Yoichi Kamagata

Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of redox-associated functions is coupled with loss of nucleotide biosynthesis, raising a fundamental question of how such metabolically reduced organisms sustain cell growth. One of the most widespread and diverse lineages of prokaryotes, Minisyncoccota or Patescibacteriota, constitutes the majority of lineages exhibiting this pattern. To investigate how such organisms persist, we cultivated and characterized a representative of this lineage from a deep aquifer. The organism attaches to and penetrates growing bacterial host cells, and directly uptakes host RNA, concomitant with its depletion in the host. The metabolically reduced parasite cleaves host-derived RNA to directly supply cellular energy currencies and precursors for RNA/DNA synthesis, NTPs, without invoking canonical metabolic pathways. Codon usage in the parasite is complementary to that of its host, potentially minimizing translation of host-derived mRNA. Comparative genomics and phylogenetics indicate that these features are widespread and likely ancestral across the lineage. Exploitation of host RNA as a metabolic resource reveals a previously unrecognized metabolic strategy that demonstrates cellular metabolism can be sustained through direct utilization of informational macromolecules and thereby taps into an omnipresent energy reservoir, potentially supporting the environmental ubiquity of the metabolically reduced lineage.

We report the complete genome sequence of strain MRC-7, which represents a potentially novel genus within the family Opitutaceae. The genome was 4,342,534 bp in size and contained 3,428 protein-coding sequences, several of which were predicted to be involved in pectin degradation.

Nitrite-oxidizing bacteria (NOB) play a crucial role in global nitrogen cycling, yet their presence and adaptations in acidic environments remain poorly understood. This study unveils the cultivation and characterization of a novel acid-tolerant NOB, NS4 culture, affiliated with lineage II ( Nitrospira _ D ) within the genus Nitrospira . Enriched and isolated from a freshwater pond sediment, NS4 culture exhibits remarkable physiological and genomic traits that shed light on NOB survival strategies in low pH conditions. NS4 culture demonstrates the optimal growth at pH 6 and 0.5 mM nitrite concentration, with a maximum growth rate of 0.62 day⁻¹. Kinetic analyses reveal a high affinity for nitrite ( K _{m (app)} = 4.02 µM), suggesting adaptation to oligotrophic environments. Phylogenomic and genomic-relatedness analyses position NS4 culture as a novel member within the genus Nitrospira , for which we propose as “ Candidatus Nitrospira acidotolerans.” Genomic investigations indicate the presence of a complete reductive tricarboxylic acid cycle and genes for nitrite oxidation, confirming its chemolithoautotrophic lifestyle. Intriguingly, NS4 genome lacks complete pathways for cobalamin biosynthesis, implying a potential dependence on symbiotic partners for this essential cofactor. The NS4 genome harbors genes associated with acid resistance, including chaperones, transporters, and amino acid metabolism, suggesting a genetic potential for adaptation or resistance to low pH conditions. This discovery expands our understanding of NOB diversity and adaptability, offering insights into nitrogen cycling in acid-impacted ecosystems. The physiological and genomic traits of this acid-tolerant NOB open new insights for exploring the ecological significance of NOB in previously overlooked acidic habitats. IMPORTANCE: Nitrite-oxidizing bacteria (NOB) are integral to the global nitrogen cycle, yet their adaptations to acidic environments remain poorly understood. This study introduces Candidatus Nitrospira acidotolerans, an acid-tolerant NOB highly enriched from freshwater pond sediment. By combining physiological and genomic analyses, this work reveals unique adaptations that enable survival and nitrite oxidation under low pH conditions. Notably, the NS4 culture demonstrates high nitrite affinity and resistance to acidic stress, suggesting its ecological significance in acid-impacted ecosystems. Additionally, NS4 genomic traits reveal genetic potential of metabolic dependencies, including reliance on symbiotic partners for cobalamin synthesis. These findings expand our understanding of NOB diversity and their role in nitrogen cycling under extreme conditions, offering novel insights into microbial ecology and potential applications in managing nitrogen processes in acidic environments.

Duckweeds are small, fast-growing aquatic plants with high starch and protein content, making them promising candidates for next-generation plant biomass resources. Despite their importance, little is known about their interactions with microorganisms, particularly plant growth-promoting bacteria (PGPB), which play key roles in enhancing plant productivity. In this study, we report the plant growth-promoting effects of strain LA-C6, a member of the phylum Armatimonadota, isolated from duckweed fronds. Based on 16S rRNA gene analysis, this strain represents a novel genus-level lineage, and is referred to as Fimbriimonadaceae bacterium strain LA-C6. In axenic co-culture experiments, strain LA-C6 promoted duckweed growth, increasing the frond proliferation of four duckweed species (Lemna minor, Lemna aequinoctialis, Spirodela polyrhiza, and Landoltia punctata) by 1.8- to 4.0-fold compared with uninoculated controls. Importantly, three other phylogenetically distinct Armatimonadota species also exhibited significant plant growth-promoting effects on L. minor, increasing frond number by up to 2.3-fold and dry weight by up to 2.4-fold. This finding highlights the broader potential of diverse Armatimonadota members as PGP bacteria. A survey of the IMNGS database showed that strain LA-C6 and other Armatimonadota species are widely distributed across diverse plant-associated environments. Biochemical assays and gene prediction analyses revealed that strain LA-C6 produces indole-3-acetic acid (IAA) as a representative PGP trait, whereas no additional PGP-associated traits were detected. These results suggest that diverse bacterial lineages within the phylum Armatimonadota exert growth-promoting effects on aquatic plants, potentially through yet-to-be-identified mechanisms.

Methane, a greenhouse gas and energy source, is commonly studied using stable isotope signals as proxies for its formation processes. In subsurface environments, methane often exhibits equilibrium isotopic signals, but the equilibration process has never been demonstrated in the laboratory. We cocultured a hydrogenotrophic methanogen with an H ₂ -producing bacterium under conditions (55°C, 10 megapascals) simulating a methane-bearing subsurface. This resulted in near-complete reversibility of methanogenesis, leading to equilibria for both hydrogen and carbon isotopes. The methanogen not only equilibrated kinetic isotope signals of initially produced methane but also modified the isotope signals of amended thermogenic methane. These findings suggest that hydrogenotrophic methanogenesis can overwrite the isotope signals of subsurface methane, distorting proxies for its origin and formation temperature—insights crucial for natural gas exploration.

A Gram-negative, obligatory anaerobic, chemoheterotrophic bacterium, designated strain IA91^T, was isolated from sediments and formation water from deep aquifers in Japan. IA91^T derives its peptidoglycan, energy and carbon from exogenous cell wall fragments, namely muropeptides, released from actively reproducing bacteria, and is dependent on other bacteria for cell wall formation, growth and even cell shape: IA91^T is irregular rod-shaped but coccoids when muropeptide is absent. IA91^T grew in a temperature range of 25–45 °C with optimum growth at 40 °C. IA91^T utilized limited substrates, yeast extract, muropeptides and d-lactate. The major end products from yeast extract degradation were acetate, hydrogen and carbon dioxide. Co-cultivation with a hydrogen-scavenging methanogenic archaeon promoted IA91^T growth. No anaerobic respiration with nitrate, nitrite, sulphate or Fe(III) was observed. The major cellular fatty acids are C16 : 0, C18 : 1 trans9, C18 : 0 and C17 : 0. The G+C content of the genomic DNA was 45.6 mol%. Phylogenetic analysis based on 16S rRNA gene and conserved protein sequences involved in replication, transcription and translation indicated that IA91^T belonged to the candidate phylum Marine Group A (MG-A, SAR406 or Ca. Marinimicrobia) with no cultivated representatives. Based on the phenotypic and phylogenomic characteristics, a new genus and species, Fidelibacter multiformis gen. nov., sp. nov., is proposed for IA91^T (= JCM 39387^T = KCTC 25736^T). In addition, a new bacterial phylum named Fidelibacterota phyl. nov. is proposed for the candidate phylum MG-A represented by F. multiformis and Fidelibacteraceae fam. nov., Fidelibacterales ord. nov. and Fidelibacteria classis nov.

なぜ多くの微生物は培養できないのか?培養の困難さを第一の理由に挙げることも多いが、実際のところ、これまでの微生物学が依拠してきた手法論に根ざす本質的な理由が大きいと言ってよい。大規模シークエンシングに基づく膨大なメタゲノム情報の蓄積と旧来的な培養手法、そしてその培養手法そのものが持つ問題点などを理解することによって、まずは難培養の根幹が見えてくる。その一方でメタゲノムに基づく微生物のゲノム情報（metagenome-assembled genomes: MAGs）の増加はとどまるところを知らず、これまでの微生物の分類・同定・命名のルールを大きく揺るがそうとしてる。本総説ではそうした点に触れながら難培養性微生物の実体について概観したい。

Most of Earth’s prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or ‘Candidatus Marinimicrobia’) that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria. Reliance on exogenous muropeptides is traceable to the phylum’s ancestor, with evidence of vertical inheritance across several classes. This dependency may be widespread across bacteria (16 phyla) based on the absence of key peptidoglycan synthesis genes. These results suggest that uptake of exogenous cell wall components could be a relevant and potentially common survival strategy in energy-limited habitats like the deep biosphere.

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA–DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.