Past and recent biodiversity profiling in ancient Lake Chalco Mexico by a metagenomics analysis

For decades, paleoecological studies in lake sediments have focused on reconstructing the environments of the past and explaining phenomena linked to climatic variations. Recent advances in high-throughput DNA sequencing have allowed access to environmental DNA (eDNA) and ancient sedimentary DNA (sedaDNA) as a new and efficient proxy for past and present biodiversity. The basin of Mexico (BM) is located in the central part of the Trans-Mexican Volcanic Belt at 2,200 m a.s.l.; with the southern portion harboring the Chalco sub-basin. Lake Chalco is one of the last remaining natural aquatic ecosystems within the ever-expanding urban area surrounding Mexico City. The paleoenvironmental history of this lake has been previously characterized using sedimentological and geochemical proxies, as well as preserved microfossils (diatoms, pollen) with a temporal framework based on multiple radiocarbon dates. However, information for the remaining taxonomic groups and metabolic pathways remained unexplored. Here, we present the first metagenomics-based study for the Holocene in a high-altitude lake in Central Mexico –Lake Chalco. We explored the relationship between the lake’s paleoenvironmental condition and estimations of taxonomic and metabolic profiles across the sedimentary sequence (2.5 meters long). Multiple biological and abiotic variables revealed three main environmental phases: 1) a cool freshwater lake (FW1: 11,500-11,000 cal years BP), 2) a warm hyposaline lake (HS2: 11,000-6,000 cal years BP), and 3) a temperate, subsaline lake (SS3, <6,000 cal years BP). We describe the structure of the microbiota community and taxonomy richness turnover in the three Holocene paleoenvironmental phases. During the past 12 000 years BP the most abundant domains in Lake Chalco sediments were Bacteria, followed by Archaea, and Eukarya (36,722 genera). The analysis of functional proteins showed high biodiversity with a total of 27,636,243 proteins identified, but it was only possible to annotate 3,227,398 of them. Also, we identified several genes associated with some relevant pathways, such as methanogenesis. Altogether, this study allowed us to reconstruct the natural history of lake Chalco and its surroundings.