Interspecies chemical signalling in a methane-oxidizing bacterial community

Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide a carbon and energy source for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structure and function these communities. Here we show that many members of the Methylomonas genus possess a LuxR-type acyl-homoserine lactone (acyl-HSL) receptor/transcription factor highly homologous to MbaR from the quorum sensing (QS) system of Methylobacter tundripaludum, another methane-oxidizer that has been isolated from the same environment. We reconstitute this detection system in Escherichia coli and also use mutant and transcriptomic analysis to show that the receptor from Methylomonas species strain LW13 (LW13) is active and alters LW13 gene expression in response to the acyl-HSL produced by M. tundripaludum. These findings provide a molecular mechanism for how two species of bacteria that may compete for resources in the environment can interact in a specific manner through a chemical signal. In order to determine which genes MmsR regulates in response to acyl-HSL signal, we compared the transcriptome of exponentially growing LW13 in the presence or absence of 3-OH-C10-HSL. As a control for gene changes that are not the result of signal binding to MmsR, we constructed an unmarked, in-frame deletion of mmsR (∆mmsR) and also compared the transcriptome of this strain in the presence and absence of signal. For each condition, we sequenced the transcriptomes of two biological replicates.

厌氧生态系统产生甲烷后，环境中多种细菌会对其进行氧化代谢。这些微生物为自身无法氧化甲烷的物种提供了碳源与能量来源，不仅在相应生态位中发挥关键作用，还能在这种强效温室气体进入大气前将其固定封存。
解析甲烷氧化细菌在环境中的互作分子机制，有助于我们理解调控这类群落结构与功能的重要方面。
本研究发现，甲基单胞菌属（Methylomonas）的多个菌株均携带一类LuxR型酰基高丝氨酸内酯（acyl-HSL）受体/转录因子，其与苔原甲基杆菌（Methylobacter tundripaludum）群体感应（QS）系统中的MbaR高度同源；苔原甲基杆菌是另一种可从相同环境中分离得到的甲烷氧化细菌。
我们在大肠杆菌（Escherichia coli）中重构了这套检测系统，并通过突变体与转录组学分析证实，甲基单胞菌菌株LW13（LW13）的该受体具有活性，可响应苔原甲基杆菌产生的acyl-HSL并调控LW13的基因表达。
上述研究结果为两种可能在环境中竞争资源的细菌如何通过化学信号进行特异性互作提供了分子层面的机制解释。
为明确MmsR在响应acyl-HSL信号时调控的靶基因，我们对比了指数生长期的LW13菌株在添加与不添加3-OH-C10-HSL条件下的转录组。
为排除非信号结合MmsR所致的基因表达变化，我们构建了mmsR的无痕框内缺失突变株（∆mmsR），并同样对比了该菌株在添加与不添加信号分子条件下的转录组。
针对每一组实验条件，我们均对两份生物学重复样本进行了转录组测序。