MOLECULAR SYSTEMATICS, MICROBIAL ECOLOGY AND SINGLE CELL
ANALYSIS
E. F. DeLong
Biology Department
Woods Hole Oceanographic Institution
Woods Hole MA, 02543
ABSTRACT
Molecular approaches in taxonomy and systematics are providing a unifying framework for understanding the
phylogenetic relationships of diverse biological species. The methods rely on comparison of nucleic acid or amino
acid sequences, which can serve as yardsticks for measuring evolutionary divergence. Direct sequence analysis
can largely circumvent problems inherent in phenotypic comparisons of widely divergent taxa. Macromolecular
sequence information is particularly useful in situations where directly comparable phenotypic properties are
scarce or difficult to assess. Additionally, macromolecular sequence data bases are valuable resources for
determining the phylogenetic affiliations of previously unstudied or uncharacterized organisms. In particular,
current understanding of the evolutionary relationships of microbial species has been greatly advanced through
molecular phylogenetic comparisons of small subunit ribosomal RNA (rRNA) sequences.
The molecular data employed in systematic and evolutionary studies are also proving useful for ecological
studies. By directly retrieving phylogenetically informative gene sequences from mixed microbial populations,
it is possible to infer phylogenetic affiliations of individual popUlation constituents. This allows identification of
community members without requiring their cultivation, and so avoids some selective biases associated with pure
culture methods. In addition, short segments of sequence, such as those found in small subunit rRNA, can be
taxa-specific. These sequences may therefore serve as diagnostic markers for particular groups. In conjunction
with epifluorescence microscopy, fluor-labeled, rRNA-targeted probes that bind to these diagnostic sequences
may be used to determine the phylogenetic identity of individual cells. Thus, macromolecular sequence
information can be employed to detect the presence of partiCUlar species, and to study their spatial and temporal
variability. Recent applications, including molecular phylogenetic analyses of mixed bacterioplankton populations,
demonstrate the utility of this approach.
INTRODUCTION
Single cell analyses have proven extremely useful for determining the abundance, activities
and variability of microbial species in their natural habitats. In the field of oceanography,
recent studies of marine cyanobacteria exemplify the utility of this approach (Waterbury et al. ,
1986). Their unique size and autofluorescent properties permit the rapid, direct identification
and enumeration of marine Synechococcus (Waterbury et al., 1979). This in turn has led to
detailed understanding of the temporal and spatial distribution and abundance of these
NATO AS! Series. Vol. G 27
Particle Analysis in Oceanography
Edited by S. Demers
© Springer-Verlag Berlin Heidelberg 1991
ANALYSIS
E. F. DeLong
Biology Department
Woods Hole Oceanographic Institution
Woods Hole MA, 02543
ABSTRACT
Molecular approaches in taxonomy and systematics are providing a unifying framework for understanding the
phylogenetic relationships of diverse biological species. The methods rely on comparison of nucleic acid or amino
acid sequences, which can serve as yardsticks for measuring evolutionary divergence. Direct sequence analysis
can largely circumvent problems inherent in phenotypic comparisons of widely divergent taxa. Macromolecular
sequence information is particularly useful in situations where directly comparable phenotypic properties are
scarce or difficult to assess. Additionally, macromolecular sequence data bases are valuable resources for
determining the phylogenetic affiliations of previously unstudied or uncharacterized organisms. In particular,
current understanding of the evolutionary relationships of microbial species has been greatly advanced through
molecular phylogenetic comparisons of small subunit ribosomal RNA (rRNA) sequences.
The molecular data employed in systematic and evolutionary studies are also proving useful for ecological
studies. By directly retrieving phylogenetically informative gene sequences from mixed microbial populations,
it is possible to infer phylogenetic affiliations of individual popUlation constituents. This allows identification of
community members without requiring their cultivation, and so avoids some selective biases associated with pure
culture methods. In addition, short segments of sequence, such as those found in small subunit rRNA, can be
taxa-specific. These sequences may therefore serve as diagnostic markers for particular groups. In conjunction
with epifluorescence microscopy, fluor-labeled, rRNA-targeted probes that bind to these diagnostic sequences
may be used to determine the phylogenetic identity of individual cells. Thus, macromolecular sequence
information can be employed to detect the presence of partiCUlar species, and to study their spatial and temporal
variability. Recent applications, including molecular phylogenetic analyses of mixed bacterioplankton populations,
demonstrate the utility of this approach.
INTRODUCTION
Single cell analyses have proven extremely useful for determining the abundance, activities
and variability of microbial species in their natural habitats. In the field of oceanography,
recent studies of marine cyanobacteria exemplify the utility of this approach (Waterbury et al. ,
1986). Their unique size and autofluorescent properties permit the rapid, direct identification
and enumeration of marine Synechococcus (Waterbury et al., 1979). This in turn has led to
detailed understanding of the temporal and spatial distribution and abundance of these
NATO AS! Series. Vol. G 27
Particle Analysis in Oceanography
Edited by S. Demers
© Springer-Verlag Berlin Heidelberg 1991