Molecular phylogeny of Archaea from soil

Abstract

Cultivation methods have contributed to our present knowledge about the presence and diversity of microbes in naturally occurring communities. However, it is well established that only a small fraction of prokaryotes have been cultivated by standard methods and, therefore, the prokaryotes that are cultivated may not reflect the composition and diversity within those communities. Of the two prokaryotic phylogenetic domains, Bacteria and Archaea, members of the former have been shown to be ubiquitous in nature, with ample evidence of vast assemblages of uncultured organisms. There is also now increasingly compelling evidence that the Archaea, which were once thought to occupy a limited number of environments, are also globally widespread. Here we report the use of molecular phylogenetic techniques, which are independent of microbial cultivation, to conduct an assessment of Archaea in a soil microbial community. Small subunit ribosomal RNA genes of Archaea were amplified from soil and cloned. Phylogenetic and nucleotide signature analyses of these cloned small subunit ribosomal RNA gene sequences revealed a cluster of Archaea from a soil microbial community that diverge deeply from the crenarchaeotal line of descent and has the closest affiliation to the lineage of planktonic Archaea. The identification and phylogenetic classification of this archaeal lineage from soil contributes to our understanding of the ecological significance of Archaea as a component of microbial communities in non-extreme environments.

Figure 1

Inferred unrooted phylogenetic tree of archaeal SSU rRNA gene sequences cloned from soil, illustrating close affiliation of these sequences (designated SCA clones) with those of the Group I marine sequences of the Crenarchaeota. Tree was inferred by neighbor-joining analysis of 637 homologous positions of sequence from each organism or clone. Scale bar represents 10 mutations per 100 nt of homologous sequence positions. The percentage of 100 bootstrap resamplings that support some of the major topological elements in neighbor joining (above line) and parsimony (below line) analyses is indicated.

Figure 2

Inferred phylogenetic tree of archaeal SSU rRNA gene sequences cloned from soil, illustrating close affiliation of these sequences (designated SCA clones) with those within the planktonic Archaea. The tree was rooted to the korarchaeotal sequence JP27 (8). Planktonic Archaea clones used in this analysis are from marine bacterioplankton (NH49-9; ref. 7), soil (PAD19 and FIE16; ref. 11), and a marine holothurian mid-gut (JM-2, JM-4, JM-7, and JM-8; ref. 18). Tree was inferred by maximum likelihood analysis of 261 homologous positions of sequence from each clone. Scale bar represents 10 mutations per 100-nt of homologous sequence positions. The percentage of 100 bootstrap resamplings that support some of the major topological elements in maximum likelihood (above line) and parsimony (below line) analyses is indicated. Only bootstrap values >60 are shown for these analyses.