MnOxGeneTool: A Comprehensive Tool for Identifying and Quantifying Mn(II)-Oxidizing Genes, Revealing Phylogenetic Diversity and Environmental Drivers of Mn(II)-Oxidizers

IF 10.8 1区环境科学与生态学 Q1 ENGINEERING, ENVIRONMENTAL

环境科学与技术 Pub Date : 2025-06-03 DOI:10.1021/acs.est.5c01235

Yuhan Wang, Zhengkai Pan, Yuyu Shi, Yaohui Bai, Jinsong Liang, Aijie Wang, Jiuhui Qu

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引用次数: 0

Abstract

Manganese (Mn) oxides are crucial for degrading organic pollutants and driving biogeochemical cycles. Microorganisms drive Mn(II) oxidation, but traditional cultivation-dependent identification methods are inefficient and error-prone. To overcome these limitations, we developed MnOxGeneTool, a bioinformatics tool for identifying and quantifying Mn(II)-oxidizing genes from genomic and metagenomic data. MnOxGeneTool consists of three main components: (1) a curated database of known Mn(II)-oxidizing proteins and their homologues, (2) a hidden Markov models (HMMs) database derived from this protein data set, and (3) a computational pipeline that integrates bioinformatics tools (e.g., HMMER and BLASTX) to identify and quantify Mn(II)-oxidizing genes. We assessed the accuracy and sensitivity of these HMMs through cross-validation, demonstrating their effectiveness in identifying Mn(II)-oxidizing genes in bacterial genomes. Using MnOxGeneTool, we explored the phylogenetic diversity of Mn(II)-oxidizers and identified 824 bacterial genera containing Mn(II)-oxidizing genes, significantly expanding previous knowledge in this field. Additionally, we analyzed metagenomic data from various environments to explore environmental drivers of Mn(II)-oxidizing genes, identifying two potential drivers: oligotrophic conditions and alkaline environments. These findings enable targeted discovery of novel Mn(II)-oxidizers and genetic determinants through identification of their ecological niches and expression optima, thereby expanding MnOxGeneTool’s predictive coverage of uncatalogued Mn(II)-oxidizing proteins. By providing an innovative bioinformatics tool that enables efficient identification and quantification of Mn(II)-oxidizing genes from both genomic and metagenomic data, this study offers significant advancements in the research of biogenic Mn(II) oxidation. The tool is available at https://github.com/wyh19990121/MnOxGeneTool.

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MnOxGeneTool：一个鉴定和定量Mn（II）氧化基因的综合工具，揭示Mn（II）氧化基因的系统发育多样性和环境驱动因素

锰氧化物对降解有机污染物和推动生物地球化学循环至关重要。微生物驱动Mn（II）氧化，但传统的依赖培养的鉴定方法效率低下且容易出错。为了克服这些限制，我们开发了MnOxGeneTool，这是一种生物信息学工具，用于从基因组和宏基因组数据中鉴定和定量Mn（II）氧化基因。MnOxGeneTool由三个主要组成部分组成：(1)已知Mn（II）氧化蛋白及其同源物的策划数据库，(2)从该蛋白质数据集衍生的隐马尔可夫模型（hmm）数据库，以及(3)集成生物信息学工具（例如HMMER和BLASTX）的计算管道，以识别和量化Mn（II）氧化基因。我们通过交叉验证评估了这些hmm的准确性和敏感性，证明了它们在鉴定细菌基因组中Mn（II）氧化基因方面的有效性。利用MnOxGeneTool，我们探索了Mn(II)-氧化剂的系统发育多样性，并鉴定出824个含有Mn(II)-氧化基因的细菌属，大大扩展了该领域的先前知识。此外，我们分析了来自不同环境的宏基因组数据，以探索Mn（II）氧化基因的环境驱动因素，确定了两个潜在的驱动因素：寡营养条件和碱性环境。这些发现使得有针对性地发现新的Mn(II)-氧化剂和遗传决定因子，通过鉴定其生态位和最佳表达，从而扩大了MnOxGeneTool对未分类Mn(II)-氧化蛋白的预测覆盖范围。通过提供一种创新的生物信息学工具，可以从基因组和宏基因组数据中高效地识别和定量Mn（II）氧化基因，本研究为生物源性Mn（II）氧化研究提供了重大进展。该工具可在https://github.com/wyh19990121/MnOxGeneTool上获得。

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来源期刊

环境科学与技术环境科学-工程：环境

CiteScore

17.50

自引率

9.60%

发文量

12359

审稿时长

2.8 months

期刊介绍： Environmental Science & Technology (ES&T) is a co-sponsored academic and technical magazine by the Hubei Provincial Environmental Protection Bureau and the Hubei Provincial Academy of Environmental Sciences. Environmental Science & Technology (ES&T) holds the status of Chinese core journals, scientific papers source journals of China, Chinese Science Citation Database source journals, and Chinese Academic Journal Comprehensive Evaluation Database source journals. This publication focuses on the academic field of environmental protection, featuring articles related to environmental protection and technical advancements.