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Phylogenetic and Gene Expression Analysis of Cyanobacteria and Diatoms in the Twilight Waters of the Temperate Northeast Pacific Ocean

  • Environmental Microbiology
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Abstract

In this study, to explore the microbial community structure and its functionality in the deep-sea environments, we initially performed a 16S ribosomal RNA (rRNA)-based community structure analyses for microbial communities in the sea water collected from sites of 765–790 m in depth in the Pacific Ocean. Interestingly, in the clone library we detected the presence of both photoautotrophic bacteria such as cyanobacteria and photoheterotrophic bacteria, such as Chloroflexus sp. To further explore the existence and diversity of possible light-utilizing microorganisms, we then constructed and analyzed a 23S rRNA plastid gene cloning library. The results showed that the majority of this cloning library was occupied by oxygenic photoautotrophic organisms, such as diatoms Thalassiosira spp. and cyanobacterium Synechococcus sp. In addition, the diversity of these oxygenic photoautotrophic organisms was very limited. Moreover, both reverse-transcription PCR and quantitative reverse-transcription PCR approaches had been employed to detect expression of the genes involved in protein synthesis and photosynthesis of photoautotrophic organisms, and the positive results were obtained. The possible mechanisms underlying the existence of very limited diversity of photosynthetic organisms at this depth of ocean, as well as the positive detection of rRNA and mRNA of diatom and cyanobacteria, were discussed.

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Acknowledgements

We would like to thank the crew of the R/V Thompson TN221 Research Cruise with chief scientists Dr. John Delaney and Dr. Deborah Kelley of the University of Washington, and Dr. Joseph Shih-Hui Chao and Dr. Cody Youngbull from the Center for Biosignatures Discovery Automation in the Biodesign Institute at Arizona State University (ASU) for their help with the water sampling. We also thank ASU for the support of this research.

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  1. Center for Biosignatures Discovery Automation, the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-6501, USA

    Weimin Gao, Xu Shi, Jieying Wu, Yuguang Jin, Weiwen Zhang & Deirdre R. Meldrum

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  1. Weimin Gao
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  2. Xu Shi
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  3. Jieying Wu
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Correspondence to Weiwen Zhang.

Electronic Supplementary Materials

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Supplementary Figure 1

Phylogenetic analysis of Archaea belonging to the uncultured marine group I Crenarchaeote found in the deep-sea water (PPT 93 kb)

Supplementary Figure 2

Phylogenetic analysis of bacteria found in the deep-sea water (PPT 88 kb)

Supplementary Figure 3

Rarefaction analysis of Archaea marine group I clones (3A) and 23 rRNA clone library (3B) (PPT 80 kb)

Supplementary Table 1

A summary of phylogeny affiliation of bacterial clones (DOC 37 kb)

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Gao, W., Shi, X., Wu, J. et al. Phylogenetic and Gene Expression Analysis of Cyanobacteria and Diatoms in the Twilight Waters of the Temperate Northeast Pacific Ocean. Microb Ecol 62, 765–775 (2011). https://doi.org/10.1007/s00248-011-9891-y

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