The future of genomics in polar and alpine cyanobacteria

Abstract

In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria. In this article, we present ways that genomic techniques might be used to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology. Existing examples from other environments (e.g. marine/hot springs) are used to discuss how methods developed there might be used to investigate specific questions in the cryosphere. Phylogenomics, comparative genomics and population genomics are identified as methods for understanding the evolution and biogeography of polar and alpine cyanobacteria. Transcriptomics will allow us to investigate gene expression under extreme environmental conditions, and metagenomics can be used to complement tradition amplicon-based methods of community profiling. Finally, new techniques such as single cell genomics and metagenome assembled genomes will also help to expand our understanding of polar and alpine cyanobacteria that cannot readily be cultured.

Strong in combination: Polyphasic approach enhances arguments for cold‐assigned cyanobacterial endemism

“…Several molecular studies have focused on the cyanobacterial diversity of aquatic ecosystems in the Arctic and Antarctica (Comte et al., ; Strunecký et al, ; Taton et al., ), but studies focusing on the terrestrial ecosystems dominated by BSCs have been scarce (Pushkareva et al., ; Wood, Rueckert, Cowan, & Cary, ). Additionally, little is known concerning their phylogenetic affiliations, geographic distribution, physiology, and bioactive metabolites combined with the aspect of a limited number of Antarctic, Arctic or Alpine cyanobacterial strains available in culture collections.…”

“…Correct assignments of 16S rRNA sequences to publicly available sequences of species with unambiguous morphological characteristics such as the "eyespot" of Oculatella species proves the validity of the approach applied in this study. Although multigene analysis such as a combination of 16S and ITS is preferred, we could demonstrate that sequencing parts of the 16S in combination with light microscopy contributes to recent investigation pipelines for cyanobacteria of cold biomes (Chrismas et al, 2018).…”

“…Insights into cyanobacterial community compositions were made to critically challenge questions regarding biogeographic aspects. As recently highlighted by the group of Chrismas et al (2018), the applied approach contributes to genomic techniques to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology.…”

Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

“…Details about genome bins are available in Table S2. We released scaffolded assemblies and protein predictions for all the bins having a completeness >90%, whether classified as cyanobacterial (14) or probable microbiome organisms (13). Raw read data for the 17 cyanobacterial cultutes have been deposited in the NCBI SRA (SAMN08623419 to SAMN08623435; bioproject PRJNA436342).…”

“…Cyanobacteria are notoriously difficult to isolate and keep axenic in culture (1), especially polar strains (13), hence the need for tedious purification protocols (14). In consequence, all cyanobacterial culture collections include a majority of non-axenic cultures (e.g., Czech Collection of Algae and Cyanobacteria, CCALA; University of Toronto Culture Collection of Algae and Cyanobacteria, UTCC), with the notable exception of the Pasteur Culture Collection of Cyanobacteria, PCC.…”