1
|
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.
Collapse
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:
| |
Collapse
|
2
|
Li Y, Wu J, Liu Y, Chen F, Guan J, Shao Y, Wang J, Zhang L, Goel R, Sun X, Wang Q, Zhang R, Song H, Liu B. The effect of sludge retention time (SRT) on the Nitrifier typical kinetics at ambient temperature under the low ammonia density. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 85:617-632. [PMID: 35100143 DOI: 10.2166/wst.2021.624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sludge retention time (SRT) regulation is one of the essential management techniques for refined control of the main-sidestream treatment process under the low ammonia density. It is indispensable to understand the effect of SRTs changes on the Nitrifier kinetics to obtain the functional separation of the Nitrifier and the refined control of the nitrification process. In this study, Nitrifier was cultured with conditions of 35 ± 0.5 °C, pH 7.5 ± 0.2, DO 5.0 ± 0.5 mg-O/L, and SRTs were controlled for 40 d, 20 d, 10 d, and 5 d. The net growth rate (μm), decay rate (b), specific growth rate (μ), the yield of the Nitrifier (YA), temperature parameter (TA), and inhibition coefficient (KI) have been measured and extended with the SRT decreases. Instead, the half-saturation coefficient (KS) decreased. In addition, the limited value of pH inhibition occurs (pHUL), and the pH of keeping 5% maximum reaction rate (pHLL) was in a relatively stable state. The trade of kinetics may be induced by the change of species structure of Nitrifier. The Nitrosomonas proportion was increased, and the Nitrospira was contrary with the SRT decreasing. It is a match for the functional separation of Nitrifier when SRTs was 20 d at ambient temperature under the low ammonia density. The kinetics of ammonia-oxidizing organisms (AOO) and nitrite-oxidizing organisms (NOO) in Nitrifier under different SRT conditions should be measured respectively to the refined control of the partial nitrification process in future study.
Collapse
Affiliation(s)
- Yifan Li
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail: ; These authors contributed equally to this work and should be considered co-first authors
| | - Jinzhu Wu
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail: ; These authors contributed equally to this work and should be considered co-first authors
| | - Yongjie Liu
- Shandong Institute for Product Quality Inspection, Jinan, 250102, China
| | - Feiyong Chen
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| | - Jie Guan
- Shandong Institute for Product Quality Inspection, Jinan, 250102, China
| | - Yuanyuan Shao
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| | - Jing Wang
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| | - Lijie Zhang
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| | - Rajeev Goel
- Hydromantis Environmental Software Solutions, Inc., 407 King Street West, Hamilton, Ontario, Canada
| | - Xiuqin Sun
- Nuclear Engineering Lihua Technology Engineering Co. Ltd, Beijing, China
| | - Quanyong Wang
- Shandong Branch of China Urban Construction Research Institute, No. 1299, Xinluo Street, Jinan, China
| | - Ruina Zhang
- Shanghai Environmental & Sanitary Engineering Design Institute Co., Ltd, No.11, 345 Lane, Shilong RD, Shanghai, China
| | - Hengyu Song
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| | - Bing Liu
- Resources and Environment Innovation Institute, School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China E-mail:
| |
Collapse
|
3
|
Fujita Y, Walton M, Das G, Dohnalkova A, Vanzin G, Anderko A. Impacts of anthropogenic gadolinium on the activity of the ammonia oxidizing bacterium Nitrosomonas europaea. CHEMOSPHERE 2020; 257:127250. [PMID: 32600781 DOI: 10.1016/j.chemosphere.2020.127250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/01/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Widespread use of gadolinium-based contrast agents in medical imaging has resulted in increased Gd inputs to municipal wastewater treatment plants. Others have reported that typical wastewater treatment does not attenuate Gd, resulting in discharges to natural waters. However, whether elevated Gd impacts the performance of biological treatment has not been investigated. We examined whether gadolinium chloride or Gd chelated with diethylenetriaminepentaacetic acid (DTPA) affected the activity of the model nitrifying bacterium Nitrosomonas europaea. At nominal GdCl3 additions ranging from 1 to 500 μM, no impact was observed compared to the control. Most (>98%) of the added Gd precipitated, and extracellular GdPO4 nanoparticles were observed. When chelated with DTPA, Gd remained soluble, but no statistically significant impact on ammonia oxidation was observed until the highest concentrations tested. At 300 and 500 μM Gd-DTPA, a temporary reduction of nitrite production relative to the control (effect size 1.3 mg l-1 and 1.5 mg l-1, respectively, at 24 h) was seen. By itself, DTPA was highly inhibitory. Modeling suggested that DTPA likely chelated other metals, but adjusting the concentrations of the most abundant metals in the medium, calcium and magnesium, indicated that lowering their free ion activities was probably not the cause of inhibition. Complexation of other essential metals was more likely. Our studies indicate that while the low bioavailability of Gd may limit its ecosystem impacts, the role of synthetic ligands used with Gd and other rare earth elements should be considered as the production, use and disposal of these elements increases.
Collapse
Affiliation(s)
- Yoshiko Fujita
- Idaho National Laboratory, Biological & Chemical Science & Engineering Department, Idaho Falls, ID, 83415-2203, United States.
| | - Michelle Walton
- Idaho National Laboratory, Biological & Chemical Science & Engineering Department, Idaho Falls, ID, 83415-2203, United States
| | - Gaurav Das
- OLI Systems, Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, NJ, 07927, United States
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Gary Vanzin
- Colorado School of Mines, Department of Civil & Environmental Engineering, 1012 14th Street, Golden, CO, 80401, United States
| | - Andre Anderko
- OLI Systems, Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, NJ, 07927, United States
| |
Collapse
|
4
|
Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME JOURNAL 2018; 12:2389-2402. [PMID: 29899515 DOI: 10.1038/s41396-018-0191-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 01/17/2023]
Abstract
Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.
Collapse
|
5
|
Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea. Appl Environ Microbiol 2016; 82:3310-3318. [PMID: 27016565 DOI: 10.1128/aem.00294-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/19/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2 IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on the dilution rate and Na2CO3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3 oxidation from growth and increased N2O production. IMPORTANCE Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO2) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of Nitrosomonas europaea, a model ammonia-oxidizing bacterium, and report on increased production of N2O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N2O emissions from nitrification in soils and wastewater treatment.
Collapse
|
6
|
Papp B, Török T, Sándor E, Fekete E, Flipphi M, Karaffa L. High cell density cultivation of the chemolithoautotrophic bacterium Nitrosomonas europaea. Folia Microbiol (Praha) 2015; 61:191-8. [PMID: 26358065 DOI: 10.1007/s12223-015-0425-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/02/2015] [Indexed: 01/13/2023]
Abstract
Nitrosomonas europaea is a chemolithoautotrophic nitrifier, a gram-negative bacterium that can obtain all energy required for growth from the oxidation of ammonia to nitrite, and this may be beneficial for various biotechnological and environmental applications. However, compared to other bacteria, growth of ammonia oxidizing bacteria is very slow. A prerequisite to produce high cell density N. europaea cultures is to minimize the concentrations of inhibitory metabolic by-products. During growth on ammonia nitrite accumulates, as a consequence, N. europaea cannot grow to high cell concentrations under conventional batch conditions. Here, we show that single-vessel dialysis membrane bioreactors can be used to obtain substantially increased N. europaea biomasses and substantially reduced nitrite levels in media initially containing high amounts of the substrate. Dialysis membrane bioreactor fermentations were run in batch as well as in continuous mode. Growth was monitored with cell concentration determinations, by assessing dry cell mass and by monitoring ammonium consumption as well as nitrite formation. In addition, metabolic activity was probed with in vivo acridine orange staining. Under continuous substrate feed, the maximal cell concentration (2.79 × 10(12)/L) and maximal dry cell mass (0.895 g/L) achieved more than doubled the highest values reported for N. europaea cultivations to date.
Collapse
Affiliation(s)
- Benedek Papp
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1, Debrecen, Hungary
| | - Tibor Török
- Safety and Environmental Department, TEVA Pharmaceutical Ltd., H-4032, Pallagi u. 13, Debrecen, Hungary
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, H-4032, Böszörményi út 138, Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1, Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1, Debrecen, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1, Debrecen, Hungary.
| |
Collapse
|
7
|
Fujita Y, Barnes J, Eslamimanesh A, Lencka MM, Anderko A, Riman RE, Navrotsky A. Effects of Simulated Rare Earth Recycling Wastewaters on Biological Nitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:9460-8. [PMID: 26132866 PMCID: PMC5380465 DOI: 10.1021/acs.est.5b01753] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Increasing rare earth element (REE) supplies by recycling and expanded ore processing will result in generation of new wastewaters. In some cases, disposal to a sewage treatment plant may be favored, but plant performance must be maintained. To assess the potential effects of such wastewaters on biological treatment, model nitrifying organisms Nitrosomonas europaea and Nitrobacter winogradskyi were exposed to simulated wastewaters containing varying levels of yttrium or europium (10, 50, and 100 ppm), and the extractant tributyl phosphate (TBP, at 0.1 g/L). Y and Eu additions at 50 and 100 ppm inhibited N. europaea, even when virtually all of the REE was insoluble. Provision of TBP with Eu increased N. europaea inhibition, although TBP alone did not substantially alter activity. For N. winogradskyi cultures, Eu or Y additions at all tested levels induced significant inhibition, and nitrification shut down completely with TBP addition. REE solubility was calculated using the previously developed MSE (Mixed-Solvent Electrolyte) thermodynamic model. The model calculations reveal a strong pH dependence of solubility, typically controlled by the precipitation of REE hydroxides but also likely affected by the formation of unknown phosphate phases, which determined aqueous concentrations experienced by the microorganisms.
Collapse
Affiliation(s)
- Yoshiko Fujita
- Idaho National Laboratory, Idaho Falls, ID 83415
- Corresponding Author Contact Information: ; Tel. (+1) 208-526-1242; Fax (+1) 208 526 0828, . Mail Stop: 83415-2203
| | - Joni Barnes
- Idaho National Laboratory, Idaho Falls, ID 83415
| | - Ali Eslamimanesh
- OLI Systems Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, NJ 07927
| | | | - Andrzej Anderko
- OLI Systems Inc., 240 Cedar Knolls Road, Suite 301, Cedar Knolls, NJ 07927
| | - Richard E. Riman
- Rutgers, The State University of New Jersey, Department of Materials Science and Engineering, 607 Taylor Road, Piscataway, NJ 08855
| | - Alexandra Navrotsky
- Peter A. Rock Thermochemistry Laboratory and NEAT ORU, University of California Davis, Davis, CA 95616
| |
Collapse
|
8
|
Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H. The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. BMC PLANT BIOLOGY 2015; 15:78. [PMID: 25848894 PMCID: PMC4358910 DOI: 10.1186/s12870-015-0467-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes. RESULTS We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species. CONCLUSIONS The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.
Collapse
Affiliation(s)
- Jiří Bárta
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - James D Stone
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
- />Institute of Botany CAS, Zámek 1, Průhonice, 25243 Czech Republic
| | - Jiří Pech
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Dagmara Sirová
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Lubomír Adamec
- />Institute of Botany CAS, Section of Plant Ecology, Dukelská 135, Treboň, 37982 Czech Republic
| | - Matthew A Campbell
- />Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, 4442 New Zealand
| | - Helena Štorchová
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
| |
Collapse
|
9
|
Gorman-Lewis D, Martens-Habbena W, Stahl DA. Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea. GEOBIOLOGY 2014; 12:157-171. [PMID: 24589203 DOI: 10.1111/gbi.12075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
The ammonia-oxidizing archaeon Nitrosopumilus maritimus strain SCM1 (strain SCM1), a representative of the Thaumarchaeota archaeal phylum, can sustain high specific rates of ammonia oxidation at ammonia concentrations too low to sustain metabolism by ammonia-oxidizing bacteria (AOB). One structural and biochemical difference between N. maritimus and AOB that might be related to the oligotrophic adaptation of strain SCM1 is the cell surface. A proteinaceous surface layer (S-layer) comprises the outermost boundary of the strain SCM1 cell envelope, as opposed to the lipopolysaccharide coat of Gram-negative AOB. In this work, we compared the surface reactivities of two archaea having an S-layer (strain SCM1 and Sulfolobus acidocaldarius) with those of four representative AOB (Nitrosospira briensis, Nitrosomonas europaea, Nitrosolobus multiformis, and Nitrosococcus oceani) using potentiometric and calorimetric titrations to evaluate differences in proton-ionizable surface sites. Strain SCM1 and S. acidocaldarius have a wider range of proton buffering (approximately pH 10-3.5) than the AOB (approximately pH 10-4), under the conditions investigated. Thermodynamic parameters describing proton-ionizable sites (acidity constants, enthalpies, and entropies of protonation) are consistent with these archaea having proton-ionizable amino acid side chains containing carboxyl, imidazole, thiol, hydroxyl, and amine functional groups. Phosphorous-bearing acidic functional groups, which might also be present, could be masked by imidazole and thiol functional groups. Parameters for the AOB are consistent with surface structures containing anionic oxygen ligands (carboxyl- and phosphorous-bearing acidic functional groups), thiols, and amines. In addition, our results showed that strain SCM1 has more reactive surface sites than the AOB and a high concentration of sites consistent with aspartic and/or glutamic acid. Because these alternative boundary layers mediate interaction with the local external environment, these data provide the basis for further comparisons of the thermodynamic behavior of surface reactivity toward essential nutrients.
Collapse
Affiliation(s)
- D Gorman-Lewis
- University of Washington, Department of Earth and Space Sciences, Seattle, WA, USA
| | | | | |
Collapse
|
10
|
Hu YS, Zhao YQ, Zhao XH, Kumar JLG. Comprehensive analysis of step-feeding strategy to enhance biological nitrogen removal in alum sludge-based tidal flow constructed wetlands. BIORESOURCE TECHNOLOGY 2012; 111:27-35. [PMID: 22357288 DOI: 10.1016/j.biortech.2012.01.165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/24/2012] [Accepted: 01/26/2012] [Indexed: 05/31/2023]
Abstract
Step-feeding strategies have been extensively studied and comprehensively analyzed in this study for a four-stage alum sludge-based tidal flow constructed wetlands (AlS-TFCWs) system. Enhanced total nitrogen removal of 83% is achieved under high nitrogen loading rate of 19.1 g N/m(2)d. The key issues towards the success of a significant nitrogen removal in step-feeding TFCWs are the bed resting time (which provides better aeration for nitrification) and up flow stage/delayed input of side stream(s) (which ensure favorable environment for better denitrification). Simultaneous nitrification and denitrification (SND) was found effective in the 1st stage of the system and SND via nitrite is the main nitrogen conversion mechanism. The optimal influent distribution fraction for step-feeding purpose can be estimated from a theoretical basis, which is a function of the influent BCOD/TKN ratio. Therefore the influent distribution fraction should be adjusted according to the variety of influent characteristics, rather than a fixed value.
Collapse
Affiliation(s)
- Y S Hu
- Centre for Water Resources Research, School of Civil, Structural and Environmental Engineering, University College Dublin, Newstead Building, Belfield, Dublin 4, Ireland
| | | | | | | |
Collapse
|
11
|
Schmidt I. Chemoorganoheterotrophic growth of Nitrosomonas europaea and Nitrosomonas eutropha. Curr Microbiol 2009; 59:130-8. [PMID: 19452213 DOI: 10.1007/s00284-009-9409-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/27/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
The ammonia oxidizers Nitrosomonas europaea and Nitrosomonas eutropha are able to grow chemoorganotrophically under anoxic conditions with pyruvate, lactate, acetate, serine, succinate, alpha-ketoglutarate, or fructose as substrate and nitrite as terminal electron acceptor. The growth yield of both bacteria is about 3.5 mg protein (mmol pyruvate)(-1) and the maximum growth rates of N. europaea and N. eutropha are 0.094 d(-1) and 0.175 d(-1), respectively. In the presence of pyruvate and CO2 about 80% of the incorporated carbon derives from pyruvate and about 20% from CO2. Pyruvate is used as energy and only carbon source in the absence of CO2 (chemoorganoheterotrophic growth). CO2 stimulates the chemoorganotrophic growth of both ammonia oxidizers and the expression of ribulose bisphosphate carboxylase/oxygenase is down-regulated at increasing CO2 concentration. Ammonium, although required as nitrogen source, is inhibitory for the chemoorganotrophic metabolism of N. europaea and N. eutropha. In the presence of ammonium pyruvate consumption and the expression of the genes aceE, ppc, gltA, odhA, and ppsA (energy conservation) as well as nirK, norB, and nsc (denitrification) are reduced.
Collapse
Affiliation(s)
- Ingo Schmidt
- Department Microbiology, University of Bayreuth, Universitaetsstrasse 30, 95447, Bayreuth, Germany.
| |
Collapse
|
12
|
Güven D, Schmidt I. Specific activity and viability of Nitrosomonas europaea during discontinuous and continuous fermentation. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
13
|
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 2008; 105:2134-9. [PMID: 18250313 PMCID: PMC2538889 DOI: 10.1073/pnas.0708857105] [Citation(s) in RCA: 552] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Indexed: 02/07/2023] Open
Abstract
The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46 degrees C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as "Candidatus Nitrososphaera gargensis," is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.
Collapse
Affiliation(s)
| | - Elena V. Lebedeva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia; and
| | - Eva Spieck
- University of Hamburg, Biocenter Klein Flottbek, Microbiology, Ohnhorststrasse 18, D-22609 Hamburg, Germany
| | | | - Andreas Richter
- Chemical Ecology and Ecosystem Research, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | | | | |
Collapse
|
14
|
Chung YC, Huang C, Tseng CP. Biological elimination of H2S and NH3 from wastegases by biofilter packed with immobilized heterotrophic bacteria. CHEMOSPHERE 2001; 43:1043-1050. [PMID: 11368219 DOI: 10.1016/s0045-6535(00)00211-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Biotreatment of various ratios of H2S and NH3 gas mixtures was studied using the biofilters, packed with co-immobilized cells (Arthrobacter oxydans CH8 for NH3 and Pseudomonas putida CH11 for H2S). Extensive tests to determine removal characteristics, removal efficiency, removal kinetics, and pressure drops of the biofilters were performed. To estimate the largest allowable inlet concentration, a prediction model was also employed. Greater than 95%, and 90% removal efficiencies were observed for NH3 and H2S, respectively, irrespective of the ratios of H2S and NH3 gas mixtures. The results showed that H2S removal of the biofilter was significantly affected by high inlet concentrations of H2S and NH3. As high H2S concentration was an inhibitory substrate for the growth of heterotrophic sulfur-oxidizing bacteria, the activity of H2S oxidation was thus inhibited. In the case of high NH3 concentration, the poor H2S removal efficiency might be attributed to the acidification of the biofilter. The phenomenon was caused by acidic metabolite accumulation of NH3. Through kinetic analysis, the presence of NH3 did not hinder the NH3 removal, but a high H2S concentration would result in low removal efficiency. Conversely, H2S of adequate concentrations would favor the removal of incoming NH3. The results also indicated that maximum inlet concentrations (model-estimated) agreed well with the experimental values for space velocities of 50-150 h(-1). Hence, the results would be used as the guideline for the design and operation of biofilters.
Collapse
Affiliation(s)
- Y C Chung
- Science & Technology information Center, National Science Council, Taipei, Taiwan, ROC
| | | | | |
Collapse
|
15
|
Grunditz C, Dalhammar G. Development of nitrification inhibition assays using pure cultures of Nitrosomonas and Nitrobacter. WATER RESEARCH 2001; 35:433-440. [PMID: 11228996 DOI: 10.1016/s0043-1354(00)00312-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Restricted requirements for nitrogen reduction at wastewater treatment plants have increased the need for assays determining the inhibition of nitrification. In this paper, two new assays studying ammonia oxidation and nitrite oxidation, respectively, are presented. As test organisms, pure cultures of Nitrosomonas and Nitrobacter isolated from activated sludge are used. The assays are performed in test tubes where the bacteria are incubated with the compound or wastewater to be tested. The nitrification rate is measured during 4 h and compared with reference samples. The test organisms were characterised with respect to temperature, pH and cell activity. Optimum temperature was 35 degrees C for Nitrosomonas and 38 degrees C for Nitrobacter; optimum pH was 8.1 for Nitrosomonas and 7.9 for Nitrobacter. There was a linear relationship between the nitrification rate and the cell concentration in the studied interval. The cell activity decreased slightly with storage time. A significant level of inhibition was calculated to 11% for the Nitrosomonas assay, and to 9% for the Nitrobacter assay. The assays are applicable to determination of nitrification inhibition in samples of industrial waste waters or influents of treatment plants, or chemical substances likely to be found in wastewater.
Collapse
Affiliation(s)
- C Grunditz
- Department of Biotechnology, Royal Institute of Technology (KTH), SE-100 44 Stockholm, Sweden
| | | |
Collapse
|
16
|
Chung YC, Huang C, Tseng CP, Pan JR. Biotreatment of H2S- and NH3-containing waste gases by co-immobilized cells biofilter. CHEMOSPHERE 2000; 41:329-336. [PMID: 11057594 DOI: 10.1016/s0045-6535(99)00490-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gas mixture of H2S and NH3 in this study has been the focus in the research area concerning gases generated from the animal husbandry and the anaerobic wastewater lagoons used for their treatment. A specific microflora (mixture of Thiobacillus thioparus CH11 for H2S and Nitrosomonas europaea for NH3) was immobilized with Ca-alginate and packed inside a glass column to decompose H2S and NH3. The biofilter packed with co-immobilized cells was continuously supplied with H2S and NH3 gas mixtures of various ratios, and the removal efficiency, removal kinetics, and pressure drop in the biofilter was monitored. The results showed that the efficiency remained above 95% regardless of the ratios of H2S and NH3 used. The NH3 concentration has little effect on H2S removal efficiency, however, both high NH3 and H2S concentrations significantly suppress the NH3 removal. Through product analysis, we found that controlling the inlet ratio of the H2S/NH3 could prevent the biofilter from acidification, and, therefore, enhance the operational stability. Conclusions from bioaerosol analysis and pressure drop in the biofilter suggest that the immobilized cell technique creates less environmental impact and improves pure culture operational stability. The criteria for the biofilter operation to meet the current H2S and NH3 emission standards were also established. To reach Taiwan's current ambient air standards of H2S and NH3 (0.1 and 1 ppm, respectively), the maximum inlet concentrations should not exceed 58 ppm for H2S and 164 ppm for NH3, and the residence time be kept at 72 s.
Collapse
Affiliation(s)
- Y C Chung
- Science and Technology Information Center, National Science Council, Taipei, Taiwan, ROC
| | | | | | | |
Collapse
|
17
|
Estimation of nitrifying bacterial activities by measuring oxygen uptake in the presence of the metabolic inhibitors allylthiourea and azide. Appl Environ Microbiol 1998; 64:2266-8. [PMID: 9603846 PMCID: PMC106310 DOI: 10.1128/aem.64.6.2266-2268.1998] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The effects of two metabolic inhibitors on an enriched nitrifying biomass during incubation for short periods of time were investigated by determining respirometric measurements. Allylthiourea (86 &mgr;M) and azide (24 &mgr;M) were shown to be strong, selective inhibitors of ammonia and nitrite oxidation, respectively. Consequently, a differential respirometry method for estimating nitrifying and heterotrophic bacterial activities within a mixed biomass is proposed.
Collapse
|
18
|
Dynamic modeling of immobilized Nitrosomonas europaea: Implementation of diffusion limitation over expanding microcolonies. Enzyme Microb Technol 1995. [DOI: 10.1016/0141-0229(94)00105-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
Properties of a new strain of Nitrosomonas isolated from an aerobic biofilm in a domestic sewage-treatment system. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0922-338x(94)90004-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Sato C, Schnoor JL, McDonald DB. Effects of copper and nickel on the growth ofnitrosomonas europaea. ACTA ACUST UNITED AC 1986. [DOI: 10.1002/tox.2540010307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|