Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers

Abstract

To investigate the phylogenetic diversity of putative chemolithoautotrophs possessing the RubisCO form II gene (cbbM) in various environments, we designed a new PCR primer set targeting this gene. The primer set was designed to cover more diverse and longer sequences of cbbM genes than those reported previously. We analyzed various samples (i.e., benthic sands, basement rocks, sulfide chimneys, vent fluids and overlying bottom seawater) collected in a deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, by PCR-based analysis using the designed primer set. Most of the cbbM phylotypes recovered from the liquid samples were related to those of the SUP05 group that belongs to the Gammaproteobacteria and includes putative sulfide-oxidizing chemolithoautotrophs. In contrast, the cbbM phylotypes recovered from the solid samples were related to environmental clones with low similarity (74-90%) and not closely related to the SUP05 group (69-74%). The cbbM phylotypes recovered from the liquid samples were different from those of the solid samples. Furthermore, the cbbM phylotypes recovered from the solid samples were different from each other. Our results expand knowledge of the phylogenetic diversity and distribution of putative chemolithoautotrophs possessing RubisCO form II cbbM genes in deep-sea hydrothermal fields.

Quantitative PCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System (Lō'ihi Seamount, Hawai'i)

“…3 and 5B and C), suggesting that, while the gene sequence for aclB is present at Lo 'ihi, the rTCA cycle is not as widely used as the CBB cycle. As the rTCA cycle operates in the Epsilonproteobacteria and generally at higher-temperature deepsea vents, the abundance of cbbM relative to that of aclB supports the hypothesis that although aclB genes are present, Zetaproteobacteria at Lo 'ihi use the CBB cycle as their primary means of carbon fixation (10,23,38).…”

“…Nondegenerate qPCR primers were designed for carbon fixation genes using PCRcloned sequences. PCR primers for ribulose-1,5-bisphosphate carboxylase (RubisCO) type II (cbbM) and ATP citrate lyase (aclB) genes were first obtained from previous studies (38,39). These degenerate primer sets for cbbM and aclB were used to amplify and sequence PCR products from Lo 'ihi 2013 BMS samples.…”

Functional Gene Analysis of Freshwater Iron-Rich Flocs at Circumneutral pH and Isolation of a Stalk-Forming Microaerophilic Iron-Oxidizing Bacterium

“…DNA was extracted from the samples (approximately 0.5 g) using the FastDNA spin kit for soil and the FastPrep instrument (MP Biomedicals, Santa Ana, CA, USA). PCR was performed with the following oligonucleotide primers: Bac27F (26) and Uni1406R (18) for the bacterial 16S rRNA gene, Arc9F (27) and Uni1406R for the archaeal 16S rRNA gene, A189f and A682r (28) for pmoA, and cbbM343F and cbbM1226R (29) for cbbM. In addition, PCRs for pmoA and cbbM were also performed for the DNA extracts from the iron-rich microbial mat collected previously in Budo Pond, Hiroshima University, Japan (20).…”

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities

“…The cbbL gene is found in plants, green algae, Cyanobacteria and many chemolithoautotrophs, whereas cbbM is reported to occur in several photosynthetic bacteria, aerobic and facultative anaerobic chemoautotrophic bacteria and dinoflagellates [6]. The occurrence of the cbbM gene has been exclusively investigated for chemolithoautotrophy from aquatic habitats such as hydrothermal vents [5], hypersaline habitats [7], soda lake sediments [8], thermal Springs [9], Movile Cave in Romania [10], with only one study from a terrestrial ecosystem reported so far [11].…”