Abdallah Rehab Z, Elbehery Ali H A, Ouf Amged, Siam Rania
Biology Department, The American University in Cairo, Cairo, Egypt.
Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt.
Curr Res Microb Sci. 2025 Jul 1;9:100433. doi: 10.1016/j.crmicr.2025.100433. eCollection 2025.
Microbial dark matter (MDM) represents a vast, uncultured fraction of microbial life with largely unknown ecological roles, particularly in extreme environments. This study investigates MDM in the hypersaline microbial mats of Solar Lake, Taba, Egypt, using shotgun metagenomics (∼70 M reads/sample; triplicate sampling across four sites). A total of 364 metagenome-assembled genomes (MAGs) were recovered, of which 116 (∼30 %) were classified as MDM, comprising 55 % archaeal and 45 % bacterial lineages. Functional annotation revealed that ∼14 % of the MDM MAGs had the genetic potential to fix carbon. The genetic makeup of . Lokiarchaeota (5 MAGs, 4.3 %) and Heimdallarchaeota (1 MAG, 0.86 %) suggest a mixotrophic lifestyle. Some non-methanogenic MAGs had the genetic capacity to utilize methanol and glycine-betaine as carbon sources. In addition, . Marinisomatota MAGs had the genetic potential to degrade polysaccharides, while KSB1 MAGs harbored genes for carbohydrate degradation, denitrification, and nitrogen fixation. The high relative abundance of the SOX gene complex, in . Asgardarchaeota and . Coatesbacteria (RBG-13-66-14), highlights MDM community involvment in thiosulfate oxidation. Additionally, a novel Myxococcota MAG encoded a complete photosynthetic gene cluster, including photosystem II, suggesting phototrophic activity along with Cyanobacteria. Collectively, the genetic makeup of the Solar Lake MDM community underpins key processes such as carbon cycling, sulfur reduction, thiosulfate oxidation, nitrogen fixation, and denitrification, driving the biogeochemical dynamics of this unique hypersaline ecosystem.
微生物暗物质（MDM）代表了微生物生命中庞大的未培养部分，其生态作用大多未知，尤其是在极端环境中。本研究利用鸟枪法宏基因组学（约7000万条 reads/样本；在四个地点进行重复采样）对埃及塔巴太阳湖的高盐度微生物垫中的MDM进行了调查。总共获得了364个宏基因组组装基因组（MAG），其中116个（约30%）被归类为MDM，包括55%的古菌谱系和45%的细菌谱系。功能注释显示，约14%的MDM MAG具有固定碳的遗传潜力。洛基古菌门（5个MAG，4.3%）和海姆达尔古菌门（1个MAG，0.86%）的基因组成表明其具有混合营养型生活方式。一些非产甲烷MAG具有利用甲醇和甘氨酸 - 甜菜碱作为碳源的遗传能力。此外，海洋体菌门MAG具有降解多糖的遗传潜力，而KSB1 MAG含有碳水化合物降解、反硝化和固氮基因。在阿斯加德古菌门和科茨氏菌属（RBG - 13 - 66 - 14）中，SOX基因复合体的相对丰度较高，突出了MDM群落参与硫代硫酸盐氧化。此外，一个新的粘球菌门MAG编码了一个完整的光合基因簇，包括光系统II，表明其与蓝细菌一起具有光养活性。总体而言，太阳湖MDM群落的基因组成支撑了碳循环、硫还原、硫代硫酸盐氧化、固氮和反硝化等关键过程，推动了这个独特的高盐生态系统的生物地球化学动态。
