Pyrosequencing Revealed SAR116 Clade as Dominant dddP-Containing Bacteria in Oligotrophic NW Pacific Ocean

Abstract

Dimethyl sulfide (DMS) is a climatically active gas released into the atmosphere from oceans. It is produced mainly by bacterial enzymatic cleavage of dimethylsulfoniopropionate (DMSP), and six DMSP lyases have been identified to date. To determine the biogeographical distribution of bacteria relevant to DMS production, we investigated the diversity of dddP—the most abundant DMS-producing gene—in the northwestern Pacific Ocean using newly developed primers and the pyrosequencing method. Consistent with previous studies, the major dddP-containing bacteria in coastal areas were those belonging to the Roseobacter clade. However, genotypes closely related to the SAR116 group were found to represent a large portion of dddP-containing bacteria in the surface waters of the oligotrophic ocean. The addition of DMSP to a culture of the SAR116 strain Candidatus Puniceispirillum marinum IMCC1322 resulted in the production of DMS and upregulated expression of the dddP gene. Considering the large area of oligotrophic water and the wide distribution of the SAR116 group in oceans worldwide, we propose that these bacteria may play an important role in oceanic DMS production and biogeochemical sulfur cycles, especially via bacteria-mediated DMSP degradation.

Niche partitioning of picocyanobacterial lineages in the oligotrophic northwestern Pacific Ocean

“…Two liter water samples were passed through a 0.2-µm Supor filter (Gelman Sciences, Ann Arbor, MI, USA), and the filters were frozen at -80°C after adding 1 mL STE buffer (100 mM NaCl, 10 mM Tris-HCl, 1 mM EDTA, pH 8.0). DNA was extracted using the method of Choi et al (2015).…”

Seasonal Variation of Picocyanobacterial Community Composition in Seawaters Around Dokdo, Korea

“…DNA의 추출 및 정제는 lysozyme, SDS 및 proteinase K로 세포를 용해시킨 후 DNeasy blood and tissue kit(Qiagen)을 이용하였다 (Choi et al, 2015).…”

Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines

“…Pelagibacter , a member of the SAR11 clade, was recently shown to assimilate dimethylsulfoniopropionate (DMSP) producing dimethyl sulfide (DMS), an important compound for climate regulation ( Sun et al, 2016 ). Another DMS-producer, SAR116 (under class Alphaproteobacteria), which has been shown to be abundant in the northwest Pacific Ocean ( Choi et al, 2015 ), was also detected in the BR dataset. The abundance of archaea in the Benham Rise UMP corroborates the finding that archaea dominate the mesopelagic layer of the Pacific Ocean ( Karner, DeLong & Karl, 2001 ).…”