Frozen soil to explore cold-adapted microbial trends and enzymes

Permafrost represents a reservoir for the bioprospecting of new compounds and cold-adapted proteins. Cold-adapted proteins are advantageous in several industrial settings because, thanks to their low enzymatic optimum temperature, they do no require heating steps, being more energy sustainable and giving high reaction yields and fewer unwanted secondary chemical reactions. Comparison between thermophilic, mesophilic and psychrophilic proteins can give important information for the bioengineering optimization of cold-adapted proteins. We collected frozen soil samples from 34 different locations along a transect starting at the Greenland Ice Sheet (GrIS) edge and going further away ranging a variety of habitats and geochemical specific site conditions with the aim to obtain a deep read coverage assembly i) to analyze the cold-adapted community in this area, studying the DNA and cDNA microbial distribution in proglacial upper permafrost layer, ii) and to reconstruct high- and medium- quality Metagenome-Assembled Genomes (MAGs) and create a Cold-Adapted Predicted Protein (CAPP) database. The cold-adapted community converged to similar taxonomic composition along the transect and showed solid permafrost-shaped community rather than microbial trends of typical of proglacial systems. However, whereas DNA profiles were conditioned by the distance from the ice edge, cDNA showed major correlation to geochemical trends highlighting how microbial activity is determined by environmental conditions. The construction of the assembly of this conserved frozen soil community led to the retrieval of 69 high- and medium- quality MAGs, 213 complete biosynthetic gene clusters (BGCs) and more than three million predicted proteins. The latter constitutes the CAPP database whose aim is to provide cold-adapted protein sequence information for a protein- and taxon- focused amino acid sequence modification and ultimately to facilitate protein engineering of cold-adapted enzymes.

永久冻土（Permafrost）是新型化合物与冷适应蛋白（cold-adapted proteins）生物勘探的重要储库。冷适应蛋白在诸多工业场景中具备显著优势：因其酶促最适温度较低，无需加热步骤，兼具更高的能源利用可持续性，可实现更高的反应产率且副化学反应更少。对嗜热蛋白、嗜温蛋白与嗜冷蛋白进行比较，可为冷适应蛋白的生物工程优化提供关键信息。本研究从以格陵兰冰盖（Greenland Ice Sheet, GrIS）边缘为起点的样带的34处不同点位采集了冻土样本，覆盖多样生境与位点特异性地球化学条件，旨在完成深度读长覆盖度组装，以实现两大研究目标：其一，分析该区域的冷适应群落，研究冰缘上层永久冻土层中的DNA与互补DNA（cDNA）微生物分布；其二，构建高质量及中等质量的宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs），并创建冷适应预测蛋白（Cold-Adapted Predicted Protein, CAPP）数据库。沿该样带分布的冷适应群落呈现出相似的分类组成，其群落结构受永久冻土塑造，而非遵循典型冰缘系统的微生物分布规律。不过，DNA图谱受距冰盖边缘的距离所调控，而cDNA则与地球化学趋势呈现更强相关性，这揭示了微生物活性由环境条件决定的机制。对该保守冻土群落的组装构建，共获得69个高质量及中等质量的MAGs、213个完整生物合成基因簇（biosynthetic gene clusters, BGCs）以及超过300万个预测蛋白。上述预测蛋白构成了CAPP数据库，其旨在为聚焦蛋白与分类群的氨基酸序列修饰提供冷适应蛋白序列信息，最终助力冷适应酶的蛋白工程改造。