Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America.
PLoS One. 2011;6(8):e23973. doi: 10.1371/journal.pone.0023973. Epub 2011 Aug 23.
The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique) genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF)-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of (14)C-labeled compounds to (14)CO(2) indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT), trimethylamine (TMA), trimethylamine N-oxide (TMAO), and dimethylsulfoniopropionate (DMSP) were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of (14)C-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27-35%) than of C1 compounds (2-6%) into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO(2) in the upper ocean.
海洋中最丰富的异养生物是 SAR11α 变形菌，它们被认为在矿化海洋溶解有机碳方面发挥着重要作用。它们的基因组是已知自由生活异养细胞中最小的基因组之一，这引发了一个问题，即它们如何成功地利用具有有限代谢途径的复杂有机物。在这里，我们表明 SAR11 亚群 Ia（疑似 Pelagibacter ubique）基因组中的保守基因编码了各种一碳化合物和甲基化化合物中甲基基团的氧化途径。这些途径预计通过四氢叶酸 (THF) 介导的氧化产生能量，但不能支持从 C1 化合物中净同化生物质。细胞内 ATP 含量的测量和（14）C 标记化合物的氧化表明甲醇、甲醛、甲胺和甘氨酸甜菜碱 (GBT)、三甲胺 (TMA)、三甲胺 N-氧化物 (TMAO) 和二甲亚砜 (DMSP) 的甲基基团可被 SAR11 菌株 Ca. P. ubique HTCC1062 的无菌培养物氧化。对宏基因组数据的分析表明，C1 代谢基因在自然 SAR11 种群中高频出现。在短期培养中，马尾藻海微生物浮游生物的自然群落表现出氧化（14）C 标记的甲酸盐、甲醛、甲醇和 TMAO 的潜力，这与培养的 SAR11 细胞相似，并且与培养的 SAR11 细胞一样，将丙酮酸和葡萄糖（27-35%）的比例纳入生物量的比例明显高于 C1 化合物（2-6%）。总的来说，这些基因组、细胞和环境数据表明 SAR11 培养物和以 SAR11 为主导的自然微生物群落中存在令人惊讶的脱甲基和 C1 氧化能力，并支持 C1 氧化可能是将溶解有机碳循环回上层海洋 CO2 的重要途径的结论。
