Table_2_Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.xlsx

Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.

糖杆菌候选门（Saccharibacteria）的生物体常作为烃类降解群落的活跃成员被检出，但其在烃类降解中的实际作用仍不明晰。本研究采用基因组解析宏基因组学（genome-resolved metagenomics），对3批添加烃类的地下水样品富集培养物展开分析，以解析土著糖杆菌候选门生物的代谢潜能。基于核糖体蛋白的群落谱分析结果显示，尽管培养条件完全一致，各富集培养物的群落组成差异显著，重现性极差。通过核糖体蛋白聚类与重建基因组读段比对分析，3批富集培养物间共享的群落成员占比仅分别为17.5%与12.5%。在其中一批富集培养物中，2株糖杆菌候选门菌株以16.6%的相对丰度成为群落优势类群，我们成功获取了二者的近完整基因组。对其有限代谢网络的详细剖析表明，此类菌株具备肽降解能力，可利用多种己糖进行乳酸发酵，且提示其采取 scavenging生存模式，即从外界获取分子构建单元。与此前认为糖杆菌候选门生物直接参与烃类降解的研究结论相悖，本研究的分析结果证实，此类生物可在群落中成为丰度较高的 scavenger类群，其角色更偏向有机碳汇，而非烃类降解者。