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UCYN‐A3, a newly characterized open ocean sublineage of the symbiotic N2‐fixing cyanobacterium Candidatus Atelocyanobacterium thalassa

Cornejo‐Castillo, Francisco M., Muñoz‐Marín, Maria del Carmen, Turk‐Kubo, Kendra A., Royo‐Llonch, Marta, Farnelid, Hanna, Acinas, Silvia G., Zehr, Jonathan P.
Environmental microbiology 2019 v.21 no.1 pp. 111-124
Cyanobacteria, Haptophyta, genes, genetic variation, hosts, metagenomics, nitrogen, nitrogen fixation, nitrogenase, nucleotide sequences, oceans, plankton, quantitative polymerase chain reaction, ribosomal RNA, surveys, symbiosis, Hawaii
The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN‐A) is one of the most abundant and widespread nitrogen (N₂)‐fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN‐A1, UCYN‐A2, UCYN‐A3 and UCYN‐A4. However, very little is known about UCYN‐A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD‐FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN‐A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN‐A3 sublineage. We designed new CARD‐FISH probes that allowed us to distinguish and observe UCYN‐A2 in a coastal location (SIO Pier; San Diego) and UCYN‐A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN‐A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN‐A3 symbiosis in open ocean waters suggesting that the different UCYN‐A sublineages are distributed along different size fractions of the plankton defined by the cell‐size ranges of their prymnesiophyte hosts.