Genomics of Antarctic Cyanobacteria from Lakes Fryxell and Vanda: Sulfide Tolerant Oxygenic Photosynthesis, Implications of Polar Light Cycles, and Biogeography with Large-Scale k-mer Searching

Antarctic cyanobacteria form microbial mats in perennially ice-covered lakes in the McMurdo Dry Valleys, Antarctica. These mats demonstrate a variety of ecological and metabolic behaviors consistent with Antarctic conditions as well as specific challenges between and within the lakes. In this thesis, I explore the survival of cyanobacteria in Antarctic conditions focusing on sulfide stress, polar light availability, and their biogeographical distribution in other environments.In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1-2 mm thick layer of 50 µmol L-1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. A metagenome-assembled genome (MAG) of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, it is unknown whether the organism can perform anoxygenic photosynthesis using sqr and PS I while PS II is sulfide-inhibited. The seasonal light availability of polar environments has implications for the functioning of circadian clocks in Antarctic cyanobacteria. However, polar cyanobacteria are underrepresented in available genomic data, limiting opportunities to study their genetic adaptations to this and other polar challenges. Chapter 2 presents four new Antarctic cyanobacteria MAGs, bringing the total number of polar MAGs and genomes to ten. These new cyanobacteria are from microbial mats in Lake Vanda located in the McMurdo Dry Valleys in Antarctica. The four MAGs were taxonomically categorized as a Leptolyngyba, Pseudanabaena, Microcoleus, and Neosynechococcus. The sizes of these MAGs range from 2.76 Mpb – 6.07 Mbp and the bin completion ranges from 74.2% – 92.57%. Furthermore, the four novel cyanobacteria have ANIs below 90% with each other and below 77% with existing polar cyanobacteria MAGs and genomes, which demonstrates genomic diversity among polar cyanobacteria genomes. Analysis of the gene content of all ten polar cyanobacteria demonstrates that they have metabolic capacity for photosynthesis and various cold tolerance mechanisms. Standard circadian rhythm genes are present in the majority of cyanobacteria studied with the Leptolyngbya and Neosynechococcus containing kaiB3, a divergent homolog of kaiB. Although some work has been done on the biogeography of cyanobacteria within Antarctica, the global distribution of polar cyanobacteria is not well understood. It is not known if polar cyanobacteria are specialists of their environments or opportunists that tolerate survival in the cryosphere. These questions can be addressed by identifying the distribution of Antarctic cyanobacteria across global locations, but this is logistically complicated to do using 16S amplicon sequences, which is standard for biogeography studies. However, novel sourmash MAGsearch software based on large-scale k-mer searching allows for MAGs of interest to be identified in publicly available metagenomic data. Chapter 3 used five Antarctic cyanobacteria MAGs from Lake Vanda (Microcoleus, Neosynechococcus, Leptolyngbya, and Pseudanabaena) and Lake Fryxell (P. pseudopriestleyi), as search queries. The sourmash MAGsearch revealed that the Microcoleus MAG was widely dispersed in a variety of environmental conditions, the P. pseudopriestleyi MAG was present in harsh environments, and the Neosynechococcus, Leptolyngbya, and Pseudanabaena MAGs were present in polar and a few non-polar environments. The search technique can be used to search for any organism present in metagenomes and has exciting implications for future biogeography studies