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Research Article

Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium

  • Liang Ran equal contributor,

    equal contributor Contributed equally to this work with: Liang Ran, John Larsson

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • John Larsson equal contributor,

    equal contributor Contributed equally to this work with: Liang Ran, John Larsson

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • Theoden Vigil-Stenman,

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • Johan A. A. Nylander,

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • Karolina Ininbergs,

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • Wei-Wen Zheng,

    Affiliation: Biotechnology Research Center, Fujian Agriculture and Forestry University, Fuzhou, China

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  • Alla Lapidus,

    Affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

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  • Stephen Lowry,

    Affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

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  • Robert Haselkorn,

    Affiliation: Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America

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  • Birgitta Bergman mail

    bergmanb@botan.su.se

    Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden

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  • Published: July 08, 2010
  • DOI: 10.1371/journal.pone.0011486
  • Published in PLOS ONE

Reader Comments (1)

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Regarding genus assignment

Posted by Dimitra on 06 Sep 2010 at 15:12 GMT

First I would like to cordially congratulate my colleagues for their very interesting and important work. It is to my greatest pleasure that the genome of the Azolla cyanobiont is both available and so finely analyzed.

However, I would like to argue against renaming the cyanobiont genus to Nostoc instead of the original assignment to the genus Anabaena. Older and also more recent work conducted by myself and colleagues (Papaefthimiou et al. 2008a, 2008b) has shown the much closer relatedness of the Azolla cyanobiont to aquatic species of genus Anabaena. These findings are also supported by the fact that Azolla is actually an aquatic fern.
I strongly believe that it would be very important to include all available genomes from the Nostocaceae family to an eventual phylogenetic analysis that would resolve the taxonomic assignment of the Azolla cyanobiont.

I make this comment only for the best benefit of science and with the greatest respect for my former colleagues at the Department of Botany, Stockholm University.

Bibliography:
Papaefthimiou, D., Van Hove, C., Lejeune, A., Rasmussen, U., Wilmotte, A. 2008a. Diversity and host specificity of Azolla cyanobionts. Journal of Phycology, 44:1529-8817.

Papaefthimiou, Dimitra, Hrouzek, Pavel, Mugnai, Maria Angela, Lukesova, Alena, Turicchia, Silvia, Rasmussen, Ulla, Ventura, Stefano. 2008b. Differential patterns of evolution and distribution of the symbiotic behaviour in nostocacean cyanobacteria. Int J Syst Evol Microbiol 58: 553-564.

No competing interests declared.

RE: Regarding genus assignment

bergmanb replied to Dimitra on 10 Sep 2010 at 20:46 GMT


Thank you very much for your interest in our article and for your question. We are not sure about assigning the Azolla cyanobiont to the genus Nostoc. However, we are not convinced it should be assigned to Anabaena either. For lack of something better we chose Nostoc when the genome was to be submitted as this cyanobacterium is symbiotic - all other plant symbionts are ascribed to the genus Nostoc - and as the cyanobiont forms hormogonia, a character assigned to the genus Nostoc.
In addition, there are several conflicting reports on the phylogenetic identity of the cyanobiont of Azolla: Plazinski et al. 1990 reported it as being closer to Nostoc, while Baker et al. 2003 argue that is is neither Anabaena nor Nostoc while the studies by you and your colleagues suggest it to be closer to Anabaena. However, our phylogenetic analysis so far do indicate that the cyanobiont is not closer to either Nostoc nor Anabaena, but forms a sister-group to these two. In addition, we are basing our findings on a "core-gene-set" based on alignments of 400+ genes present in all genomes tested, while you used 16S+ITS and DGGE. There is no doubt that the "core-gene-set" is more revealing when it comes to reletedness between organisms.
Ultimately, the assignment to one or the other will depend on the type of phylogenetic analysis made. But the entire taxonomic cyanobacterial nomenclature, as it exists today, has difficulties fitting into the wealth of new genomic information. Work by Muriel Gugger at the Pasteur Culture Collection shows that none of the taxonomical groupings of cyanobacteria are completely coherent. With all due respect to the taxonomic classification that has been done already, some of the nomenclature used for cyanobacteria is merely confusing - not so much when examining the morphology, but surely much so at the genomic level. Hence, more cyanobacterial genomes need to be sequenced (especially filamentous species) to better resolve the cyanobacterial phylogenies. The Azolla cyanobiont may be neither Anabaena nor Nostoc, and these names may not be kept in the genomic era to come.

Bibliography:
Baker, J.A. et al. (2003) "The cyanobiont in an Azolla fern is neither Anabaena nor Nostoc." Fems Microbiology Letters 229(1): 43-47

Plazinski, J. et al. (1990) "DNA probes show genetic-variation in cyanobacterial symbionts of the Azolla fern and a closer relationship to free-living Nostoc strains than to free-living Anabaena strains." Applied and Environmental Microbiology 56(5):1263-1270

No competing interests declared.