Biology subjects

Fukuyama, Y.

Publications and source records attributed to Fukuyama, Y..

5 recordsLinked to original sources

bioRxiv2026

Microorganisms consume trace gases present throughout the Mariana Trench water column

Dark waters harbour two-thirds of the ocean's bacterial and archaeal cells, yet the energy sources sustaining microbial life at these depths remain poorly understood. Here we integrate hydrographic profiles with metagenomic analyses and ex situ activity measurements to investigate whether carbon monoxide (CO) and molecular hydrogen (H2) are viable energy sources for epipelagic and mesopelagic microbial populations in the Mariana Trench region. Both gases were detected from 5 to 9,371 m, with concentrations generally higher in the photic zone but anomalously high in several deeper waters. Metagenomic analyses indicate a shift from phototrophic towards lithotrophic energy acquisition with depth. Microbial populations encoding CO dehydrogenases increased from 6.1% at 5 m to 45% at 1,000 m, while those encoding uptake hydrogenases were much less abundant, but increased from 0.34% to 0.63%. Ex situ incubations revealed that in situ cell-specific CO oxidation rates declined with depth, whereas corresponding H2 oxidation rates were significantly higher at 1,000 m than at the surface. At 1,000 m, cell-specific H2 oxidation rates were approximately 4,500-fold higher than those of CO. These contrasting trends suggest that CO oxidation is a widespread auxiliary energy-acquisition strategy, whereas H2 oxidation may sustain hydrogenotrophic growth in dark waters. Together, our results suggest H2 and CO are readily available to pelagic microbial populations and are biologically oxidised in the dark zone, supporting microbial energy acquisition and oceanic biogeochemical cycling.

microbiology↗

bioRxiv2025

Direct carbon monoxide fixation via the bacterial and archaeal Wood-Ljungdahl pathways

The Wood-Ljungdahl (WL) pathway, which is widely distributed in both archaea and bacteria, is an ancient carbon fixation pathway from CO2. CO2 fixation proceeds via two branches of pathway: progressive reduction to the methyl group in the methyl branch and one-step reduction to CO in the carbonyl branch. In the final step of the pathway, the methyl group, CO, and CoA are combined into a carbon monoxide dehydrogenase (CODH)/acetyl-CoA synthase (ACS) complex to form acetyl-CoA. Here, we show direct CO fixation to the carbonyl group of acetyl-CoA in both archaeal and bacterial WL pathways under hydrogenogenic growth conditions using 13C tracer-based metabolomics. A combination of metabolomics and proteomics suggested that the hydrogenotrophically grown Thermodesulfatator indicus and Archaeoglobus sp. strain MCR cells, directly fixed CO using free-form ACS in the carbonyl branch with relatively low CO availability. In contrast, carboxydotrophically grown Archaeoglobus cells utilize the CODH/ACS complex for CO2 fixation rather than CO fixation. Direct CO fixation by free-form ACS is more advantageous for conserving reduced ferredoxin compared with the thermodynamically challenged CO2 reduction by CODH. These findings provide further insight into the origin and evolution of the most ancient inorganic carbon fixation pathway and geochemical cycles on early Earth.

microbiology↗

bioRxiv2025

Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria

The Wood-Ljungdahl (WL) pathway and reductive tricarboxylic acid (rTCA) cycle are the dominant chemolithotrophic CO2 fixation pathways in bacteria inhabiting aphotic geothermal and deep-sea hydrothermal ecosystems. However, the activity of these bacterial metabolic systems in ecosystems with available organic carbons remains unclear. Here, we examined the impact of extracellular acetate on the CO2-fixation pathways of three thermophilic hydrogen-oxidizing and non-acetogenic bacteria using 13C tracer-based metabolomics. Under chemolithoautotrophic conditions, Thermodesulfatator indicus and Hydrogenobacter thermophilus fixed CO2 through the WL pathway and rTCA cycle, respectively, whereas Thermovibrio ammonificans, which has been suggested to operate both of these pathways, exhibited significant CO2 fixation through only the rTCA cycle. Under chemolithomixotrophic conditions with acetate, H. thermophilus and T. ammonificans assimilated both CO2 and acetate via the rTCA cycle. In contrast, acetate suppressed CO2 fixation through the WL pathway in T. indicus and was used as the primary carbon source under chemolithomixotrophic conditions. These results suggest that the contribution of the WL pathway for CO2 fixation might be overestimated in ecosystems where acetate is available. Moreover, the present findings indicate that simultaneous CO2 fixation through both the WL pathway and rTCA cycle in a cell, which has been proposed as a possible metabolic strategy for CO2-fixation in ancestral life, is not advantageous in extant microorganisms.

microbiology↗

bioRxiv2023

Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen

Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 L of 100 nmol/L mol amino acids comparable to a mere 1 x 104-5 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the co-occurrence of the Wood-Ljungdahl pathway and an incomplete reductive TCA cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acid, genomic information, and public database. Among them, the presence of the alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS is the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to in any kind of isolated microbe.

microbiology↗

bioRxiv2021

Isolation and characterization of novel temperate virus Aeropyrum globular virus 1 infecting hyperthermophilic archaeon Aeropyrum

We isolate a novel archaeal temperate virus named Aeropyrum globular virus 1 (AGV1) from the host Aeropyrum culture. Reproduction of AGV1 was induced by adding 20 mM tris-acetate buffer to exponentially growing host cells. Negatively stained virions showed spherical morphology (60 {+/-}2 nm in diameter) similar to Globuloviridae viruses. The double-stranded circular DNA genome of AGV1 contains 18,222 bp encoding 34 open-reading frames. No ORFs showed significant similarity with Globuloviridae viruses. AGV1 shares three genes, including an integrase gene, with reported spindle-shaped temperate viruses. However we couldnt detect its integration site in the host genome. Moreover AGV1 seemed not to replicate autonomously because there are no origin recognition boxes in the genome. qPCR results showed that the genome copy number of AGV1 was lower than that of the host genome (10-3 copies per host genome). Upon the addition of tris-acetate buffer, a steep increase in the AGV1 genome copy number (9.5-26 copies per host genome at 2 days post-treatment) was observed although clustered regularly interspaced short palindromic repeat (CRISPR) elements of the host genome showed significant matches with AGV1 protospacers. Our findings suggest that AGV1 is a novel globular virus exhibiting an unstable carrier state in the growing host and in that way AGV1 can escape from the host defense system and propagate under stressful host conditions. ImportanceStudying archaeal viruses yields novel insights into the roles of virospheres and viruses in the evolutionary process of their hosts. Here, we isolated a novel spherical virus named Aeropyrum globular virus 1. AGV1 has integrase gene but its genome is not integrated into the host genome. AGV1 could not replicate autonomously due to the lack of origin recognition boxes and thus its copy number was too low (10-3 copies per host genome) without any inducing stimulus. However, upon the addition of tris-acetate buffer, the AGV1 genome copy number steeply increased instead of a perfect sequence match between the spacer of the host CRISPR/Cas system and the protospacer. Our findings suggest that AGV1 can escape from the host defense system and propagate under stressful conditions for the host by establishing an unstable carrier state. These results reveals a novel aspect of host-virus interactions in extreme environments.

microbiology↗