Nature Biotechnology: Chinese scientists establish the world’s first glacier microbial database

The Tibetan Plateau is known as the world’s “Third Pole” and “Asian Water Tower”. In addition to the North and South Poles, it is the world’s largest glacier distribution area, with more than 20,000 glaciers, an area of more than 20,000 square kilometers, and is also the source of more than ten major rivers on which 2 billion people in China and Asia depend for their survival. Glaciers on the Tibetan Plateau are natural reservoirs of microorganisms, sequestering microorganisms from different historical periods.

Now, the world’s first glacier microbial genome and gene dataset (TG2G) built by Chinese scientists has been officially released. The study, which was rated as “highly innovative” by many reviewers, was published in Nature Biotechnology on the evening of June 27, Beijing time.

This is the result of the Pan-Third Pole Environmental Center of Lanzhou University, the Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, the Institute of Microbiology of the Chinese Academy of Sciences, australia and Denmark, which brings together more than 25 million genetic information of 30 phyla species of 21 glaciers on the Qinghai-Tibet Plateau, and systematically discusses the microbial diversity and functions of glaciers on the Qinghai-Tibet Plateau.

“This is a very meaningful piece of work that fills a major gap in the knowledge of microbial community sequencing in glacial habitats.” Nikos Kyrpides, one of the leaders of the Earth Microbiome Project and head of the U.S. Department of Energy’s Joint Genome Research Institute, commented as a special guest commentator for the journal.

The first glacier microbial data “bank”

The research team sequenced and assembled 85 metagenomes from 21 glaciers on the Qinghai-Tibet Plateau, obtained 2358 metagenomic loaded genomes, and combined them with the genomes of 883 bacterial culture plants isolated from the glaciers of the Qinghai-Tibet Plateau to construct the glacier microbial genome and gene dataset TG2G on the Qinghai-Tibet Plateau.

TG2G contains the genomes of 3241 glacial bacteria and archaea, which can be divided into 30 phylums, 69 orders, 12 orders, 22 families, 475 genera and 968 species. Compared with the genomic data in the polar ocean, the Earth’s microbial database and the species classification database, 88.3% to 100% of the glacier microorganisms on the Qinghai-Tibet Plateau are potential new species, which are mainly endemic species mainly distributed in a single glacier, with strong spatial and habitat specificity.

Meanwhile, the genetic data in the TG2G dataset includes 25,320,330 different genes in the glacial environment, of which 15,954 genes may be associated with secondary metabolite synthesis, with only 8.4% existing in existing databases. This finding confirms that the TG2G database contains a large number of secondary metabolites with novel functions. Secondary metabolites, i.e. organic compounds that are not directly involved in the growth, development, or reproduction of life, but play an important role in interactions between organisms and environmental adaptations.

“This is the first detailed glacial ecosystem genome and genetic catalog.” The editorial team of Nature Biotechnology commented. A peer-reviewed expert from the journal also noted that the work was “highly innovative because little microbial genomic information associated with the glacial environment has been known.”

Recognize the “glacier visitor” for the benefit of human health

Although the number of glacial microbial genomes currently obtained is only 3241, which is far lower than the amount of gut microbial data. The editors and reviewers of the paper argue that the study is of great significance in the context of global warming and the loss of glacial microbial diversity.

These “glacier visitors” are rich in genetic resources that benefit humanity, including many compounds that have the potential to synthesize antibiotics or anti-cancer drugs.

For example, terpenoids are widely used as secondary metabolites in industry, medicine and health, etc., and terpene synthesis-related genes are the most diverse secondary metabolite synthesis gene types in the Tibetan Plateau genomic data (26%), which may be related to the need for microbial synthetic pigments to resist ultraviolet radiation and capture light energy.

Metabolites of non-ribosomal polypeptide synthase, polyketone synthase, and non-ribosomal polypeptide synthetase-polyketone synthase complex protein coding genes are associated with antibiotic synthesis, which account for 21% of the gene diversity associated with synthesis of all secondary metabolites, and need to be further explored.

On the other hand, Glacial Proteus, Pachychomycetes and Actinomycetes on the Tibetan Plateau carry genes related to biofilm synthesis, cell motility and cytotoxin synthesis, which are part of the microbial adaptation to the glacial environment and the interaction mechanism between microorganisms and predators. Of these, 14,301 (52% of the total) have significant similarities with virulence factors present in the Earth’s Microbiome (GEM) database, and the potential pathogenic factors in 396 genomes are manipulated by gene-moving elements such as plasmids and bacteriophages. This suggests that during glacier ablation, there is a possibility of rapid release of toxin genes, some of which may have an impact when they come into contact with humans, animals and plants. The associated risks require further assessment of the abundance, pathogenic risk and interaction mechanisms of these potentially pathogenic microorganisms after contact with downstream ecosystems.

Several peer-reviewed experts noted that both the description of new genes associated with secondary metabolite biosynthesis and the identification of potentially toxicity-related genes demonstrate the useful value of this unique dataset. “This data can provide a very useful resource for people and should be used for other types of analysis.” Kyrpides commented.

The database has made genomic and genetically-level data publicly available on the China National Oemics Data Encyclopedia NODE platform. Some reviewers hope that the dataset will also be open to the International Nucleotide Database Cooperation Organization (INSDC) database.

Figure 1 Overview of glacial microbial gene sets on the Tibetan Plateau. a. Species classification and evolutionary relationships of the acquired metagenomic loading genome (MAG) and the pure bacterial genome; b. Classification and proportion of synthesis-related genes of secondary metabolites in gene concentrations; c. Association of mobile elements of gene sets with toxin genes

Awareness is the first step to protection

The TG2G dataset also establishes a standardized process for data processing and comparison of microbes in the glacial environment. This data processing process is not only applicable to the Qinghai-Tibet Plateau, but also to global glaciers, serving the comparative study of global glacier microorganisms. When using this gene set as a metagenomic sequencing assembly template, the average sequence assembly ratio can be increased from 68% to 85%, which effectively improves the utilization rate of sequencing data.

The research team used the analysis process of TG2G to compare microbial metagenomic data of glaciers in the Arctic and European Alps, and obtained 405 glacial microbial genomes representing 215 new species. Comparative studies have found that the composition of glacial microbial communities on the Tibetan Plateau and other regions is significantly different, and the relative abundance of glacial algae (green algae and red algae) in the Arctic and Tibetan Plateau is similar, but both are significantly lower than those in the Alps.

The team also found that for bacterial communities, spatial distance caused by community diffusion restrictions had a greater impact than the differences between different habitats of glaciers. However, at the functional level, the effect of differences in glacier habitats is greater than the impact of diffusion restriction, with ice dust habitats enriching genes related to nucleic acid and lipid metabolic synthesis, while snow ice habitat microorganisms have more genes associated with secondary metabolite synthesis and coenzyme synthesis, which may be driven by differences in environmental selection pressures in different habitats.

In the context of the rapid retreat of global glaciers, it is significant to establish a platform for archiving, analyzing and comparing glacier microorganisms at the genomic and genetic levels. Due to the extremely low proportion of microorganisms in the environment that can be cultured by conventional methods (between 0.1% and 0.01%), digital preservation of genomic sequences will be a way to conserve biodiversity. It will also be possible to obtain information on the response of glacier microorganisms to the climatic environment, and explore their adaptation mechanisms to the glacier environment to better protect and utilize glacier microbial resources.

The database will help to develop anaeolyte products with high catalytic efficiency at low temperatures but rapid inactivation at high temperatures; Identify potential pathogenic microbial taxa in glaciers on the Tibetan Plateau and assess their ecological risks released downstream with glacial meltwater; Understand their driving role in the process of glacial carbon and nitrogen cycles, and play a role as an ecological security barrier on the Tibetan Plateau; It reveals the unique microbial taxa and its environmental adaptation mechanism adapted to the low-temperature strong ultraviolet environment, providing clues for the exploration of extraterrestrial life.

The TG2G dataset is the first step in understanding the microbial adaptation mechanism, carbon and nitrogen cycle process, biological resource development and assessment of downstream ecological impacts in glacial ecosystems, and more in-depth research will provide a theoretical basis for assessing the impact of climate change on carbon fluxes on the Tibetan Plateau, and further enhance the ecological barrier effect of the Qinghai-Tibet Plateau.

The study was co-participated by the Biogeochemical Cycle Team of the Pan-Third Pole Environmental Center of Lanzhou University, the Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, the Institute of Microbiology of the Chinese Academy of Sciences, as well as the University of Queensland in Australia and the University of Aarhus in Denmark. The research has been funded by the Second Comprehensive Scientific Expedition to the Tibetan Plateau and the Major Research Program of the Hydrosphere of the National Natural Science Foundation of China.

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