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Terrestrial geothermal springs, reminiscent of early Earth conditions, host diverse and abundant populations of Archaea. In this study, we reconstructed 2,949 metagenome-assembled genomes (MAGs) from 152 metagenomes collected over six years from 48 geothermal springs in Tengchong, China. Among these MAGs, 1,431 (49%) were classified as high-quality, while 1,518 (51%) were considered as medium-quality. Phylogenomic analysis revealed that these MAGs spanned 12 phyla, 27 classes, 67 orders, 147 families, 265 genera, and 475 species. Notably, 575 (19%) MAGs represented new taxa at various taxonomic levels, and 2,075 (70%) lacked nomenclature and effective descriptions. The most abundant phyla of archaeal genomes were Thermoproteota, Thermoplasmatota, and Micrarchaeota. The DRTY, ZMQ, and ZZQ geothermal springs were predominated by Archaea, particularly by Thermoproteia and Thermoplasmata. These draft genomes provide new data for studying species diversity and function within terrestrial geothermal spring archaeal communities, thus contributing to the conservation and utilization of thermophilic and hyperthermophilic microbial resources., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes 1 . However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved 2-4 . Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells., (© 2023. The Author(s).)

Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites., (© 2023. The Author(s).)

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) has recently been developed for simultaneously removing nitrogen and phosphorus from saline sewage with minimal sludge production. This novel process could potentially enable sustainable wastewater treatment. Yet, the core functional bacteria and their roles are unknown. Here, we used high-throughput 16S rRNA gene sequencing coupled with principal coordinates analysis and ANOVA with Tukey's test to unravel the spatiotemporal heterogeneity of functional bacteria and their synergetic and competitive interactions. We did not find any obvious spatial heterogeneity within the bacterial population in different size-fractionated sludge samples, but the main functional bacteria varied significantly with operation time. Thauera was enriched (9.26~13.63%) as become the core functional genus in the DS-EBPR reactors and links denitrifying phosphorus removal to sulfide oxidation. The other two functional genera were sulfate-reducing Desulfobacter (4.31~12.85%) and nitrate-reducing and sulfide-oxidizing Thiobacillus (4.79~9.92%). These bacteria cooperated in the DS-EBPR process: Desulfobacter reduced sulfate to sulfide for utilization by Thiobacillus, while Thauera and Thiobacillus competed for nitrate and sulfide as well as Thauera and Desulfobacter competed for acetate. This study is the first to unravel the interactions among core functional bacteria in DS-EBPR, thus improving our understanding of how this removal process works.

Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments.