Hydrogen is a fundamental electron donor in diverse microbial metabolisms and it is considered the energetic currency exchanged within microbial communities in anaerobic environments. Hydrogen is also the major actor in the transition to alternative low-carbon energy sources, primarily due to its dual role as energy source and energy carrier and to the production of water as a byproduct of its combustion. The geological storage of hydrogen gas produced from diverse sources in stable terrestrial reservoirs, known also as Underground Hydrogen Storage (UHS), is a key prerequisite to decouple production from utilization. UHS targets include depleted porous natural gas reservoirs, salt caverns and deep aquifers. Studies carried out in the past 30 years have unveiled a large subsurface ecosystem able to interact with the geochemical cycles and volatiles present in Earth’s crust. When hydrogen is stored underground, the microbial communities present in situ can interact with it, consuming it as electron donor, potentially producing undesired metabolic byproducts capable of affecting the success of UHS operations. Additionally, subsurface microbial communities might impact the geological production, migration and accumulation of hydrogen in natural reservoirs. Here, we review the current state of knowledge in hydrogenotrophic metabolisms capable of affecting UHS operations and natural hydrogen prospecting, and discuss how the microbiology of natural hydrogen-rich springs can be used as analog to model the state space of hydrogen operations. We discuss our current knowledge of the limits of life in the context of hydrogen economy, and the complex trophic network that hydrogen might sustain in the subsurface. While energy demands increase globally, the ability to effectively operate geological hydrogen storage and identify natural hydrogen deposits will become a key prerequisite to reduce the global carbon footprint. Understanding the potential for microbes to interact with hydrogen in the subsurface is therefore at the forefront of the ecological transition.

The term ”thermophilic prokaryotes” covers an immense taxonomic and functional diversity of bacteria and archaea, spanning the length and breadth of the prokaryotic Tree of Life. Indeed, thermophiles are found within most major prokaryotic lineages and their functional diversity runs the gamut of biochemical and physiological adaptations. Thus, examples can be found of thermophilic lithoautotrophs as well as chemoheterotrophs, obligate anaerobes and aerophiles, extreme halophiles, acidophiles and alkaliphiles, and more. Their ecology is likewise diverse, with thermophiles found in a variety of habitats ranging from hydrothermal vents to desert soil to industrial settings and wastewater treatment facilities. It goes without saying that such immense diversity cannot be reviewed comprehensively in a relatively short book chapter. We thus aim to present examples pulled from diverse taxa within the vast menagerie of prokaryotic thermophiles in order to give insights into the metabolic, taxonomic, and ecological diversity of thermophilic prokaryotes rather than attempting an exhaustive review.

The Antarctic Circumpolar Current (ACC) is the major current in the Southern Ocean, isolating the warm stratified subtropical waters from the more homogeneous cold polar waters. The ACC flows from west to east around Antarctica and generates an overturning circulation by fostering deep-cold water upwelling and the formation of new water masses, thus affecting the Earth's heat balance and the global distribution of carbon. The ACC is characterized by several water mass boundaries or fronts, known as the Subtropical Front (STF), Subantarctic Front (SAF), Polar Front (PF), and South Antarctic Circumpolar Current Front (SACCF), identified by typical physical and chemical properties. While the physical characteristics of these fronts have been characterized, there is still poor information regarding the microbial diversity of this area. Here we present the surface water bacterioplankton community structure based on 16S rRNA sequencing from 13 stations sampled in 2017 between New Zealand to the Ross Sea crossing the ACC Fronts. Our results show a distinct succession in the dominant bacterial phylotypes present in the different water masses and suggest a strong role of sea surface temperatures and the availability of Carbon and Nitrogen in controlling community composition. This work represents an important baseline for future studies on the response of Southern Ocean epipelagic microbial communities to climate change.

The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.

Non-coding RNAs represent the largest part of transcribed mammalian genomes and prevalently exert regulatory functions. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) can modulate the activity of each other. Skeletal muscle is the most abundant tissue in mammals. It is composed of different cell types with myofibers that represent the smallest complete contractile system. Considering that lncRNAs and miRNAs are more cell type-specific than coding RNAs, to understand their function it is imperative to evaluate their expression and action within single myofibers. In this database, we collected gene expression data for coding and non-coding genes in single myofibers and used them to produce interaction networks based on expression correlations. Since biological pathways are more informative than networks based on gene expression correlation, to understand how altered genes participate in the studied phenotype, we integrated KEGG pathways with miRNAs and lncRNAs. The database also integrates single nucleus gene expression data on skeletal muscle in different patho-physiological conditions. We demonstrated that these networks can serve as a framework from which to dissect new miRNA and lncRNA functions to experimentally validate. Some interactions included in the database have been previously experimentally validated using high throughput methods. These can be the basis for further functional studies. Using database information, we demonstrate the involvement of miR-149, -214 and let-7e in mitochondria shaping; the ability of the lncRNA Pvt1 to mitigate the action of miR-27a via sponging; and the regulatory activity of miR-214 on Sox6 and Slc16a3. The MyoData is available at https://myodata.bio.unipd.it.

The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem, as the abundance of its biomass affects trophic levels both below it and above. Major changes in climate conditions observed in the Antarctic Peninsula region in the last decades have the potential to alter the distribution of the krill population and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species, and of the molecular mechanisms behind them, are urgently needed. The availability of a large body of RNA-seq assays gave us the opportunity to extend the current knowledge of the krill transcriptome, considerably reducing errors and redundancies. The study covered the entire developmental process, from larval stages to adult individuals, information which are of central relevance for ecological studies. We describe KrillDB2 database, which combines the latest annotation of the krill transcriptome with a series of analyses specifically targeting genes and molecular processes relevant to krill physiology. KrillDB2 provides in a single resource the most complete collection of experimental data and bioinformatic annotations: it includes an extended catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions such as developmental stages, geographical regions, seasons, and sexes. Finally, it provides information about non-coding RNAs, a class of molecules whose contribute to krill physiology, which have never been reported before.