Metagenomic Investigation into 300 Years of Cyanobium Population Dynamics in Mono Lake
Abstract
Mono Lake, CA is a hypersaline soda lake in the eastern Sierra Nevada Mountain range that fluctuates on seasonal and annual cycles of mono- or meromixis. Preservation of high-quality relic DNA in lake sediments allows for the investigation of historical microbial populations and tracking genetic variation within extant communities in the water column. We applied genome-resolved metagenomics to sediment core samples spanning roughly 300 years (~1 m) of sediment deposition as well as modern samples from the water column. We focused on the picocyanobacterium Cyanobium whose deposition in lake sediment serves as a record of water column phototrophy. The persistence and high relative abundance of Cyanobium in the water column through periods of mono- and meromixis make it a model organism for studying trends in past and present genetic diversity. Shotgun metagenomes were generated for 12 water column samples (0-35 m depths) collected in Sept. 2017 and May 2018 and nine samples from a sediment core collected May 2018 to a depth of 96 cm. Two high quality Cyanobium metagenome-assembled genomes (MAGs) were constructed from the 96 cm sediment and 24 m water column metagenomes. We used these MAGs as references to frame our investigation of Cyanobium genetic diversity of Mono Lake through time and differing environments. We compared Mono Lake Cyanobium MAGs to other known Cyanobium genomes available on NCBI by creating a pangenome using anvio. 97 genes were unique to both Mono Lake MAGs, including a glycine betaine transporter protein (betS) that is potentially involved in hypersaline adaptation. We also mapped reads from all 24 water and sediment metagenomes onto our ~300 year old sediment MAG, representing the oldest recovered Cyanobium population, to understand how gene coverage and nucleotide diversity have varied in the population through time. Linear regression models of gene coverage over water column or sediment core depth identified candidate ancient genes based on their abundance in older Cyanobium populations and absence in modern populations. Interestingly, some candidate ancient genes were replaced by variant that were rare but detectable in the deeper sediments. Altogether, we document the dynamics of genetic variation in a key photoautotroph from an extreme environment.
- Publication:
-
AGU Fall Meeting Abstracts
- Pub Date:
- December 2021
- Bibcode:
- 2021AGUFM.B15K1563S