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論文

Clades of huge phages from across Earth's ecosystems

Al-Shayeb, B.*; Sachzdeva, 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

 被引用回数:20 パーセンタイル:0.48(Multidisciplinary Sciences)

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.

論文

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. M.*; 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

 被引用回数:8 パーセンタイル:18.27(Multidisciplinary Sciences)

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$$_{2}$$ and other terminal electron acceptors. The type C heme-copper oxygen reductase found in Melainabacteria BJ4A may be adapted to low O$$_{2}$$ 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$$_{2}$$, thus are adapted to low O$$_{2}$$ levels. These contemporary lineages have representatives with fermentative H$$_{2}$$-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$$_{2}$$ metabolism were central metabolic features.

論文

Spin-orbital short-range order on a honeycomb-based lattice

中辻 知*; 久我 健太郎*; 木村 健太*; 佐竹 隆太*; 片山 尚幸*; 西堀 英治*; 澤 博*; 石井 梨恵子*; 萩原 政幸*; Bridges, F.*; et al.

Science, 336(6081), p.559 - 563, 2012/05

 被引用回数:96 パーセンタイル:4.01(Multidisciplinary Sciences)

フラストレートした磁性体においても最低温度まで乱れが残る場合がある。その一例がBa$$_3$$CuSb$$_2$$O$$_9$$であり、微視的に見ると磁気的に非対称である一方、長さ,時間スケールともに平均的に見ると対称な状態にある。われわれは、この物質において静的なヤーンテラー歪を示すことなくCu$$^{2+}$$イオンのハニカム格子が、フラストレートした状態にあることを見いだした。このハニカム格子においては、スピン1/2同士が2次元的にランダムに結合しており、スピンダイマー的なブロードな励起があり、また低エネルギーのスピン自由度が残ることが見られた。

口頭

Sulfur and hydrogen metabolism linked to CO$$_{2}$$ fixation by abundant Nitrospirae in the deep subsurface

天野 由記; Anantharaman, K.*; Tomas, B. C.*; Olm, M.*; Burstein, D.*; Castelle, C. J.*; 別部 光里*; 宮川 和也; 岩月 輝希; 鈴木 庸平*; et al.

no journal, , 

The bacterial phylum Nitrospirae is phylogenetically diverse. There are relatively few isolated representatives available for laboratory study and the physiology, functions and distributions of these bacteria across environments remain largely unknown. To understand the ecological role of Nitrospirae in the deep subsurface, we analyzed metagenomically-derived near complete genomes from groundwaters associated with granite and sedimentary rock where Nitrospirae are very abundant. The bacteria are autotrophs that fix CO$$_{2}$$ via the Wood-Ljungdahl pathway and reductive TCA cycles. The genomes encode versatile energy-generating pathways that involve sulfate reduction, hydrogen oxidation and nitrite reduction. Phylogenetic analyses indicate that the organisms are most similar to the isolated magnetotactic bacterium, Candidatus Magnetobacterium bavaricum, with only 89-91% 16S rRNA gene sequence identity. These Nitrospirae bacteria appear to play critical ecosystem roles as primary producers and they are likely central to sulfur cycling in the deep subsurface.

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