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 COoxidizing 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.Several distinct functional groups comprise the bacterial lithotrophs. Obligate lithotrophs include sulfide-, sulfur-, metal-, ammonium-, and nitrite-oxidizing bacteria, many of which have been described in detail previously (2-5, 14-16, 28, 29, 35, 36, 39). In contrast, facultative lithotrophs include aerobic hydrogen-and CO-oxidizing bacteria, few of which have been described (22)(23)(24). Most facultative lithotrophs are heterotrophs that preferentially oxidize organic substrates or that grow mixotrophically with CO (or hydrogen) and organics (22,23). However, in spite of their physiological, ecological, and phylogenetic diversity, all lithotrophs are united by their ability to incorporate CO 2 for cell carbon through the activity of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO).RubisCO, the most abundant protein on Earth (33), has been thoroughly characterized (8,10,13,17,20,30,32,33,37,40). Based on various biochemical analyses, two forms have been documented. All known lithotrophic bacteria contain form I, while a relatively small number of bacteria, e.g., Hydrogenovibrio marinus, Rhodobacter capsulatus, Rhodobacter sphaeroides, and several Thiobacillus species, also contain form II (33). Sequence analyses of the gene coding for the large subunit of RubisCO (rbcL) have revealed two major phylogenetically distinct form I groups, a green alga-like group and a red alga...

Interactions between bacterial carbon monoxide and hydrogen consumption and plant development on recent volcanic deposits

“…Previous analyses of Kilauea volcano based on multiple sites that constituted a chronosequence from 21-to 300-year old showed that atmospheric CO and hydrogen utilization occurred early in successional development and contributed significantly to respiratory metabolism (King, 2003a). Molecular ecological analyses also revealed significant differentiation among CO-oxidizing and lithotrophic communities colonizing deposits of different ages and successional development (Dunfield and King, , 2005Nanba et al, 2004). In this study, we report interactions between successional development, specific functional processes (CO and hydrogen oxidation and acetylene reduction) and related microbiological and biogeochemical variables for Kilauea volcano deposits with uniform ages and climatic regimes.…”

“…Sites were established near Kilauea caldera on a 1959 tephra deposit (Pu'u Puai-PP) and a 1969 lava flow (Mauna Ulu-MU), aspects of which have been previously described (King, 2003a;Dunfield and King, 2004;Nanba et al, 2004;Gomez-Alvarez et al, 2007). The PP site consists of islands of closedcanopy woody vegetation (mixed Metrosideros polymorpha (Ohia) and Morella faya (also Myrica faya or fire tree) interspersed with extensive unvegetated patches comprised of tephra (or volcanic cinders); the cinders were approximately 1 cm in diameter.…”

“…Vitousek and co-workers have addressed some of these issues through their research on nitrogen fixation and nitrogen mineralization on Hawaiian volcanic deposits (Riley and Vitousek, 1995;Vitousek, 1999;Crews et al, 2001;Pearson and Vitousek, 2001). Nü sslein and Tiedje (1998), Nanba et al (2004) and Dunfield and King (2004) have documented various aspects of microbial community structure and function on recent Hawaiian volcanic deposits (44-300 years old), and shown in particular that relatively young deposits harbored very distinct assemblages, especially where plants were present. Analyses of quinone profiles on Mt Pinatubo mudflows also suggested possible associations of Actinobacteria with developing plant communities (Ohta et al, 2003).…”

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

“…PCRs were carried out using 50-l volumes (13). A 492-to 495-bp cbbL fragment was amplified and sequenced using primers K2 and V2 as previously described by Nanba et al (22). OMP coxL genes (form I; about 1,260 bp) and putative coxL genes (BMS, form II; about 1,260 bp) were also amplified from the isolates and sequenced as we have described previously (13).…”

Salinisphaera hydrothermalis sp. nov., a mesophilic, halotolerant, facultatively autotrophic, thiosulfate-oxidizing gammaproteobacterium from deep-sea hydrothermal vents, and emended description of the genus Salinisphaera

“…A 500 bp fragment of the gene encoding form I RuBisCO (rbcL/cbbL) from S. shabanensis DSM 14853 T was amplified as described previously (Nanba et al, 2004), and its sequence was determined. Internal primers ss rbcLF (59-GGTCTATGAAAGCGCTCAAGG-39) and ss rbcLR (59-ATCCATTTCGAGATCACGCGG-39) were designed based on the rbcL sequence from S. shabanensis DSM 14853 T (using the IDT OligoAnalyser 3.1 program; http:// www.idtdna.com), and were used to amplify a 400 bp fragment of the rbcL gene from the three novel strains.…”