Shino Suzuki

Abstract Ribosomes are essential for protein synthesis and require ribosome biogenesis factors (RBFs) for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed that Candidate Phyla Radiation (CPR), also known as the phylum Patescibacteria, characterized by reduced genomes and smaller ribosomes, has about half the average number of RBFs compared with non-CPR bacteria. Notably, key RBFs such as der, obgE, and rbfA, considered indispensable, are conserved in only around 20%–70% of CPR genomes. Since such repertoires were not observed in reduced genomes of other phyla, CPR presumably diverged early in bacterial evolution. We further confirmed that ribosomal structural changes correlate with reduced RBFs, evidencing co-evolution between RBFs and the ribosome. These findings suggest that ribosomal biogenesis is more flexible than recognized, and the small cell and genome sizes of CPR bacteria and their early divergence may influence the unusual repertoires of RBFs. Teaser Ribosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional views of this essential process in evolution.

Serpentinization, a geochemical process found on modern and ancient Earth, provides an ultra-reducing environment that can support microbial methanogenesis and acetogenesis. Several groups of archaea, such as the order Methanocellales, are characterized by their ability to produce methane. Here, we generate metagenomic sequences from serpentinized springs in The Cedars, California, and construct a circularized metagenome-assembled genome of a Methanocellales archaeon, termed Met12, that lacks essential methanogenesis genes. The genome includes genes for an acetyl-CoA pathway, but lacks genes encoding methanogenesis enzymes such as methyl-coenzyme M reductase, heterodisulfide reductases and hydrogenases. In situ transcriptomic analyses reveal high expression of a multi-heme c-type cytochrome, and heterologous expression of this protein in a model bacterium demonstrates that it is capable of accepting electrons. Our results suggest that Met12, within the order Methanocellales, is not a methanogen but a CO2-reducing, electron-fueled acetogen without electron bifurcation.

<jats:p>Planetary protection is a guiding principle aiming to prevent microbial contamination of the solar system by spacecraft (forward contamination) and extraterrestrial contamination of the Earth (backward contamination). Bioburden reduction on spacecraft, including cruise and landing systems, is required to prevent microbial contamination from Earth during space exploration missions. Several sterilization methods are available; however, selecting appropriate methods is essential to eliminate a broad spectrum of microorganisms without damaging spacecraft components during manufacturing and assembly. Here, we compared the effects of different bioburden reduction techniques, including dry heat, UV light, isopropyl alcohol (IPA), hydrogen peroxide (H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>), vaporized hydrogen peroxide (VHP), and oxygen and argon plasma on microorganisms with different resistance capacities. These microorganisms included <jats:italic>Bacillus atrophaeus</jats:italic> spores and <jats:italic>Aspergillus niger</jats:italic> spores, <jats:italic>Deinococcus radiodurans</jats:italic>, and <jats:italic>Brevundimonas diminuta</jats:italic>, all important microorganisms for considering planetary protection. <jats:italic>Bacillus atrophaeus</jats:italic> spores showed the highest resistance to dry heat but could be reliably sterilized (i.e., under detection limit) through extended time or increased temperature. <jats:italic>Aspergillus niger</jats:italic> spores and <jats:italic>D. radiodurans</jats:italic> were highly resistant to UV light. Seventy percent of IPA and 7.5% of H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> treatments effectively sterilized <jats:italic>D. radiodurans</jats:italic> and <jats:italic>B. diminuta</jats:italic> but showed no immediate bactericidal effect against <jats:italic>B. atrophaeus</jats:italic> spores. IPA immediately sterilized <jats:italic>A. niger</jats:italic> spores, but H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> did not. During VHP treatment under reduced pressure, viable <jats:italic>B. atrophaeus</jats:italic> spores and <jats:italic>A. niger</jats:italic> spores were quickly reduced by approximately two log orders. Oxygen plasma sterilized <jats:italic>D. radiodurans</jats:italic> but did not eliminate <jats:italic>B. atrophaeus</jats:italic> spores. In contrast, argon plasma sterilized <jats:italic>B. atrophaeus</jats:italic> but not <jats:italic>D. radiodurans</jats:italic>. Therefore, dry heat could be used for heat-resistant component bioburden reduction, and VHP or plasma for non-heat-resistant components in bulk bioburden reduction. Furthermore, IPA, H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>, or UV could be used for additional surface bioburden reduction during assembly and testing. The systemic comparison of sterilization efficiencies under identical experimental conditions in this study provides basic criteria for determining which sterilization techniques should be selected during bioburden reduction for forward planetary protection.</jats:p>

Abstract Developing a cleanroom and clean chambers (CCs) for Hayabusa2 returned samples has been discussed with the committee for Hayabusa2 sample curation facility since 2015. One major difference from the specifications of the CCs used for Itokawa samples is that a part of samples was decided to be handled and preserved in vacuum to avoid terrestrial nitrogen contamination with organics or unknown materials that might easily react with the samples. Thus, the CCs for Hayabusa2 samples were divided into two CCs for vacuum processes and three CCs for purified nitrogen conditions. The cleanroom was built in summer 2017, while the CCs were installed in the summer of 2018. After the installation of the CCs, instruments for initial descriptions, sample containers, handling tools for powder and particle samples, and jigs to assist handling samples were developed in parallel with functional checks and repeated rehearsals between the fall of 2018 and the fall of 2020. The curatorial works on Hayabusa2-retuned samples were conducted as previously planned. Simultaneously, contaminations and influences of inorganics, organics, microbial, and magnetic constructs have been assessed to evaluate their potential effects on the analysis of the returned samples. Additionally, the tools used to touch samples directly have been demagnetized to avoid sample magnetization during their handling and the tool magnetization was measured before and after their usages. The series of developments and experiences from the curatorial works of Hayabusa2-returned samples represent valuable implications for future sample return missions. Graphical Abstract