Genomic diversity and CRISPR-Cas systems in the cyanobacterium Nostoc in the High Arctic

Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture

Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.

Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems

The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

Breaking the Ice: A Review of Phages in Polar Ecosystems

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean

Interactions between marine viruses and microbes are a critical part of the oceanic carbon cycle. The impacts of virus-host interactions range from short-term disruptions in the mobility of microbial biomass carbon to higher trophic levels through cell lysis (i.e., the viral shunt) to long-term reallocation of microbial biomass carbon to the deep sea through accelerating the biological pump (i.e., the viral shuttle). The biogeochemical backdrop of the ocean-the physical, chemical, and biological landscape-influences the likelihood of both virus-host interactions and particle formation, and the fate and flow of carbon. As climate change reshapes the oceanic landscape through large-scale shifts in temperature, circulation, stratification, and acidification, virus-mediated carbon flux is likely to shift in response. Dynamics in the directionality and magnitude of changes in how, where, and when viruses mediate the recycling or storage of microbial biomass carbon is largely unknown. Integrating viral infection dynamics data obtained from experimental models and field systems, with particle motion microphysics and global observations of oceanic biogeochemistry, into improved ecosystem models will enable viral oceanographers to better predict the role of viruses in marine carbon cycling in the future ocean.

Metagenome-Assembled Genome of Cyanocohniella sp. LLY from the Cyanosphere of Llayta, an Edible Andean Cyanobacterial Macrocolony

Cyanobacterial macrocolonies known as Llayta are found in Andean wetlands and have been consumed since pre-Columbian times in South America. Macrocolonies of filamentous cyanobacteria are niches for colonization by other microorganisms. However, the microbiome of edible Llayta has not been explored. Based on a culture-independent approach, we report the presence, identification, and metagenomic genome reconstruction of Cyanocohniella sp. LLY associated to Llayta trichomes. The assembled genome of strain LLY is now available for further inquiries and may be instrumental for taxonomic advances concerning this genus. All known members of the Cyanocohniella genus have been isolated from salty European habitats. A biogeographic gap for the Cyanocohniella genus is partially filled by the existence of strain LLY in Andes Mountains wetlands in South America as a new habitat. This is the first genome available for members of this genus. Genes involved in primary and secondary metabolism are described, providing new insights regarding the putative metabolic capabilities of Cyanocohniella sp. LLY.