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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation. iScience 2024; 27:109596. [PMID: 38638570 PMCID: PMC11024918 DOI: 10.1016/j.isci.2024.109596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Siegfried E. Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
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Feng B, Chen J, Wang C, You G, Lin J, Gao H, Han S, Ma J. Ofloxacin weakened treatment performance of rural domestic sewage in an aerobic biofilm system by affecting biofilm resistance, bacterial community, and functional genes. ENVIRONMENTAL RESEARCH 2024; 246:118036. [PMID: 38163543 DOI: 10.1016/j.envres.2023.118036] [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: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Ofloxacin (OFL) is a typical fluoroquinolone antibiotic widely detected in rural domestic sewage, however, its effects on the performance of aerobic biofilm systems during sewage treatment process remain poorly understood. We carried out an aerobic biofilm experiment to explore how the OFL with different concentrations affects the pollutant removal efficiency of rural domestic sewage. Results demonstrated that the OFL negatively affected pollutant removal in aerobic biofilm systems. High OFL levels resulted in a decrease in removal efficiency: 9.33% for chemical oxygen demand (COD), 18.57% for ammonium (NH4+-N), and 8.49% for total phosphorus (TP) after 35 days. The findings related to the chemical and biological properties of the biofilm revealed that the OFL exposure triggered oxidative stress and SOS responses, decreased the live cell number and extracellular polymeric substance content of biofilm, and altered bacterial community composition. More specifically, the relative abundance of key genera linked to COD (e.g., Rhodobacter), NH4+-N (e.g., Nitrosomonas), and TP (e.g., Dechlorimonas) removal was decreased. Such the OFL-induced decrease of these genera might result in the down-regulation of carbon degradation (amyA), ammonia oxidation (hao), and phosphorus adsorption (ppx) functional genes. The conventional pollutants (COD, NH4+-N, and TP) removal was directly affected by biofilm resistance, functional genes, and bacterial community under OFL exposure, and the bacterial community played a more dominant role based on partial least-squares path model analysis. These findings will provide valuable insights into understanding how antibiotics impact the performance of aerobic biofilm systems during rural domestic sewage treatment.
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Affiliation(s)
- Bingbing Feng
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Junkai Lin
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Shanrui Han
- PowerChina Huadong Engineering Corporation Limited, No.201, Gaojiao Road, Yuhang District, Hangzhou, Zhejiang 311122, PR China
| | - Junchao Ma
- PowerChina Huadong Engineering Corporation Limited, No.201, Gaojiao Road, Yuhang District, Hangzhou, Zhejiang 311122, PR China
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Ghimire-Kafle S, Weaver ME, Kimbrel MP, Bollmann A. Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments. Appl Environ Microbiol 2024; 90:e0169823. [PMID: 38349190 PMCID: PMC10952389 DOI: 10.1128/aem.01698-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.
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Affiliation(s)
| | - Matt E. Weaver
- Department of Microbiology, Miami University, Oxford, Ohio, USA
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Williamson G, Harris T, Bizior A, Hoskisson PA, Pritchard L, Javelle A. Biological ammonium transporters: evolution and diversification. FEBS J 2024. [PMID: 38265636 DOI: 10.1111/febs.17059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Paul Alan Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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5
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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Aarts R, Tabury K, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity. NPJ Microgravity 2024; 10:3. [PMID: 38200027 PMCID: PMC10781756 DOI: 10.1038/s41526-024-00345-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Raf Aarts
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Kevin Tabury
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium.
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6
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Sasi R, Suchithra TV. Wastewater microbial diversity versus molecular analysis at a glance: a mini-review. Braz J Microbiol 2023; 54:3033-3039. [PMID: 37723328 PMCID: PMC10689596 DOI: 10.1007/s42770-023-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023] Open
Abstract
Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.
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Affiliation(s)
- R Sasi
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601
| | - T V Suchithra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601.
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7
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Oshiki M, Saito T, Nakaya Y, Satoh H, Okabe S. Growth of the Nitrosomonas europaea cells in the biofilm and planktonic growth mode: Responses of extracellular polymeric substances production and transcriptome. J Biosci Bioeng 2023; 136:430-437. [PMID: 37925312 DOI: 10.1016/j.jbiosc.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Nitrosomonas europaea, an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Takahiro Saito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yuki Nakaya
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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8
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Xue Y, Zheng M, Cheng Z, Li S, Yang S, Liu Y, Qian Y, Huang X. Dynamic Simulation of Nitrifying Microbial Communities for Establishing Acidic Partial Nitritation in Suspended Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17542-17552. [PMID: 37909179 DOI: 10.1021/acs.est.3c01282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Acidic partial nitritation (PN) is a promising technology to achieve low-cost and energy-efficient shortcut nitrogen removal from wastewater. However, a comprehensive understanding of the acidic PN under dynamic changes of pH in a sequencing batch reactor (SBR) is still lacking. In this study, we successfully established acidic PN (NO2- accumulation ratio >80%) under dynamic pH variation from 7.0 to 4.5 in a lab-scale SBR. By accumulating in situ free nitrous acid (FNA) generation based on the dynamic pH change, acidic PN maintained stability even at a low NH4+ concentration of 100 mg N L-1. The microbial community analysis revealed that two ammonium-oxidizing bacteria (AOB) genera, Nitrosospira and Nitrosomonas, successfully coexisted and cooperated during acidic PN. None of the species of nitrite-oxidizing bacteria (NOB) showed adaptation to intermittent inhibition of in situ FNA even under high DO conditions (>4.0 mg O2 L-1). Furthermore, we innovatively incorporated the classic nitrification model with the growth and decay of different nitrifying bacterial species and their inhibition by pH, FNA, and free ammonia (FA) to predict the nitrifying microbial communities shifting for establishing acidic PN. The extended model was calibrated by using short-term batch experiments and was validated by using long-term dynamic data of the nitrifying microbial community during SBR operation. The validated model was further used to identify feasible influent conditions for the SBR PN process, including influent HCO3- concentration, NH4+ concentration and molar ratio (HCO3/NH4+). Outcomes from this study support the optimal design of acidic PN-based short-cut nitrogen removal processes for future application.
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Affiliation(s)
- Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Zhao Cheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Siqi Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shaolin Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yi Qian
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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9
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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10
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Tsujino S, Masuda R, Shimizu Y, Azuma Y, Kanada Y, Fujiwara T. Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification. Antonie Van Leeuwenhoek 2023; 116:1037-1055. [PMID: 37596503 DOI: 10.1007/s10482-023-01862-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.
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Affiliation(s)
- Shuhei Tsujino
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Ryota Masuda
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yoshiyuki Shimizu
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuichi Azuma
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yutaro Kanada
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
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11
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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12
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Li J, Zhao C, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, He X, Qiu Z, Wang J. Multidrug-resistant plasmid RP4 increases NO and N 2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation. WATER RESEARCH 2023; 242:120266. [PMID: 37421866 DOI: 10.1016/j.watres.2023.120266] [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: 01/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.
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Affiliation(s)
- Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
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13
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Bizior A, Williamson G, Harris T, Hoskisson PA, Javelle A. Prokaryotic ammonium transporters: what has three decades of research revealed? MICROBIOLOGY (READING, ENGLAND) 2023; 169:001360. [PMID: 37450375 PMCID: PMC10433425 DOI: 10.1099/mic.0.001360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
The exchange of ammonium across cellular membranes is a fundamental process in all domains of life. In plants, bacteria and fungi, ammonium represents a vital source of nitrogen, which is scavenged from the external environment. In contrast, in animal cells ammonium is a cytotoxic metabolic waste product and must be excreted to prevent cell death. Transport of ammonium is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. In addition to their function as transporters, Amt/Mep/Rh proteins play roles in a diverse array of biological processes and human physiopathology. Despite this clear physiological importance and medical relevance, the molecular mechanism of Amt/Mep/Rh proteins has remained elusive. Crystal structures of bacterial Amt/Rh proteins suggest electroneutral transport, whilst functional evidence supports an electrogenic mechanism. Here, focusing on bacterial members of the family, we summarize the structure of Amt/Rh proteins and what three decades of research tells us concerning the general mechanisms of ammonium translocation, in particular the possibility that the transport mechanism might differ in various members of the Amt/Mep/Rh superfamily.
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Affiliation(s)
- Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
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14
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Chen H, Liu K, Yang E, Chen J, Gu Y, Wu S, Yang M, Wang H, Wang D, Li H. A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159462. [PMID: 36257429 DOI: 10.1016/j.scitotenv.2022.159462] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.
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Affiliation(s)
- Hong Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China; Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Ke Liu
- China Machinery International Engineering Design & Research Institute Co., Ltd, Changsha 410007, China
| | - Enzhe Yang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Jing Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Yanling Gu
- School of Materials Science and Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Sha Wu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China.
| | - Min Yang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Hong Wang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410004, China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Hailong Li
- School of Energy Science and Engineering, Central South University, Changsha 410083, China.
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15
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Yuan D, Zheng L, Liu YX, Cheng H, Ding A, Wang X, Tan Q, Wang X, Xing Y, Xie E, Wu H, Wang S, Zhu G. Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:810-821. [PMID: 36459424 DOI: 10.1021/acs.est.2c06234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The thawing of dormant plateau permafrost emits nitrous oxide (N2O) through wetlands; however, the N2O production mechanism in plateau wetlands is still unclear. Here, we used the 15N-18O double tracer technique and metagenomic sequencing to analyze the N2O production mechanism in the Yunnan-Kweichow and Qinghai-Tibet plateau wetlands during the summer of 2020. N2O production activity was detected in all 16 sediment samples (elevation 1020-4601 m: 2.55 ± 0.42-26.38 ± 3.25 ng N g-1 d-1) and was promoted by nitrifier denitrification (ND). The key functional genes of ND (amoA, hao, and nirK) belonged to complete ammonia oxidizing (comammox) bacteria, and the key ND species was the comammox bacterium Nitrospira nitrificans. We found that the comammox bacterial species N. nitrificans and the ammonia oxidizing bacterial (AOB) species Nitrosomonas europaea cooperate to produce N2O in the plateau wetland sediments. Furthermore, we inferred that environmental factors (elevation and total organic matter (TOM)) influence the cooperation pattern via N. nitrificans, thus affecting the N2O production activity in the plateau wetland sediments. Our findings advance the mechanistic understanding of nitrifiers in biogeochemical cycles and global climate change.
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Affiliation(s)
- Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Hongguang Cheng
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing100083, China
| | - Haoming Wu
- College of Water Sciences, Beijing Normal University, Beijing100875, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
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16
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Faust V, van Alen TA, Op den Camp HJ, Vlaeminck SE, Ganigué R, Boon N, Udert KM. Ammonia oxidation by novel " Candidatus Nitrosacidococcus urinae" is sensitive to process disturbances at low pH and to iron limitation at neutral pH. WATER RESEARCH X 2022; 17:100157. [PMID: 36262799 PMCID: PMC9574496 DOI: 10.1016/j.wroa.2022.100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/06/2022] [Accepted: 10/02/2022] [Indexed: 05/06/2023]
Abstract
Acid-tolerant ammonia-oxidizing bacteria (AOB) can open the door to new applications, such as partial nitritation at low pH. However, they can also be problematic because chemical nitrite oxidation occurs at low pH, leading to the release of harmful nitrogen oxide gases. In this publication, the role of acid-tolerant AOB in urine treatment was explored. On the one hand, the technical feasibility of ammonia oxidation under acidic conditions for source-separated urine with total nitrogen concentrations up to 3.5 g-N L-1 was investigated. On the other hand, the abundance and growth of acid-tolerant AOB at more neutral pH was explored. Under acidic conditions (pH of 5), ammonia oxidation rates of 500 mg-N L-1 d-1 and 10 g-N g-VSS-1 d-1 were observed, despite high concentrations of 15 mg-N L-1 of the AOB-inhibiting compound nitrous acid and low concentration of 0.04 mg-N L-1 of the substrate ammonia. However, ammonia oxidation under acidic conditions was very sensitive to process disturbances. Even short periods of less than 12 h without oxygen or without influent resulted in a complete cessation of ammonia oxidation with a recovery time of up to two months, which is a problem for low maintenance applications such as decentralized treatment. Furthermore, undesirable nitrogen losses of about 10% were observed. Under acidic conditions, a novel AOB strain was enriched with a relative abundance of up to 80%, for which the name "Candidatus (Ca.) Nitrosacidococcus urinae" is proposed. While Nitrosacidococcus members were present only to a small extent (0.004%) in urine nitrification reactors operated at pH values between 5.8 and 7, acid-tolerant AOB were always enriched during long periods without influent, resulting in an uncontrolled drop in pH to as low as 2.5. Long-term experiments at different pH values showed that the activity of "Ca. Nitrosacidococcus urinae" decreased strongly at a pH of 7, where they were also outcompeted by the acid-sensitive AOB Nitrosomonas halophila. The experiment results showed that the decreased activity of "Ca. Nitrosacidococcus urinae" correlated with the limited availability of dissolved iron at neutral pH.
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Affiliation(s)
- Valentin Faust
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- ETH Zürich, Institute of Environmental Engineering, 8093 Zürich, Switzerland
| | - Theo A. van Alen
- Department of Microbiology, RIBES, Radboud University Nijmegen, 0268 Nijmegen, The Netherlands
| | - Huub J.M. Op den Camp
- Department of Microbiology, RIBES, Radboud University Nijmegen, 0268 Nijmegen, The Netherlands
| | - Siegfried E. Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, Faculty of Science, University of Antwerp, 2020 Antwerpen, Belgium
- Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), 9052 Gent, Belgium
| | - Ramon Ganigué
- Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), 9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
| | - Nico Boon
- Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), 9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
| | - Kai M. Udert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- ETH Zürich, Institute of Environmental Engineering, 8093 Zürich, Switzerland
- Corresponding author at: Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
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17
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Ayub H, Kang MJ, Farooq A, Jung MY. Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu. Life (Basel) 2022; 12:1806. [PMID: 36362966 PMCID: PMC9693385 DOI: 10.3390/life12111806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Interactions between metals and microbes are critical in geomicrobiology and vital in microbial ecophysiological processes. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing microorganisms (AOM) are key members in aerobic environments to start the C and N cycles. Ammonia and methane are firstly oxidized by copper-binding metalloproteins, monooxygenases, and diverse iron and copper-containing enzymes that contribute to electron transportation in the energy gain pathway, which is evolutionally connected between MOB and AOM. In this review, we summarized recently updated insight into the diverse physiological pathway of aerobic ammonia and methane oxidation of different MOB and AOM groups and compared the metabolic diversity mediated by different metalloenzymes. The elevation of iron and copper concentrations in ecosystems would be critical in the activity and growth of MOB and AOM, the outcome of which can eventually influence the global C and N cycles. Therefore, we also described the impact of various concentrations of metal compounds on the physiology of MOB and AOM. This review study could give a fundamental strategy to control MOB and AOM in diverse ecosystems because they are significantly related to climate change, eutrophication, and the remediation of contaminated sites for detoxifying pollutants.
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Affiliation(s)
- Hina Ayub
- Interdisciplinary Graduate Programm in Advance Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
| | - Min-Ju Kang
- Interdisciplinary Graduate Programm in Advance Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
| | - Adeel Farooq
- Research Institute for Basic Sciences (RIBS), Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programm in Advance Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
- Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea
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18
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Campbell K, Wang J. Understanding the role of activated sludge in oxygen transfer: Effects of sludge settleability, solids retention time, and nitrification reaction. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10806. [PMID: 36352319 DOI: 10.1002/wer.10806] [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: 07/25/2022] [Revised: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The current understanding on the oxygen transfer in activated sludge process is primarily developed based on two-phase systems, focusing only on oxygen transfer from air to water. However, this research demonstrates that activated sludge particles significantly impact oxygen transfer from air all the way to the microorganisms. Three bench-scale complete-mix activated sludge reactors, operated under the same influent loading and dissolved oxygen level but different solids retention times (SRTs), were used to develop oxygen transfer performance data as effects of different sludge property parameters. These reactors were also operated under batch modes to further validate the effect of nitrification reaction on oxygen transfer. Results indicate that high overall oxygen transfer efficiency (OTE) is associated with low mixed liquor viscosity, long SRT, and nitrification reaction. Further analyses suggest that low mixed liquor viscosity, which resulted from high sludge settleability or low settled volume of sludge, reduces the thickness of liquid films at all interfaces and the size of air bubbles. Long SRT results in high active nitrifier population and low specific extracellular polymeric substance (EPS). Nitrification reaction, which serves as the rate-limiting step for oxygen transfer, may increase the oxygen transfer driving force. High active nitrifier population also promotes direct air-sludge contact. All of these factors help facilitate oxygen transfer. This research provides a new approach to improve energy efficiency for wastewater treatment, which is to change the activated sludge property by adjusting treatment plant design and operational parameters. PRACTITIONER POINTS: High sludge settleability reduces viscosity therefore liquid film thickness. Long SRT increases active microorganism population and reduces specific EPS content. Nitrification reaction increases oxygen transfer driving force. Direct air-particle contact adds another pathway for oxygen transfer. Nitrification reaction is the rate-limiting step of the oxygen transfer process.
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Affiliation(s)
- Ken Campbell
- Department of Civil, Architectural and Environmental Engineering, Missouri University of Science and Technology, Rolla, Missouri, USA
| | - Jianmin Wang
- Department of Civil, Architectural and Environmental Engineering, Missouri University of Science and Technology, Rolla, Missouri, USA
- The Center for Research in Energy and Environment (CREE), Missouri University of Science and Technology, Rolla, Missouri, USA
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19
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Wang J, Zheng F, Yu Z, Chen J, Lu H. Dissolved organic nitrogen derived from wastewater denitrification: Composition and nitrogenous disinfection byproduct formation. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129775. [PMID: 35994914 DOI: 10.1016/j.jhazmat.2022.129775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/23/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Microbially derived dissolved organic nitrogen (mDON) is a major fraction of effluent total nitrogen at wastewater treatment plants with enhanced nutrient removal, which stimulates phytoplankton blooms and formation of toxic nitrogenous disinfection by-products (N-DBPs). This study identified denitrifiers as major contributors to mDON synthesis, and further revealed the molecular composition, influential factors and synthetic microorganisms of denitrification-derived mDON compounds leading to N-DBP formation. The maximum mDON accumulated during denitrification was 8.92% of converted inorganic nitrogen, higher than that of anammox (4.24%) and nitrification (2.76%). Sodium acetate addition at relatively high C/N ratio (5-7) favored mDON formation, compared with methanol and low C/N (1-3). Different from acetate, methanol-facilitated denitrification produced 13-69% more lignin-like compounds than proteins using Orbitrap LC-MS. The most abundant N-DBPs formed from denitrification-derived mDON were N-nitrosodibutylamine and dichloroacetonitrile (13.32 μg/mg mDON and 12.21 μg/mg mDON, respectively). Major amino acids, aspartate, glycine, and alanine were positively correlated with typical N-DBPs. Biosynthesis and degradation pathways of these N-DBP precursors were enriched in denitrifiers belonging to Rhodocyclaceae, Mycobacteriaceae and Hyphomicrobiaceae. As intensive disinfection is applied at worldwide wastewater treatment plants during COVID-19, carbon source facilitated denitrification should be better managed to reduce both effluent inorganic nitrogen and DON, mitigating DON and N-DBP associated ecological risks in receiving waters.
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Affiliation(s)
- Jie Wang
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Fang Zheng
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Zhaoniao Yu
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Jinrong Chen
- Zhejiang Fuchun Ziguang Environmental Protection Co., Ltd., 310000 Hangzhou, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China.
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20
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Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method. mSphere 2022; 7:e0032422. [PMID: 35938727 PMCID: PMC9429940 DOI: 10.1128/msphere.00324-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Until recently, the de facto method for short-read-based amplicon reconstruction was a sequence similarity threshold approach (operational taxonomic units [OTUs]). This has changed with the amplicon sequence variant (ASV) method where distributions are fitted to abundance profiles of individual genes using a noise-error model. While OTU-based approaches are still useful for 16S rRNA/18S rRNA genes, where thresholds of 97% to 99% are used, their use for functional genes is still debatable as there is no consensus on clustering thresholds. Here, we compare OTU- and ASV-based reconstruction approaches and taxonomy assignment methods, the naive Bayesian classifier (NBC) and Bayesian lowest common ancestor (BLCA) algorithm, using a functional gene data set from the microbial nitrogen-cycling community in the Brouage mudflat (France). A range of OTU similarity thresholds and ASVs were used to compare amoA (ammonia-oxidizing archaea [AOA] and ammonia-oxidizing bacteria [AOB]), nxrB, nirS, nirK, and nrfA communities between differing sedimentary structures. Significant effects of the sedimentary structure on weighted UniFrac (WUniFrac) distances were observed for AOA amoA when using ASVs, an OTU at a threshold of 97% sequence identity (OTU-97%), and OTU-85%; AOB amoA when using OTU-85%; and nirS when using ASV, OTU-90%, and OTU-85%. For AOB amoA, significant effects of the sedimentary structures on UniFrac distances were observed when using OTU-97% but not ASVs, and the inverse was found for nrfA. Interestingly, conclusions drawn for nirK and nxrB were consistent between amplicon reconstruction methods. We also show that when the sequences in the reference database are related to the environment in question, the BLCA algorithm leads to more phylogenetically relevant classifications. However, when the reference database contains sequences more dissimilar to the ones retrieved, the NBC obtains more information. IMPORTANCE Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets. In this paper, we argue that the recently developed ASV approach offers a better opportunity to achieve such standardization than OTUs for functional genes. We also propose a comprehensive framework for quality filtering of the sequencing reads based on protein sequence verification.
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21
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Rapid detection of nitrite based on nitrite-oxidizing bacteria biosensor and its application in surface water monitoring. Biosens Bioelectron 2022; 215:114573. [PMID: 35853327 DOI: 10.1016/j.bios.2022.114573] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 11/22/2022]
Abstract
Timely and sensitive detection of nitrite is of great significance for human health protection and water pollution treatment. However, many biosensors can only determine the comprehensive toxicity of the water, and there are few electroactive biofilm (EAB) sensors for the specific detection of pollutants. Biofilms formed by bacteria with specific functions can improve the specificity of nitrite identification by biosensors. This study developed a novel, rapidly responding, high sensitivity (958.6 μAμM-1cm-2), wide detection range and anti-interference electrochemical biosensor based on electroactive nitrite-oxidizing bacteria. The biosensor could accurately detect nitrite in the range of 0.3-100 mg/L within 3 min by the cyclic voltammetry (CV) method. The bioelectrode could perform stable detection of nitrite over 200 cycles. The specificity of the biosensor for detecting nitrite was demonstrated by the presence of nitrite oxidizing bacteria (NOB) and nitrite oxidase enzyme (NXR) on the electrode biofilm. The biosensor performed well in wetlands and rivers, with an RSD <14.8% in the detection of nitrite at low concentrations, and further revealed the nitrification occurrence. Our study provided a feasible way for the development of a highly sensitive, rapidly responding and stable electrochemical biosensor, which also exhibited potential applications for long-term detection of nitrite and assessment of ecological function in surface water (rivers, lakes, wetlands, marshes, etc.).
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22
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Yang M, Qiu S, Wang L, Chen Z, Hu Y, Guo J, Ge S. Effect of short-term light irradiation with varying energy densities on the activities of nitrifiers in wastewater. WATER RESEARCH 2022; 216:118291. [PMID: 35313179 DOI: 10.1016/j.watres.2022.118291] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Microalgal-bacterial consortium (MBC) process has been proposed as an alternative to conventional activated sludge process for nitrogen removal from wastewater. As one of the most influencing parameters, light irradiation effects on microalgae have been extensively investigated. However, light influence on the performance of nitrifiers in activated sludge and its mechanism remains unclear. In this study, the effects of three factors (light irradiation power, irradiation time and sludge concentration) on activities and physiological characteristics of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were systematically studied through both the Design of Experiments driven response surface methodology (RSM) approach and light-nitrification kinetic modeling. Results indicated that light irradiation with the specific light energy density (Es) at 0.0203-0.1571 kJ·mg-1 VSS (80-160 W/400-1000 μmol·m-2·s-1, 2.0-5.0 h and 2750-4250 mg·L-1) stimulated the relative AOB activities (rAOB) by 120.0%. This was supported by the increased electron transport system activity, key enzyme activity (AMO) , gene expression (amoA) and energy generation (ATP consumption) in the light treatment. Moreover, further Es increasing up to 0.18 kJ·mg-1 VSS inhibited both AOB and NOB activities. The inhibition was ascribed to the joint light responses of metabolic disorders and lipid peroxidation. The findings enhance our understanding of nitrifiers' physiological responses to short-term light irradiation, and promote the development of MBC as a sustainable approach for wastewater treatment.
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Affiliation(s)
- Mingzhu Yang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China
| | - Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China
| | - Lingfeng Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China
| | - Zhipeng Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China
| | - Yanbing Hu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China
| | - Jianhua Guo
- Australian Center for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing, Jiangsu 210094, China.
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Wu J, Hong Y, He X, Liu X, Ye J, Jiao L, Li Y, Wang Y, Ye F, Yang Y, Du J. Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 2022; 25:104333. [PMID: 35602962 PMCID: PMC9118673 DOI: 10.1016/j.isci.2022.104333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022] Open
Abstract
The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiang He
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lijing Jiao
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Juan Du
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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24
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Jiang C, Wang X, Wang H, Xu S, Zhang W, Meng Q, Zhuang X. Achieving Partial Nitritation by Treating Sludge With Free Nitrous Acid: The Potential Role of Quorum Sensing. Front Microbiol 2022; 13:897566. [PMID: 35572707 PMCID: PMC9095614 DOI: 10.3389/fmicb.2022.897566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Partial nitritation is increasingly regarded as a promising biological nitrogen removal process owing to lower energy consumption and better nitrogen removal performance compared to the traditional nitrification process, especially for the treatment of low carbon wastewater. Regulating microbial community structure and function in sewage treatment systems, which are mainly determined by quorum sensing (QS), by free nitrous acid (FNA) to establish a partial nitritation process is an efficient and stable method. Plenty of research papers reported that QS systems ubiquitously existed in ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), and various novel nitrogen removal processes based on partial nitritation were successfully established using FNA. Although the probability that partial nitritation process might be achieved by the regulation of FNA on microbial community structure and function through the QS system was widely recognized and discussed, the potential role of QS in partial nitritation achievement by FNA and the regulation mechanism of FNA on QS system have not been reviewed. This article systematically reviewed the potential role of QS in the establishment of partial nitritation using FNA to regulate activated sludge flora based on the summary and analysis of the published literature for the first time, and future research directions were also proposed.
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Affiliation(s)
- Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xu Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Huacai Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Shengjun Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Qingjie Meng
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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25
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Taylor AE, Mellbye BL. Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature. Front Microbiol 2022; 13:817986. [PMID: 35620102 PMCID: PMC9127996 DOI: 10.3389/fmicb.2022.817986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.
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Affiliation(s)
- Anne E. Taylor
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Brett L. Mellbye
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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26
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Kang Z, Li X, Li Y, Ye L, Zhang B, Zhang X, Penttinen P, Gu Y. Black Truffles Affect Quercus aliena Physiology and Root-Associated nirK- and nirS-Type Denitrifying Bacterial Communities in the Initial Stage of Inoculation. Front Microbiol 2022; 13:792568. [PMID: 35572648 PMCID: PMC9096950 DOI: 10.3389/fmicb.2022.792568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.
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Affiliation(s)
- Zongjing Kang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yan Li
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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27
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Duhan N, Norton JM, Kaundal R. deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning. Brief Bioinform 2022; 23:6553605. [PMID: 35325031 DOI: 10.1093/bib/bbac071] [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] [Received: 11/12/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 11/12/2022] Open
Abstract
Nitrogen is essential for life and its transformations are an important part of the global biogeochemical cycle. Being an essential nutrient, nitrogen exists in a range of oxidation states from +5 (nitrate) to -3 (ammonium and amino-nitrogen), and its oxidation and reduction reactions catalyzed by microbial enzymes determine its environmental fate. The functional annotation of the genes encoding the core nitrogen network enzymes has a broad range of applications in metagenomics, agriculture, wastewater treatment and industrial biotechnology. This study developed an alignment-free computational approach to determine the predicted nitrogen biochemical network-related enzymes from the sequence itself. We propose deepNEC, a novel end-to-end feature selection and classification model training approach for nitrogen biochemical network-related enzyme prediction. The algorithm was developed using Deep Learning, a class of machine learning algorithms that uses multiple layers to extract higher-level features from the raw input data. The derived protein sequence is used as an input, extracting sequential and convolutional features from raw encoded protein sequences based on classification rather than traditional alignment-based methods for enzyme prediction. Two large datasets of protein sequences, enzymes and non-enzymes were used to train the models with protein sequence features like amino acid composition, dipeptide composition (DPC), conformation transition and distribution, normalized Moreau-Broto (NMBroto), conjoint and quasi order, etc. The k-fold cross-validation and independent testing were performed to validate our model training. deepNEC uses a four-tier approach for prediction; in the first phase, it will predict a query sequence as enzyme or non-enzyme; in the second phase, it will further predict and classify enzymes into nitrogen biochemical network-related enzymes or non-nitrogen metabolism enzymes; in the third phase, it classifies predicted enzymes into nine nitrogen metabolism classes; and in the fourth phase, it predicts the enzyme commission number out of 20 classes for nitrogen metabolism. Among all, the DPC + NMBroto hybrid feature gave the best prediction performance (accuracy of 96.15% in k-fold training and 93.43% in independent testing) with an Matthews correlation coefficient (0.92 training and 0.87 independent testing) in phase I; phase II (accuracy of 99.71% in k-fold training and 98.30% in independent testing); phase III (overall accuracy of 99.03% in k-fold training and 98.98% in independent testing); phase IV (overall accuracy of 99.05% in k-fold training and 98.18% in independent testing), the DPC feature gave the best prediction performance. We have also implemented a homology-based method to remove false negatives. All the models have been implemented on a web server (prediction tool), which is freely available at http://bioinfo.usu.edu/deepNEC/.
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Affiliation(s)
- Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA
| | - Jeanette M Norton
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA.,Bioinformatics Facility, Center for Integrated BioSystems, UT 84322 USA.,Department of Computer Science, College of Science; Utah State University, Logan, UT 84322 USA
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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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29
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Phosphorous (V) Corrole Fluorophores for Nitrite Assessment in Environmental and Biological Samples. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10030107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two phosphorous (V) corrole complexes, [5,10,15-pentafluorophenyl corrole] phosphorous (V) (PFCorr) and [10-(4-trimethylsilylphenyl)-5,15-dimesityl-corrole] phosphorous (V) (PCorr) were synthesized and tested as nitrite-sensitive fluorophores. Fluorimetry studies on ligand sensitivity towards anions were carried out in solution, then inside polymeric membrane optodes deposited on glass, and finally by functionalized SiO2 nanoparticles deposited on a paper support. The selective fluorescence quenching was registered upon addition of an increasing amount of NO2− ions for both ligands. The influence on the PFCorr optode’s response of the lipophilic sites’ functionalization was investigated. The sensors’ suitability for nitrite assessment in natural waters at levels 10-fault lower than the WHO’s recommended maximum concentration level of 3 mg/L was demonstrated.
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Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.
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Sim JXF, Doolette CL, Vasileiadis S, Drigo B, Wyrsch ER, Djordjevic SP, Donner E, Karpouzas DG, Lombi E. Pesticide effects on nitrogen cycle related microbial functions and community composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150734. [PMID: 34606862 DOI: 10.1016/j.scitotenv.2021.150734] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The extensive application of pesticides in agriculture raises concerns about their potential negative impact on soil microorganisms, being the key drivers of nutrient cycling. Most studies have investigated the effect of a single pesticide on a nutrient cycling in single soil type. We, for the first time, investigated the effect of 20 commercial pesticides with different mode of actions, applied at their recommended dose and five times their recommended dose, on nitrogen (N) microbial cycling in three different agricultural soils from southern Australian. Functional effects were determined by measuring soil enzymatic activities of β-1,4-N-acetyliglucosaminidase (NAG) and l-leucine aminopeptidase (LAP), potential nitrification (PN), and the abundance of functional genes involved in N cycling (amoA and nifH). Effects on nitrifiers diversity were determined with amplicon sequencing. Overall, the pesticides effect on N microbial cycling was dose-independent and soil specific. The fungicides flutriafol and azoxystrobin, the herbicide chlorsulfuron and the insecticide fipronil induced a significant reduction in PN and β-1,4-N-acetylglucosaminidase activity (P < 0.05) (NAG) in the alkaline loam soil with low organic carbon content i.e. a soil with properties which typically favors pesticide bioavailability and therefore potential toxicity. For the nitrifier community, the greatest pesticide effects were on the most dominant Nitrososphaeraceae (ammonia-oxidizing archaea; AOA) whose abundance increased significantly compared to the less dominant AOA and other nitrifiers. The inhibiting effects were more evident in the soil samples treated with fungicides. By testing multiple pesticides in a single study, our findings provide crucial information that can be used for pesticide hazard assessment.
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Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis 41500, Greece
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Ethan R Wyrsch
- iThree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia; University of South Australia, UniSA STEM, Mawson Lakes, South Australia 5095, Australia
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Canto-Encalada G, Tec-Campos D, Tibocha-Bonilla JD, Zengler K, Zepeda A, Zuñiga C. Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. PLoS Comput Biol 2022; 18:e1009828. [PMID: 35108266 PMCID: PMC8853641 DOI: 10.1371/journal.pcbi.1009828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 02/17/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022] Open
Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production. Nitrosomonas europaea catalyzes the first step of the nitrification process (ammonia to nitrite). It has been recognized as one of the most important members of microbial communities of wastewater treatment processes. Genome-scale models are powerful tools in process optimization since they can predict the organism’s behavior under different growth conditions. The final genome-scale model of N. europaea ATCC19718, iGC535, can predict growth and oxygen uptake rates with 90.52% accuracy under chemolithotrophic and chemolitoorganotrophic conditions. Moreover, iGC535 can predict the simultaneous oxidation of ammonia and wastewater pollutants, such as benzene, toluene, phenol and, chlorobenzene. iGC535 represents the most comprehensive knowledge-base for a nitrifying organism available to date. The genome-scale model reconstructed in this work brings us closer to understanding N. europaea’s role in a community with other nitrifying bacteria.
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Affiliation(s)
| | - Diego Tec-Campos
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, México
- Department of Pediatrics, University of California, San Diego, California, United States of America
| | - Juan D. Tibocha-Bonilla
- Department of Pediatrics, University of California, San Diego, California, United States of America
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, California, United States of America
- Department of Bioengineering, University of California, San Diego, California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, California, United States of America
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, México
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, California, United States of America
- * E-mail:
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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Wang L, Liu Z, Jiang X, Li A. Aerobic granulation of nitrifying activated sludge enhanced removal of 17α-ethinylestradiol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149546. [PMID: 34438142 DOI: 10.1016/j.scitotenv.2021.149546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
The positive correlation between the nitrification activity of activated sludge and 17α-ethinylestradiol (EE2) removal has been widely reported. However, up to now the effect of the granulation of nitrifying activated sludge (NAS) on EE2 removal has not been determined. In this study, nitrifying granular sludge (NGS) exhibited more effective EE2 removal efficiency with 3.705 μgEE2∙(gMLSS∙h)-1 in a sequential batch reactor (SBR). Through the artificial neural network (ANN) model and Spearman correlation analysis, nitrite accumulation was demonstrated to be the key factor affecting EE2 removal. Notably, under the same aeration condition (0.15 L/min), nitrite accumulation was more easily achieved in NGS because of its dense structure. Full-length 16S rRNA gene sequencing suggested that EE2 could strongly influence the microbial communities of NAS and NGS. NGS exhibited an increase in community diversity and richness, but NAS exhibited a decrease. In addition, the relative abundance of Nitrosomonas (ammonia-oxidizing bacteria, AOB) decreased considerably in both NAS and NGS, whereas the expression of amoA and nirK genes in Nitrosomonas was upregulated. It was suggested that Nitrosomonas was forced to regulate its gene expression to resist the negative effects of EE2. Denitrifying bacteria, such as Comamonas, were enriched in both NAS and NGS, and there were more species of heterotrophs that can degrade micropollutants in NGS with exposure to EE2. The transformation pathways of EE2 were uniform in NAS and NGS. Ammonia monooxygenase (AMO) in AOB directly biotransformed EE2 while reactive species produced by AOB chemically transformed EE2. Heterotrophs degraded EE2 and its transformation products (TPs) generated by AOB. According to TPs and microbial structure, NGS exhibited better performance than NAS regarding the collaborative removal of EE2 by AOB and heterotrophs. These results provide important information for the development and application of NGS to treat wastewater containing estrogen and high-strength ammonium.
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Affiliation(s)
- Lili Wang
- Key Laboratory of Water and sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zhifang Liu
- Key Laboratory of Water and sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xiaoman Jiang
- Key Laboratory of Water and sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Anjie Li
- Key Laboratory of Water and sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
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Baruch M, Tejedor-Sanz S, Su L, Ajo-Franklin CM. Electronic control of redox reactions inside Escherichia coli using a genetic module. PLoS One 2021; 16:e0258380. [PMID: 34793478 PMCID: PMC8601525 DOI: 10.1371/journal.pone.0258380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/26/2021] [Indexed: 11/22/2022] Open
Abstract
Microorganisms regulate the redox state of different biomolecules to precisely control biological processes. These processes can be modulated by electrochemically coupling intracellular biomolecules to an external electrode, but current approaches afford only limited control and specificity. Here we describe specific electrochemical control of the reduction of intracellular biomolecules in Escherichia coli through introduction of a heterologous electron transfer pathway. E. coli expressing cymAmtrCAB from Shewanella oneidensis MR-1 consumed electrons directly from a cathode when fumarate or nitrate, both intracellular electron acceptors, were present. The fumarate-triggered current consumption occurred only when fumarate reductase was present, indicating all the electrons passed through this enzyme. Moreover, CymAMtrCAB-expressing E. coli used current to stoichiometrically reduce nitrate. Thus, our work introduces a modular genetic tool to reduce a specific intracellular redox molecule with an electrode, opening the possibility of electronically controlling biological processes such as biosynthesis and growth in any microorganism.
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Affiliation(s)
- Moshe Baruch
- The Molecular Foundry, Biological Nanostructures Facility, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sara Tejedor-Sanz
- The Molecular Foundry, Biological Nanostructures Facility, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Lin Su
- The Molecular Foundry, Biological Nanostructures Facility, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Caroline M. Ajo-Franklin
- The Molecular Foundry, Biological Nanostructures Facility, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- Institute for Biosciences and Bioengineering, Rice University, Houston, Texas, United States of America
- * E-mail:
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36
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Chun SJ, Kim YJ, Cui Y, Nam KH. Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117851. [PMID: 34358869 DOI: 10.1016/j.envpol.2021.117851] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/13/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.
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Affiliation(s)
- Seong-Jun Chun
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea
| | - Young-Joong Kim
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea
| | - Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyong-Hee Nam
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea.
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Verbeelen T, Leys N, Ganigué R, Mastroleo F. Development of Nitrogen Recycling Strategies for Bioregenerative Life Support Systems in Space. Front Microbiol 2021; 12:700810. [PMID: 34721316 PMCID: PMC8548772 DOI: 10.3389/fmicb.2021.700810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
To enable long-distance space travel, the development of a highly efficient and robust system to recover nutrients from waste streams is imperative. The inability of the current physicochemical-based environmental control and life support system (ECLSS) on the ISS to produce food in situ and to recover water and oxygen at high enough efficiencies results in the need for frequent resupply missions from Earth. Therefore, alternative strategies like biologically-based technologies called bioregenerative life support systems (BLSSs) are in development. These systems aim to combine biological and physicochemical processes, which enable in situ water, oxygen, and food production (through the highly efficient recovery of minerals from waste streams). Hence, minimalizing the need for external consumables. One of the BLSS initiatives is the European Space Agency's (ESA) Micro-Ecological Life Support System Alternative (MELiSSA). It has been designed as a five-compartment bioengineered system able to produce fresh food and oxygen and to recycle water. As such, it could sustain the needs of a human crew for long-term space exploration missions. A prerequisite for the self-sufficient nature of MELiSSA is the highly efficient recovery of valuable minerals from waste streams. The produced nutrients can be used as a fertilizer for food production. In this review, we discuss the need to shift from the ECLSS to a BLSS, provide a summary of past and current BLSS programs and their unique approaches to nitrogen recovery and processing of urine waste streams. In addition, compartment III of the MELiSSA loop, which is responsible for nitrogen recovery, is reviewed in-depth. Finally, past, current, and future related ground and space demonstration and the space-related challenges for this technology are considered.
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Affiliation(s)
- Tom Verbeelen
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Ghent, Belgium
| | - Felice Mastroleo
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments. Appl Environ Microbiol 2021; 87:e0103821. [PMID: 34347515 DOI: 10.1128/aem.01038-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite - can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.
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Wang N, Gao J, Liu Y, Wang Q, Zhuang X, Zhuang G. Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review. CHEMOSPHERE 2021; 274:129970. [PMID: 33979914 DOI: 10.1016/j.chemosphere.2021.129970] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhang J, Hu Z, Liu T, Wang Z, Guo J, Yuan Z, Zheng M. Feasibility of methane bioconversion to methanol by acid-tolerant ammonia-oxidizing bacteria. WATER RESEARCH 2021; 197:117077. [PMID: 33812128 DOI: 10.1016/j.watres.2021.117077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/08/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Bioconversion of biogas to value-added liquids has received increasing attention over the years. However, many biological processes are restricted under acidic conditions owing to the excessive carbon dioxide (CO2, 30-40% v/v) in biogas. Here, using an enriched culture dominated by acid-tolerant ammonia-oxidizing bacteria (AOB) 'Candidatus Nitrosoglobus', this study examined the feasibility of producing methanol from methane in the CO2-acidified environment (i.e. pH of 5.0). Within the tested dissolved methane range (0.1-0.9 mM), methane oxidation by the acid-tolerant AOB culture followed first-order kinetics, with the same rate constant (i.e. 0.43 (L/(g VSS‧h)) between pH 7.0 and 5.0. The acidic methane oxidation showed robustness against high dissolved concentrations of CO2 (up to 4.06 mM) and hydrogen sulfide (H2S up to 0.11 mM), which led to a high methanol yield of about 30-40%. As such, the raw biogas containing toxic CO2 and H2S can directly serve for methanol production by this acid-tolerant AOB culture, economizing a conventionally costly biogas upgradation process. Afterwards, two batch reactors fed with methane and oxygen intermittently both obtained a final concentration of 1.5 mM CH3OH (equal to 72 mg chemical oxygen demand/L) in the liquid, suggesting it is a useful carbon source to enhance denitrification in wastewater treatment systems. In addition, ammonia availability was identified to be critical for a higher rate of this AOB-mediated methanol production. Overall, our results for the first time demonstrated the capability of a novel acid-tolerant AOB culture to oxidize methane, and also illustrated the technical feasibility to utilize raw biogas for methanol production at acidic conditions.
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Affiliation(s)
- Junji Zhang
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Zhetai Hu
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Tao Liu
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Zhiyao Wang
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Min Zheng
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia.
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41
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Yadav P, Yadav R, Jain S, Vaidya A. Caspase-3: A primary target for natural and synthetic compounds for cancer therapy. Chem Biol Drug Des 2021; 98:144-165. [PMID: 33963665 DOI: 10.1111/cbdd.13860] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/29/2021] [Accepted: 04/18/2021] [Indexed: 12/21/2022]
Abstract
Caspases, a group of protease enzymes (cysteine proteases), exist as inactive zymogens in the cells and execute apoptosis (programmed cell death). Caspase-3, an executioner caspase, plays an imperative role in apoptosis and becomes a primary target for cancer treatment. A number of analogues of quinazoline, quinazolinone, indoloquinazolines, quinone, naphthoquinones, pyrroloiminoquinones, styrylquinolines, tetheredtetrahydroquinoline, fluoroquinolone, thiosemicarbazones, benzotriazole, pyrimidines, chalcone, and carbazoles have been reported till date, representing caspase-3 mediated apoptosis for cancer therapy. Simultaneously, plant isolates, including lysicamine, podophyllotoxin, and majoranolide, have also been claimed for caspase-3-mediated apoptosis-induced cytotoxicity. Procaspase-activating compound-1 (PAC-1) is the first FDA approved orphan drug, and its synthetic derivative WF-208 also showed fascinating caspase-3 mediated anticancer activity. Till date, a large number of compounds have been reported and patented for their caspase-3-mediated cytotoxicity and now scientist is also focusing to introduce new compounds in market to encompass anticancer activity.
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Affiliation(s)
- Poonam Yadav
- Department of Pharmacology and Toxicology, NIPER, Hajipur, India
| | - Ramakant Yadav
- Department of Neurology, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - Shweta Jain
- Sir Madan Lal Institute of Pharmacy, Etawah, India
| | - Ankur Vaidya
- Pharmacy College Saifai, Uttar Pradesh University of Medical Sciences, Saifai, India
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Huddy RJ, Sachdeva R, Kadzinga F, Kantor RS, Harrison STL, Banfield JF. Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. Front Microbiol 2021; 12:643368. [PMID: 33897653 PMCID: PMC8061750 DOI: 10.3389/fmicb.2021.643368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/09/2021] [Indexed: 01/14/2023] Open
Abstract
Thiocyanate (SCN–) contamination threatens aquatic ecosystems and pollutes vital freshwater supplies. SCN–-degrading microbial consortia are commercially adapted for remediation, but the impact of organic amendments on selection within SCN–-degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN– could be reproducibly selected for based on SCN– loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN–-contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN–-degrading consortium. Five experiments were conducted over 790 days, and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to break down SCN– using a novel thiocyanate desulfurase, oxidize resulting reduced sulfur, degrade product cyanate to ammonia and CO2 via cyanate hydratase, and fix CO2 via the Calvin–Benson–Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN– at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.
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Affiliation(s)
- Robert J Huddy
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Fadzai Kadzinga
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Rose S Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States.,Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States.,School of Earth Sciences, University of Melbourne, Melbourne, VIC, Australia
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43
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Picone N, Pol A, Mesman R, van Kessel MAHJ, Cremers G, van Gelder AH, van Alen TA, Jetten MSM, Lücker S, Op den Camp HJM. Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium. THE ISME JOURNAL 2021; 15:1150-1164. [PMID: 33303933 PMCID: PMC8115276 DOI: 10.1038/s41396-020-00840-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Ammonia oxidation was considered impossible under highly acidic conditions, as the protonation of ammonia leads to decreased substrate availability and formation of toxic nitrogenous compounds. Recently, some studies described archaeal and bacterial ammonia oxidizers growing at pH as low as 4, while environmental studies observed nitrification at even lower pH values. In this work, we report on the discovery, cultivation, and physiological, genomic, and transcriptomic characterization of a novel gammaproteobacterial ammonia-oxidizing bacterium enriched via continuous bioreactor cultivation from an acidic air biofilter that was able to grow and oxidize ammonia at pH 2.5. This microorganism has a chemolithoautotrophic lifestyle, using ammonia as energy source. The observed growth rate on ammonia was 0.196 day-1, with a doubling time of 3.5 days. The strain also displayed ureolytic activity and cultivation with urea as ammonia source resulted in a growth rate of 0.104 day-1 and a doubling time of 6.7 days. A high ammonia affinity (Km(app) = 147 ± 14 nM) and high tolerance to toxic nitric oxide could represent an adaptation to acidic environments. Electron microscopic analysis showed coccoid cell morphology with a large amount of intracytoplasmic membrane stacks, typical of gammaproteobacterial ammonia oxidizers. Furthermore, genome and transcriptome analysis showed the presence and expression of diagnostic genes for nitrifiers (amoCAB, hao, nor, ure, cbbLS), but no nirK was identified. Phylogenetic analysis revealed that this strain belonged to a novel bacterial genus, for which we propose the name "Candidatus Nitrosacidococcus tergens" sp. RJ19.
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Affiliation(s)
- Nunzia Picone
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Arjan Pol
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Rob Mesman
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Maartje A. H. J. van Kessel
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Geert Cremers
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Antonie H. van Gelder
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Theo A. van Alen
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Mike S. M. Jetten
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - Huub J. M. Op den Camp
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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45
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A simple and sensitive direct mRNA multiplexed detection strategy for amoA-targeted monitoring of ammonia-oxidizing activity in water environment. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Han P, Wu D, Sun D, Zhao M, Wang M, Wen T, Zhang J, Hou L, Liu M, Klümper U, Zheng Y, Dong HP, Liang X, Yin G. N 2O and NO y production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers. WATER RESEARCH 2021; 190:116728. [PMID: 33326897 DOI: 10.1016/j.watres.2020.116728] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) and NOy (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO2)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N2O and NOy emissions. Yet, little is known about HONO and NO2 production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N2O and NOy production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NOy production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N2O based on results from NH2OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH2OH) and NO transformation enzymatic activities may lead to a buildup of NH2OH/NO which can abiotically react to N2O ; iv) collectively confirm restrained N2O and NOy emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.
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Affiliation(s)
- Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Dianming Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Mengdi Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Lijun Hou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, 01062, Germany
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
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47
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Wang F, Xu Z, Wang C, Guo Z, Yuan Z, Kang H, Li J, Lu F, Liu Y. Biochemical characterization of a tyrosinase from Bacillus aryabhattai and its application. Int J Biol Macromol 2021; 176:37-46. [PMID: 33571594 DOI: 10.1016/j.ijbiomac.2021.02.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/05/2023]
Abstract
Although lots of tyrosinases have been isolated from bacteria, few studies are focused on tyrosinases from Bacillus sp.. In this study, a tyrosinase from B. aryabhattai TCCC 111983 (TYR) was functionally expressed, purified, and then biochemically characterized. The recombinant tyrosinase (rTYR) presented a good catalytic activity in a broad temperature and pH range, retaining over 60% of the relative activity at 30 °C-90 °C and 45% at pH 3.0 to 10.0. Especially, rTYR exhibited 20% of its maximum activity at 0 °C, and it also showed a variable stability towards different effectors. It presented high tolerance towards salinity and chloride, retaining 81% of its original activity in 2 M NaCl. Kinetic parameters indicated that rTYR displayed a relatively good affinity for both l-tyrosine and l-DOPA. Additionally, rTYR demonstrated remarkable advantages on efficient decolorizing azo and anthraquinonic food dyes (carmine and erythrosin), and more five industrial dyes with or without mediators in acidic, neutral, and alkaline conditions. As the first report on the tyrosinase from B. aryabhattai, the aforementioned results indicated that rTYR would be potential for food industrial applications.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zehua Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Chen Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zehui Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zhaoting Yuan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hongwei Kang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jingwen Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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48
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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49
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Zheng F, Wang J, Xiao R, Chai W, Xing D, Lu H. Dissolved organic nitrogen in wastewater treatment processes: Transformation, biosynthesis and ecological impacts. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116436. [PMID: 33493760 DOI: 10.1016/j.envpol.2021.116436] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/08/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
With the upgrade of wastewater treatment plants (WWTPs) to meet more stringent discharge limits for nutrients, dissolved organic nitrogen (DON) is present at an increasing percentage (up to 85%) in the effluent. Discharged DON is of great environmental concern due to its potentials in stimulating algal growth and forming toxic nitrogenous disinfection by-products (N-DBPs). This article systematically reviewed the characteristics, transformation and ecological impacts of wastewater DON. Proteins, amino acids and humic substances are the abundant DON compounds, but a large fraction (nearly 50%) of DON remains uncharacterized. Biological treatment processes play a dominant role in DON transformation (65-90%), where DON serves as both nutrient and energy sources. Despite of the above progress, critical knowledge gaps remain in DON functional duality, relationship with dissolved inorganic nitrogen (DIN) species, and coupling/decoupling with the dissolved organic carbon (DOC) pool. Development of more rapid and accurate quantification methods, modeling transformation processes, and assessing DON-associated eutrophication and N-DBP formation risks should be given priority in further investigations.
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Affiliation(s)
- Fang Zheng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jie Wang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Rui Xiao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Wenbo Chai
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058, Hangzhou, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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50
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Nechayeva A, Boyarshin K, Bespalova O, Klyueva V, Makanina O, Batlutskaya I. Analysis of 16S rRNA gene variability in soil nitrifying bacteria of the genus Nitrosomonas. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213005007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The main goal of the work was to assess variability of 16S rRNA gene sequence within the nitrifying bacterial genus Nitrosomonas to find specific sequences for its detection. To achieve it, we had to find and to assess sequences that are highly conservative on the level of the genus and to find and to assess sequences variable on the level of genus but conserved on the level of species. In the SILVA database of ribosomal RNA sequences, 231 sequences of 16S rRNAs of bacteria of the genus Nitrosomonas were collected, of which were sorted 132 sequences by length from 1400 to 1541 (full-sized gene) nucleotides. We conducted an analysis of the taxon-specificity of sequences conserved at the genus level. More than a hundred full matches were found by the BLAST program in the nr database with other genera of the same and other families. So, in Nitrosomonas 16S rRNA gene are present some highly conservative regions, but they are not genus-specific due to high coincidence with other genera. Wherein, a variable region 994-1041 is highly species-specific for the species N. eutropha. Generally, the sequence of 994-1041 region of Nitrosomonas 16S rRNA genes tends to be clustered, being very close between some species.
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