CiteULike: vrich's Chisholm

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior

Edward Delong — 2006-01-27T15:51:55-00:00

Science, Vol. 311, No. 5760. (27 January 2006), pp. 496-503.

Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.

Phytoplankton population dynamics at the Bermuda Atlantic Time-series station in the Sargasso Sea

Michele Durand — 2005-11-09T16:47:29-00:00

Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 48, No. 8-9. (2001), pp. 1983-2003.

Phytoplankton populations were analyzed using flow cytometry in monthly samples at the Bermuda Atlantic Time-series Study (BATS) station in the Sargasso Sea from 1989-1994 for picoplankton (Synechococcus and Prochlorococcus) and from 1992-1994 for eukaryotic phytoplankton in order to better understand the mechanisms that dictate seasonal and inter-annual patterns in the phytoplankton community. The eukaryotic phytoplankton were dominated by populations of small nanoplankton (mostly 2-4 [mu]m diameter), though populations of coccolithophores and sometimes pennate diatoms also could be distinguished. Flow cytometric measurements of population abundances, individual cell light scattering (which can be related to cell size), and chlorophyll fluorescence were made. Synechococcus and the eukaryotic phytoplankton reached their greatest concentrations during the spring bloom each year when the water column was deeply mixed and nutrients were detectable in surface waters. The maximum cell concentration for Prochlorococcus was in the summer and fall of each year, with a deeper sub-surface maximum than Synechococcus. Picoplankton chlorophyll fluorescence and estimated cell size were greater at depth than near the surface, and were lowest in midsummer for both Synechococcus and Prochlorococcus. In the summer and fall, Prochlorococcus cells were often smallest at mid-depth, even when fluorescence per cell and cell concentration were lower at the surface. For the eukaryotes (including coccolithophores), cell concentrations were high during the spring in both 1992 and 1993, and in fall 1992. At these times, mean cell size and fluorescence were low. Improved size and carbon estimates were made and it was found that the estimated contribution of phytoplankton carbon to total particulate organic carbon, integrated over the upper 200 m, averaged 33% (range 21-43%) with no pronounced seasonal pattern.

Emergent biogeography of microbial communities in a model ocean.

MJ Follows — 2007-04-02T11:00:39-00:00

Science, Vol. 315, No. 5820. (30 March 2007), pp. 1843-1846.

A marine ecosystem model seeded with many phytoplankton types, whose physiological traits were randomly assigned from ranges defined by field and laboratory data, generated an emergent community structure and biogeography consistent with observed global phytoplankton distributions. The modeled organisms included types analogous to the marine cyanobacterium Prochlorococcus. Their emergent global distributions and physiological properties simultaneously correspond to observations. This flexible representation of community structure can be used to explore relations between ecosystems, biogeochemical cycles, and climate change.

Sequencing genomes from single cells by polymerase cloning

Kun Zhang — 2006-06-13T09:43:51-00:00

Nature Biotechnology, Vol. 24, No. 6. (28 May 2006), pp. 680-686.

Code and context: Prochlorococcus as a model for cross-scale biology

Maureen Coleman — 2008-05-09T02:18:14-00:00

Trends in Microbiology, Vol. 15, No. 9. (September 2007), pp. 398-407.

Prochlorococcus is a simple cyanobacterium that is abundant throughout large regions of the oceans, and has become a useful model for studying the nature and regulation of biological diversity across all scales of complexity. Recent work has revealed that environmental factors such as light, nutrients and predation influence diversity in different ways, changing our image of the structure and dynamics of the global Prochlorococcus population. Advances in metagenomics, transcription profiling and global ecosystem modeling promise to deliver an even greater understanding of this system and further demonstrate the power of cross-scale systems biology.

Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients

Zackary Johnson — 2006-04-18T15:59:09-00:00

Science, Vol. 311, No. 5768. (24 March 2006), pp. 1737-1740.

Prochlorococcus is the numerically dominant phytoplankter in the oligotrophic oceans, accounting for up to half of the photosynthetic biomass and production in some regions. Here, we describe how the abundance of six known ecotypes, which have small subunit ribosomal RNA sequences that differ by less than 3%, changed along local and basin-wide environmental gradients in the Atlantic Ocean. Temperature was significantly correlated with shifts in ecotype abundance, and laboratory experiments confirmed different temperature optima and tolerance ranges for cultured strains. Light, nutrients, and competitor abundances also appeared to play a role in shaping different distributions. 10.1126/science.1118052