Phylogenetic diversity and ecology of environmental Archaea
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.
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