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Polyphasic characterization of an epilithic biofilm from a lava cave in Kīlauea Caldera, Hawaiʻi

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Item Summary

Title: Polyphasic characterization of an epilithic biofilm from a lava cave in Kīlauea Caldera, Hawaiʻi
Authors: Saw, Jimmy Hser Wah
Keywords: epilithic biofilm
lava cave
Kīlauea Caldera
Issue Date: Dec 2012
Publisher: [Honolulu] : [University of Hawaii at Manoa], [December 2012]
Abstract: The microbial community in an epilithic biofilm on an lava cave wall in Kīlauea Caldera, Hawaiʻi, was characterized by a polyphasic approach. Ribosomal-pyrotag and metagenomic sequencing revealed phylogenetic diversity rivaling that in a Guerrero Negro hypersaline microbial mat. Targeted cultivations led to the isolation, characterization, and genome sequencing of a deeply divergent novel cyanobacterium. Diverse Bacteria and Archaea lineages were detected. The most abundant sequences, representing ~24% of the metagenomic reads analyzed, affiliated with Burkholderia. Comparative metagenomic analyses revealed community composition and function most similar to those in soils. Two novel cyanobacteria detected in metagenomic data were cultivated; JS1 is related to Gloeobacter violaceus PCC 7421T , the only cultivated Gloeobacter species. JS2 may represent a new genus in the Oscillatoriales since it shares <95% 16S rRNA gene sequence identity with its nearest neighbor, a Leptolyngbya sp. A third cultivated cyanobacterium (JS3) not detected in clone libraries, ribosomal-pyrotag or metagenomic data sets, belongs in the true-branching filamentous Stigonematales; JS3 shares 98.1% 16S rRNA gene sequence identity with Fischerella muscicola PCC 7414, and may be a new Fischerella sp.
Comparing the complete genome sequence of JS1 with that of G. violaceus PCC 7421T revealed JS1 represents a new species, despite sharing 98.7% 16S rRNA gene sequence identity with PCC7421T . The name Candidatus Gloeobacter kilaueaensis is proposed, with JS1T the Type strain. Maximum likelihood phylogenetic trees based on 16S rRNA gene sequences and 43 concatenated ribosomal proteins showed Candidatus Gloeobacter kilaueaensis JS1T places in the deep-branching Gloeobacter clade, but is less basal than G. violaceus. Divergence times based on Bayesian analyses suggested these Gloeobacter species diverged 150-300 MYA. The isolation, characterization, and genome sequencing of a deeply divergent novel Gloeobacter is significant given that for forty years we have known only one species in the entire order. Of broader significance is confirmation that by integrating molecular and cultivation methods we can target for cultivation specific Bacteria and or Archaea only detected in molecular analyses; a range of scripts was also developed to analyze and visualize sequence data.
Description: Ph.D. University of Hawaii at Manoa 2012.
Includes bibliographical references.
URI/DOI: http://hdl.handle.net/10125/100817
Appears in Collections:Ph.D. - Microbiology



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