Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.

Rhodothalassium (Rts.) salexigens is a halophilic purple nonsulfur bacterium and the sole species in the genus Rhodothalassium, which is itself the sole genus in the family Rhodothalassiaceae and sole family in the order Rhodothalassiales (class Alphaproteobacteria). The genome of this phylogenetically unique phototroph comprises 3.35 Mb and is highly chimeric, with nearly half of its genes originating from families other than the Rhodothalassiaceae, many of which lack phototrophic species. Photosynthesis genes in Rts. salexigens are not arranged in a typical photosynthesis gene cluster but are scattered across the genome, suggesting an origin from horizontal transfers. Despite an encoded RuBisCO, autotrophy has not been observed in Rts. salexigens, and enzymes that oxidize common inorganic electron donors are not encoded. Phospholipid biosynthesis in Rts. salexigens is restricted, and phosphoglycerolipids are the only phospholipids present in its intracytoplasmic membranes. Rts. salexigens fixes nitrogen using a Mo-containing nitrogenase and uses ammonia despite previous results that indicated it was a glutamate auxotroph. Glycine betaine is the sole osmolyte in Rts. salexigens, and enzymes are encoded that facilitate both its uptake and its biosynthesis from glycine. The genomic data also support chemotactic swimming motility, growth over a range of salinities, and the production of membrane-strengthening hopanoids.

Bdelloid rotifers are major components of zooplankton worldwide and have been reported in glacier ice in both Northern and Southern Hemispheres. Curiously, no reports of psychrophilic bdelloids have surfaced in North America despite exhaustive surveys of other ice-dwelling invertebrates, e.g., glacier ice worms. This distribution gap may be partially explained by a predator-prey relationship between these two animals, but the current study suggests that ice worms and bdelloids can co-inhabit at least some glacial ecosystems over geological time. Here we report the first ice-inhabiting bdelloid rotifer from North America, collected from the northern aspect of Mt. Deception, WA, USA. Nuclear and mitochondrial genotyping identified sister-species relationships within a clade of Nordic ice-dwelling bdelloids, and close evolutionary relationships with Antarctic/New Zealand specimens. Intrapopulation genetic divergences suggest that bdelloids arrived in North America near the onset of the Pleistocene (2.58 myr BP), but their circumpolar dispersal capabilities and robustness (e.g., freeze-thaw tolerance, ability to propagate at elevated temperatures and under extreme laboratory conditions) cannot rule out multiple transoceanic dispersal events throughout the Quaternary.

In this study, we report the draft genome sequence of strain A2. The genome size was 3.8 Mbp, the GC content was 67.4%, and it was predicted to contain 3520 protein-coding genes, 62 tRNA genes, 8 rRNA genes, and 4 snRNA genes. Phylogenetic analysis of the 16S rRNA gene in different databases suggests that strain A2 belongs to Halomonas salifodinae. Also, Multilocus Sequence Typing analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic of the core genes and comparative genomic analysis using the Average Nucleotide Identity, digital DNA-DNA Hybridization, Average Amino acid Identity, the Percentage of Conserved Proteins values indicators, and the Genome Taxonomy Database indicates that strain A2 is identified as H. salifodinae and suggest that this species has a closer phylogenetic relationship with the genus Bisbaumannia than with Halomonas. The pangenomic analysis of A2 against 100 reference genomes of described Halomonas and another related genus shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome genes, and 691 unique genes. A2 has 261 signature genes that it shares only with Bisbaumannia and Halomonas salifodinae. For strain A2 we found 29 genes for secretion systems, 23 genes for Na+ and K+ ion transport, 6 Biosynthetic Gene Clusters groups, a total of 12 genomic islands, an 8.2 kb gene prophage region, 15 regions associated with CRISPR and one CAS-TypeIF cas gene cluster region, 12 genes of biotechnological importance, 38 unique genes essential for adaptability and biotechnological relevance, as well as, 35 genes for the synthesis of compatible solutes. Comparative genomics analysis shows that strain A2 has multiple unique genetic features that could be useful for biotechnological applications. The result of this study places the species Halomonas salifodinae in a very close relationship with the genus Bisbaumannia than with Halomonas, so its reclassification to the genus Bisbaumannia is proposed for future validation.

The thermophilic methanogenic archaea Methanothermobacter spp. are applied as archaeal cell factories in industrial processes for methane production. Recently, secretion of commodity chemicals by M. marburgensis, such as amino acids, organic acids, or lipids has been observed. Together with the genetic tools available, genetically engineered cell factories for commodity chemical production from CO2 can be developed. However, the toxicity of the commonly used trace metal chelator Nitrilotriacetic acid (NTA) for M. marburgensis blocks potential regulatory approval for human applications. Therefore, we identified EDDS and hEDTA as suitable non-toxic alternatives as metal chelators for M. marburgensis. While EDDS reduces the specific growth rate (µ) of M. marburgensis by 40%, hEDTA shows the same µ as with NTA usage. Additionally, hEDTA offers cost wise a sustainable economic alternative to NTA with 23 € m− 3 of growth medium compared to 13 € m− 3 with NTA. With hEDTA as a harmless alternative to NTA, we are one step closer to industrial sustainable commodity chemical production from CO2 with M. marburgensis.

The Atacama Desert, one of the most extreme environments on our planet, harbors a plethora of unique microbial communities adapted to the harsh conditions of the habitat. In this study, strain ATCH4T, a novel Gram-stain-negative, curved rod-shaped bacterium, was isolated from the Llamara salt pan, located in the Atacama Desert in the north of Chile. ATCH4T was capable of growth within a range of 3–12% (w/v) NaCl, 4–40 °C, and pH 6–9. Comparative 16S rRNA analysis placed the strain within the genus Idiomarina, with its closest related type species being I. loihiensis, I. ramblicola, and I. abyssalis. Genomic analysis revealed the presence of several genes linked to halophilicity as well as unique metabolic pathways, including the ability to synthesize C5 and C10–C20 isoprenoids, which may contribute to the isolate’s survival in hypersaline conditions. The observed isoprenoid biosynthesis pathways suggest potential applications in various biotechnological fields, including the production of biofuels, pharmaceuticals, and other valuable chemicals. Levels of DNA-DNA relatedness, average nucleotide identity, and several phenotypic and chemotaxonomic markers clearly indicate that strain ATCH4T represents a novel species of the genus Idiomarina, for which the designation Idiomarinaaminovorans sp. nov. (type strain ATCH4T = DSM 114475 = LMG 32710) is proposed.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00792-025-01399-x.

Among the many ice-binding proteins (IBPs) found in microorganisms (bacteria, archaea, fungi and algae), the canonical DUF3494 beta-barrel type is the most common. Until now, little variation has been found in this structure: an initial coil leads into an alpha helix that directs the following coils into a reverse stack, with the final coil ending up next to the initial coil. Here, I show that there exist many bacterial proteins whose AlphaFold-predicted structures deviate from the DUF3494 structure so that they are not recognized as belonging to an existing DUF or Pfam family. In these non-canonical DUF3494 (ncDUF3494) proteins, the number of coils in the alpha helix is highly variable, often being as high as 14. The putative ice-binding sides of each of 13 proteins modeled have a well-aligned row of hydrophilic residues, with spacings that are close to the repeat distance on the ice a-axis. A recombinant protein made for one of the proteins showed that it had ice-binding activity, even in the µg/ml range. The ncDUF3494 proteins appear to be found only in bacteria, the great majority of which live in icy habitats. C-terminal PEP-Cterm motifs, which are rare in DUF3494s, are present in most of the ncDUF3494s, possibly indicating a secretory function. The relatively narrow distribution of ncDUF3494 proteins suggests that they are a later development in DUF3494 evolution.

The novel esterase gene lipP1, which encodes HjEstP1, was discovered in the genome of the extremely halophilic archaeon Haloarcula japonica. A homology search and sequence alignment revealed that HjEstP1 is a member of family IV esterases with conserved GXSXG and HGGG motifs. lipP1 was expressed in its parental strain, and recombinant HjEstP1 was purified and characterized. Optimal pH and temperature of HjEstP1 were 6.0 and > 60 °C, respectively. HjEstP1 showed higher activity with increasing NaCl concentration, and optimal NaCl concentration was > 4.5 M. Furthermore, HjEstP1 preferentially hydrolyzed pNP and glycerol esters with short chain fatty acids. To our knowledge, this is the first report of an esterase from an extremely halophilic archaeon obtained via homologous expression.

The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.