Diversity of Bacteria and Archaea in hypersaline sediment from Death Valley National Park, California

• Published in: MicrobiologyOpen (Weinheim) 2012-06, Vol.1 (2), p.135-148
• Main Authors: Kim, Jong‐Shik, Makama, Mfundi, Petito, Janine, Park, Nyun‐Ho, Cohan, Frederick M., Dungan, Robert S.
• Format: Article
• Language: English
• Subjects: 16S rRNA gene; Actinobacteria; Archaea; Bacilli; Bacillus; Bacteria; Bacteroidetes; Cloning; Cyanobacteria; Deoxyribonucleic acid; DNA; Domains; Ecotype Simulation; Ecotypes; Estimates; Firmicutes; Gemmatimonadetes; Genes; Halobacteriaceae; hypersaline sediment; Microorganisms; National parks; New genera; Original Research; Phylogenetics; Phylogeny; Polymerase chain reaction; Primers; Proteobacteria; rRNA 16S; Sediments; Simulation; Simulation analysis; Taxonomy
• ISSN: 2045-8827; 2045-8827
• DOI: 10.1002/mbo3.20

The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain‐specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus‐Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis–B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates in hypersaline sediment from Death Valley National Park were examined. A phylogenetic analysis of 16S rRNA gene sequences revealed that the sediment contained a variety of previously undiscovered genera, species, and ecotypes from the domains Bacteria and Archaea. While many of the clone sequences were affiliated with extreme and moderate halophiles, many of the bacterial isolates may not be halophiles but instead only halotolerant, since they were cultivated on media containing low salt concentrations.