Chesapeake Bay Virioplankton Metagenome

Viruses are all around us. The first indication of the amazing abundance of viruses within marine and freshwater environments came through direct observations of water samples using powerful electron microscopes. The productive waters of estuaries, like the Chesapeake Bay, typically contain around 1 to 10 million virus particles per milliliter. This means that the Chesapeake, which holds more than 18 trillion gallons of water, contains around 10,000,000,000,000,000,000,000 (~1 X 10e22) virus particles.

Bacterial Abundance Heat Diagram
Click to enlarge.

Large numbers such as these are typically used in astronomy when describing the number of stars in the Milky Way, 200,000,000,000 (2 X 10e11 stars) or in the Universe, 40,000,000,000,000,000,000,000 (4 X 10e22 stars). Considering all the environments of earth put together, microbial ecologists estimate that our biosphere contains around 1031 virus particles. Thus, the enormous numbers used to describe the amount of stars in the universe, can also be used to describe the abundance of viruses on planet Earth.

We now refer to free-floating (planktonic) viruses within natural waters as virioplankton. This is similar to calling planktonic bacteria-bacterio- plankton or planktonic unicellular algae-phyto- plankton. The discovery, over 15 years ago, of the vast abundance of virioplankton lead to two central questions on the influence of viruses on co-existing populations of bacterio- and phytoplankton:

1) How does viral infection influence the net productivity (growth) of bacterio- and phytoplankton?
2) How do viruses alter the genetic composition of bacterio- and phytoplankton communities?

The Microbial Observatory for Virioplankton Ecology was established in May 2002, through a grant from the National Science Foundation, Microbial Observatories program. The overall goal of the project is examine interannual changes in the abundance, activity, and diversity of virioplankton over the yearly biological cycle of the Chesapeake Bay estuary. The Chesapeake was chosen as this marine ecosystem experiences dramatic seasonal changes in phytoplankton growth (primary productivity). Because it is a slightly stratified salt- wedge estuary, the Chesapeake presents dramatic changes in salinity, temperature and dissolved oxygen both along its length and from surface to bottom waters. Our initial suspicion that the dynamic nature of the Bay would be reflected within its smallest residents has been correct.

Recently, we have applied metagenomic sequencing approaches to characterize the genetic diversity and community structure of dsDNA viruses within the Cheseapeake. Viruses within large volume water samples collected across the Chesapeake in September, 2002 were concentrated into a small volume. DNA from the viral concentrate was randomly sheared and PCR-amplified after the addition of linkers to either end of the sheared products. A small insert library (~2-3 kb DNA inserts) was constructed from this linker amplified DNA by Lucigen Corporation (Middleton, WI) using a vector (pSMART) that prevents transcription of insert DNA. From this library ~2,900 clones were bi-directionally sequenced generating ~4.4 Mb of DNA sequence data. Preliminary analyses indicate that the library contains an astoundingly high proportion (~70%) of sequences with no known homologs. This an other evidence indicates that natural viral communities contain the highest proportion of unknown genetic diversity on earth.