Article
Microbiology
Simon Mills, Anna Christine Trego, Piet N. L. Lens, Umer Zeeshan Ijaz, Gavin Collins
Summary: This study investigated the microbial ecology of granule formation in high-rate, up-flow anaerobic bioreactors and proposed an ecological granulation model. By analyzing the microbial communities actively undergoing growth, breakage, and reformation within the granules, important ecological roles influencing granule formation and stability were identified, leading to the development of a stepwise ecological model for granulation.
MICROBIOLOGY SPECTRUM
(2021)
Article
Engineering, Environmental
Tzu-Yu Lin, Wen-Tso Liu
Summary: This study further validated the ecological genomics (ecogenomics)-based mass balance (EGMB) models and demonstrated the feasibility of using metagenome-based EGMB model to reveal microbial activity and function. The results showed highly comparable community profiles in the mock community and the bioreactor, and also identified the contribution of uncultivated populations in degrading the feed biomass.
Article
Biochemistry & Molecular Biology
Magdalena Nagler, Sabine Marie Podmirseg, Markus Mayr, Judith Ascher-Jenull, Heribert Insam
Summary: Microbiome studies using next generation sequencing are commonly performed on the total DNA pool, which includes extracellular- and intracellular DNA fractions. Results show that total DNA has lower species richness and unique reads compared to intracellular DNA when tracking microbial community changes over time. The extracellular DNA fraction may qualitatively bias microbiome studies due to abundant sequences masking overall results, while intracellular DNA provides more reliable genetic information about potentially alive microbes.
Article
Microbiology
HyunWoo Lee, Temesgen M. Fitamo, Camilla L. Nesbo, Nigel G. H. Guilford, Kart Kanger, Minqing Ivy Yang, Elizabeth A. Edwards
Summary: The objective of this study was to identify relationships between process parameters and the microbial community. The study found that increasing food waste led to a large increase in the absolute microbial abundance in the circulating leachate, while more cryptic Candidatus Roizmanbacteria and Spirochaetaceae specifically correlated with enhanced methane from the fiber fraction.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Agricultural Engineering
Gi-Beom Kim, Roent Dune A. Cayetano, Jungsu Park, Yura Jo, Seong Yeob Jeong, Myung Yeol Lee, Sang-Hyoun Kim
Summary: Low-thermal pretreatment of undigested and dewatered sludge at 10% total solids improved net energy production, sludge treatment efficiency, and digestion stability in a lab-scale anaerobic bioreactor. The highest biomethane yield and production rate were achieved at an SRT of 16 days, with a shift in methanogenic population from hydrogenotrophic to acetoclastic. This strategy could be a feasible approach for managing sludge from small wastewater treatment plants.
BIORESOURCE TECHNOLOGY
(2021)
Article
Environmental Sciences
Celine Lavergne, Polette Aguilar-Munoz, Natalia Calle, Frederic Thalasso, Maria Soledad Astorga-Espana, Armando Sepulveda-Jauregui, Karla Martinez-Cruz, Laure Gandois, Andres Mansilla, Rolando Chamy, Maialen Barret, Lea Cabrol
Summary: Freshwater ecosystems play a significant role in methane emissions and this study investigated the effects of temperature on microbial community structure and methane production pathways in sub-Antarctic lake sediments. The research found that temperature had a significant impact on methane production rates, particularly when methanogenic precursors such as acetate and H-2/CO2 were introduced.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Microbiology
Barbara Tonanzi, Simona Crognale, Andrea Gianico, Stefano Della Sala, Paola Miana, Maria Chiara Zaccone, Simona Rossetti
Summary: The study found that the majority of the reads in the anaerobic digester were affiliated with fermentative bacteria, followed by an increase in the proportion of Bacteroidetes over time and Methanosaeta as the most abundant methanogenic component. Specific quantitative data from real-time PCR showed an enrichment of bacteria and methanogens once the steady state was reached.
Article
Agriculture, Dairy & Animal Science
Giovana Slanzon, William Sischo, Craig McConnel
Summary: This study assessed the differences in the fecal microbiome of organic dairy cows receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. The results showed that there were differences in microbial diversity between pasture-based and TMR-based diets, but little difference in the relative abundance of methanogens. The good quality pasture and TMR in this study, combined with the allowance for feeding high levels of TMR, may have contributed to the lack of differences in the fecal archaeal community. Therefore, the development of novel strategies independent of pasture management is needed to reduce enteric methane emissions on organic dairies.
Article
Environmental Sciences
Simon Mills, Thi Phi Yen Nguyen, Umer Zeeshan Ijaz, Piet N. L. Lens
Summary: In this study, the effects of long-term bioreactor (un)stability on resistance to shock loads were evaluated. The results showed that the reactor with stable operation performed better in terms of resistance to a sudden increase in organic loading rate, despite having lower microbial community diversity. The operation history of a reactor plays a crucial role in determining its ability to withstand environmental perturbations.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Energy & Fuels
Cecilia Callejas, Ivan Lopez, Patricia Bovio-Winkler, Claudia Etchebehere, Liliana Borzacconi
Summary: The treatment of sugarcane vinasse is a challenge in sustainable bioethanol production, with anaerobic digestion being the most promising method. This study investigated the dynamics of microbial communities in a 100m(3) UASB methanogenic reactor during bioethanol production. Firmicutes were found to play a specific role in vinasse treatment, and the adaptation of inoculum to vinasse influenced microbiota diversity. The microbial community structure adapted to changes in feed and persisted during starvation periods in the reactor.
BIOMASS CONVERSION AND BIOREFINERY
(2022)
Article
Plant Sciences
Chakrit Bunyoo, Peerapat Roongsattham, Sirikorn Khumwan, Juthaporn Phonmakham, Passorn Wonnapinij, Arinthip Thamchaipenet
Summary: This study investigated the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions using 16S rRNA amplicon sequencing. The results showed that Proteobacteria was the dominant phylum in duckweed samples. A total of 24 microbial genera were identified as a core microbiome, with consistent proportions across all duckweed subtypes. The diversity of microbial communities decreased after nutrient-deficient stress, but the relative abundance of certain genera significantly increased. Functional prediction of the metagenome data revealed enrichment of essential pathways involved in DAB colonization and biodegradation under stress condition.
Article
Engineering, Environmental
Wenjie Guo, Dunjie Li, Zhipeng Zhang, Rongrong Mo, Yongzhen Peng, Yongmei Li
Summary: This study investigates a novel methodology for fractionation of organic components and microbial degraders in waste activated sludge (WAS) using modern instrumental analysis and 16S rRNA gene sequence analysis to modify the fractions in the anaerobic digestion model No 1 (ADM1). The combination of Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), and nuclear magnetic resonance (NMR) analyses accurately fractionated the organic matters in WAS, which was validated by other extraction methods. Based on microbial diversity analysis, the initial fractions of microbial degraders in ADM1 were reset. The ADM1 with full parameter modification (ADM1-FPM) showed significantly improved simulation of methane production in WAS. Rating: 8/10.
Article
Plant Sciences
Yumeng Wang, Chunyan Ma, Deqiang Dou
Summary: The aim of this study is to explore whether ginseng can be used with semen raphani to remedy acute and chronic fatigue conditions. The combination of ginseng with semen raphani does not influence acute fatigue effect compared with ginseng alone and can benefit for the fireness side-effect of ginseng. However, the more ratios of semen raphani in the combination with ginseng, the less the power of treating chronic fatigue is.
JOURNAL OF ETHNOPHARMACOLOGY
(2022)
Article
Engineering, Environmental
Evangelina Ripoll, Ivan Lopez, Liliana Borzacconi
Summary: This article discusses the anaerobic digestion technology used for organic-based solid waste management, as well as the issue of specific methanogenic activity tests. It is found that in solid digesters, the dilution of micro-organisms by substrate and organic inert material can affect the activity tests and distort the results. To address this, correction factors are proposed to adjust for the dilution effects. Experimental results show that the use of correction factors can reduce result distortion and improve the accuracy of the data.
Article
Engineering, Environmental
Najoua Mlaik, Fatma Karray, Sami Sayadi, Firas Feki, Sonia Khoufi
Summary: The study examined the anaerobic digestion of organic fraction of municipal solid waste (OFMSW) and its impact on the microbial community. The results showed that the biogas yield decreased with increased organic loading rates (OLRs) and the microbial community composition changed during the digestion process.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Hiroki Nagasawa, Takahiko Kagawa, Takuji Noborio, Masakoto Kanezashi, Atsushi Ogata, Toshinori Tsuru
Summary: The study demonstrates the ultrafast synthesis of silica membranes in atmospheric-pressure, low-temperature plasma, with direct deposition leading to the formation of a thin silica layer on the substrate. Increased deposition temperature improved the inorganic nature of the plasma-deposited layer and enhanced membrane performance. The resulting membranes showed outstanding permeance for small gas molecules, providing a nonthermal alternative for silica-based membranes fabrication.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Microbiology
Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Kuhl, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada, Vera Thiel
Summary: This study identified two different modes of energy metabolism of Chloroflexus aggregans in hot spring microbial mats through metatranscriptomic analyses and microscale measurements, showing that the organism exhibits phototrophy and chemomixotrophy under dynamic environmental conditions.
Article
Microbiology
Yuxin Chen, Arisa Nishihara, Takao Iino, Moriya Ohkuma, Shin Haruta
Summary: YA01T, a novel nitrogen-fixing fermentative bacterium isolated from Nakabusa hot springs in Japan, represents a new species of the genus Caldicellulosiruptor, with distinct phylogenetic position, biochemical and physiological characteristics, and major cellular fatty acids differentiating it from other Caldicellulosiruptor species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Yuya Sato, Eiji Tanaka, Tomoyuki Hori, Hiroyuki Futamata, Keita Murofushi, Hiroshi Takagi, Takuto Akachi, Teruhiko Miwa, Tomohiro Inaba, Tomo Aoyagi, Hiroshi Habe
Summary: The study demonstrates the potential industrial application of comammox in producing high-quality nitrate solution for hydroponic fertilizer. Comammox Nitrospira was found to be the main driver of stable and efficient ammonia oxidation in the system. Microbial co-occurrence analysis revealed strong positive correlations between Nitrospira and certain other OTUs, which may help stabilize Nitrospira abundance in the biofilm.
Article
Microbiology
Joval N. Martinez, Arisa Nishihara, Shin Haruta
Summary: Draft genome sequences of potentially novel bacteria were assembled from the metagenome of epilithic biofilm samples collected from the Tama River in Japan. Binning resulted in 31 metagenome-assembled genomes (MAGs) with >= 50% completeness.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Multidisciplinary Sciences
Yuya Sato, Seonghan Jang, Kazutaka Takeshita, Hideomi Itoh, Hideaki Koike, Kanako Tago, Masahito Hayatsu, Tomoyuki Hori, Yoshitomo Kikuchi
Summary: The study reveals a symbiotic bacteria that degrades insecticide into a non-insecticidal but bactericidal compound, offering a new strategy to address insecticide resistance.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Yong Guo, Tomo Aoyagi, Tomoyuki Hori
Summary: The draft genome sequences of two Geobacter sp. strains, AOG1 and AOG2, isolated from enrichment cultures, revealed the presence of numerous genes encoding multiheme c-type cytochromes and pilA-N genes encoding the pilin monomer of nanowires in their genomes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Yong Guo, Hideyuki Ihara, Tomo Aoyagi, Tomoyuki Hori, Yoko Katayama
Summary: This study presents the draft genome sequences of two sulfur-oxidizing chemolithoautotrophic bacteria, Sulfurovum spp. TSL1 and TSL6, isolated from tsunami-launched marine sediment in the Great East Japan earthquake.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
So Muramatsu, Setsuko Hirose, Takao Iino, Moriya Ohkuma, Satoshi Hanada, Shin Haruta
Summary: A novel bacterium strain N10(T) containing bacteriochlorophyll was isolated from a hot spring in Nagano Prefecture, Japan. The strain exhibited aerobic anoxygenic phototrophic characteristics and could not grow anaerobically even under illumination. Genome analysis revealed the presence of genes related to bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes, and type-2 photosynthetic reaction centre. Phylogenetic analysis placed strain N10(T) in a distinct lineage near Tabrizicola and Xinfangfangia genera and some species in the genus Rhodobacter. The strain showed low sequence identity with species in the family Rhodobacteraceae based on 16S rRNA gene. Accordingly, a new genus and species, Neotabrizicola shimadae, are proposed for strain N10(T).
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Shigeru Kawai, Mikako Ishikawa, Satoshi Hanada, Shin Haruta
Summary: A novel thermophilic chemotrophic bacterium, Hydrogenophilus thiooxidans sp. nov., was isolated from Nakabusa Hot Spring in Japan. The bacterium can grow both chemoheterotrophically and autotrophically under different conditions.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Megumi Kono, Joval N. Martinez, Takeshi Sato, Shin Haruta
Summary: This study presents the genome sequence of a thermophilic unicellular cyanobacterium isolated from a thermal pool at Yellowstone National Park.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Agronomy
Shota Shirane, Noriaki Momma, Toshiyuki Usami, Chiharu Suzuki, Tomoyuki Hori, Tomo Aoyagi, Seigo Amachi
Summary: Anaerobic soil disinfestation (ASD) is an ecofriendly alternative to chemical fumigation for eliminating soil-borne plant pathogens. This study found that caproate, produced by a specific strain of bacteria, is a key disinfestation factor in ethanol-based ASD, and the direct application of caproate to soil could be a promising strategy for rapid and stable soil disinfection.
Article
Microbiology
Md. Gahangir Alam, Shin Haruta
Summary: We report the whole-genome sequence of a thermophilic chemolithotrophic sulfate-reducing bacterium, Thermodesulfomicrobium sp. strain WS (class Deltaproteobacteria), isolated from the Onikobe geothermal field in Miyagi Prefecture, Japan. The genome consists of a 2,357,780-bp chromosome with a GC content of 62.9% and 2,196 protein-coding sequences.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Engineering, Environmental
Xinyi Zhou, Taku Fujiwara, Taira Hidaka, Fumitake Nishimura, Tomohiro Nakanishi, Akihiko Terada, Tomoyuki Hori
Summary: In this study, a microaerobic activated sludge process (MAS) was proposed as a pretreatment method to retain NH4-N from high-strength nitrogenous wastewater. The MAS systems achieved high NH4-N retention rates and TOC removal rates. The emissions of CO2 and N2O during MAS were evaluated, and the mechanisms of N2O emission from each reactor were investigated. The study highlighted the importance of N2O mitigation in the MAS process, especially under acidic conditions.
Article
Engineering, Environmental
Ralph Rolly Gonzales, Keizo Nakagawa, Kazuo Kumagai, Susumu Hasegawa, Atsushi Matsuoka, Zhan Li, Zhaohuan Mai, Tomohisa Yoshioka, Tomoyuki Hori, Hideto Matsuyama
Summary: This study demonstrates a hybrid osmotically assisted reverse osmosis (OARO) and reverse osmosis (RO) process for the enrichment and recovery of ammoniacal nitrogen in wastewater, resulting in energy-saving and economic benefits.
