Genomic perspectives in microbial oceanography

  title={Genomic perspectives in microbial oceanography},
  author={Edward F. Delong and David M. Karl},
The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine… 
Genomics, metagenomics, and microbial oceanography—A sea of opportunities
The application of genomics and metagenomics in microbial oceanography is reviewed and future directions are suggested that have important implications in global carbon cycle, climate change, and ecosystem function.
Microbial structuring of marine ecosystems
The need to examine the biochemical interactions of microorganisms with ocean systems at the nanometre to millimetre scale is stressed — a scale that is relevant to microbial activities and must be scaled up to make useful predictions of how marine ecosystems in the whole ocean might respond to global change.
Linking bacterial community structure to carbon fluxes in marine environments
Microbial oceanography is undergoing a dramatic revolution thanks to the rapid development of novel techniques that allow the examination of microbial diversity and functions via molecular methods,
Ocean microbial metagenomics
Sensitivity of the biological oceanic nitrogen cycle to changes in dissolved oxygen
The sampling, construction of large insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomics clones are described.
Marine microbial genomics in Europe: current status and perspectives
A multinational, multidisciplinary approach is now needed to understand and finally predict the complex responses of the marine ecosystem to ongoing global changes and reveal a wealth of new metabolic processes and functions, which have a high potential for biotechnological applications.
Deciphering ocean carbon in a changing world
Questions being addressed using recent methodological and technological developments in analytical chemistry, microbiology, and informatics are considered and how these advances are transforming the authors' understanding of some of the most important reactions of the marine carbon cycle are considered.
Molecular diversity and ecology of microbial plankton
The history of microbial evolution in the oceans is probably as old as the history of life itself, but whether microbial plankton populations harbour organisms that are models of adaptive sophistication remains to be seen.
Priorities for ocean microbiome research.
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food
Microbial community transcriptional networks are conserved in three domains at ocean basin scales
It is reported that common temporal and ecological dynamics underpin disparate marine microbial communities, providing the first evidence that trans-Pacific diurnal transcriptional patterns in these communities may regulate ecological and biogeochemical processes across the ocean.


Microbial community genomics in the ocean
  • E. Delong
  • Environmental Science
    Nature Reviews Microbiology
  • 2005
Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea, and are poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.
From genes to ecosystems: the ocean's new frontier
The application of new molecular and genomic techniques to the ocean is driving a scientific revolution in marine microbiology. Discoveries range from previously unknown groups of organisms and novel
The Evolution of Modern Eukaryotic Phytoplankton
The geological, geochemical, and biological processes that contributed to the rise of the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis are examined.
Bacterial photosynthesis in surface waters of the open ocean
The first biophysical evidence demonstrating that aerobic bacterial photosynthesis is widespread is reported, indicating that these organisms account for 2–5% of the photosynthetic electron transport in the upper ocean.
Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics
Genetic analyses of methane-oxidizing Archaea from deep-sea sediments show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs, which supports previous hypotheses and provides an informed foundation for metabolic modeling of anaerobic methane oxidation.
Comparative Metagenomics of Microbial Communities
This work characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments.
Marine phage genomics.
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
The genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade, is described, indicating that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds to supplement heterotrophy.
The Ecological Role of Water-Column Microbes in the Sea*
Evidence is presented to suggest that numbers of free bacteria are controlled by nanoplankton~c heterotrophic flagellates which are ubiquitous in the marine water column, thus providing the means for returning some energy from the 'microbial loop' to the conventional planktonic food chain.
Microbial Ecology and Genomics: A Crossroads of Opportunity
The explosion of new information in microbial biology made available by recent advances in molecular technology is examined--and the important questions that remain are looked at.