Checking out the Molecular Barcodes of Loricate Choanoflagellates

In recent years, a sharp increase in the capacity of high throughput DNA sequencing (HTS) has been met with a concomitant decrease in its cost (Caporaso et al, 2012). As a result, vast databases of marine microbial metagenomes and -barcodes have been gathered from research cruises across the global oceans. One such cruise was the Tara Oceans expedition (2009-2013), which sampled 210 oceanic stations. Like other HTS studies, Tara Oceans revealed swathes of OTU molecular barcodes unidentified at high taxonomic resolutions. This problem highlights a key issue in the HTS age of marine microbiology: the paucity of curated sequences coupled to morphological and taxonomic descriptions. Nitsche and colleagues (2016) set out to remedy this problem, by creating a database of curated rDNA barcodes from acanthoecid (loricate) choanoflagellates. Unlike their naked cousins, acanthoecid choanoflagellates are strictly marine and synthesise a complex, silica lorica with species-specific morphology. As abundant bacterivorous nanoflagellates, choanoflagellates can too have a considerably effect on marine carbon flow. Therefore, the ecological importance and well-defined morphology of this group make the acanthoecid choanoflagellates good candidates as a proof of concept to resolve the identity of unknown HTS barcodes.

Although 115 species of this group have been described, <10% of them have been sequenced. Therefore, the authors collected choanoflagellates from Danish coastal waters and manipulated mixed cultures at the single cell level, to characterise both lorica morphology and ribosomal DNA sequence. Their curated findings supplemented and re-described previous species characterisations, which covered 45 morphospecies. For the first time, 9 species and 5 genera were characterised at the barcode level. The authors used their sequences to mine the Tara Ocean database for acanthoecid V9 barcodes and make a startling discovery – that one of their characterised species (Calliacantha natans) represented the second most abundant choanoflagellate in the global oceans, which was previously unidentified. This study, with relatively little effort, doubled the curated sequence database of this potentially biogeochemically important clade and showed that locally collected choanoflagellates from Danish waters have a global distribution and abundance.

On the surface, this study is taxonomically dense and offers little to those not passionately interested in details of acanthoecid classification. However, this study acts as a proof of concept to stress the importance of curating large HTS databases. The identification of the second most globally abundant choanoflagellate from the Tara Oceans is a big achievement and, while monocultures were not achieved by this study, I believe a fascinating next step would be to isolate C. natans and explore its cell biology and trophodynamics in the lab. This could yield real insights into global marine carbon flow. As well as this, I think a great candidate for future work of this type would be the tintinnid ciliates, who share with the acnathoecids a distinct loricate morphology and global distribution (Dolan et al, 2012).

Overall this study is a small, but impressive, step forward into coupling morphological and HTS barcode data and offers a simple technique to answer some of the larger questions surrounding unidentified barcoded taxa.

Reviewed Paper: Nitsche, F., Thomsen, H. A., & Richter, D. J. (2016). Bridging the gap between morphological species and molecular barcodes− exemplified by loricate choanoflagellates. European Journal of Protistology. http://www.sciencedirect.com/science/article/pii/S0932473916301080

HTS: Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., ... & Gormley, N. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal, 6(8), 1621-1624. http://www.nature.com/ismej/journal/v6/n8/abs/ismej20128a.html

Tintinnids: Dolan, J. R., Montagnes, D. J., Agatha, S., Coats, D. W., & Stoecker, D. K. (Eds.). (2012). The biology and ecology of tintinnid ciliates: Models for marine plankton. John Wiley & Sons.