Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84

IF 11.4 1区环境科学与生态学 Q1 ENGINEERING, ENVIRONMENTAL

Water Research Pub Date : 2025-04-16 DOI:10.1016/j.watres.2025.123598

Jiapeng Li , Xiaotian Zuo , Qianqian Chen , Yanting Lin , Fangang Meng

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Abstract

Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.

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基因组解析宏基因组分析揭示了来自SC-I-84属的一种具有截断亚硝酸盐还原途径的新型反硝化菌

了解部分反硝化（PD）细菌的基因组和生态学特性对开发废水处理技术具有重要意义。在这项研究中，一个基于PD的生物反应器被操作，产生了一个由潜在的新型PD功能细菌（SC-I-84）主导的混合培养。在SC-I-84富集体系中，硝酸盐还原活性和亚硝酸盐生成活性逐渐增加，而亚硝酸盐还原活性总是可以忽略不计。系统发育分析表明，cs - i -84与未培养的β -变形菌（99%）亲缘关系密切，而其反硝化功能基因（napA、napB、narV和narY）显示出与Burkholderiales铜属染色体基因共同进化的证据。在SC-I-84的遗传图谱中，只鉴定到硝酸盐还原基因（nar和nap），而亚硝酸盐还原基因（nir）缺失。值得注意的是，硝酸盐还原基因与碳代谢基因（如b /C， mdh, idh）相邻，并且发现了高丰度的三羧酸（TCA）循环基因。这可以提高SC-I-84中硝酸盐还原基因对电子供体的利用效率，从而提高反硝化活性。SC-I-84与部分参与氮碳代谢的细菌及其他PD菌呈正合作关系，与全反硝化菌呈负相互作用。这些结果表明，SC-I-84的富集限制了全反硝化细菌的生长，有助于维持PD过程的稳定。总之，新的PD功能细菌的元基因组分析有望增强我们对PD过程的理解，并有助于开发基于PD的废水处理工艺。

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来源期刊

Water Research 环境科学-工程：环境

CiteScore

20.80

自引率

9.40%

发文量

1307

审稿时长

38 days

期刊介绍： Water Research, along with its open access companion journal Water Research X, serves as a platform for publishing original research papers covering various aspects of the science and technology related to the anthropogenic water cycle, water quality, and its management worldwide. The audience targeted by the journal comprises biologists, chemical engineers, chemists, civil engineers, environmental engineers, limnologists, and microbiologists. The scope of the journal include: •Treatment processes for water and wastewaters (municipal, agricultural, industrial, and on-site treatment), including resource recovery and residuals management; •Urban hydrology including sewer systems, stormwater management, and green infrastructure; •Drinking water treatment and distribution; •Potable and non-potable water reuse; •Sanitation, public health, and risk assessment; •Anaerobic digestion, solid and hazardous waste management, including source characterization and the effects and control of leachates and gaseous emissions; •Contaminants (chemical, microbial, anthropogenic particles such as nanoparticles or microplastics) and related water quality sensing, monitoring, fate, and assessment; •Anthropogenic impacts on inland, tidal, coastal and urban waters, focusing on surface and ground waters, and point and non-point sources of pollution; •Environmental restoration, linked to surface water, groundwater and groundwater remediation; •Analysis of the interfaces between sediments and water, and between water and atmosphere, focusing specifically on anthropogenic impacts; •Mathematical modelling, systems analysis, machine learning, and beneficial use of big data related to the anthropogenic water cycle; •Socio-economic, policy, and regulations studies.