Celerinatantimonas yamalensis sp. nov., a cold-adapted diazotrophic bacterium from a cold permafrost brine

Harmony in diversity: Reorganizing the families within the order Pseudomonadales

An accurate and coherent bacterial taxonomy is essential for studying the ecological aspects of microorganisms and for understanding microbial communities and their dynamics. The order Pseudomonadales is of particular importance in biological research due to its ability to interact with eukaryotic hosts, including taxa of clinical relevance (e.g.: Pseudomonas, Moraxella, Acinetobacter), or due to its functions in soil and water ecosystems. Despite their relevance, we have identified several inconsistencies in the organisation of genera within families in this order. Here, we perform comprehensive phylogenetic and phylogenomic analyses to reorganise these taxa. Average amino acid identity (AAI) values shared within and between families support our reclassifications. We propose seven new families, including new ecologically relevant families (e.g.: Oceanobacteraceae fam. nov.), as well as several taxonomic emendations. Our results also support the inclusion of Cellvibrionales and Oceanospirillales within Pseudomonadales. This revised organisation provides a robust delineation of these taxa into families, characterised by AAI values ranging from 60% to 77%. AAI distances between families are predominantly below 60%. This reclassification contributes to establishment of a more reliable taxonomic framework within Gammaproteobacteria, providing the basis for a more comprehensive understanding of their evolution.

Microbial Assemblages in Pressurized Antarctic Brine Pockets (Tarn Flat, Northern Victoria Land): A Hotspot of Biodiversity and Activity

Two distinct pressurized hypersaline brine pockets (named TF4 and TF5), separated by a thin ice layer, were detected below an ice-sealed Antarctic lake. Prokaryotic (bacterial and archaeal) diversity, abundances (including virus-like particles) and metabolic profiles were investigated by an integrated approach, including traditional and new-generation methods. Although similar diversity indices were computed for both Bacteria and Archaea, distinct bacterial and archaeal assemblages were observed. Bacteroidetes and Gammaproteobacteria were more abundant in the shallowest brine pocket, TF4, and Deltaproteobacteria, mainly represented by versatile sulphate-reducing bacteria, dominated in the deepest, TF5. The detection of sulphate-reducing bacteria and methanogenic Archaea likely reflects the presence of a distinct synthrophic consortium in TF5. Surprisingly, members assigned to hyperthermophilic Crenarchaeota and Euryarchaeota were common to both brines, indicating that these cold habitats host the most thermally tolerant Archaea. The patterns of microbial communities were different, coherently with the observed microbiological diversity between TF4 and TF5 brines. Both the influence exerted by upward movement of saline brines from a sub-surface anoxic system and the possible occurrence of an ancient ice remnant from the Ross Ice Shelf were the likely main factors shaping the microbial communities.

Desulfovibrio gilichinskyi sp. nov., a cold-adapted sulfate-reducing bacterium from a Yamal Peninsula cryopeg

A psychrotolerant non-spore-forming sulfate-reducing bacterium, strain K3S^T, was isolated from a Yamal Peninsula cryopeg within permafrost. Strain K3S^T grew at subzero temperatures and required Na⁺ for growth. The new bacterium was able to use lactate, formate, pyruvate, fumarate, alanine, ethanol and molecular hydrogen as electron donors in the presence of sulfate, and used sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors in the presence of lactate. Fe(III)-citrate and Fe(III)-EDTA were reduced without visible growth. Major polar lipids were рhosphatidylserine, рhosphatidylethanolamine, phospholipids, cardiolipin and aminolipid; major cellular fatty acids were C16 : 1ω7, C16 : 0 and C18 : 1ω7; and the predominant isoprenoid quinone was MK-6 (H2). The genomic DNA G+C content was found to be 42.33 mol%. Phylogenetic analysis showed that the closest relative of the new isolate was Desulfovibrio ferrireducens strain 61^T with 97.1 % 16S rRNA gene similarity. In addition, the ANI value between strain K3S^T and D. ferrireducens 61^T was 82.1 %. On the basis of the genomic and polyphasic taxonomy data of strain K3S^T, we conclude that the strain is a representative of a novel species Desulfovibrio gilichinskyi sp. nov. (=VKM B-2877^T=DSM 100341^T).

Evidence for marine origin and microbial-viral habitability of sub-zero hypersaline aqueous inclusions within permafrost near Barrow, Alaska

Cryopegs are sub-surface hypersaline brines at sub-zero temperatures within permafrost; their global extent and distribution are unknown. The permafrost barrier to surface and groundwater advection maintains these brines as semi-isolated systems over geological time. A cryopeg 7 m below ground near Barrow, Alaska, was sampled for geochemical and microbiological analysis. Sub-surface brines (in situtemperature of -6 °C, salinity of 115 ppt), and an associated sediment-infused ice wedge (melt salinity of 0.04 ppt) were sampled using sterile technique. Major ionic concentrations in the brine corresponded more closely to other (Siberian) cryopegs than to Standard seawater or the ice wedge. Ionic ratios and stable isotope analysis of water conformed to a marine or brackish origin with subsequent Rayleigh fractionation. The brine contained ∼1000× more bacteria than surrounding ice, relatively high viral numbers suggestive of infection and reproduction, and an unusually high ratio of particulate to dissolved extracellular polysaccharide substances. A viral metagenome indicated a high frequency of temperate viruses and limited viral diversity compared to surface environments, with closest similarity to low water activity environments. Interpretations of the results underscore the isolation of these underexplored microbial ecosystems from past and present oceans.

The microbial ecology of permafrost

Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.