Table_9_Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan.xlsx

Sulfur-oxidizing bacteria play a crucial role in various processes, including mine bioleaching, biodesulfurization, and treatment of sulfur-containing wastewater. Nevertheless, the pathway involved in sulfur oxidation is highly intricate, making it complete comprehension a formidable and protracted undertaking. The mechanisms of sulfur oxidation within the Acidithiobacillus genus, along with the process of energy production, remain areas that necessitate further research and elucidation. In this study, a novel strain of sulfur-oxidizing bacterium, Acidithiobacillus Ameehan, was isolated. Several physiological characteristics of the strain Ameehan were verified and its complete genome sequence was presented in the study. Besides, the first genome-scale metabolic network model (AMEE_WP1377) was reconstructed for Acidithiobacillus Ameehan to gain a comprehensive understanding of the metabolic capacity of the strain.The characteristics of Acidithiobacillus Ameehan included morphological size and an optimal growth temperature range of 37-45°C, as well as an optimal growth pH range of pH 2.0-8.0. The microbe was found to be capable of growth when sulfur and K2O6S4 were supplied as the energy source and electron donor for CO2 fixation. Conversely, it could not utilize Na2S2O3, FeS2, and FeSO4·7H2O as the energy source or electron donor for CO2 fixation, nor could it grow using glucose or yeast extract as a carbon source. Genome annotation revealed that the strain Ameehan possessed a series of sulfur oxidizing genes that enabled it to oxidize elemental sulfur or various reduced inorganic sulfur compounds (RISCs). In addition, the bacterium also possessed carbon fixing genes involved in the incomplete Calvin-Benson-Bassham (CBB) cycle. However, the bacterium lacked the ability to oxidize iron and fix nitrogen. By implementing a constraint-based flux analysis to predict cellular growth in the presence of 71 carbon sources, 88.7% agreement with experimental Biolog data was observed. Five sulfur oxidation pathways were discovered through model simulations. The optimal sulfur oxidation pathway had the highest ATP production rate of 14.81 mmol/gDW/h, NADH/NADPH production rate of 5.76 mmol/gDW/h, consumed 1.575 mmol/gDW/h of CO2, and 1.5 mmol/gDW/h of sulfur. Our findings provide a comprehensive outlook on the most effective cellular metabolic pathways implicated in sulfur oxidation within Acidithiobacillus Ameehan. It suggests that the OMP (outer-membrane proteins) and SQR enzymes (sulfide: quinone oxidoreductase) have a significant impact on the energy production efficiency of sulfur oxidation, which could have potential biotechnological applications.

硫化菌在多种过程中扮演着至关重要的角色，包括矿山生物浸出、生物脱硫以及含硫废水处理。然而，硫化作用的途径极其复杂，其完全的解析是一项艰巨且漫长的任务。酸硫杆菌属中硫化作用的机制，以及能量产生过程，仍然是亟需进一步研究和阐明的领域。在本研究中，一种新型的硫化菌菌株——酸硫杆菌阿米汉（Acidithiobacillus Ameehan）被分离出来。研究验证了该菌株的多种生理特性，并呈现了其完整的基因组序列。此外，针对酸硫杆菌阿米汉，构建了首个基因组规模代谢网络模型（AMEE_WP1377），以全面了解该菌株的代谢能力。阿米汉菌株的特征包括形态尺寸、最佳生长温度范围为37-45°C，以及最佳生长pH范围为pH 2.0-8.0。该微生物被发现能够在以硫和K2O6S4作为能量源和电子供体进行二氧化碳固定的条件下生长。相反，它不能利用Na2S2O3、FeS2和FeSO4·7H2O作为能量源或电子供体进行二氧化碳固定，也不能以葡萄糖或酵母提取物作为碳源生长。基因组注释揭示了阿米汉菌株拥有一系列硫化作用基因，使其能够氧化单质硫或各种还原无机硫化合物（RISCs）。此外，该细菌还拥有涉及不完全卡尔文-本森-贝什曼（CBB）循环的碳固定基因。然而，该细菌缺乏氧化铁和固定氮的能力。通过实施基于约束的通量分析预测存在71种碳源时的细胞生长，观察到与实验Biolog数据的吻合度达到88.7%。模型模拟发现了五种硫化作用途径。最佳硫化作用途径具有最高的ATP生产速率（14.81 mmol/gDW/h）、NADH/NADPH生产速率（5.76 mmol/gDW/h），消耗了1.575 mmol/gDW/h的二氧化碳和1.5 mmol/gDW/h的硫。我们的研究结果为酸硫杆菌阿米汉中涉及硫化作用的细胞代谢途径提供了全面概述。它表明，外膜蛋白（OMP）和硫化物-醌氧化还原酶（SQR酶）对硫化作用的能量产生效率具有显著影响，这可能在生物技术应用中具有潜力。