Enhanced metabolic potentials and functional gene interactions of microbial stress response towards high elevation in freshwater lakes

Elevation has strong influence on microbial community composition, but its influence on aquatic microbial functional genes remains unclear. Here, we compared the functional gene structure of microbial communities in surface water between two low-elevation lakes (LELs, with elevation of ca. 530 meters) and two high-elevation lakes (HELs, with elevation of ca. 4,600 meters) by using a metagenomic approach of Geo Chip-based functional gene arrays. We found significant differences in composition but not in richness of the microbial functional genes between the HELs and the LELs. In the HELs, the microbial communities had higher functional capacities in stress responses than those in LELs, which include cold shock, oxygen limitation, osmotic stress, nitrogen limitation, phosphate limitation, glucose limitation, radiation stress, heat shock, protein stress, and sigma factors genes. We also observed higher metabolic potentials in the degradation of aromatic, chitin, cellulose and hemicellulose in HELs than in LELs. By performing network analyses, we found enhanced interactions and complexity among the co-occurring functional genes in the HELs than those in the LELs in terms of network size, links, connectivity, and clustering coefficients. Notably, more functional genes of stress response played module-hub roles in the network of HELs. Overall, we observed contrasting patterns of microbial metabolic potentials and functional gene interactions in different elevational freshwater lakes, and found that the microbial communities developed functional strategies to cope with the harsh conditions at the high elevational lakes. IMPORTANCEElevational patterns of biodiversity have attracted scientific interest in the fields of microbial ecology and biogeography. The influence of elevation on aquatic microbial functional gene structure and their metabolic potentials remains unclear. We compared the functional gene structure of microbial communities in surface water between two low-elevation lakes and two high-elevation lakes with a more than 4,000-meter difference in elevation along a mountainside by using GeoChip 5.0, which covered in total 144,000 gene sequences from 393 functional gene families. We found apparent differences in functional gene structures in lakes between the two different elevations. We also found enhanced metabolic potentials and functional gene interactions for microbial stress response with increasing elevation in freshwater lakes. These results highlighted that limnetic microbial communities could develop functional strategies to cope with harsh conditions towards high elevations.