PDF(Pubmed)
Abstract：
BACKGROUND: 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).
RESULTS: 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 CH4 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.
CONCLUSIONS: 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.
RESULTS: 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 CH4 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.
CONCLUSIONS: 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.
摘要：
背景：生物聚合物厌氧分解的最后一步是产甲烷。稻田土壤是甲烷的主要人为来源，稻草通常用作水稻种植中的肥料。这里,我们旨在破译产甲烷群落在菲律宾稻田的长期缺氧孵化（120天）过程中对稻草添加的结构和功能响应。该研究结合了过程测量，特定生物标志物的定量实时PCR和RT-PCR(16SrRNA，mcrA)，和元组学（环境基因组学和转录组学）。
结果：分析方法共同揭示了两个主要的细菌和产甲烷活动阶段：早期（第7至21天）和晚期（第28至60天）社区反应，通过微生物基因和转录本丰度以及CH4生产率的显着瞬时下降而分开。两个产甲烷活性阶段对应于甲烷科的最大rRNA和mRNA丰度，但表达的产甲烷途径不同。虽然在早期活动阶段，三个遗传上不同的甲烷杆菌属种群促进了乙酸碎屑甲烷生成，后期活动阶段由单个甲烷弧菌基因组进行的甲基营养甲烷生成定义。与甲烷紧密相关。MSH10X1，将环境转录本映射到宏基因组组装的基因组（MAGs）和特定于种群的参考基因组上，揭示了该基因组物种是乙酰分解和甲基营养甲烷生成的关键参与者。厌氧食物网是由复杂的细菌群落驱动的，地细菌科和Peptococaceae被认为是与甲烷藻功能相互作用的候选者。甲烷科的成员是氢营养甲烷生成的关键参与者，只有在非常晚的社区反应中才能检测到甲烷科成员的切屑活性。
结论：单个甲烷杆菌属物种对乙酰碎屑和甲基营养甲烷生成的主要但时移表达代表了一个新发现，扩展了我们迄今为止对稻田土壤中高表达的甲烷生成途径的认识。视频摘要。
结果：分析方法共同揭示了两个主要的细菌和产甲烷活动阶段：早期（第7至21天）和晚期（第28至60天）社区反应，通过微生物基因和转录本丰度以及CH4生产率的显着瞬时下降而分开。两个产甲烷活性阶段对应于甲烷科的最大rRNA和mRNA丰度，但表达的产甲烷途径不同。虽然在早期活动阶段，三个遗传上不同的甲烷杆菌属种群促进了乙酸碎屑甲烷生成，后期活动阶段由单个甲烷弧菌基因组进行的甲基营养甲烷生成定义。与甲烷紧密相关。MSH10X1，将环境转录本映射到宏基因组组装的基因组（MAGs）和特定于种群的参考基因组上，揭示了该基因组物种是乙酰分解和甲基营养甲烷生成的关键参与者。厌氧食物网是由复杂的细菌群落驱动的，地细菌科和Peptococaceae被认为是与甲烷藻功能相互作用的候选者。甲烷科的成员是氢营养甲烷生成的关键参与者，只有在非常晚的社区反应中才能检测到甲烷科成员的切屑活性。
结论：单个甲烷杆菌属物种对乙酰碎屑和甲基营养甲烷生成的主要但时移表达代表了一个新发现，扩展了我们迄今为止对稻田土壤中高表达的甲烷生成途径的认识。视频摘要。
