The future of genomics in polar and alpine cyanobacteria

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

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.

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.

Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.

The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.

Survivability of Anhydrobiotic Cyanobacteria in Salty Ice: Implications for the Habitability of Icy Worlds

Two anhydrobiotic strains of the cyanobacterium Chroococcidiopsis, namely CCMEE 029 and CCMEE 171, isolated from the Negev Desert in Israel and from the Dry Valleys in Antarctica, were exposed to salty-ice simulations. The aim of the experiment was to investigate the cyanobacterial capability to survive under sub-freezing temperatures in samples simulating the environment of icy worlds. The two strains were mixed with liquid solutions having sub-eutectic concentration of Na₂SO₄, MgSO₄ and NaCl, then frozen down to different final temperatures (258 K, 233 K and 203 K) in various experimental runs. Both strains survived the exposure to 258 K in NaCl solution, probably as they migrated in the liquid veins between ice grain boundaries. However, they also survived at 258 K in Na₂SO₄ and MgSO₄-salty-ice samples-that is, a temperature well below the eutectic temperature of the solutions, where liquid veins should not exist anymore. Moreover, both strains survived the exposure at 233 K in each salty-ice sample, with CCMEE 171 showing an enhanced survivability, whereas there were no survivors at 203 K. The survival limit at low temperature was further extended when both strains were exposed to 193 K as air-dried cells. The results suggest that vitrification might be a strategy for microbial life forms to survive in potentially habitable icy moons, for example in Europa's icy crust. By entering a dried, frozen state, they could be transported from niches, which became non-habitable to new habitable ones, and possibly return to metabolic activity.

Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology

Cyanobacteria are important photoautotrophs in extreme environments such as the McMurdo Dry Valleys, Antarctica. Terrestrial Antarctic cyanobacteria experience constant darkness during the winter and constant light during the summer which influences the ability of these organisms to fix carbon over the course of an annual cycle. Here, we present a unique approach combining community structure, genomic and photophysiological analyses to understand adaptation to Antarctic light regimes in the cyanobacterium Leptolyngbya sp. BC1307. We show that Leptolyngbya sp. BC1307 belongs to a clade of cyanobacteria that inhabits near-surface environments in the McMurdo Dry Valleys. Genomic analyses reveal that, unlike close relatives, Leptolyngbya sp. BC1307 lacks the genes necessary for production of the pigment phycoerythrin and is incapable of complimentary chromatic acclimation, while containing several genes responsible for known photoprotective pigments. Photophysiology experiments confirmed Leptolyngbya sp. BC1307 to be tolerant of short-term exposure to high levels of photosynthetically active radiation, while sustained exposure reduced its capacity for photoprotection. As such, Leptolyngbya sp. BC1307 likely exploits low-light microenvironments within cyanobacterial mats in the McMurdo Dry Valleys.

Prokaryotic community shifts during soil formation on sands in the tundra zone

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but they have not been considered for the tundra zone, where the environmental conditions are unfavourable for the establishment of complicated biocoenoses. In this research, we characterized the prokaryotic diversity and abundance of microbial genes found in a typical tundra and wooded tundra along a gradient of increasing vegetation—unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. Microbial communities from typical tundra and wooded tundra plots at three stages of sand fixation were compared using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing of 16S rRNA gene libraries. The abundances of ribosomal genes increased gradually in both chronosequences, and a similar trend was observed for the functional genes related to the nitrogen cycle (nifH, bacterial amoA, nirK and nirS). The relative abundance of Planctomycetes increased, while those of Thaumarchaeota, Cyanobacteria and Chloroflexi decreased from unfixed sands to mature soils. According to β-diversity analysis, prokaryotic communities of unfixed sands were more heterogeneous compared to those of mature soils. Despite the differences in the plant cover of the two mature soils, the structural compositions of the prokaryotic communities were shaped in the same way. Thus, sand fixation in the tundra zone increases archaeal, bacterial and fungal abundances, shifts and unifies prokaryotic communities structure.

Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat

Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.

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

Cyanobacteria of biological soil crusts (BSCs) represent an important part of circumpolar and Alpine ecosystems, serve as indicators for ecological condition and climate change, and function as ecosystem engineers by soil stabilization or carbon and nitrogen input. The characterization of cyanobacteria from both polar regions remains extremely important to understand geographic distribution patterns and community compositions. This study is the first of its kind revealing the efficiency of combining denaturing gradient gel electrophoresis (DGGE), light microscopy and culture‐based 16S rRNA gene sequencing, applied to polar and Alpine cyanobacteria dominated BSCs. This study aimed to show the living proportion of cyanobacteria as an extension to previously published meta‐transcriptome data of the same study sites. Molecular fingerprints showed a distinct clustering of cyanobacterial communities with a close relationship between Arctic and Alpine populations, which differed from those found in Antarctica. Species richness and diversity supported these results, which were also confirmed by microscopic investigations of living cyanobacteria from the BSCs. Isolate‐based sequencing corroborated these trends as cold biome clades were assigned, which included a potentially new Arctic clade of Oculatella. Thus, our results contribute to the debate regarding biogeography of cyanobacteria of cold biomes.

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

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.