Kyohei Kuroda

National Institute of Advanced Industrial Science and Technology

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Takashi Narihiro

National Institute of Advanced Industrial Science and Technology

Takashi Yamaguchi

Nagaoka University of Technology

Masashi Hatamoto

Nagaoka University of Technology

Masaru K. Nobu

Japan Agency for Marine-Earth Science and Technology

Masayoshi Yamada

National Cancer Center Hospital East

Masahito Yamauchi

National Institute of Technology, Kagoshima College

Hazuki Kurashita

National Institute of Advanced Industrial Science and Technology

Yuga Hirakata

National Institute of Advanced Industrial Science and Technology

Kengo Kubota

Tohoku University

Ryosuke Nakai

National Institute of Advanced Industrial Science and Technology

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Nagaoka University of Technology

National Institute of Advanced Industrial Science and Technology

The University of Tokyo

Nagaoka University

Hiroshima University

Hokkaido University

National Institute of Technology, Kagoshima College

Tohoku University

National Institute of Technology, Miyakonojo College

Nagaoka National College of Technology

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Improvement of Generic Skills by Working in Diverse Groups and Establishment of Students’ Evaluation Approaches

Journal of JSEE (2017)

Kyohei Kuroda Tsuyoshi Danshita Shinya MAKI Tomohiro Yamaguchi Makoto ICHITSUBO

A global and innovative human resource development is essential in recent Japanese industry because of rapid globalization of today’ s world. To address the needs in the industries, we performed the development program of innovative and global human resources in collaboration with 11 “Kosen” during Dec. 26-28, 2015. A total of 35 students and 8 professors in “Kosen” and Nagaoka University of Technology participated in this program. Through the hackathon-based facilitation and project management exercises, we grouped 6 teams, and evaluated students’ generic skills improvements. By using spearman’ s correlation test and network analysis, we could visualize the students’ development and interaction in each team. Besides, we propose that diversities of their educational institutions/majors and numbers of female students are the critical factors for effective team building based on principal component analysis of students’ diversities.

Facilitation

10.4307/jsee.65.1_58

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Citations (1)

Thermodynamically diverse syntrophic aromatic compound catabolism

Environmental Microbiology (2017)

Masaru K. Nobu Takashi Narihiro Miaomiao Liu Kyohei Kuroda Ran Mei

Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO2 , H2 and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H2 and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.

Euryarchaeota

Catabolism

Microbial Metabolism

Metabolic pathway

10.1111/1462-2920.13922

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Citations (34)

Draft genome sequences of Corallococcus strains KH5-1 and NO1, isolated from activated sludge

Microbiology Resource Announcements (2024)

Shun Tomita Ryosuke Nakai Kyohei Kuroda Hazuki Kurashita Masashi Hatamoto

Myxobacteria are known as prolific producers of secondary metabolites with a unique and wide spectrum of bioactivities. Here, we report draft genome sequences of KH5-1 and NO1, myxobacteria isolated from activated sludge, which consist of 9.89 and 9.86 Mb, both of which have G + C contents of 70.7%.

Myxobacteria

10.1128/mra.01104-23

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A novel cultivation method for growing oyster mushrooms with low potassium content using brewer’s grain, an agro-waste

Environmental Technology & Innovation (2023)

Keigo Nakakubo Kei Kariyazono Takahiro Watari Fumio Yagi Kyohei Kuroda

A novel cultivation method was established for growing low-potassium oyster mushrooms to benefit patients with kidney disease by adding various ratios of KCl, NaCl, and glycerol to a basal medium containing conifer sawdust and brewer's grain. The basal medium contained 265 mg of potassium (6.8 meq)/kg medium, which is close to the minimum amount required for the vegetative growth for oyster mushrooms, corresponding to 8.1% of potassium of the control medium containing conifer sawdust and rice bran. Of the media tested, the medium containing total potassium and sodium of 487 and 584 mg (12.5 and 25.4 meq)/kg medium, respectively, was good in fruiting bodies yield and reduction of potassium amount. Addition of osmolyte glycerol [32.5 g (352.9 meq)/kg bed] to this medium resulted in fruiting bodies with 70% less potassium compared to that of the control medium. These results suggest that agro-wastes can be effectively used for producing low-K mushrooms.

Sawdust

Potassium nitrate

10.1016/j.eti.2023.103240

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Development of slow sponge sand filter (SpSF) as a post-treatment of UASB-DHS reactor effluent treating municipal wastewater

Water Science & Technology (2016)

Namita Maharjan Kyohei Kuroda Kazuya Dehama Masashi Hatamoto Takashi Yamaguchi

In this study, conventional slow sand filter (SSF) and modified slow sponge sand filter (SpSF) were investigated for the post-treatment of up-flow anaerobic sludge blanket (UASB)-down-flow hanging sponge (DHS) reactor effluent. The seasonal variation did not show significant differences in removal efficiencies of both filters. However in summer, both filters were able to achieve high total suspended solids and total biochemical oxygen demand removal averaging 97% and 99%, respectively. Contrary to organic removal, total nitrogen removal efficiency was satisfactory, showing increased removal efficiencies averaging 58% and 62% for SSF and SpSF in summer. On the other hand, average total coliform removal of SSF and SpSF was 4.2 logs and 4.4 logs and corresponding Escherichia coli removal was 4.0 logs and 4.1 logs, respectively. From our observation, it could be concluded that the relative performance of SpSF for nutrients and coliforms was better than SSF due to the effectiveness of sponge media over fine sands. Moreover, microbial community analysis revealed that the members of phylum Proteobacteria were predominant in the biofilms of both filters, which could have contributed to pollutant removal. Therefore, SpSF could be concluded to be a suitable post-treatment of UASB-DHS system in warmer conditions.

Total suspended solids

Biochemical oxygen demand

10.2166/wst.2016.164

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Development of the Button Mushroom Cultivation Technology Based on the Combined Use of Sewage Sludge Compost and Cow Manure

Journal of Japan Society of Civil Engineers Ser G (Environmental Research) (2017)

Masahito Yamauchi Shoji Ikeda Yutarou NIIHARA Masayoshi Yamada Fumio Yagi

本研究では，下水汚泥堆肥の成分特性を把握後，マッシュルーム(ツクリタケ，Agaricus bisporus)の栽培を試みた．その結果，下水汚泥堆肥を単独の栄養材として利用した試験区では，収量が対照区（牛糞堆肥区）と比較して極端に少なかった．これは，菌糸の生殖成長期に利用されるセルロースやカリウムが培地中に極端に少なかったことが影響していると考えられた．一方，下水汚泥堆肥と牛糞堆肥を併用した試験区では，収量が対照区と比較して1.2～1.8倍に増加した．また，子実体中の重金属含有量は対照区と同等であったこと，さらに一般成分，アミノ酸含有量などの栄養成分についても対照区と遜色ないことから，下水汚泥堆肥はマッシュルーム培地に利用できると考えられた．

Agaricus bisporus

Cow dung

Sewage sludge

Agaricus

10.2208/jscejer.73.iii_397

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Citations (2)

Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach

Microbes and Environments (2022)

Shuka Kagemasa Kyohei Kuroda Ryosuke Nakai Yu‐You Li Kengo Kubota

Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana-lyses. The amplicon ana-lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana-lysis of the 0.45-0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.

10.1264/jsme2.me22027

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Citations (11)

Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems

mBio (2024)

Kyohei Kuroda Meri Nakajima Ryosuke Nakai Yuga Hirakata Shuka Kagemasa

To verify whether members of the phylum

Candidatus

10.1128/mbio.03102-23

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Citations (7)

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

Scientific Reports (2016)

Ran Mei Takashi Narihiro Masaru K. Nobu Kyohei Kuroda Wen‐Tso Liu

Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

Digestion

10.1038/srep34090

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Citations (98)

Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage

Microbes and Environments (2015)

Azrina A. Aida Kyohei Kuroda Masamitsu Yamamoto Akinobu Nakamura Masashi Hatamoto

We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors.

Mesophile

Anammox

10.1264/jsme2.me14105

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Citations (15)