals took place in situ and formed a dense, chaotic meshwork of needle-like crystallites. We did not observe deposition of calcified needles that had already precipitated in the transported vesicles, which challenges the previous model of miliolid mineralization. Hence, Foraminifera utilize less divergent calcification pathways, following the recently discovered biomineralization principles. Mesocrystalline chamber walls are therefore apparently created by accumulating and assembling particles of pre-formed liquid amorphous mineral phase within the extracellular organic matrix enclosed in a biologically controlled privileged space by active pseudopodial structures. Both calcification pathways evolved independently in the Paleozoic and are well-conserved in two clades that represent different chamber formation modes.

evolutionary biology↗

bioRxiv2021

High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA based techniques and especially environmental DNA (eDNA) metabarcoding is becoming a powerful monitoring tool. However, current approaches are based on genetic target regions <500 nucleotides, which offer limited taxonomic resolution. We developed a method for eDNA metabarcoding, based on nanopore sequencing of a longer amplicon, enabling improved identification of fish species. We designed a universal primer pair targeting a 2kb region of fish mitochondria, and compared it to the commonly used MiFish primer pair that targets only [~]170bp. In sillico and mock community testing showed that the 2kb fragments improved the accurate identification of genetically closely related species. eDNA was amplified, and sequenced using the Oxford Nanopore MinION in combination with the sequence read processing pipeline Decona. Analyzing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, but both approaches also identified unique species in the aquarium eDNA. Next, both primer pairs were used on multiple eDNA samples from the North Sea. Here, similar location specific fish communities were obtained from both approaches. More species were identified through the MiFish approach in the field samples. Interestingly, this difference was not observed in the aquarium, suggesting that 2kb fragment based metabarcoding potentially detects more recent occurrences of animals. This new method has the potential to improve and expand the molecular toolbox for eDNA based monitoring approaches.

molecular biology↗

bioRxiv2020

What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach

The unprecedented threats to coral reef ecosystems from global climate change (GCC) require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g.: GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential "single observer" effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.

genetics↗