title: Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.
abstract: A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass.
authors.affiliation: Laboratory of Aquatic Biology and Environmental Science, Graduate School of Agricultural Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Nanba
authors.forename: G M
authors.initials: GM
authors.lastname: King
authors.forename: K
authors.initials: K
authors.lastname: Dunfield
mesh_terms: D001420:Bacteria, Aerobic / Q000145:classification / Q000201:enzymology* / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D002248:Carbon Monoxide / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D014644:Genetic Variation; D006254:Hawaii; D008969:Molecular Sequence Data; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry / Q000235:genetics*; D012988:Soil Microbiology; D018707:Volcanic Eruptions
chemical_list: D004269:DNA, Bacterial; D002248:Carbon Monoxide; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase