Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.

中文翻译：

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嗜热堆肥的基因组解析宏基因组和宏转录组分析揭示了关键细菌参与者及其代谢相互作用

堆肥是有机材料环保降解的重要技术，是微生物驱动的过程。以前的堆肥宏基因组研究对其微生物种群的分类和功能多样性进行了一般描述，但缺乏有关在此过程中活跃的关键生物体的更具体信息。在这里，我们展示并分析了从两个嗜热堆肥细胞的时间序列样本中恢复的 60 个大部分高质量的宏基因组组装基因组 (MAG)，其中 47 个是潜在的新细菌物种；其中 24 个在两个公共 MAG 数据集中没有任何 95% 平均核苷酸同一性水平的命中。根据其中一个细胞的元转录组数据对基因内容和表达功能进行分析，在 99 天的堆肥过程中将 MAG 分为三个簇。通过应用代谢建模方法，我们能够预测 MAG 之间的代谢依赖性。这些模型表明辅助细菌的重要性，这些细菌不进行木质纤维素降解，但可能有助于活性氧的管理，并具有提高堆肥生物能效率的酶，例如氢化酶和N2O还原酶。MAG 之间预测的强代谢依赖性揭示了依赖于 H+、NH3、O2 和 CO2 以及葡萄糖、谷氨酸、琥珀酸、富马酸等交换的关键相互作用，强调了生物质转化过程中功能分层和互养相互作用的重要性。我们的模型包括从一个堆肥单元数据中恢复的 49 个 MAG 中的 22 个。基于这个模型，我们强调红热菌、双孢热双孢菌和一种新型的伽玛变形杆菌是化学营养代谢和交叉喂养相互作用中的主要参与者。获得的结果扩展了我们对堆肥细菌的分类和功能多样性的了解，并提供了它们动态代谢相互作用的模型。