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PLoS One. 2016 May 19;11(5):e0155757. doi: 10.1371/journal.pone.0155757. eCollection 2016.

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Author information

1
Department of Molecular Genetic and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Casilla 114-D, C.P. 651 3677, Santiago, Chile.
2
Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Box 1031, 171 21 Solna, Sweden.
3
Center for Climate Change and Resilience Research (CR)2, Santiago, Chile.
4
BILS/Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50003, SE-10405, Stockholm, Sweden.
5
Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA 92037, United States of America.
6
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States of America.
7
Informatics Group, J. Craig Venter Institute, San Diego, CA 92037, United States of America.
8
Informatics Group, J. Craig Venter Institute, Rockville, MD 20850, United States of America.
9
Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47401, United States of America.

Abstract

Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

PMID:
27196065
PMCID:
PMC4890579
DOI:
10.1371/journal.pone.0155757
[Indexed for MEDLINE]
Free PMC Article

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