Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany.
Present address: Institute of Agricultural and Nutritional Sciences, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Strasse 5, Halle (Saale), Germany.
Microbiome. 2024 Feb 26;12(1):39. doi: 10.1186/s40168-023-01739-z.
The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).
The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.
The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.
生物聚合物的厌氧分解的最后一步是产甲烷作用。稻田土壤是甲烷的主要人为来源，稻草通常用作稻田施肥。在这里，我们旨在解析甲烷菌群落结构和功能对菲律宾稻田土壤延长缺氧培养（120 天）中添加稻草的响应。该研究结合了过程测量、特定生物标志物（16S rRNA、mcrA）的定量实时 PCR 和 RT-PCR，以及元组学（环境基因组学和转录组学）。
分析方法共同揭示了两个主要的细菌和产甲烷活性阶段：早期（第 7 天至 21 天）和晚期（第 28 天至 60 天）群落响应，微生物基因和转录物丰度以及 CH4 产生率的显著瞬态下降将两者分开。两个产甲烷活性阶段对应于 Methanosarcinaceae 的最大 rRNA 和 mRNA 丰度，但表达的产甲烷途径不同。虽然三个遗传上不同的 Methanosarcina 种群在早期活性阶段有助于乙酸营养型产甲烷作用，但晚期活性阶段由单个 Methanosarcina 基因组种执行的甲基营养型产甲烷作用定义。与 Methanosarcina sp. MSH10X1 密切相关，将环境转录物映射到宏基因组组装基因组（MAG）和种群特异性参考基因组上，揭示了该基因组种是乙酸营养型和甲基营养型产甲烷作用的关键参与者。厌氧食物网由一个复杂的细菌群落驱动，Geobacteraceae 和 Peptococcaceae 是与 Methanosarcina 功能相互作用的潜在候选者。Methanocellaceae 成员是氢营养型产甲烷作用的关键参与者，而 Methanotrichaceae 成员的乙酸营养活性仅在群落反应的后期才能检测到。
由单个 Methanosarcina 基因组种优先但时间转移表达的乙酸营养型和甲基营养型产甲烷作用代表了一个新的发现，扩展了我们迄今为止对在稻田土壤中高度表达的产甲烷途径的知识。
