SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment.
SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment.
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DOI：
10.1038/ismej.2015.37
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发表时间：
2015-11
期刊：
影响因子：
--
通讯作者：
Schäfer H
中科院分区：
文献类型：
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作者：
Eyice Ö;Namura M;Chen Y;Mead A;Samavedam S;Schäfer H
二甲基硫（DMS）在全球硫循环和大气化学中具有重要作用。微生物利用二甲基硫作为唯一的碳、硫或能量来源，有助于二甲基硫在各种生态系统中的循环。人们对陆地环境中降解二甲硫醚的微生物种群的多样性知之甚少。根据培养研究，从陆地生态系统中分离出的各种细菌都能降解二甲硫醚，但仍不清楚这些细菌中是否有任何一种在原地发挥重要作用。在这项研究中，我们确定细菌使用DMS作为碳源和能源在陆地环境中，农业土壤和湖泊沉积物，通过DNA稳定同位素探测（SIP）。通过变性梯度凝胶电泳、SIP梯度组分的高通量测序和phi 29扩增的群落DNA的宏基因组测序分析了参与DMS降解的微生物群落。标签模式的时间进程SIP实验确定的Methylophilaceae家庭的成员，以前没有牵连的DMS降解，占主导地位的DMS降解人口在土壤和湖泊沉积物。硫杆菌属在SIP孵育的13 C-DNA中也检测到。宏基因组测序还表明参与甲基嗜菌科在DMS降解，并进一步表明在DMS同化社区的功能配置文件中的甲基营养和无机硫化合物的氧化线的转变。总体而言，这些数据表明，与在海洋环境中通过SIP将γ蛋白细菌群体鉴定为DMS降解剂不同，β蛋白细菌嗜甲基菌科可能在陆地环境中的DMS循环中发挥关键作用。
Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in 13C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments.