Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China.
Microb Ecol. 2023 Nov;86(4):3043-3056. doi: 10.1007/s00248-023-02307-6. Epub 2023 Oct 13.
Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.
海洋中微生物碳泵（MCP）产生的顽固溶解有机碳（RDOC）对于碳封存和调节地球历史上的气候变化至关重要。然而，微生物在陆地水生系统（如河流和湖泊）中形成 RDOC 的重要性仍有待确定。通过整合宏基因组（MG）和宏转录组（MT）测序，我们定义了中国西南典型喀斯特河流——漓江的水和底泥中的微生物群落及其转录活性。β变形菌在水中占优势，是重塑溶解有机碳（DOC）的最常见种群。从水和底泥中回收了 45 个宏基因组组装基因组（MAG）。MAG 的功能注释表明，尽管变形菌门广泛存在纤维素和几丁质利用基因，但在降解复杂碳方面的多功能性较差，而拟杆菌门在利用大分子有机碳方面具有很高的潜力。代谢重塑表明，细菌群落中增加的共享代谢物与 DOC 浓度的增加有关，这突出了微生物在产生和重塑碳成分过程中合作的重要性。β-氧化、亮氨酸降解和甲羟戊酸（MVA）模块与 RDOC 的浓度呈显著正相关。在喀斯特河流中，Limnohabitans 和 UBA4660 相关 MAG 中的亮氨酸降解途径被阻断与 RDOC 的减少有关，而含有完整亮氨酸降解途径的 Fluviicola 相关 MAG 与 RDOC 浓度呈正相关。总的来说，我们的研究揭示了细菌代谢过程与碳封存之间的联系。这为微生物在喀斯特河流碳汇中的作用提供了新的见解。
