New genome of a Chlorella-like microeukaryote from permanently stratified Meromictic Lake Cadagno

Meromictic Lake Cadagno, situated at 1921m altitude,  features a persistent microbial bloom at an oxic-anoxic boundary known as the chemocline. The chemocline separates the upper oxic and lower sulfur-rich anoxic zone.
Published in Microbiology
New genome of a Chlorella-like microeukaryote from permanently stratified Meromictic Lake Cadagno
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Meromictic Lake Cadagno, situated at 1921m altitude,  features a persistent microbial bloom at an oxic-anoxic boundary known as the chemocline. The chemocline separates the upper oxic and lower sulfur-rich anoxic zone. Our story revisits the finding of Milucka et al. published in ISMEJ in 2015, which hypothesized the coupling of in situ oxygen production by photosynthetic algae and diatoms with methane-oxidizing bacteria in the chemocline. However, what was lacking was robust information on the identity of oxygenic phototrophs present in the chemocline. So, which microbial species supply in situ oxygen, given that the oxygen availability is limited in the zone of chemocline? This was one of the intriguing questions for the microbiology of Meromictic Lake Cadagno. 

Schematic of Meromictic Lake Cadagno water column

Previous studies reported cyanobacteria associated with oxygen production in the chemocline (Danza et al. 2018; Luedin et al. 2019). However, these studies used flow cytometry to identify cyanobacteria, and information on the cyanobacterial species was lacking. Thus, 16S gene amplicon sequencing was used to learn more about the cyanobacterial species. This was one of the main aims of our study, to focus on the bacterial population. Nonetheless, our research shifted towards microbial eukaryotes when cyanobacteria were found to be rare, but chloroplasts were abundant in the chemocline (Saini et al. 2022). Yes! You read it right, 16S bacterial gene amplification hinted at the presence of eukaryotes. Indeed these surprising findings led us to use metagenomics to identify eukaryotic phytoplankton present in Lake Cadagno. However, our journey was not easy, as assembling a eukaryotic genome from a metagenomic dataset is known to be a daunting task, and a workflow needs to be constructed. 

Metagenomics pipeline to study microbial eukaryotes

Fortunately, we separated the eukaryotic metagenome-assembled genome (MAG) from the hundreds of bacterial MAGs. After spending months crafting, we presented the first high-quality genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno. Our team provisionally named this genome Chlorella-like MAG, as it belongs to the genus Chlorella according to taxonomic and phylogenomic analyses. However, there is no well-established system for naming novel microbial eukaryotes identified using metagenomics. We hope some nomenclature system will soon be applied to eukaryotes to help researchers name species identified using sequencing approaches. 

The metabolic potential predicted from its genomic information offered a better understanding of the role of microeukaryotes in carbon, sulfur, and nitrogen metabolism in the chemocline of Lake Cadagno. Not only was this new microeukaryote well equipped for in situ oxygen production for phototrophic sulfur bacteria, but it also had the potential to metabolize sulfur and nitrogen in the chemocline. One thing seems to be likely, ongoing cooperation between microeukaryotes and phototrophic sulfur bacteria in meromictic Lake Cadagno, and this made it to the title of the study. 

https://www.nature.com/articles/s41396-023-01396-y

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