Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

J. Kirk Harris, J. Gregory Caporaso, Jeffrey J. Walker, John R. Spear, Nicholas J. Gold, Charles E. Robertson, Philip Hugenholtz, Julia Goodrich, Daniel McDonald, Dan Knights, Paul Marshall, Henry Tufo, Rob Knight, Norman R. Pace

Research output: Contribution to journalArticlepeer-review

112 Scopus citations

Abstract

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only 1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional 119 000 nearly full-length sequences and 28 000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.

Original languageEnglish (US)
Pages (from-to)50-60
Number of pages11
JournalISME Journal
Volume7
Issue number1
DOIs
StatePublished - Jan 2013

Bibliographical note

Funding Information:
We thank the Exportadora de Sal SA for access and assistance in working on-site. We are grateful for the enabling support of David DesMarais, Brad Bebout and Tori Hoehler, NASA Ames, Moffat Field, CA. Sanger sequencing was provided by the Joint Genome Institute Community Sequencing Program. JRS was supported by an NSF Microbial Biology Postdoctoral start-up fund. Work in the Knight lab was supported in part by the National Institutes of Health and the Howard Hughes Medical Institute. Work in the Pace laboratory was supported by grants from the NASA Astrobiology Institute. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. Data deposition: the sequences were assigned GenBank accession numbers JN427016–JN539989.

Keywords

  • Guerrero Negro
  • QIIME
  • microbial ecology
  • microbial mats
  • rRNA phylogeny

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