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

Abstract

Summary 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.

Unexpected presence of the nitrogen‐fixing symbiotic cyanobacterium UCYN‐A in Monterey Bay, California

“…The images show that the size of Braarudosphaera bigelowii is larger (ca. 20 µm) than previous reports (5-10 µm) as well as the size of the UCYN-A2 cyanobacteria cell, approximately 7 µm in diameter (Thompson et al 2014, Cornejo-Castillo et al 2019. As CARD-FISH hybridizations require active cells with many rRNA molecules, these images also verify that these cells were alive and active.…”

“…It has been hypothesized that UCYN-A2 is a coastal strain or ecotype that sometimes co-occurs with UCYN-A4, while UCYN-A1 and UCYN-A3 are open ocean strains (Turk-Kubo et al 2017). However, UCYN-A1 and UCYN-A2 have been reported to co-occur in coastal waters in the Southern California Bight (Needham et al 2018), the Scripps Pier (Thompson et al 2014, Cornejo-Castillo et al 2019, in the Western Tropical South Pacific (Turk-Kubo et al 2015, Messer et al 2016, Henke et al 2018, Stenegren et al 2018, and in the Bering Sea off Nome, Alaska (Harding et al 2018; Fig. 1).…”

“…In order to visualize the UCYN-A/prymnesiophyte symbiosis detected at the SCMW, a CARD-FISH sample (100 mL of seawater fixed with formaldehyde at 1.8% final concentration) was collected in September 2018 and filtered onto a 0.6 µm pore-size polycarbonate filter. The UCYN-A2 association was targeted using a double CARD-FISH hybridization with specific probes UCYN-A2-732 and UBRADO69 and competitors as described elsewhere (Cabello et al 2016, Cornejo-Castillo et al 2019. Samples were inspected under epifluorescence on a Leica DM500B epifluorescence microscope (University of California, Santa Cruz Life Sciences Microscopy Center) and micrographs were taken under ultraviolet (DAPI signal of the nucleus), blue (green labeled host with Alexa 488 stain), and green (red labeled UCYN-A with Cy3) excitation wavelengths using LAS X 3.6 software.…”

“…In the present study, we examine diazotroph diversity based on the nifH gene over an 8-year time-period (2011-2018) at a near-shore station located at the Santa Cruz Municipal Wharf in MB, and report for the first time the presence of the cyanobacterium UCYN-A. Prior to this study, UCYN-A had been reported in several regions of the Southern California Bight, including the San Pedro Ocean time-series (SPOT; Hamersley et al, 2011), Catalina Island (Needham et al 2018), and the Scripps Institute of Oceanography pier (SIO, La Jolla/San Diego; Thompson et al 2014, Cornejo-Castillo et al 2019, but it was not previously detected in the nifH surveys of MB (Turk-Kubo et al 2017). Our findings show that UCYN-A assemblages in coastal MB waters are mainly dominated by the UCYN-A2 sublineage, have seasonal patterns in abundance, and were detected much more frequently and at higher abundances when climatological conditions in the MB shifted from cold to warm.…”

Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments

“…The haptophyte provides photosynthetically fixed C to UCYN-A in exchange for N supplied by UCYN-A from N 2 fixation [ 7 ]. Two genetically distinct UCYN-A symbionts, UCYN-A1 and UCYN-A2, have similarly streamlined genomes [ 9 ], but are associated with morphologically and physiologically distinct haptophyte hosts [ 10 , 11 ].…”