Phylogenetic diversity and ecology of environmental Archaea

https://doi.org/10.1016/j.mib.2005.10.003Get rights and content

On the basis of culture studies, Archaea were thought to be synonymous with extreme environments. However, the large numbers of environmental rRNA gene sequences currently flooding into databases such as GenBank show that these organisms are present in almost all environments examined to date. Large sequence databases and new fast phylogenetic software allow more precise determination of the archaeal phylogenetic tree, but also indicate that our knowledge of archaeal diversity is incomplete. Although it is apparent that Archaea can be found in all environments, the chemistry of their ecological context is mostly unknown.

Introduction

Carl Woese first realized that the ribosome, the ubiquitous molecular machine that conducts protein synthesis, offers a way to investigate systematically the relationships between all forms of life. Woese's approach was to determine the sequences of the RNAs that makes up the ribosome, particularly the small subunit of ribosomal RNA (rRNA). Comparisons of nucleotide sequences of ribosomal genes from different organisms allowed inference of the evolutionary relationships between the organisms: the greater the similarity or difference between the rRNA sequences, the more or less closely related the organisms are. Subsequent work by many investigators formalized the mathematics of sequence comparisons and adopted phylogenetic tree diagrams as the graphical means to display the relationships between sequences (nominally organisms).

Woese's results using the rudimentary sequencing technology available in the mid-1970s determined that there are three phyla of organisms: Eucarya, Bacteria and Archaea [1]. This sequence-based framework for the description of microbial diversity provided a foundation in the mid-1980s for a significant step in microbial ecology — the culture-independent analysis of rRNA gene sequences from environmental samples [2]. Even early results demonstrated that the microbial world is much larger and more diverse than previously predicted from historical culture studies. Environmental sequences have contributed dramatically to our understanding of archaeal diversity, which continues to expand. Figure 1 shows the accumulation of archaeal rRNA sequences submitted to GenBank. As environmental sequences have accumulated it has become evident that Archaea are a cosmopolitan group that are not limited to ‘extreme’ environments. The expanded sequence collection also affords the opportunity to develop more comprehensive phylogenetic trees than previously possible.

New software has become available that allows phylogenetic trees to be constructed from much larger numbers of RNA sequences than had heretofore been possible. Statistical analysis of phylogenetic trees based on large, predominantly environmentally derived, RNA sequence data sets shows that much of the complex branching traditionally associated with the Archaea is not supported. The complex branching pattern collapses to many branches radiating from single points, known as polytomies or star radiations. Although the wealth of new environmental RNA sequence data show the Archaea to be present in all environments, little progress has been made regarding precisely how the organisms obtain energy from their ecological niches.

Section snippets

Construction of large phylogenetic trees

Various software tools are used to analyze the phylogenetics of rRNA datasets. ARB has become a common phylogenetic software package to use [3]. ARB manages, aligns and annotates sequences as well as managing and printing phylogenetic trees. ARB is often supplemented with additional software packages such as PAUP [4] and more recently MrBayes [5]. PAUP and MrBayes are phylogenetic software tools that are specifically focused on the algorithms used to generate phylogenetic trees.

The most

Archaeal ecology: no longer just extremophiles

Although the phrase ‘archaeal ecology’ is popularly synonymous with ‘extreme’ environments, this is clearly an anthropocentric view. Representatives of Archaea occur everywhere, in samples from ocean water [12], ocean sediments [13], solid gas hydrates [14], tidal flat sediments [15], freshwater lakes [16], soil [17], plant roots [18], peatlands [19], petroleum-contaminated aquifers [20] and the human mouth and gut [21], to cite just a few reports. Archaea commonly occupy a significant

Conclusions

The rate of archaeal sequence submission to public sequence databases has increased dramatically in recent years. Most of the new data are rRNA gene sequences derived from environmental samples. Recently developed phylogenetic tree software makes the analysis of large sequence datasets possible with readily available computers. Archaeal phyla, the phylogenetic location of which was previously unstable, assume a fixed position in phylogenetic trees based on large sequence datasets, probably

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

Special thanks to Alexandros Stamatakis for his quick responses to our questions and to our requests for new features in his RAxML software package. This research was supported in part by the NASA Astrobiology Institute.

References (28)

  • C.R. Woese et al.

    Phylogenetic structure of the prokaryotic domain: the primary kingdoms

    Proc Natl Acad Sci USA

    (1977)
  • N.R. Pace et al.

    Analyzing natural microbial populations by rRNA sequences

    ASM News

    (1985)
  • W. Ludwig et al.

    ARB: a software environment for sequence data

    Nucleic Acids Res

    (2004)
  • D. Swofford

    PAUP*: Phylogenetic analysis using parsimony (* and other methods)

    (1999)
  • J.P. Huelsenbeck et al.

    MRBAYES: Bayesian inference of phylogenetic trees

    Bioinformatics

    (2001)
  • D.H. Hillis et al.

    An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis

    Syst Biol

    (1993)
  • M. Holder et al.

    Phylogeny estimation: traditional and Bayesian approaches

    Nat Rev Genet

    (2003)
  • A. Stamatakis et al.

    RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

    Bioinformatics

    (2005)
  • H. Huber et al.

    A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont

    Nature

    (2002)
  • C. Brochier et al.

    Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

    Genome Biol

    (2005)
  • L. Cubonova et al.

    Histones in crenarchaea

    J Bacteriol

    (2005)
  • E.F. DeLong

    Microbial community genomics in the ocean

    Nat Rev Microbiol

    (2005)
  • K. Knittel et al.

    Diversity and distribution of methanotrophic archaea at cold seeps

    Appl Environ Microbiol

    (2005)
  • H.J. Mills et al.

    Characterization of microbial community structure in Gulf of Mexico fas hydrates: comparative analysis of DNA- and RNA-derived clone libraries

    Appl Environ Microbiol

    (2005)
  • Cited by (0)

    View full text