Tomoyuki Hori

• Chief Senior Researcher at National Institute of Advanced Industrial Science and Technology

Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and iso...

1,4-Dioxane is one of the most common and persistent artificial pollutants in petrochemical industrial wastewaters and chlorinated solvent groundwater plumes. Despite its possible biological treatment in natural environments, the identity and dynamics of the microorganisms involved are largely unknown. Here, we identified active and diverse 1,4-dio...

Pathogens are known to survive in compost and to regrow under the influence of certain factors, such as moisture content, temperature and nutrient availability. Dead biomass, by providing available nutrients, is a factor that may affect pathogen regrowth. However, the indigenous microorganisms, including pathogens, that grown on the dead biomass of...

In anaerobic membrane bioreactor (AnMBR) treating organic solid waste, acetate is one of the most important precursors to CH4. However, the identity and diversity of anaerobic acetate degraders are largely unknown, possibly due to their slow growth rates and low abundances. Here, we identified acetate-degrading microorganisms in the AnMBR sludges b...

Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB...

Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system pe...

Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge (MAS) system for retaining ammonia while removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the MAS system is essential to optimize s...

The gut microbiome is crucial for the metabolic health and pathogen resistance of various host animals; however, the impact of the wild gut microbiome on host health remains poorly understood. This study examined the gut microbiome of medaka ( Oryzias latipes species complex), comparing domesticated and wild populations, to assess the wild gut micr...

Rapid sand filters (RSFs) are employed in a drinking water treatment to remove undesirable elements such as suspended solids and dissolved metal ions. At a closed uranium (U) mine site, two sets of tandemly linked paired RSF systems (RSF1-RSF2 and RSF1-RSF3) were utilized to remove iron and manganese from mine water. In this study, a 16S rRNA-based...

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement...

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, minorit...

Microbial methane oxidation has a significant impact on the methane flux from marine gas hydrate areas. However, the environmental fate of methane remains poorly constrained. We quantified the relative contributions of aerobic and anaerobic methanotrophs to methane consumption in sediments of the gas hydrate-bearing Sakata Knoll, Japan, by in situ...

We investigated relationships between features of benthic macrofaunal communities and geochemical parameters in and around microbial mat-covered sediments associated with a methane seepage on Sakata Knoll in the eastern Japan Sea. A depression on top of the knoll corresponds to a gas-hydrate-bearing area with seepage of methane-rich fluid, and micr...

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 fer...

A transition to ammonia recovery from wastewater has started; however, a technology for sustainable nitrogen retention in the form of ammonia and organic carbon removal is still in development. This study validated a microaerophilic activated sludge (MAS) system to efficiently retain ammonia from high-strength nitrogenous wastewater. The MAS is bas...

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of...

The discharge of high-strength oily wastewater adversely affects the environment; therefore, the treatment of wastewater containing fats, oils, and grease from the food industry is of importance. In this study, we used a membrane bioreactor (MBR) to treat Ramen noodle-soup wastewater, and we evaluated the optimal oil concentration in the wastewater...

Anaerobic soil disinfestation (ASD) consists of the application of labile organic materials to soil, flooding, and covering the soil surface with plastic film. Anaerobic soil disinfestation is a widely used ecofriendly alternative to chemical fumigation for eliminating soil-borne plant pathogens. However, the exact mode of action of ASD has not bee...

Difficulty in treating ironworks wastewater with high concentrations of nitrate is a major issue in steel manufacturing. We developed an N2 gas aerated anaerobic membrane bioreactor (AnMBR) and further assessed its nitrate removal capacity at the bench (0.026 m³) and pilot (4 m³) scales using a comprehensive microbiome survey. Both scale AnMBRs wer...

A transition to ammonia recovery from wastewater has started; however, a technology for sustainable nitrogen retention in the form of ammonia is still in development. This study validated a microaerophilic activated sludge (MAS) system to efficiently retain ammonia from high-strength nitrogenous wastewater. The MAS is based on conventional activate...

The decolorization of 11 dyes by granular sludge from an anaerobic expanded granular sludge bed (EGSB) reactor was evaluated. Biological decolorization of Reactive Red 21, 23, and 180, and Reactive Yellow 15, 17, and 23 in model textile wastewater was observed for the first time after a 7-day incubation (over 94% decolorization). According to the s...

Intensive research on molecular microbiological methods has accelerated the development of cutting-edge technologies, e.g., a high-throughput sequencer, microscopy, and mass spectrometry, at a surprisingly fast pace. The development of these technologies has allowed researchers, whose expertise does not lie in environmental microbiology and microbi...

Urban rivers receive used water derived from anthropogenic activities and are a crucial source of the potent greenhouse gas nitrous oxide (N2O). However, considerable uncertainties still exist regarding the variation and mechanisms of N2O production in response to the discharge of treated sewage from municipal wastewater treatment plants (WWTPs). T...

Sulfurovum spp. TSL1 and TSL6 are sulfur-oxidizing chemolithoautotrophic bacteria isolated from the tsunami-launched marine sediment in the Great East Japan earthquake. This announcement describes the draft genome sequences of the two isolates that possess the gene sets for the sulfur oxidation pathway.

Insecticide resistance is one of the most serious problems in contemporary agriculture and public health. Although recent studies revealed that insect gut symbionts contribute to resistance, the symbiont-mediated detoxification process remains unclear. Here we report the in vivo detoxification process of an organophosphorus insecticide, fenitrothio...

Here, we report the draft genome sequences of two Geobacter sp. strains, AOG1 and AOG2, isolated from enrichment cultures using crystalline Fe(III) oxides as electron acceptors. Strains AOG1 and AOG2 possess numerous genes encoding multiheme c-type cytochromes and pilA-N genes encoding the pilin mono-mer of nanowires in their genomes.

Here, we report the draft genome sequences of two Geobacter sp. strains, AOG1 and AOG2, isolated from enrichment cultures using crystalline Fe(III) oxides as electron acceptors. Strains AOG1 and AOG2 possess numerous genes encoding multiheme c -type cytochromes and pilA-N genes encoding the pilin monomer of nanowires in their genomes.

The hallmark of eusocial insects, honeybees, ants, and termites, is division of labor between reproductive and non-reproductive worker castes. In addition, environmental adaption and ecological dominance are also underpinned by symbiotic associations with beneficial microorganisms. Microbial symbionts are generally considered to be maintained in an...

Typically, sulfate-reducing bioreactors used to treat acid mine drainage (AMD) undergo an initial incubation period of a few weeks to acclimatize sulfate-reducing bacteria (SRB), although necessity of this preincubation has rarely been evaluated. To reduce time and economic cost, we developed an SRB acclimatization method using the continuous flow...

In the Seto Inland Sea, Japan, chemical oxygen demand has increased over recent decades, while average dissolved oxygen concentrations in the bottom water have increased. In this study, we investigated responses of organic carbon (OC) in hypoxic sediment to changes of redox conditions using experimental columns containing sediment and overlying wat...

Background: Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible application in bioremediation and bioelectrochemical engineering, some of phylogenetically close Desulfuromonas spp. strains have be...

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...

Waste rocks generated from tunnel excavation contain the metalloid selenium (Se) and its concentration sometimes exceeds the environmental standards. The possibility and effectiveness of dissolved Se removal by the indigenous microorganisms are unknown. Chemical analyses and high-throughput 16S rRNA gene sequencing were implemented to investigate t...

The Great East Japan Earthquake caused a serious accident at the first Fukushima nuclear power plant (NPP), which in turn released a large amount of radionuclides. Little attention has been paid to in-situ soil microorganisms exposed to radioactive contamination by the actual NPP accident. We herein investigated bacterial communities in the radioac...

Anaerobic membrane bioreactor (AnMBR) is used for the treatment of organic solid waste. Clogging of filtration membrane pores, called membrane fouling, is one of the most serious issues for the sustainable operation of AnMBR. Although the physical and chemical mechanisms of the membrane fouling have been widely studied, the biological mechanisms ar...

The adoption of anaerobic membrane bioreactors (AnMBRs) for organic solid waste management is important for the recovery of energy and high-quality treated water. However, few studies have focused on AnMBR treatment of high-strength organic solid waste and the microorganisms involved under deteriorated operating conditions. In the present study, a...

Population shifts in the activated sludge microbiome of a membrane bioreactor (MBR) during the treatment of Ramen noodle-soup wastewater were analyzed by high-throughput sequencing. An MBR underwent stable treatment of wastewater containing increasing oil concentrations (from 135 to 1,350 mg/L) for 26 days; however, after feeding with wastewater co...

Excess sludge reduction is a central challenge in wastewater treatment, requiring a cost-effective technology. Here, we report the pilot-scale implementation of two Modified Ludzack-Ettinger (MLE) processes with and without a high-pressure jet device (HPJD) as a sludge reduction method based on physically decomposing bacterial cells in activated sl...

Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, d...

Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 M...

Methane-oxidizing bacteria (MOB) possess the metabolic potential to assimilate the highly potent greenhouse gas, CH4, and can also synthesize valuable products. Depending on their distinct and fastidious metabolic pathways, MOB are mainly divided into Type I and Type II; the latter are known as producers of polyhydroxyalkanoate (PHA). Despite the m...

Desulfuromonas sp. strain AOP6, with iron(III)-reducing activity, was isolated from subseafloor sediment in Nankai Trough. We report the complete genome of this strain determined by Illumina MiSeq sequencing and PCR/Sanger sequencing-based gap closing. The genome includes the genes encoding c-type cytochromes, type IV pili, and fatty acid degradati...

Simultaneous enzymatic saccharification and comminution (SESC) was used for large-scale anaerobic digestion of wood lignocellulose to generate methane and unmodified lignin. During SESC, 10% aqueous mixture of powdered debarked wood from various species was subjected to bead milling with hydrolytic enzymes to generate particles below 1 μm. This slu...

In this study, anaerobic membrane bioreactor (AnMBR) was applied for the treatment of a model slurry of high-strength organic solid waste. Continuous monitoring of reactor performances by chemical analyses and fine-scale tracing of the AnMBR sludge microbiome by high-throughput 16S rRNA gene sequencing were conducted during the long-term operation...

Although membrane fouling is a major issue when operating membrane bioreactors (MBRs), information regarding MBR performance and the sludge microbiome after the development of fouling remains limited. For the present study, two MBRs were operated for approximately 1 month under conditions of membrane fouling to investigate the effects of highly str...

Changes in microbial communities are observed during the long-term operation of activated sludge systems employing an excess sludge reduction technology. Short-term changes are also significant to confirm if key microbes are damaged, but they have not been investigated due to the absence of an appropriate method. We report a methodology to identify...

Aerobic anoxygenic phototrophic bacteria (AAnPB) are widely distributed and regarded as key players driving the carbon cycle in surface water of global oceans, coastal and estuary areas and in other freshwater environments (e.g., ponds and lakes). However, the abundance and spatial distribution of AAnPB in rivers is much less well-known. Here we in...

The natural microbial communities involved in arsenic (As) extraction under biostimulated conditions are still unclear. In this study, soil slurry was incubated with arsenate [As(V)]-laden Fe(III) or Al (hydr)oxides with lactate or acetate. After 40 d, dissolved As released from As(V)-laden Fe(III) accounted for 54% of the initial solid-phase As in...

The recent discovery of nitrous oxide (N2O)-reducing bacteria suggests a potential biological sink for the potent greenhouse gas N2O. While some N2O-reducing bacteria have been described, characterization of more isolates will be required for an application towards N2O mitigation. Here, we describe the successful enrichment and isolation of high-af...

Five types of sulfate-reducing passive bioreactors with rice bran as substrate were operated at three different mine sites under various operating conditions to investigate and compare the dominant sulfate-reducing bacteria (SRBs) involved in acid mine drainage (AMD) treatment. In all bioreactors, AMD was properly treated under the national effluen...

Abstract Levulinic acid (LA) is a building block alternative to fermentable sugars derived from cellulosic biomass. Among LA catabolic processes in Pseudomonas putida KT2440, ligation of coenzyme A (CoA) to LA by levulinyl-CoA synthetase (LvaE) is known to be an initial enzymatic step in LA metabolism. To identify the genes involved in the first st...

With a focus on marine sediment launched by the tsunami accompanying the Great East Japan Earthquake, we examined the vertical (i.e., depths of 0–2, 2–10, and 10–20 mm) profiles of reduced inorganic sulfur species and microbial community using a newly improved sulfur-fractionation method and 16S rRNA gene sequencing. S0 accumulated at the largest q...

The prokaryotic and eukaryotic microbial communities of activated sludge in a chemical plant wastewater treatment facility, processing relatively oligotrophic wastewater containing aromatic compounds and high-strength bromide ions, were characterized by high-throughput sequencing of rRNA genes based on DNA and RNA extracts. The microbial community...

Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly–based metatranscriptomics to a complex microbiome, activated sludge, which has b...

The aims of this study were to investigate the feasibility of partial nitrification (PN) in a sequencing batch reactor (SBR) fed with real wastewater discharged from the washing process at a semiconductor factory, to evaluate the efficacy of online control for nitrite buildup, and to examine the microbial community composition. To this end, online...

Here, we report a draft genome sequence of the Sporomusaceae bacterial strain FL31, a novel lactate-fermenting bacterium of the family Sporomusaceae within the class Negativicutes . This genome furthers our understanding of the physiological functions of this taxonomic group in natural environments.

The present study characterized the interactions of microbial populations in activated sludge systems during the operational period after an increase in the wastewater flow rate and consequential ammonia accumulation using a 16S rRNA gene sequencing-based network analysis. Two hundred microbial populations accounting for 81.8% of the total microbio...

Reverse osmosis (RO) system at a stage after membrane bioreactor (MBR) is used for the wastewater treatment and reclamation. One of the most serious problems in this system is membrane fouling caused by biofilm formation. Here, microbiomes and chemical components of the feed water and membrane-attached biofilm of RO system to treat MBR effluents we...

Sulfate-reducing passive bioreactor is an option for treating acid mine drainage (AMD) for a long period of time without maintenance. A 35-L packed-bed sulfate-reducing bioreactor containing rice bran was continuously operated for over 800 days, however, reactor performance became progressively worsened after day 871, resulting in the effluent zinc...

Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The draft genome sequence will aid the study of the LA catabolic pathway, which will allow for more applications of...

We report here a draft genome sequence of Azospira sp. strain I13 in the class Betaproteobacteria , a facultative anaerobic bacterium responsible for nitrous oxide (N 2 O) reduction. Deciphering this genome would pave the way for the use of Azospira sp. strain I13 to facilitate N 2 O consumption in a nitrogen-removing bioreactor emitting N 2 O.

The goal of this study was to develop a startup strategy for a high-rate anaerobic ammonium oxidation (anammox) reactor to treat waste brine with high concentrations of ammonium from a natural gas plant. An upflow anaerobic sludge blanket (UASB) anammox reactor with an effective volume of 294 L was fed continuously with waste brine with a salinity...

Insecticide resistance is a serious concern in modern agriculture, and an understanding of the underlying evolutionary processes is pivotal to prevent the problem. The bean bug Riptortus pedestris, a notorious pest of leguminous crops, acquires a specific Burkholderia symbiont from the environment every generation, and harbors the symbiont in the m...

Long-term exposure of nitrifiers to high concentrations of free ammonia (FA) and free nitrous acid (FNA) may affect nitrifiers activity and nitrous oxide (N2O) emission. Two sequencing batch reactors (SBRs) were operated at influent ammonium nitrogen (NH4-N) concentrations of 800 mg/L (SBRH) and 335 mg/L (SBRL), respectively. The NH4-N removal rate...

This study investigated the effect of the feedstock-to-inoculum (F/I) ratio on performance of the solid-state anaerobic co-digestion of pig urine and rice straw inoculated with a solid digestate, and clarified the microbial community succession. A 44-day biochemical methane potential test at F/I ratios of 0.5, 1, 2 and 3 at 55 °C and a 35-day large...