A Predicted CRISPR-mediated symbiosis between uncultivated archaea

Esser, S. P.*; Rahlff, J.*; Zhao, W.*; Predl, M.*; Plewka, J.*; Sures, K.*; Wimmer, F.*; Lee, J.*; Adam, P. S.*; McGonigle, J.*; et al.

Nature Microbiology (Internet), 8(9), p.1619 - 1633, 2023/09

https://doi.org/10.1038/s41564-023-01439-2

CRISPR-Cas systems defend prokaryotic cells from viruses, plasmids, and other mobile genetic elements. Capitalizing on multi-omics approaches, we show here that the CRISPR-Cas systems of uncultivated archaea also play an integral role in mitigating potentially detrimental interactions with episymbionts. A comprehensive analysis of CRISPR-Cas-based infection histories revealed that uncultivated deep-subsurface archaeal primary-producers defend themselves from archaeal episymbionts of the DPANN superphylum of archaea, some of which are known to fuse their membranes with their host. We show that host cells counter these attacks by deploying one of two CRISPR-Cas systems (type I-B and type III-A) to target and disrupt essential genes in the episymbiont. However, genome-scale modeling of metabolic interactions between two deep subsurface host-symbiont systems revealed that host cells also benefit from the symbionts via metabolic complementation. We speculate that populations of these uncultivated archaeal episymbionts are currently transitioning from a parasitic lifestyle to one of mutualism, as must have occurred in countless mutualistic systems known today. By expanding our analysis to thousands of archaeal genomes, we conclude that CRISPR-Cas mediated resistance to archaeal episymbiosis evolved independently in various archaeal lineages and may be a wide-spread evolutionary phenomenon.

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

Jaffe, A. L.*; Thomas, A. D.*; He, C.*; Keren, R.*; Valentin-Alvarado, L. E.*; Munk, P.*; Bouma-Gregson, K.*; Farag, I. F.*; 天野 由記; Sachdeva, R.*; et al.

mBio, 12(4), p.e00521-21_1 - e00521-21_21, 2021/08

https://doi.org/10.1128/mBio.00521-21

Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions amongst these habitats remain unclear. Hear, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain TM7 have broad bacterial host ranges and constrain possible host relationships for SR1 and Gracilibacteria. Full-proteome analyses show that animal-associated TM7 have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater TM7 encodea putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events, but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa, and were reinforced by acquisition and loss of some capacities.

Clades of huge phages from across Earth's ecosystems

Al-Shayeb, B.*; Sachdeva, R.*; Chen, L.-X.*; Ward, F.*; Munk, P.*; Devoto, A.*; Castelle, C. J.*; Olm, M. R.*; Bouma-Gregson, K.*; 天野 由記; et al.

Nature, 578(7795), p.425 - 431, 2020/02

https://doi.org/10.1038/s41586-020-2007-4

Phage typically have small genomes and depend on their bacterial hosts for replication. We generated metagenomic datasets from many diverse ecosystems and reconstructed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, initiation and elongation factors and ribosomal proteins. Phage CRISPR have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. Some phage repurpose bacterial systems for phage-defense to eliminate competing phage. We phylogenetically define seven major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that large gene inventories reflect a conserved biological strategy, observed across a broad bacterial host range and resulting in the distribution of huge phage across Earth's ecosystems.

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Matheus Carnevali, P. B.*; Schulz, F.*; Castelle, C. J.*; Kantor, R. S.*; Shih, P.*; Sharon, I.*; Santini, J.*; Olm, M. R.*; 天野 由記; Thomas, B. C.*; et al.

Nature Communications (Internet), 10, p.463_1 - 463_15, 2019/01

https://doi.org/10.1038/s41467-018-08246-y

The metabolic platform in which microbial aerobic respiration evolved is tightly linked to the origins of Cyanobacteria (Oxyphotobacteria). Melainabacteria and Sericytochromatia, close phylogenetic neighbores to Oxyphotobacteria comprise both fermentative and aerobic representatives, or clades that are capablee of both. Here, we predict the metabolisms of Margulisbacteria from two distinct environments and Saganbacteria, and compare them to genomes of organisms from the related lineages. Melainabacteria BJ4A obtained from Mizunami site are potentially able to use O and other terminal electron acceptors. The type C heme-copper oxygen reductase found in Melainabacteria BJ4A may be adapted to low O levels, as expected for microaerophilic or anoxic environments such as the subsurface. Notably, Melainabacteria BJ4A seems to have a branched electron transport chain, with one branch leading to a cytochrome d ubiquinol oxidoreductase and the other one leading to the type C heme-copper oxygen reductase. Both these enzymes have high affinity for O, thus are adapted to low O levels. These contemporary lineages have representatives with fermentative H-based metabolism, lineages capable of aerobic or anaerobic respiration, and lineages with both. Our findings support the idea that the ancestor of these lineages was an anaerobe in which fermentation and H metabolism were central metabolic features.

Uncertainty analysis of far-field precipitation from used nuclear fuel

Salazar, A.*; Fratoni, M.*; Ahn, J.*; 平野 史生

Proceedings of 2017 International High-Level Radioactive Waste Management Conference (IHLRWM 2017) (CD-ROM), p.600 - 607, 2017/04

The safety assessment of a geological repository for used nuclear fuel must ensure that future generations are shielded from radiation from fission products, in particular those released by re-criticality events. An investigation is required to understand whether or not criticality can actually be achieved. In fulfilling this end, this study assesses the uncertainty in the composition and total mass of precipitates forming in the far-field due to variation in transport parameters. The Latin Hypercube Sampling technique is employed to generate an accurate, random distribution of variables employed in the transport model and to assess the uncertainty of attaining a critical mass. The average characteristics of the damaged fuel from the Fukushima Daiichi reactor cores is used as the reference waste form. Results are compared to the minimum critical masses of previous studies to assess the criticality safety margin.

Effects of random geometry on post-closure repository criticality safety

Liu, X.*; Fratoni, M.*; Ahn, J.*; 平野 史生

Proceedings of 2017 International High-Level Radioactive Waste Management Conference (IHLRWM 2017) (CD-ROM), p.595 - 599, 2017/04

The present work aims to study the effect of random geometry on the long-term criticality safety. Preliminary considerations on uranium depositions in randomly fractured rocks have been obtained through an approximated analytical solution to calculate spherical fuel lumps with random locations. With stochastic and heterogeneous conditions applied, the present work examines the conservatives of the neutronic models for repository criticality safety assessment, and provides deeper understandings of the system. The major finding is that, when parameters are chosen to optimized the criticality, effective multiplication factor for systems with the random geometries can be well-bounded by the average case.

A New view of the tree of life

Hug, L. A.*; Baker, B. J.*; Anantharaman, K.*; Brown, C. T.*; Probst, A. J.*; Castelle, C. J.*; Butterfield, C. N.*; Hernsdorf, A. W.*; 天野 由記; 伊勢 孝太郎; et al.

Nature Microbiology (Internet), 1(5), p.16048_1 - 16048_6, 2016/05

https://doi.org/10.1038/nmicrobiol.2016.48

生命の系統樹は生物学において最も重要な中心テーマの一つである。遺伝子調査によると、莫大な数のブランチの存在が示唆されているが、フルスケールに近い系統樹でさえわかりにくいのが現状である。本研究では、これまでに報告されてきた配列情報に加えて、新たに取得した未培養生物のゲノム情報を用いて、バクテリア,アーキア,真核生物を含む系統樹を更新した。系統樹の描写は、全体的な概容とそれぞれの主要な系統における多様性のスナップショットの両方について行った。その結果、バクテリアの多様化の優勢性が示され、培養されていない生物種の重要性とともに主要な放射構造においてそれらの生物種の重要な進化が集中している現象が強調された。

Repository criticality analysis for damaged fuels; Geometry effect in the modeling of uranium and plutonium deposition in geological formations

Liu, X.*; Ahn, J.*; 平野 史生

Proceedings of 14th International High-Level Radioactive Waste Management Conference (IHLRWMC 2013) (CD-ROM), p.527 - 534, 2013/04

本研究では溶融燃料を地層処分した場合の臨界安全性に注目し、MCNPモデルで仮定する地層中でのウランとプルトニウムの析出物の幾何学的形状の影響について検討した。東京電力福島第一原子力発電所の炉内溶融燃料を地層処分することを想定して、多様なパラメータに対して保守的な数値解析を実施した結果、臨界状態を生起させる系の条件の組合せが存在することが観察された。また、鉄を多く含む母岩の場合は臨界の可能性が顕著に低減できることが示された。

地層処分に有効な分離変換概念研究

池上 哲雄; Ahn, J.*

JAEA-Research 2006-045, 17 Pages, 2006/07

JAEA-Research-2006-045.pdf:1.55MB

地層処分との関係において、分離変換の対象核種と分離変換の程度に関する目標設定に資することを目的に、従来の高レベル廃棄物そのものの潜在的放射性毒性に代わり、処分場での長寿命核種の移行挙動を考慮した新たな指標である「環境影響」を導入して、PWRサイクル及びFBRサイクルについて評価を行った。評価にあたって必要となる長寿命核種の廃棄物固化体への初期装荷量は廃棄物処理(conditioning)モデルを用いて求めた。環境影響を評価すると同時に、処分場内での核種移行挙動にかかわる各種パラメータの不確かさが環境影響に及ぼす影響も評価した。その結果、分離変換の目標は次のように設定できると考えられる。(1)PWRサイクルの場合:本評価で想定した廃棄物への移行率:U:0.604%, Pu:0.297%に加え、Np, Am, (Pu)の移行率を1%以下に抑える。(2)FBRサイクルの場合:全アクチニドに対するサイクルシステムとしての回収率99.9%は適切な設定である。

ウラン系強磁性超伝導物質UGeとURhGeの強磁性転移に伴う臨界現象について

立岩 尚之; 芳賀 芳範; 松田 達磨*; 山本 悦嗣; Fisk, Z.

no journal, , 

ウラン強磁性超伝導物質UGeとURhGeの強磁性転移に伴う臨界現象を磁化測定により調べた。スケーリング理論等を用いた解析からこれらウラン系強磁性超伝導物質の臨界現象は非従来型であることが明らかになった。その起源について議論する。