Genetic diversity in Sargasso Sea bacterioplankton

Abstract

Bacterioplankton are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction. The analysis indicates the presence of a novel microbial group, the SAR11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs--cyanobacteria, prochlorophytes and chloroplasts--was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.

Genetic Diversity of Plankton Community as Depicted by PCR-DGGE Fingerprinting and its Relation to Morphological Composition and Environmental Factors in Lake Donghu

“…Therefore, comparative analysis of the ubiquitous rRNA genes, regardless of organisms_ developmental stage, can be universally applied to infer relationships among the organisms. The use of rRNA genes to examine relationships among organisms is relatively new, Giovannoni et al [5] having applied the method to study PCR-amplified 16S rRNA genes from natural environments. PCR-DGGE analysis of the microbial community produces a complex profile, which can be quite sensitive to spatial-temporal dynamics, and is one of the most commonly used fingerprinting methods in community characterization.…”

Bacterial diversity in an arctic lake: a freshwater SAR11 cluster

“…Such phylogenetic analysis not only extends our identification of naturally occurring picoplankton but, by comparison with cultured species, may also increase our understanding of their physiology as inferred from that of microbial taxa with very similiar rRNA genes. The phylogenetic characterization of small subunit rRNA genes (16s rRNAs; Pace et al 1986) has gained widespread acceptance as a tool to understand microbial (and macrofaunal) speciation in marine systems (Giovannoni et al 1990, Britschgi & Giovannoni 1991, Schmidt et al 1991, DeLong 1992, DeLong et al 1993, Fuhrman et al 1993, Mullins et al 1995 and in extreme environments (Ward et al 1990, Barns et al 1994. Ribosomal RNA probes have delineated marine microbial succession (Rehnstam et al 1993).…”

“…The taxonomy of microbes is often based upon their physiological abilities, and taxonomic studies have the potential of providing a great deal of ecological information about the role of microbes in natural systems and ecological succession. There is a tremendous gap between taxonomy and ecology because microbial ecologists can only culture and identify a small percentage of the microbes in soils and water (Giovannoni et al 1990, Ward et al 1990, Schmidt et al 1991, Barns et al 1994. As a result, microbial ecologists have focused on a 'process approach' to study what prokaryotes collectively do in nature (Hobbie 1988).…”

“…An unexpected result of our work was the presence of gene clones related to the SARI l cluster, a group first described in 1990. The SARI1 cluster has been found in Atlantic and Pacific open ocean water and off the Florida, Bermuda and California (USA) coasts, but not along the Oregon (USA) coast (Giovannoni et al 1990, Schmidt et al 1992. It has been regarded as a subtropical marine group.…”

Uncultivated Microorganisms

“…Novel microbial divisions were discovered by the dozen (Giovannoni et al 1990;Ward et al 1990;DeLong 1992;Fuhrman et al 1992;Liesack and Stackebrandt 1992;Barns et al 1994;Hugenholtz et al 1998;Ravenschlag et al 1999;Dojka et al 2000). From the molecular surveys of the 1990s emerged an image of the biosphere with millions of novel microbial species waiting to be discovered (Tiedje 1994;Allsopp et al 1995).…”