Tec-Campos Diego, Tibocha-Bonilla Juan D, Jiang Celina, Passi Anurag, Thiruppathy Deepan, Zuñiga Cristal, Posadas Camila, Zepeda Alejandro, Zengler Karsten
Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México.
Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, United States of America.
PLoS Comput Biol. 2025 Jan 7;21(1):e1012736. doi: 10.1371/journal.pcbi.1012736. eCollection 2025 Jan.
The denitrifying bacterium Thauera sp. MZ1T, a common member of microbial communities in wastewater treatment facilities, can produce different compounds from a range of carbon (C) and nitrogen (N) sources under aerobic and anaerobic conditions. In these different conditions, Thauera modifies its metabolism to produce different compounds that influence the microbial community. In particular, Thauera sp. MZ1T produces different exopolysaccharides with floc-forming properties, impacting the physical disposition of wastewater consortia and the efficiency of nutrient assimilation by the microbial community. Under N-limiting conditions, Thauera sp. MZ1T decreases its growth rate and accelerates the accumulation of polyhydroxyalkanoate-related (PHA) compounds including polyhydroxybutyrate (PHB), which plays a fundamental role as C and energy storage in this β-proteobacterium. However, the metabolic mechanisms employed by Thauera sp. MZ1T to assimilate and catabolize many of the different C and N sources under aerobic and anaerobic conditions remain unknown. Systems biology approaches such as genome-scale metabolic modeling have been successfully used to unveil complex metabolic mechanisms for various microorganisms. Here, we developed a comprehensive metabolic model (M-model) for Thauera sp. MZ1T (iThauera861), consisting of 1,744 metabolites, 2,384 reactions, and 861 genes. We validated the model experimentally using over 70 different C and N sources under both aerobic and anaerobic conditions. iThauera861 achieved a prediction accuracy of 95% for growth on various C and N sources and close to 85% for assimilation of aromatic compounds under denitrifying conditions. The M-model was subsequently deployed to determine the effects of substrates, oxygen presence, and the C:N ratio on the production of PHB and exopolysaccharides (EPS), showing the highest polymer yields are achieved with nucleotides and amino acids under aerobic conditions. This comprehensive M-model will help reveal the metabolic processes by which this ubiquitous species influences communities in wastewater treatment systems and natural environments.
脱氮细菌陶厄氏菌属菌株MZ1T是废水处理设施中微生物群落的常见成员，在有氧和厌氧条件下，它可以利用多种碳（C）源和氮（N）源产生不同的化合物。在这些不同条件下，陶厄氏菌会改变其代谢以产生影响微生物群落的不同化合物。特别是，陶厄氏菌属菌株MZ1T会产生具有絮凝形成特性的不同胞外多糖，影响废水菌群的物理分布以及微生物群落对养分的同化效率。在氮限制条件下，陶厄氏菌属菌株MZ1T会降低其生长速率，并加速包括聚羟基丁酸酯（PHB）在内的聚羟基链烷酸酯相关（PHA）化合物的积累，PHB在这种β-变形杆菌中作为碳和能量储存发挥着重要作用。然而，陶厄氏菌属菌株MZ1T在有氧和厌氧条件下吸收和分解代谢许多不同碳源和氮源所采用的代谢机制仍然未知。诸如基因组规模代谢建模等系统生物学方法已成功用于揭示各种微生物的复杂代谢机制。在此，我们为陶厄氏菌属菌株MZ1T（iThauera861）开发了一个综合代谢模型（M模型），该模型由1744种代谢物、2384个反应和861个基因组成。我们在有氧和厌氧条件下使用70多种不同的碳源和氮源对该模型进行了实验验证。iThauera861在各种碳源和氮源上生长的预测准确率达到95%，在反硝化条件下对芳香族化合物同化的预测准确率接近85%。随后，利用该M模型确定了底物、氧气存在以及碳氮比对PHB和胞外多糖（EPS）产生的影响，结果表明在有氧条件下，核苷酸和氨基酸可实现最高的聚合物产量。这个综合M模型将有助于揭示这种普遍存在的物种影响废水处理系统和自然环境中群落的代谢过程。
