Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock

Jessica Lumian; Christen Grettenberger; Anne D Jungblut; Tyler J Mackey; Ian Hawes; Eduardo Alatorre-Acevedo; Dawn Y Sumner

doi:10.3389/fmicb.2023.1330602

Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock

Front Microbiol. 2024 Jan 11:14:1330602. doi: 10.3389/fmicb.2023.1330602. eCollection 2023.

Authors

Jessica Lumian¹, Christen Grettenberger^{2

3}, Anne D Jungblut⁴, Tyler J Mackey⁵, Ian Hawes⁶, Eduardo Alatorre-Acevedo², Dawn Y Sumner²

Affiliations

¹ Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States.
² Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States.
³ Department of Environmental Toxicology, University of California Davis, Davis, CA, United States.
⁴ Department of Sciences, The Natural History Museum, London, United Kingdom.
⁵ Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, United States.
⁶ Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand.

Abstract

Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp - 6.07 Mbp, and the bin completion ranges from 74.2-92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.

Keywords: bioinformatics; circadian clock; cryosphere; genomics; photosynthesis; polar cyanobacteria.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The work (proposal: 10.46936/10.25585/60000736) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. Samples used in this project were collected during a field season supported by the New Zealand Foundation for Research, Science and Technology (Grant No. CO1X0306) with field logistics provided by Antarctica New Zealand (Project K-081). Sequencing was provided by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility under Contract No. CSP502867. Data analysis was supported by a US National Science Foundation Graduate Research Fellowship to JL, NSF grants OPP-1745341 and OPP-1937748 to DS, and NSF grant BII-2022126 to DS and CG.