2006 Annual Science Report

Marine Biological Laboratory Reporting  |  JUL 2005 – JUN 2006

Microbial Diversity in the Deep Ocean

Project Summary

The world’s oceans are teeming with microscopic life forms. The evolution of marine microbes over billions of years predicts the composition of microbial communities should be much greater than published estimates of a few thousand distinct kinds of microbes/liter of seawater. By adopting a massively parallel tag sequencing strategy, we explored bacterial communities of deep water masses of the North Atlantic (Figure 1) and diffuse flows associated with the hydrothermal vents of Axial Seamount (Figure 2)

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

The world’s oceans are teeming with microscopic life forms. The evolution of marine microbes over billions of years predicts the composition of microbial communities should be much greater than published estimates of a few thousand distinct kinds of microbes/liter of seawater. By adopting a massively parallel tag sequencing strategy, we explored bacterial communities of deep water masses of the North Atlantic (Figure 1) and diffuse flows associated with the hydrothermal vents of Axial Seamount (Figure 2). We extracted DNA from eight 1 liter samples and produced PCR libraries for amplicons that span the V6 hypervariable region of Bacterial small subunit ribosomal RNAs. These amplicons were sequenced using massively parallel 454 DNA sequencing technology. These sequence tags were used to query a reference data base of all published bacterial ribosomal RNAs and in a DOTUR analysis that relies upon sequence similarities to cluster related sequences into Operational Taxonomic Unites (OTUs) according to a distance criteria. The number and frequency of each OTU (defined by querying the database or by the DOTUR analysis) served as input to rarefaction analyses (Figure 3 for queries of the database and Table 1 for the DOTUR analyses) in which diversity for each sample appears to be at least two orders of magnitude more complex than previously reported for any microbial environment. For water samples from diffuse flows associated with hydrothermal vents and water samples from the oxygen minimum zone and deep waters of the North Atlantic we identified more than 50,000 different kinds of bacteria in a one-liter samples. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This “rare biosphere” is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and at different times in earth’s history may have had a profound impact on shaping planetary processes.

{{ 1 }}

{{ 2 }}

{{ 3 }}

Table 1. Similarity-based OTUs and Species Richness Estimators *.

{{ 4 }}

  • PROJECT INVESTIGATORS:
    Mitchell Sogin Mitchell Sogin
    Project Investigator
  • PROJECT MEMBERS:
    Julie Huber
    Postdoc

  • RELATED OBJECTIVES:
    Objective 5.1
    Environment-dependent, molecular evolution in microorganisms

    Objective 5.2
    Co-evolution of microbial communities