Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil
Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil
复制标题
揭示一种未培养的伽马变形杆菌的代谢特征，该细菌负责石油污染土壤中 PAH 的原位生物降解
DOI：
10.1111/1462-2920.15814
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发表时间：
2021-10-21
影响因子：
5.1
通讯作者：
Yuan, Yong
中科院分区：
文献类型：
--
作者：
Cai, Xixi;Li, Jibing;Yuan, Yong
探索土著多环芳烃降解菌的代谢特性是理解自然环境中多环芳烃生物修复机制的关键。虽然稳定同位素探测（SIP）是一种可行的方法来确定功能微生物在复杂的环境中，未培养的降解菌的代谢特征仍然是难以捉摸的。本研究采用SIP、扩增子测序和宏基因组分箱相结合的方法，研究了石油污染土壤中萘（NAP）的生物降解。基于SIP和扩增子测序结果，将未培养的γ-变形杆菌属鉴定为关键NAP降解菌。此外，通过将其16 S rRNA基因与SIP鉴定的OTU序列匹配，从C-13-DNA宏基因组成功获得了该未培养降解物的组装基因组。同时，在该基因组中鉴定了一些编码萘/多环芳烃双加氧酶的NAP降解基因，进一步证实了该土著降解剂直接参与NAP降解。该降解剂含有与多种碳源、能量物质和维生素代谢相关的基因，阐明了微生物不能培养并最终实现培养的潜在原因。我们的研究结果提供了新的信息，在原位多环芳烃生物降解的机制，并增加了我们目前的知识，通过结合SIP和宏基因组分仓培养不可培养的微生物。
Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable-isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the C-13-DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non-culturable microorganisms by combining both SIP and metagenome binning.