Uncovering the causal relationships in plant-microbe ecosystems: A time series analysis of the duckweed cultivation system for biomass production and wastewater treatment.

The complex interplay among plants, microbes, and the environment strongly affects productivity of vegetation ecosystems; however, determining causal relationships among various factors in these systems remains challenging. To address this issue, this study aimed to evaluate the potential of a data analytical framework called empirical dynamic modeling, which identifies causal links and directions solely from time series data. By cultivating duckweed, a promising aquatic plant for biomass production and wastewater treatment, we obtained a 63-day time series data of plant productivity, microbial community structure, wastewater treatment performance, and environmental factors.

Biofilm-derived membrane vesicles exhibit potent immunomodulatory activity in Pseudomonas aeruginosa PAO1.

Pathogenic bacteria form biofilms on epithelial cells, and most bacterial biofilms show increased production of membrane vesicles (MVs), also known as outer membrane vesicles in Gram-negative bacteria. Numerous studies have investigated the MVs released under planktonic conditions; however, the impact of MVs released from biofilms on immune responses remains unclear. This study aimed to investigate the characteristics and immunomodulatory activity of MVs obtained from both planktonic and biofilm cultures of Pseudomonas aeruginosa PAO1.

Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity.

A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective.

Complete genome sequences of six duckweed-associated bacterial strains for studying community assembly in synthetic plant microbiome.

We report the complete genome sequences of six bacterial strains isolated from a floating macrophyte, duckweed. These six strains, representing the six dominant families of the natural duckweed microbiome, establish a simple model ecosystem when inoculated onto sterilized duckweed. Their genomes would provide insights into community assembly in plant microbiome.

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

Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e.

Identification of genes involved in enhanced membrane vesicle formation in biofilms: surface sensing facilitates vesiculation.

Membrane vesicles (MVs) are small spherical structures (20-400 nm) produced by most bacteria and have important biological functions including toxin delivery, signal transfer, biofilm formation, and immunomodulation of the host. Although MV formation is enhanced in biofilms of a wide range of bacterial species, the underlying mechanisms are not fully understood. An opportunistic pathogen, , causes chronic infections that can be difficult to treat due to biofilm formation.

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms.

Hydroponic cultivation of Solanum lycopersicum (tomato) is important, and high tomato production depends on the use of nitrogen and phosphate fertilizers. We had developed a microbial fertilizer (MF), which is mainly composed of nitrate. To investigate the effect of MF on plant growth, hydroponic tomato was grown with MF or commercial inorganic fertilizer (IF), and the microbiomes of the rhizosphere and the liquid phase were analyzed by confocal microscopy and high-throughput sequencing.

Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility.

Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (Pres), complexed with chloride, sulfate, or salicylate at 3.52-3.

Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan.

Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their regions.

Incorporation of DNA to Bacterial Vesicles by in .

Membrane vesicles (MVs) are released by various prokaryotes and play a role in the delivery of various cell-cell interaction factors. Recent studies have determined that these vesicles are capable of functioning as mediators of horizontal gene transfer. Outer membrane vesicles (OMVs) are a type of MV that is released by Gram-negative bacteria and primarily composed of outer membrane and periplasm components; however, it remains largely unknown why DNA is contained within OMVs.

Complete Genome Sequence of Buttiauxella agrestis DSM 9389.

We report here the complete genome sequence of DSM 9389, which harbors eight 16S rRNA genes classified into three types. The genome sequence of this strain showed a high average nucleotide identity (97.3%) with that of the highly membrane vesicle-producing strain ATCC 33320.

Efficient conversion of organic nitrogenous wastewater to nitrate solution driven by comammox Nitrospira.

A bacterium capable of complete ammonia oxidation (comammox) has been widely found in various environments, whereas its industrial application is limited due to the difficulty of cultivation and/or enrichment. We developed a biological system to produce a high-quality nitrate solution for use in hydroponic fertilizer. The system was composed of two separate reactors for ammonification and nitrification and was found to have a stable and efficient performance in the conversion of organic nitrogen to nitrate.

Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, sp. Strain AQ5-07.

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source.

Synthetic Bacterial Community of Duckweed: A Simple and Stable System to Study Plant-microbe Interactions.

A complete understanding of the plant microbiome has not yet been achieved due to its complexity and temporal shifts in the community structure. To overcome these issues, we created a synthetic bacterial community of the aquatic plant, duckweed. The synthetic community established with six bacterial strains showed a stable composition for 50 days, which may have been because duckweed maintains a similar physiological status through its clonal reproduction.

Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture.

The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp.

Draft Genome Sequence of Phenol-Degrading Variovorax boronicumulans Strain c24.

We report the draft genome sequence of strain c24, which was isolated from a soil-inoculated chemostat culture amended with phenol as a sole carbon and energy source. The genome data will provide insights into phenol and other xenobiotic compound degradation mechanisms for bioremediation applications.

Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis Mutant.

Outer membrane vesicles (OMVs) are naturally released from Gram-negative bacteria and play important roles in various biological functions. Released vesicles are not uniform in shape, size, or characteristics, and little is known about this diversity of OMVs. Here, we show that deletion of , which encodes a part of the Tol-Pal system, leads to the production of multiple types of vesicles and increases overall vesicle production in the high-vesicle-forming type strain JCM 1090.

Draft Genome Sequence of Phenol-Degrading Variovorax boronicumulans Strain HAB-30.

We report the draft genome sequence of strain HAB-30, which was isolated from a phenol-degrading chemostat culture. This strain contains genes encoding a multicomponent type of phenol hydroxylase, with degradation pathways for catechol and other aromatic compounds. The genome sequence will be useful for understanding the metabolic pathways involved in phenol degradation.

Targeted delivery using membrane vesicles in prokaryotes.

Membrane vesicles (MVs) are lumen-containing spheres of lipid bilayers secreted by all prokaryotes into the extracellular milieu. They have multifunctional roles in stress response, virulence transfer, biofilm formation, and microbial interactions. Remarkably, MVs contain various components, including lytic enzymes, genetic materials, and hydrophobic signals, at high concentrations and transfer them effectively to the target microbial cells.

Draft Genome Sequence of the Phenol-Degrading Bacterium sp. Strain P-10, Isolated from Trichloroethene-Contaminated Aquifer Soil.

A batch culture was enriched on phenol with trichloroethene-contaminated aquifer soil as an inoculum. Cupriavidus sp. strain P-10 was isolated from the culture using a diluted plating method.

Bacterial communities adapted to higher external resistance can reduce the onset potential of anode in microbial fuel cells.

We investigated how bacterial communities adapted to external resistances and exhibited the performance of electricity production in microbial fuel cells (MFCs) with external resistance of 10 Ω (LR-MFC) and 1000 Ω (HR-MFC). The HR-MFC exhibited better performance than the LR-MFC. The power densities of the LR-MFC and the HR-MFC were 5.

Draft Genome Sequence of R2, Consisting of Aromatic Compound Degradation Genes for Phenol Hydroxylase.

strain R2 was isolated from a continuous culture enriched by a low concentration of phenol-oxygenating activities with low values (below 1 μM). The draft genome sequence of strain R2 reported here may contribute to determining the phenol degradation gene cluster.

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells.

Membrane vesicles (MVs) are secreted from a wide range of microbial species and transfer their content to other cells. Although MVs play critical roles in bacterial communication, whether MVs selectively interact with bacterial cells in microbial communities is unclear. In this study, we investigated the specificity of the MV-cell interactions and evaluated the potential of MVs to target bacterial cells for delivery.