Biology subjects

Futamata, H.

Publications and source records attributed to Futamata, H..

3 recordsLinked to original sources

bioRxiv2026

Competition-induced metabolic switching governs the interaction network in plant microbiome assembly

Plants are colonized by characteristic microbiomes that help maintain plant health and function. However, the mechanisms that make these communities assemble in a consistent, repeatable manner remain poorly understood. Here, we show how microbial metabolic strategies for host-derived substrates drive plant microbiome assembly, using a six-member synthetic community that captures the taxonomic diversity of natural duckweed microbiome. Contrary to expectations of metabolic niche partitioning, five of six strains adopt similar metabolic states when colonizing the host alone, consistent with the preferential use of a shared substrate, acetaldehyde. In contrast, during competition with specific community members, these strains consistently switch toward alternative substrates, including sugars and aromatics. Strikingly, this metabolic switching accompanies all negative interspecies interactions observed in the community, indicating that a single class of metabolic response dominates the inhibitory interaction network organizing community structure. By comparison, although metabolite cross-feeding is widespread, its contribution to facilitative interactions depends on the background of resource competition. Together, these findings highlight competition-induced metabolic switching as a primary driver of microbial interaction networks, and provide a cross-scale account of how microbial metabolic strategies underpin the reproducible assembly of plant microbiomes.

microbiology↗

bioRxiv2023

Rechargeable Biomineral Induced by Sulfate Reducing Bacterium Cupidesulfovibrio sp. HK-II

A black precipitate produced by a sulfate reducing bacterium Cupidesulfovibrio sp. strain HK was investigated with multidisciplinary methods. X-ray diffraction (XRD) analysis revealed that the black precipitate was mackinawite. Cyclic voltammetry analysis showed the obvious redox peaks, and the biogenic mackinawite exhibited rechargeable properties. XRD analyses showed that the form of the rechargeable biogenic mackinawite (RBM-II) was changed by discharge and recharge treatments: Field-emission transmission electron microscope analyses revealed that lepidocrocite and amorphous iron oxide were appeared from mackinawite on discharged condition, and the three kinds of minerals were intermingled via the rechargeable treatments. Physicochemical parameters were changed regularly under the treatments, suggesting that discharge would be occurred by iron oxidation and sulfur reduction, and vice versa. These results indicated that dynamics of sulfur is important key process in rechargeable mechanism, supporting that a part of mackinawite was transformed to lepidocrocite and iron oxides, and vice versa. Microbial fuel cells (MFCs) equipped with lactate, strain HK-II and anode including RBM-II consumed lactate even under opened circuit conditions, after which MFCs generated higher current density at re-closed circuit conditions. These results demonstrated that the biogenic mackinawite is one of rechargeable materials and would play important roles in geomicrobiological reactions and biotechnology.

bioengineering↗

bioRxiv2023

Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure

The way to deal with higher-order effects (i.e., modification of pairwise interactions by third-party species) has been a major consideration in community ecology. Ignoring these effects is not in line with reality, yet fully considering them make the situation overly complex. Here, we propose a simple framework incorporating higher-order effects into a bottom-up community modeling, and assessed its validity using a seven-member synthetic bacterial community on a host plant, duckweed. Our findings revealed that actual interspecies interactions in community could not be predicted from pairwise co-culturing results; however, using information from trio combinations allowed for acceptable prediction. In addition, inclusion of four-, five-, and six-member combinations did not markedly enhance the prediction accuracy from trio-based prediction, suggesting that trio combinations, the smallest unit of higher-order effects, provide a reasonable baseline to unravel complex interaction networks. Building on this finding, we developed a prediction rule to estimate the structure of 4 - 7 member communities based on information from [≤] 3-member combinations, which yielded significantly better accuracy (relative mean square percentage errors of 22.7% - 61.2%) than pairwise-based model (53.5% - 185.2%). This highlights the possibility of establishing a quantitative link between the interspecies interactions and community structure, by observing beyond-pairwise combinations.

ecology↗