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Krüger M, Chaudhari N, Thamdrup B, Overholt WA, Bristow LA, Taubert M, Küsel K, Jehmlich N, von Bergen M, Herrmann M. Differential contribution of nitrifying prokaryotes to groundwater nitrification. THE ISME JOURNAL 2023; 17:1601-1611. [PMID: 37422599 PMCID: PMC10504367 DOI: 10.1038/s41396-023-01471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.
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Affiliation(s)
- Markus Krüger
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Narendrakumar Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bo Thamdrup
- Department of Biology, Nordcee-University of Southern Denmark, Odense, Denmark
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Laura A Bristow
- Department of Biology, Nordcee-University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Ishizaki Y, Kurisu F, Furumai H, Kasuga I. Autotrophic growth activity of complete ammonia oxidizers in an upflow biological contact filter for drinking water treatment. Lett Appl Microbiol 2023; 76:ovad105. [PMID: 37679291 DOI: 10.1093/lambio/ovad105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Biological filters effectively remove ammonium from drinking water via nitrification. In a pilot-scale upflow biological contact filter (U-BCF), complete ammonia oxidizers (comammox), which are capable of oxidizing ammonia to nitrate in one cell, were more abundant than ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, little information is available on the contribution of comammox to nitrification. In this study, we evaluated the autotrophic growth activity of comammox associated with biological activated carbon (BAC) in a U-BCF by DNA-stable isotope probing (DNA-SIP). BAC samples collected from the U-BCF were continuously fed mineral medium containing 0.14 mg N L-1 ammonium and 12C- or 13C-labeled bicarbonate for 20 days. DNA-SIP analysis revealed that comammox (clades A and B) as well as AOA assimilated bicarbonate after 10 days of incubation, proving that dominant comammox could contribute to nitrification. Contrarily, AOB remained inactive throughout the observation period. Amplicon sequencing of the 13C-labeled DNA fractions of comammox revealed that specific genotypes other than the most dominant genotype in the original sample were more enriched under the incubation condition for the DNA-SIP experiment. Thus, dominant genotypes of comammox in a U-BCF might utilize organic nitrogen to fuel nitrification in ammonia-limited environments.
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Affiliation(s)
- Yuta Ishizaki
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research and Development Initiative, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
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3
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Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 PMCID: PMC9973019 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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Feng J, Li X, Yang Y, Fan X, Zhou Z, Ren J, Tan X, Li H. Insight into biofouling mechanism in biofiltration-facilitated gravity-driven membrane (GDM) system: Beneficial effects of pre-deposited adsorbents. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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5
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Zhu G, Wang X, Wang S, Yu L, Armanbek G, Yu J, Jiang L, Yuan D, Guo Z, Zhang H, Zheng L, Schwark L, Jetten MSM, Yadav AK, Zhu YG. Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154590. [PMID: 35306060 DOI: 10.1016/j.scitotenv.2022.154590] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N2O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longbin Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jie Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liping Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhongrui Guo
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hanrui Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, 24118 Kiel, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, 36525 AJ Nijmegen, the Netherlands
| | - Asheesh Kumar Yadav
- Department of Environment and Sustainability, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar 751013, India
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. WATER RESEARCH X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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Determination of 15N/ 14N of Ammonium, Nitrite, Nitrate, Hydroxylamine, and Hydrazine Using Colorimetric Reagents and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Appl Environ Microbiol 2022; 88:e0241621. [PMID: 35285242 DOI: 10.1128/aem.02416-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the nitrogen (N) cycle, nitrogenous compounds are chemically and biologically converted to various aqueous and gaseous N species. The 15N-labeling approach is a powerful culture-dependent technique to obtain insights into the complex nitrogen transformation reactions that occur in cultures. In the 15N-labeling approach, the fates of supplemented 15N- and/or unlabeled gaseous and aqueous compounds are tracked by mass spectrometry (MS) analysis, whereas MS analysis of aqueous N species requires laborious sample preparation steps and is performed using isotope-ratio mass spectrometry, which requires an expensive mass spectrometer. We developed a simple and high-throughput MS method for determining the 15N atoms percent of NH4+, NO2-, NO3-, NH2OH, and N2H4, where liquid samples (<0.5 mL) were mixed with colorimetric reagents (naphthylethylenediamine for NO2-, indophenol for NH4+, and p-aminobenzaldehyde for N2H4), and the mass spectra of the formed N complex dyes were obtained by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS. NH2OH and NO3- were chemically converted to NO2- by iodine oxidation and copper/hydrazine reduction reaction, respectively, prior to the above colorimetric reaction. The intensity of the isotope peak (M + 1 or M + 2) increased when the N complex dye was formed by coupling with a 15N-labeled compound, and a linear relationship was found between the determined 15N/14N peak ratio and 15N atom% for the tested N species. The developed method was applied to bacterial cultures to examine their N-transformation reactions, enabling us to observe the occurrence of NO2- oxidation and NO3- reduction in a hypoxic Nitrobacter winogradskyi culture. IMPORTANCE 15N/14N analysis for aqueous N species is a powerful tool for obtaining insights into the global N cycle, but the procedure is cumbersome and laborious. The combined use of colorimetric reagents and MALDI-TOF MS, designated color MALDI-TOF MS, enabled us to determine the 15N atom% of common aqueous N species without laborious sample preparation and chromatographic separation steps; for instance, the 15N atom% of NO2- can be determined from >1,000 liquid samples daily at <$1 (U.S.) per 384 samples for routine analysis. This convenient MS method is a powerful tool that will advance our ability to explore the N-transformation reactions that occur in various environments and biological samples.
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Palomo A, Dechesne A, Cordero OX, Smets BF. Evolutionary Ecology of Natural Comammox Nitrospira Populations. mSystems 2022; 7:e0113921. [PMID: 35014874 PMCID: PMC8751384 DOI: 10.1128/msystems.01139-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Otto X. Cordero
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Barth F. Smets
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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Abdelhafiz Y, Fernandes JMO, Stefani E, Albanese D, Donati C, Kiron V. Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia. Front Microbiol 2021; 12:773351. [PMID: 34867911 PMCID: PMC8636895 DOI: 10.3389/fmicb.2021.773351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/14/2021] [Indexed: 01/29/2023] Open
Abstract
Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Erika Stefani
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Wang Y, Zhu T, Chang M, Jin D. Performance of a hybrid membrane aerated biofilm reactor (H-MBfR) for shortcut nitrification. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sato Y, Tanaka E, Hori T, Futamata H, Murofushi K, Takagi H, Akachi T, Miwa T, Inaba T, Aoyagi T, Habe H. Efficient conversion of organic nitrogenous wastewater to nitrate solution driven by comammox Nitrospira. WATER RESEARCH 2021; 197:117088. [PMID: 33813172 DOI: 10.1016/j.watres.2021.117088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
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. To determine the key microbes involved and better understand the system, the microbial communities in the reactors were analyzed by 16S rRNA gene sequencing in combination with a shotgun metagenomic analysis. Canonical ammonia-oxidizing bacteria, which can only catalyze the oxidation of ammonia to nitrite, were detected with negligible relative abundances, while a comammox Nitrospira-related operational taxonomic unit (OTU) dominated the nitrification reactor. Furthermore, the comammox-type ammonia monooxygenase was found to be 500 times more highly expressed than the canonical one by quantitative PCR, indicating that comammox was the main driver of the stable and efficient ammonia oxidation in the system. A microbial co-occurrence analysis revealed a strong positive correlation between Nitrospira and several OTUs, some of which, such as Anaerolinea OTU, have been found to co-exist with comammox Nitrospira in the biofilms of water treatment systems. Given that these OTUs were abundant only on microbe-attached carriers in the system, their co-existence within the biofilm could be beneficial to stabilize the Nitrospira abundance, possibly by physically preventing oxygen exposure as well as cell spillage.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Eiji Tanaka
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroyuki Futamata
- Research Institution of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan; Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan
| | - Keita Murofushi
- Department of Environment and Energy, Industrial Research Institute of Shizuoka Prefecture, 2078 Makigaya, Aoi-ku, Shizuoka, Shizuoka 421-1298, Japan
| | - Hiroshi Takagi
- Numazu Technical Support Center, Industrial Research Institute of Shizuoka Prefecture, 3981-1 Ohoka, Numazu, Shizuoka 410-0022, Japan
| | - Takuto Akachi
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Teruhiko Miwa
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
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12
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Yao Y, Wang Z, Criddle CS. Robust Nitritation of Anaerobic Digester Centrate Using Dual Stressors and Timed Alkali Additions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2016-2026. [PMID: 33443415 DOI: 10.1021/acs.est.0c04613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nitrogen is commonly removed from wastewater by nitrification to nitrate followed by nitrate reduction to N2. Shortcut N removal saves energy by limiting ammonia oxidation to nitrite, but nitrite accumulation can be unstable. We hypothesized that repeated short-term exposures of ammonia-oxidizing communities to free ammonia (FA) and free nitrous acid (FNA) would stabilize nitritation by selecting against nitrite-oxidizing bacteria (NOB). Accordingly, we evaluated ammonium oxidation of anaerobic digester centrate in two bench-scale sequencing batch reactors (SBRs), seeded with the same inoculum and operated identically but with differing pH-control strategies. A single stressor SBR (SS/SBR) using pH set-point control produced HNO3, while a dual stressor SBR (DS/SBR) using timed alkalinity addition (TAA) produced HNO2 (ammonium removal efficiency of 97 ± 2%; nitrite accumulation ratio of 98 ± 1%). The TAA protocol was developed during an adaptation period with continuous pH monitoring. After adaptation, automated TAA enabled stable nitritation without set-point control. In the SS/SBR, repeatedly exposing the community to FA (8-10 h/exposure, one exposure/cycle) selected for FA-tolerant ammonia-oxidizing bacteria (Nitrosomonas sp. NM107) and NOB (Nitrobacter sp.). In the DS/SBR, repeatedly exposing the community to FA (2-4 h/exposure, three exposures/cycle) and FNA (4-6 h/exposure, two exposures/cycle) selected for FA- and FNA-resistant AOB (Nitrosomonas IWT514) and against NOB, stabilizing nitritation.
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Affiliation(s)
- Yinuo Yao
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Zhiyue Wang
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M. Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities. THE ISME JOURNAL 2021; 15:348-353. [PMID: 32879458 PMCID: PMC7852690 DOI: 10.1038/s41396-020-00761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.
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Affiliation(s)
- Maria Mooshammer
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Arno Schintlmeister
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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14
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Roveto PM, Gupta A, Schuler AJ. Effects of surface skewness on local shear stresses, biofilm activity, and microbial communities for wastewater treatment. BIORESOURCE TECHNOLOGY 2021; 320:124251. [PMID: 33157445 DOI: 10.1016/j.biortech.2020.124251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
This study's objective was to assess attachment surface skewness (asymmetric surface height variation) effects on biofilm development. 3D printed molds were used to create surfaces with 300 μm features to provide opposite skewness but identical roughness values. Surfaces with negative skewness had consistently greater nitrite oxidation and biomass growth than other surfaces during biofilm development when studied in annular bioreactor systems. CFD modelling predicted local shear stress differences that could explain experimental results. 16 s rRNA gene amplicon sequencing revealed population differences, including relatively high Acinetobacter and Terrimonas fractions on the negative skew surfaces, and PCoA analyses indicated the flat surface populations diverged from the skew surfaces by the study's end. The results suggest skewness is particularly important in systems where biofilms have not overgrown surface features, as in system startup, thin biofilms, and shorter time frame studies, which includes much previous microbial attachment research.
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Affiliation(s)
- Philip M Roveto
- University of New Mexico, 1 University Blvd, Albuquerque, NM 87131, United States.
| | - Adwaith Gupta
- Paanduv Applications, 124 Parwana Nagar, Bareilly, UP 243122, India.
| | - Andrew J Schuler
- University of New Mexico, 1 University Blvd, Albuquerque, NM 87131, United States.
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15
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Jantarakasem C, Kasuga I, Kurisu F, Furumai H. Temperature-Dependent Ammonium Removal Capacity of Biological Activated Carbon Used in a Full-Scale Drinking Water Treatment Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13257-13263. [PMID: 32969636 DOI: 10.1021/acs.est.0c02502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nitrification is a key function of biological activated carbon (BAC) filters for drinking water treatment. It is empirically known that the nitrification activity of BAC filters depends on water temperature, potentially resulting in the leakage of ammonium from BAC filters when the water temperature decreases. However, the ammonium removal capacity of BAC filters and factors governing the capacity remain unknown. This study employed a bench-scale column assay to determine the volumetric ammonium removal rate (VARR) of BAC collected from a full-scale drinking water treatment plant. VARR was determined at a fixed loading rate under different conditions. Seasonal variations of the VARR as well as impacts of the water matrix and water temperature on ammonium removal were quantitatively analyzed. While the VARR in an inorganic medium at 25 °C was maintained even during low water temperature periods and during breakpoint chlorination periods, the water matrix factor reduced the VARR in ozonated water at 25 °C by 33% on average. The VARR in ozonated water was dependent on water temperature, indicating that the microbial activity of BAC did not adapt to low water temperature. The Arrhenius equation was applied to reveal the relationship between VARR and water temperature. The actual ammonium removal performance of a full-scale BAC filter was predicted. VARR is useful for water engineers to reexamine the loading and filter depth of BAC filters.
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Affiliation(s)
- Chotiwat Jantarakasem
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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16
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Poghosyan L, Koch H, Frank J, van Kessel MAHJ, Cremers G, van Alen T, Jetten MSM, Op den Camp HJM, Lücker S. Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters. WATER RESEARCH 2020; 185:116288. [PMID: 32810745 DOI: 10.1016/j.watres.2020.116288] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 05/22/2023]
Abstract
Elevated concentrations of ammonium and methane in groundwater are often associated with microbiological, chemical and sanitary problems during drinking water production and distribution. To avoid their accumulation, raw water in the Netherlands and many other countries is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the top layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled from the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.
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Affiliation(s)
- Lianna Poghosyan
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Hanna Koch
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands.
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17
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Hu J, Zhao Y, Yang W, Wang J, Liu H, Zheng P, Hu B. Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters. FEMS Microbiol Ecol 2020; 96:5899051. [PMID: 32860687 DOI: 10.1093/femsec/fiaa179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/26/2020] [Indexed: 01/15/2023] Open
Abstract
Nitrification is important in drinking water treatment plants (DWTPs) for ammonia removal and is widely considered as a stepwise process mediated by ammonia- and nitrite-oxidizing microorganisms. The recent discovery of complete ammonia oxidizers (comammox) has challenged the long-held assumption that the division of metabolic labor in nitrification is obligate. However, little is known about the role of comammox Nitrospira in DWTPs. Here, we explored the relative importance of comammox Nitrospira, canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 12 surface water-fed rapid sand filters (RSFs). Quantitative PCR results showed that all the three ammonia-oxidizing guilds had the potential to dominate nitrification in DWTPs. Spearman's correlation and redundancy analysis revealed that the surface ammonium loading rate (SLR) was the key environmental factor influencing ammonia-oxidizing communities. Comammox Nitrospira were likely to dominate the nitrification under a higher SLR. PCR and phylogenetic analysis indicated that most comammox Nitrospira belonged to clade A, with clade B comammox Nitrospira almost absent. This work reveals obvious differences in ammonia-oxidizing communities between surface water-fed and groundwater-fed RSFs. The presence of comammox Nitrospira can support the stability of drinking water production systems under high SLR and warrants further investigation of their impact on drinking water quality.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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18
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Fujitani H, Momiuchi K, Ishii K, Nomachi M, Kikuchi S, Ushiki N, Sekiguchi Y, Tsuneda S. Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant. Front Microbiol 2020; 11:545190. [PMID: 33042056 PMCID: PMC7522533 DOI: 10.3389/fmicb.2020.545190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shuta Kikuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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