Abstract
The bacterial terpenoid lipids known as hopanoids are fundamental tools for interpreting ancient microbial communities. Their degradation products, the hopanes, are found in sedimentary rocks throughout the geologic record. These compounds are presumed to be analogous to the sterols of eukaryotes, yet although the eukaryotic requirement for sterols is universal, hopanoid biosynthetic capacity is not ubiquitous among marine bacteria. Among the 9.8 million shotgun reads from the Sorcerer II Global Ocean Sampling (GOS) expedition, 148 contain putative coding sequence for bacterial squalene-hopene cyclases (SHCs). SHCs encoded by α-Proteobacteria potentially related to Rhodospirillaceae dominate these hits, especially in the open ocean and in tropical regions. Planctomycetes and β-Proteobacteria contribute more SHC-encoding sequences, and therefore presumably more hopanoid production, to coastal and temperate environments. Although sequences nominally related to α- and β-Proteobacteria outnumber other taxa in marine and coastal environments, there is large phylogenetic distance between GOS sequences and known species. Assuming that the environments sampled here are broadly representative of a wide range of surface ocean climates, depositional settings and temporal periods, the data suggest a fundamental function for Proteobacteria in the development of the geologic record of hopanes.
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Acknowledgements
We thank Jan DeLeeuw for coining the term ‘lipidomics’ and members of the Pearson lab for helpful discussions. We acknowledge the Department of Energy (DOE), Office of Science, and Office of Biological and Environmental Research (DE-FG02-02ER63453), the Gordon and Betty Moore Foundation, and the J Craig Venter Science Foundation for funding to undertake this study. We gratefully acknowledge the governments of the countries of origin for the GOS samples: Canada, USA, United Kingdom, Mexico, Honduras, Panama, Costa Rica, Ecuador, French Polynesia, Australia, Seychelles, Madagascar and Tanzania. Genomic sequences from NCBI are available in the public domain courtesy of JGI (http://www.jgi.doe.gov/) and the J Craig Venter Institute. Special thanks are due to Marv Frasier, Saul Kravitz and the CAMERA team for their suggestions in support of the Advanced Reference Viewer. This work was supported by grants from the NSF and David and Lucille Packard Foundation (to AP).
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Pearson, A., Rusch, D. Distribution of microbial terpenoid lipid cyclases in the global ocean metagenome. ISME J 3, 352–363 (2009). https://doi.org/10.1038/ismej.2008.116
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