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. Overall design: 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.环境中，厌氧生态系统产生甲烷后，多种细菌可对其进行氧化代谢。这些细菌可为自身无法氧化甲烷的物种提供碳源与能量来源，不仅在相应生态位中发挥关键作用，还能在强效温室气体甲烷进入大气前将其隔离封存。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微生物群落结构与功能的重要环节。本研究发现，甲基单胞菌属（Methylomonas）的多个成员拥有一类LuxR型酰基高丝氨酸内酯（acyl-HSL）受体/转录因子，其与冻土甲基杆菌（Methylobacter tundripaludum，一种从相同环境中分离得到的甲烷氧化菌）的群体感应（QS）系统中的MbaR高度同源。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分析证实，来自甲基单胞菌菌株LW13（LW13）的该受体具有活性，可响应冻土甲基杆菌（M. tundripaludum）产生的酰基高丝氨酸内酯，进而调控LW13的基因表达。上述发现为环境中可能竞争资源的两种细菌如何通过化学信号进行特异性互作提供了分子机制解释。实验整体设计：为明确MmsR响应酰基高丝氨酸内酯信号所调控的基因，我们比较了指数生长期LW13菌株在添加与不添加3-OH-C10-HSL条件下的转录组。为排除信号不结合MmsR所导致的基因表达变化，我们构建了mmsR的无痕框内缺失突变株（ΔmmsR），并分别比较该菌株在添加与不添加信号分子时的转录组。每种实验条件均设置2次生物学重复，并对其转录组进行测序。