Men Yujie, Yu Ke, Bælum Jacob, Gao Ying, Tremblay Julien, Prestat Emmanuel, Stenuit Ben, Tringe Susannah G, Jansson Janet, Zhang Tong, Alvarez-Cohen Lisa
Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA
Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA.
Appl Environ Microbiol. 2017 Mar 31;83(8). doi: 10.1128/AEM.03508-16. Print 2017 Apr 15.
The aim of this study is to obtain a systems-level understanding of the interactions between and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid biosynthesis pathway was also assigned to the bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. The key chloroethene-dechlorinating bacterium is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of species in the communities compared to other coexisting community members in producing and providing corrinoids for species under cobalamin-limited conditions.
本研究的目的是通过分析三氯乙烯（TCE）脱氯富集培养物中的群落结构、功能组成、活性和动态变化，从系统层面了解与类咕啉供应微生物之间的相互作用。对添加和不添加外源性钴胺素的脱氯富集培养物的宏基因组和宏转录组进行了比较。从宏基因组中分类出了7个假定的草图基因组。在早期阶段（2天），在不添加外源性钴胺素的富集培养物的宏转录组中检测到的bin基因组中的基因转录本比添加了钴胺素的富集培养物中的更多。在这些基因中，不添加钴胺素时，与芽孢形成相关的基因表现出最高的差异表达，这表明类咕啉从类咕啉生产者中释放的一种可能途径。其他差异表达的基因包括参与能量守恒和营养物质运输（包括钴运输）的基因。表达量最高的类咕啉生物合成途径也被指定到bin基因组。靶向定量PCR（qPCR）分析证实，在不添加外源性钴胺素的富集培养物中，那些类咕啉生物合成基因的转录本丰度高于添加了钴胺素的富集培养物。此外，在钴胺素胁迫下，的类咕啉挽救和修饰途径被上调。本研究为钴胺素限制条件下脱氯群落成员之间的微生物相互作用和作用提供了重要见解。关键的氯乙烯脱氯细菌是一种钴胺素营养缺陷型，因此从其他群落成员那里获取类咕啉。因此，研究与群落中提供类咕啉的微生物之间的微生物-微生物相互作用很重要。本研究提供了系统层面的信息，即不同钴胺素条件下脱氯群落中支持性微生物的分类和功能组成及动态变化。这些发现揭示了在钴胺素限制条件下，与其他共存群落成员相比，物种在群落中为物种产生和提供类咕啉方面的重要作用。
