Abstract
Biological N2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients. Diazotroph genome and transcript sequences were most abundant in the transitional waters compared with lower salinity or oceanic water masses. We were able to distinguish two genetically divergent phylotypes within the Hemiaulus-associated Richelia sequences, which were the most abundant diazotroph sequences in the data set. Photosystem (PS)-II transcripts in Richelia populations were much less abundant than those in Trichodesmium, and transcripts from several Richelia PS-II genes were absent, indicating a prominent role for cyclic electron transport in Richelia. In addition, there were several abundant regulatory transcripts, including one that targets a gene involved in PS-I cyclic electron transport in Richelia. High sequence coverage of the Richelia transcripts, as well as those from Trichodesmium populations, allowed us to identify expressed regions of the genomes that had been overlooked by genome annotations. High-coverage genomic and transcription analysis enabled the characterization of distinct phylotypes within diazotrophic populations, revealed a distinction in a core process between dominant populations and provided evidence for a prominent role for noncoding RNAs in microbial communities.
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Acknowledgements
This work was sponsored in part by the Gordon and Betty Moore Foundation (GBMF) Marine Investigator award (to JPZ), GMBF ROCA award (P Yager, PI), the UCSC Microbial Environmental, Genomics, Application, Modeling, Experimental, Remote sensing (MEGAMER) facility (supported by the GBMF) and the NSF Center for Microbial Oceanography: Research and Education (EF-0424599; to JPZ). We are very grateful to MA Moran, B Crump and J Paul for their assistance throughout this project and the writing of this report. We also thank D Bombar for comments on the manuscript, and I Shilova and J Robidart for technical help and discussions.
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Hilton, J., Satinsky, B., Doherty, M. et al. Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume. ISME J 9, 1557–1569 (2015). https://doi.org/10.1038/ismej.2014.240
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DOI: https://doi.org/10.1038/ismej.2014.240
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