Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems

Abstract

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.

FIG. 1.

Cyanobacteria: diagrammatic tree of Rocky Mountain endolithic cyanobacterial sequences and reference sequences representative of cyanobacterial diversity (35). Representative endolithic sequences are indicated by bold type. The percentages indicate the abundance of sequence types in the community. Solid circles indicate nodes with ≥70% bootstrap support as determined by neighbor joining with maximum likelihood rate corrections and Bayesian inference. The tree was rooted with Escherichia coli. The following sequence groups (35) are indicated by brackets on the right: Phormidium (PHOR), Synechococcus (SO), Leptolynbia (LEPT), Pseudoanabaena (PSAN), endolith-specific group 1 (ENDO1), Nostocales (NOST), endolith-specific group 2 (ENDO2) Oscillatoria (OSC), Synechocystis/Pleurocapsa/Microcystis (S/P/M), chloroplasts (PLAST), and Gloeobacter (GBACT). Rock types are indicated as follows: SS, sandstone; LS, limestone; and GR, granite.

FIG. 2.

Actinobacteria: diagrammatic tree showing the broad distribution of endolithic rRNA gene sequences. The open wedges represent the main recognized groups within the Actinobacteria (32). The solid wedges represent new actinobacterial groups formed by endolithic sequences (Endo-1 to Endo-6). Communities with sequences that belong to a group are indicated by four-letter codes that indicate the study site (FQ, Forest Quarry; EP, Exclamation Point; OC, Owl Canyon; SC, Sinks Canyon) and the rock type (SS, sandstone; LS, limestone; GR, granite). The general topology of the tree is supported by neighbor-joining bootstrap and Bayesian analysis (not shown) and is consistent with previous phylogenetic analyses (32).

FIG. 3.

Archaea: diagrammatic tree showing the phylogenetic affiliations of representative Rocky Mountain endolithic sequences (bold type) determined in the context of a recent comprehensive archaeal phylogeny (29). The tree was rooted with bacterial sequences. Representative clones and their fractions (expressed as percentages) in the community are shown in bold type. The communities were Sinks Canyon granite (SCGR), Sinks Canyon sandstone (SCSS), and Owl Canyon limestone (OCLS).

FIG. 4.

UniFrac statistical comparison of Rocky Mountain endolithic communities based on phylogenetic compositions: pairwise UniFrac distances calculated from an Arb phylogenetic tree. (A) UPGMA tree of UniFrac distances showing the overall phylogenetic relationships of the communities. The values indicate the percent Jackknife support at each node based on 1,000 random samplings. The tree was rooted with a Yellowstone hot spring community (31). (B) Principal coordinate analysis (PCA) of UniFrac distances resulted in a clustering pattern similar to that observed by UPGMA. The rock types are sandstone (•), limestone (▪), and granite (▴).