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Data report: cultivation of microorganisms from basaltic rock and sediment cores from the North Pond on the western flank of the Mid-Atlantic Ridge, IODP Expedition 336

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      Abstract

      Cultivation experiments targeting chemolithoautotrophic microorganisms were performed using subseafloor basaltic cores (the deepest sample is from 315 meters below seafloor [mbsf] and overlying sediment cores (the deepest sample is from 91.4 mbsf) from North Pond on the western flank of the Mid-Atlantic Ridge. The cores were recovered by the R/V JOIDES Resolution during Integrated Ocean Drilling Program Expedition 336. Different bacteria were grown under different media and temperature conditions. In the enrichment cultures of the basaltic cores under aerobic conditions, frequently detected bacteria at 8°C and 25°C were members of the genera Ralstonia (the class Betaproteobacteria) and Pseudomonas (Gammaproteobacteria), whereas members of the genera Paenibacillus (Bacilli) and Acidovorax (Betaproteobacteria) were conspicuous at 37°C. Bacillus spp. (Bacilli) were outstanding at 37°C under anaerobic conditions. In the enriched cultures of the sediment cores, bacterial growth was observed at 15°C but not at 37°C, and the bacteria detected at 15°C mostly belonged to gammaproteobacterial genera such as Pseudomonas , Halomonas , and Marinobacter . All of the bacteria detected in this study were enriched only, and subcultivation of the enriched cultures in the respective original media did not succeed. The presence of hydrogenotrophic methanogens was examined by a culture-dependent or a culture-independent analysis in the basalt and sediment cores but was not proven. A fungal isolate was obtained from a single basaltic core an d belonged to the genus Exophiala of the order Chaetothyriales.

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        Archaea (archaebacteria) are a phenotypically diverse group of microorganisms that share a common evolutionary history. There are four general phenotypic groups of archaea: the methanogens, the extreme halophiles, the sulfate-reducing archaea, and the extreme thermophiles. In the marine environment, archaeal habitats are generally limited to shallow or deep-sea anaerobic sediments (free-living and endosymbiotic methanogens), hot springs or deep-sea hydrothermal vents (methanogens, sulfate reducers, and extreme thermophiles), and highly saline land-locked seas (halophiles). This report provides evidence for the widespread occurrence of unusual archaea in oxygenated coastal surface waters of North America. Quantitative estimates indicated that up to 2% of the total ribosomal RNA extracted from coastal bacterioplankton assemblages was archaeal. Archaeal small-subunit ribosomal RNA-encoding DNAs (rDNAs) were cloned from mixed bacterioplankton populations collected at geographically distant sampling sites. Phylogenetic and nucleotide signature analyses of these cloned rDNAs revealed the presence of two lineages of archaea, each sharing the diagnostic signatures and structural features previously established for the domain Archaea. Both of these lineages were found in bacterioplankton populations collected off the east and west coasts of North America. The abundance and distribution of these archaea in oxic coastal surface waters suggests that these microorganisms represent undescribed physiological types of archaea, which reside and compete with aerobic, mesophilic eubacteria in marine coastal environments.
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          The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions.

          Polymerase chain reaction conditions were established for the in vitro amplification of eukaryotic small subunit ribosomal (16S-like) rRNA genes. Coding regions from algae, fungi, and protozoa were amplified from nanogram quantities of genomic DNA or recombinant plasmids containing rDNA genes. Oligodeoxynucleotides that are complementary to conserved regions at the 5' and 3' termini of eukaryotic 16S-like rRNAs were used to prime DNA synthesis in repetitive cycles of denaturation, reannealing, and DNA synthesis. The fidelity of synthesis for the amplification products was evaluated by comparisons with sequences of previously reported rRNA genes or with primer extension analyses of rRNAs. Fewer than one error per 2000 positions were observed in the amplified rRNA coding region sequences. The primary structure of the 16S-like rRNA from the marine diatom, Skeletonema costatum, was inferred from the sequence of its in vitro amplified coding region.
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            Author and article information

            Journal
            10.2204/iodp.proc.336.2012
            Proceedings of the IODP
            Integrated Ocean Drilling Program
            1930-1014
            28 April 2015
            10.2204/iodp.proc.336.204.2015

            This work is licensed under a Creative Commons Attribution 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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            Self URI (journal page): http://publications.iodp.org/

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