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closeUCYN-A symbiosis
Posted by jzehr on 24 Jan 2018 at 20:40 GMT
This manuscript shows beautiful images of the haptophyte which is not, but is related to Braarudosphaera bigelowii, that harbors the nitrogen-fixing symbiont UCYN-A. However, the image of the proposed Prochlorococcus cell is very similar to the images of UCYN-A itself based on atomic force microscopy, nanoSIMS and FISH (and size from flow cytometry). The identification as Prochlorococcus is based only on parallel sequencing of sorted cells, and Prochlorococcus cells would be the same size as the UCYN-A cell. Since the Prochlorococcus cells were not confirmed by FISH or any other means at the cellular level, perhaps the cells are UCYN-A?
RE: UCYN-A symbiosis
mzubkov replied to jzehr on 26 Jan 2018 at 13:37 GMT
Unfortunately, Jon Zehr’s critical comment provides no alternative explanation for the presence of Prochlorococcus sequences in our next generation sequencing data.
The targeted algal cells were tightly gated using 4 cytometric parameters to maximize flow sorting purity. Therefore, the 3 dominant microbes, molecularly identified as the haptophyte, Prochlorococcus and UCYN-A, were sorted as a single particle. Because Prochlorococcus are free living cyanobacteria their only association with the haptophyte should be a result of predation. As other prymnesiophytes (e.g. Parke et al JMBA 1955) the sorted haptophyte should phagocyte prey by its cytostome. Therefore, the cell found in the haptophyte cytostome is Prochlorococcus, whilst the UCYN-A cell is the endosymbiont. Among the reported images of haptophyte-UCYN-A associations, the only high-resolution observation is by TEM, which conclusively shows UCYN-A as an intracellular symbiont (panel i on the image https://www.nature.com/ar...).
RE: RE: UCYN-A symbiosis
jzehr replied to mzubkov on 26 Jan 2018 at 22:42 GMT
Very interesting observations regardless!
For readers: "panel i" referred to in Mikhail's comment is from Japanese coastal waters, is calcified and is UCYN-A2. The endosymbiont was not identified as UCYN-directly by microscopy in that study (Hagino et al.), but by sequencing. It probably is the symbiont, but UCYN-A2 is so different from UCYN-A1 that it may be irrelevant. The calcified UCYN-A in that study (and referred to in panel i) might be a short life stage of UCYN-A2 (it is only found at one time of year) which is larger than UCYN-A1 and not really comparable to the oceanic forms addressed by this study in the tropical Atlantic.
In contrast to panel i mentioned in the reply to my comment, readers, please look at Panels d,e, g and j in the Nature Microbiology 2016 figure. These are UCYN-A1 (or the closely related UCYN-A3) which are typical oceanic UCYN-A and have been found by sequencing, qPCR, FISH and nanoSIMS in this region.
It is certainly not clear where the Prochlorococcus sequences come from! I would run a negative control bead sort to make sure there is not free DNA from the abundant Prochlorococcus. Perhaps a more likely explanation is that Prochlorococcus IS grazed, and the DNA ends up inside the host. But the feature shown in this study is exactly the same abundance (85% cells intact with UCYN-A cells that look like those reported in this paper), shape and position of UCYN-A bodies shown by multiple FISH studies.
RE: RE: RE: UCYN-A symbiosis-Explanation for presence of Prochlorococcus sequences
jzehr replied to jzehr on 27 Jan 2018 at 15:54 GMT
Probably the simplest explanation for Prochlorococcus sequences is the presence of other picoeukaryotes in the sort (16% according to this paper). We have never been able to get a pure population by Flow cytometry sorting: there is just nothing to distinguish the Braarudosphaera-like cells from the others in that class. Just a few of them being grazers would generate the observed 16S rRNA Prochlorococcus sequences seen in this study.
This is the problem of doing parallel analysis of sequences and individual cell analyses. It has to be done by single cell sorting. We have analyzed many single cells for DNA. We do not find Prochlorococcus sequences associated with single Braarudosphaera-like cells that DO contain UCYN-A and Braarudosphaera-like genomes.