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1. Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

   https://doi.org/10.1038/s41396-019-0352-9  

   Carr, Stephanie A.; Jungbluth, Sean P.; Eloe-Fadrosh, Emiley A.; Stepanauskas, Ramunas; Woyke, Tanja; Rappé, Michael S.; Orcutt, Beth N. (February 2019, The ISME Journal)

   Abstract The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life. 

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2. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

   https://doi.org/10.1128/mbio.02918-23  

   Zhang, Irene H.; Borer, Benedict; Zhao, Rui; Wilbert, Steven; Newman, Dianne K.; Babbin, Andrew R. (March 2024, mBio)

   Giovannoni, Stephen J. (Ed.)

   ABSTRACT Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%–50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCEArchaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds. 

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3. Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin

   https://doi.org/10.1002/prot.26009  

   Raut, Priyam; Glass, Jennifer B.; Lieberman, Raquel L. (October 2020, Proteins: Structure, Function, and Bioinformatics)

   Abstract Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life. In addition to eukaryotes, IAPs are encoded in metabolically diverse archaea from a wide range of environments. We found three distinct clades of archaeal IAPs: (a)Euryarchaeota(eg, halophilicHalobacteriales, methanogenicMethanosarcinalesandMethanomicrobiales, marinePoseidoniales, acidophilicThermoplasmatales, hyperthermophilicArchaeoglobusspp.), (b) DPANN, and (c)Bathyarchaeota,Crenarchaeota, andAsgard. IAPs were also present in bacterial genomes from uncultivated members of Candidate Phylum Radiation, perhaps due to horizontal gene transfer from DPANN archaeal lineages. Sequence analysis of the catalytic motif YD…GXGD (where X is any amino acid) in IAPs from archaea and bacteria reveals WD inLokiarchaeotaand many residue types in the X position. Gene neighborhood analysis in halophilic archaea shows IAP genes near corrinoid transporters (btuCDFgenes). In marineEuryarchaeota, a putative BtuF‐like domain is found in N‐terminus of the IAP gene, suggesting a role for these IAPs in metal ion cofactor or other nutrient scavenging. Interestingly, eukaryotic IAP family members appear to have evolved either fromEuryarchaeotaor fromAsgardarchaea. Taken together, our phylogenetic and bioinformatics analysis should prompt experiments to probe the biological roles of IAPs in prokaryotic secretomes. 

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4. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

   https://doi.org/10.1038/s41592-023-01940-w  

   Chklovski, Alex; Parks, Donovan H; Woodcroft, Ben J; Tyson, Gene W (August 2023, Nature Methods)

   Advances in sequencing technologies and bioinformatics tools have dramatically increased the recovery rate of microbial genomes from metagenomic data. Assessing the quality of metagenome-assembled genomes (MAGs) is a critical step before downstream analysis. Here, we present CheckM2, an improved method of predicting genome quality of MAGs using machine learning. Using synthetic and experimental data, we demonstrate that CheckM2 outperforms existing tools in both accuracy and computational speed. In addition, CheckM2’s database can be rapidly updated with new high-quality reference genomes, including taxa represented only by a single genome. We also show that CheckM2 accurately predicts genome quality for MAGs from novel lineages, even for those with reduced genome size (for example, Patescibacteria and the DPANN superphylum). CheckM2 provides accurate genome quality predictions across bacterial and archaeal lineages, giving increased confidence when inferring biological conclusions from MAGs. 

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5. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

   https://doi.org/10.1371/journal.pbio.3000954  

   Vanderpool, Dan; Minh, Bui Quang; Lanfear, Robert; Hughes, Daniel; Murali, Shwetha; Harris, R. Alan; Raveendran, Muthuswamy; Muzny, Donna M.; Hibbins, Mark S.; Williamson, Robert J.; et al (December 2020, PLOS Biology)

   Jiggins, Chris D. (Ed.)

   Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. 

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