Hideyuki Tamaki

We report the complete genome sequence of Aquabacterium sp. strain TM01, a membrane-adherent bacterium isolated from activated sludge in a labooratory-scale membrane bioreactor treating municipal sewage. The complete genome is 3,785,964 bp with a G + C content of 64.4%.

A facultatively anaerobic, thermophilic, Gram-negative bacterium, strain sy37 ^T , isolated from a deep-sea hydrothermal field and belonging to the candidate phylum WOR-3, was characterized in detail. The cells were non-motile long rods with pili and grew via respiration with 2–10% (v/v) oxygen and elemental sulphur as electron acceptors. Optimum growth was observed at 75 °C, pH 6.0 and 3.5% (w/v) NaCl with a doubling time of 10 h. iso-C _17 : 0 was found to be the major fatty acid and menaquinone-8 was identified as the major respiratory quinone. The G+C content of the genomic DNA was 60.6 mol%. Based on the results of phylogenetic analyses of the 16S rRNA gene and genome sequences, together with the phenotypic characterization of strain sy37 ^T , we propose the name Caldifarcimen microaerophilum gen. nov., sp. nov. for strain sy37 ^T (=NBRC 116057 ^T =BCRC 81450 ^T ). In addition, we propose the associated family, order, class and phylum as Caldifarciminaceae fam. nov., Caldifarciminales ord. nov., Caldifarciminia classis nov. and Caldifarciminota phyl. nov., respectively, in the bacterial kingdom Pseudomonadati .

A novel slow-growing bacterium, designated strain ag2_l2_5A ^T , was isolated from pine forest soil at Kagamiyama, Hiroshima, Japan, by using a gel microdroplet cultivation approach. The strain was characterized as a Gram-negative, non-motile bacterium with a short rod-shaped morphology. The strain formed small, circular, smooth and umbonate colonies after prolonged incubation on agar plates. Cells accumulated intracellular polyphosphate and produced membrane vesicles during the exponential growth phase. The strain grew optimally at 20–30 °C and pH 6.0–7.5, utilizing various sugars, amino acids and organic acids as carbon sources. The genomic G+C content was 62.8%. The major fatty acids were iso-C _15 : 0 , C _16 : 1 ω7c, iso-C _16 : 0 , iso-C _17 : 0 and C _16 : 0 . Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain ag2_l2_5A ^T belongs to the class Gemmatimonadetes within the phylum Gemmatimonadota . Its closest relatives were Gemmatimonas phototrophica AP64 ^T (91.3% gene sequence similarity), Gemmatimonas aurantiaca T-27 ^T and Pseudogemmatithrix spongiicola 318 ^T . Based on polyphasic characterization, the strain ag2_l2_5A ^T represents a novel genus and species of the class Gemmatimonadetes , for which the name Leucogemmata humicola gen. nov., sp. nov. is proposed. The type strain is ag2_l2_5A ^T (=NBRC 117234 ^T =DSM120521 ^T ).

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.

A hypothesis-free polymeric sensor array generates fluorescence fingerprints to rapidly identify the type, origin, and quality of complex culture supplements, enabling robust and data-driven quality assessment across diverse biological media.

We present a polymer-based chemical-tongue strategy that enables the rapid and simple detection as well as the strain-level identification of bacteria in milk, a crucial challenge for public health.

We report the draft genome sequence of Denitratisoma sp. strain agr-D3, isolated from common reed using a droplet-based cultivation method. The draft genome is 3,082,957 bp with a G + C content of 63.6%. The genome was predicted to contain 2,914 coding sequences and 4 rRNA genes.

We report the draft genome sequence of Dongia sp. strain agr-C8, isolated from the rhizosphere of Phragmites australis using a droplet-based cultivation method. The draft genome is 5,596,395 bp with a G+C content of 66.0%. The genome is predicted to contain 5,334 coding sequences and 3 rRNA genes.

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.

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.