A. L. Jaffe

Prevalence of the Calvin-Benson-Bassham cycle in chemolithoautotrophic psychrophiles and the potential for cold-adapted Rubisco

This paper identifies the Calvin-Benson-Bassham cycle as the dominant chemolithoautotrophic pathway in subzero environments and explores cold-adapted Rubisco variants in psychrophilic bacteria.

Abundant and metabolically flexible lineages within the SAR324 and gammaproteobacteria dominate the potential for rubisco-mediated carbon fixation in the dark ocean

The paper analyzes metagenomic data to show that rubisco-encoding organisms, particularly from SAR324 and gammaproteobacteria, dominate carbon fixation potential in the dark ocean.

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

The paper identifies phages capable of infecting both CPR and non-CPR bacteria, revealing their ability to use alternative genetic codes and expand host range.

Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism

The paper identifies CPR bacteria in sulfide-rich biofilms, linking them to sulfur and hydrogen metabolism through genomic and spectroscopic analyses.

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

The paper examines how geochemical gradients affect the functional potential of microbes in Lac Pavin, finding that CPR bacteria and phages show less gene content differentiation by depth compared to other microbes.

Saccharibacteria harness light energy using Type-1 rhodopsins that may rely on retinal sourced from microbial hosts

The paper identifies Saccharibacteria using Type-1 rhodopsins that pump protons and rely on retinal from microbial hosts, suggesting a symbiotic relationship for energy generation.

Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication

The paper investigates the expression of the bS21 gene in phages, finding it is active during late-stage replication and may aid in phage particle assembly.

Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria

The paper describes long-term incubation of lake water to enrich and reconstruct genomes of rare Planctomycetes and CPR bacteria, revealing metabolic traits and potential interactions with phages.

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria

This study examines gene content and co-occurrence patterns in CPR bacteria to understand their evolutionary transitions between environmental and animal-associated habitats.

Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea

The paper uses protein family content to analyze lineage relationships and pathway maintenance mechanisms in DPANN archaea, revealing metabolic and symbiotic traits.

Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea

The paper analyzes archaeal protein families to understand their phylogenetic relationships and identifies conserved hypothetical proteins that may have driven archaeal diversification.

Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil

The paper identifies unexpected diversity of CPR bacteria and nanoarchaea in grassland soil by analyzing particles less than 0.2 m, revealing new taxa and potential adaptations to aerobic conditions.

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

This study analyzes metabolic diversity in CPR bacteria, finding that gene loss and lateral transfer shape metabolic trait distribution, with conserved central pathways and patchy accessory traits.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea

The paper identifies a new RuBisCO type in CPR bacteria and DPANN archaea, showing its lateral transfer and role in carbon metabolism.