Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
School of Earth Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
Arch Microbiol. 2021 Jul;203(5):2521-2540. doi: 10.1007/s00203-021-02227-4. Epub 2021 Mar 7.
The acid ponds of the Danakil Depression in northern Ethiopia are polyextreme environments that exceed the normal physicochemical limits of pH, salinity, ion content, and temperature. We tested for the occurrence of DNA-based life in this environment using Metagenomic Shotgun DNA sequencing approaches. The obtained sequences were examined by the bioinformatic tools MetaSpades, DIAMOND and MEGAN 6-CE, and we were able to bin more than 90% of the metagenomics contigs of Dallol and Black Water to the Bacteria domain, and to the Proteobacteria phylum. Predictions of gene function based on SEED disclosed the presence of different nutrient cycles in the acid ponds. For this study, we focused on partial or completely sequenced genes involved in nitrogen metabolism. The KEGG nitrogen metabolism pathway mapping results for both acid ponds showed that all the predicted genes are involved directly or indirectly in the assimilation of ammonia and no dissimilation or nitrification process was identified. Furthermore, the deduced nitrogen fixation in the two acid ponds based on SEED classification indicated the presence of different sets of nitrogen fixing (nif) genes for biosynthesis and maturation of nitrogenase. Based on the in silico analysis, the predicted proteins involved in nitrogen fixation, especially the cysteine desulfurase and [4Fe-4S] ferredoxin, from both acid ponds are unique with less than 80% sequence similarity to the next closest protein sequence. Considering the extremity of the environmental conditions of the two acid ponds in the Danakil depression, this metagenomics dataset can add to the study of unique gene functions in nitrogen metabolism that enable thriving biocommunities in hypersaline and highly acidic conditions.
埃塞俄比亚北部达纳基尔洼地的酸性池塘是多极端环境，超过了 pH 值、盐度、离子含量和温度等正常理化极限。我们使用宏基因组鸟枪法 DNA 测序方法测试了这种环境中基于 DNA 的生命的存在。通过生物信息学工具 MetaSpades、DIAMOND 和 MEGAN 6-CE 对获得的序列进行了检查，我们能够将 Dallol 和黑水的超过 90%的宏基因组序列分类到细菌域和变形菌门。基于 SEED 的基因功能预测揭示了酸性池塘中不同的营养循环的存在。在这项研究中，我们重点研究了部分或完全测序的与氮代谢有关的基因。两个酸性池塘的 KEGG 氮代谢途径映射结果表明，所有预测的基因都直接或间接参与了氨的同化，没有发现异化或硝化过程。此外，基于 SEED 分类，两个酸性池塘中推断出的固氮作用表明存在不同的固氮（nif）基因集，用于合成和成熟固氮酶。基于计算机分析，预测的固氮相关蛋白，特别是半胱氨酸脱硫酶和[4Fe-4S]铁氧还蛋白，在两个酸性池塘中都是独特的，与下一个最接近的蛋白质序列的相似度小于 80%。考虑到达纳基尔洼地两个酸性池塘的环境条件的极端性，这个宏基因组数据集可以为研究在高盐度和强酸性条件下茁壮成长的生物群落的独特氮代谢基因功能提供补充。
