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Tschitschko B, Esti M, Philippi M, Kidane AT, Littmann S, Kitzinger K, Speth DR, Li S, Kraberg A, Tienken D, Marchant HK, Kartal B, Milucka J, Mohr W, Kuypers MMM. Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean. Nature 2024; 630:899-904. [PMID: 38723661 PMCID: PMC11208148 DOI: 10.1038/s41586-024-07495-w] [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: 11/16/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean1 and has a key role in fuelling the biological carbon pump2. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3-5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land6. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Publisher Correction: Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2024; 9:1631. [PMID: 38308099 PMCID: PMC11153124 DOI: 10.1038/s41564-024-01602-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
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Kartal B, Sahiner IT, Turhan VB, Alkurt EG. The significance of cervical discopathy diagnosis in patients with mastalgia. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2024; 28:3036-3040. [PMID: 38708461 DOI: 10.26355/eurrev_202404_36018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE The primary aim of this study was to explore the involvement of cervical discopathy in the development of non-cyclic mastalgia by employing cervical magnetic resonance imaging (MRI). PATIENTS AND METHODS A total of 407 patients were included in the study. Individualized management plans were developed for each patient. Pathological findings in MRI results were assessed by specialists in physical therapy and neurosurgery, and appropriate treatment was administered. Visual assessments of patients were conducted. The Analog Scale (VAS) scoring system was used at the initial presentation, and patients were evaluated at 1 and 3 months following the treatment. RESULTS In the MRI examinations of the patients included in the study, simultaneous cervical disc protrusion was observed in 29% (n: 124) of those with annular bulging. Comparing the VAS scores of patients before treatment, at the 1st and at the 3rd month showed a significant decrease in mastalgia pain (p < 0.001). CONCLUSIONS The diagnosis of cervical discopathy holds significant importance in the treatment of mastalgia patients. Therefore, clinicians should keep the cervical spine in mind as a potential contributing factor to mastalgia.
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
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Dietrich L, Moreno Chicano T, Almeida NM, Akram M, Jetten M, van Niftrik L, Dietl A, Kartal B, Barends TRM, Parey K. Living on hydrazine: Metabolic protein complexes from an anaerobic ammonium oxidizer. Biophys J 2023; 122:302a. [PMID: 36783511 DOI: 10.1016/j.bpj.2022.11.1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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Yang Y, Lu Z, Azari M, Kartal B, Du H, Cai M, Herbold CW, Ding X, Denecke M, Li X, Li M, Gu JD. Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance. WATER RESEARCH 2022; 226:119165. [PMID: 36257158 DOI: 10.1016/j.watres.2022.119165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.
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Hu Z, Wessels HJCT, van Alen T, Jetten MSM, Kartal B. Author Correction: Nitric oxide-dependent anaerobic ammonium oxidation. Nat Commun 2022; 13:3269. [PMID: 35672360 PMCID: PMC9174167 DOI: 10.1038/s41467-022-30986-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Wang J, Yao X, Jia Z, Zhu L, Zheng P, Kartal B, Hu B. Nitrogen input promotes denitrifying methanotrophs' abundance and contribution to methane emission reduction in coastal wetland and paddy soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119090. [PMID: 35240269 DOI: 10.1016/j.envpol.2022.119090] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) microorganisms, using nitrate/nitrite to oxidize methane, have been proved to be an important microbial methane sink in natural habitats. Increasing nitrogen deposit around the globe brings increased availability of substrates for these microorganisms. However, how elevated nitrogen level affects denitrifying methanotrophs has not been elucidated. In this study, sediment/soil samples from coastal wetland with continuous nitrogen input and paddy field with periodic nitrogen input were collected to investigate the influence of nitrogen input on the abundance and activity of denitrifying methanotrophs. The results indicated that nitrogen input significantly promoted DAMO microorganisms' abundance and contribution to methane emission reduction. In the coastal wetland, the contribution rate of DAMO process to methane removal increased from 12.1% to 33.5% along with continuously elevated nitrogen level in the 3-year tracking study. In the paddy field, the DAMO process accounted for 71.9% of total methane removal when nitrogen fertilizer was applied during the growing season, exceeding the aerobic methane oxidation process. This work would help us better understand the microbial methane cycle and reduce uncertainties in the estimations of the global methane emission.
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Ferousi C, Schmitz RA, Maalcke WJ, Lindhoud S, Versantvoort W, Jetten MSM, Reimann J, Kartal B. Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link. J Biol Chem 2021; 296:100476. [PMID: 33652023 PMCID: PMC8042395 DOI: 10.1016/j.jbc.2021.100476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.
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Garrido-Amador P, Kniaziuk M, Vekeman B, Kartal B. Learning from microorganisms: using new insights in microbial physiology for sustainable nitrogen management. Curr Opin Biotechnol 2021; 67:42-48. [PMID: 33444876 PMCID: PMC8012881 DOI: 10.1016/j.copbio.2020.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/26/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022]
Abstract
To reduce nitrate to N2 distinct nitrogen-oxide-reducing microorganisms function together. Detecting nirS, nirK or narG genes cannot be directly linked to NO and N2O emission. Nitrogen-oxide-reducing specialists can be exploited to reduce NO and N2O emission from wwtp. Aerobic methanotrophs and methane stripping must be considered for the application of N-DAMO. Ammonium recovery could be a more sustainable alternative to nitrogen removal.
Diverse nitrogen-transforming microorganisms with a wide variety of physiological properties are employed for biological nitrogen removal from wastewater. There are many technologies that achieve the required nitrogen discharge standards; however, greenhouse gas emissions and energy consumption constitute the bulk of the environmental footprint of wastewater treatment plants. In this review, we highlight current and proposed approaches aiming to achieve more energy-efficient and environment-friendly biological nitrogen removal, discuss whether new discoveries in microbial physiology of nitrogen-transforming microorganisms could be used to reduce greenhouse gas emissions, and summarize recent advances in ammonium recovery from wastewater.
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Yilmazer M, Bayrak B, Kartal B, Uzuner SK, Palabiyik B. Identification of Schizosaccharomyces pombe ird Mutants Resistant to Glucose Suppression and Oxidative Stress. Folia Biol (Praha) 2021; 67:163-173. [PMID: 35439849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Glucose is both the favourite carbon and energy source and acts as a hormone that plays a regulating role in many biological processes. Calorie restriction extends the lifespan in many organisms, including Schizosaccharomyces pombe, while uptake of high glucose leads to undesired results, such as diabetes and aging. In this study, sequence analysis of Schizosaccharomyces pombe ird5 and ird11 mutants was performed using next-generation sequencing techniques and a total of 20 different mutations were detected. ird11 is resistant to oxidative stress without calorie restriction, whereas ird5 displays an adaptive response against oxidative stress. We selected nine candidate mutations located in the non-coding (6) and coding (3) region among a total of 20 different mutations. The nine candidate mutations, which are thought to be responsible for ird5 and ird11 mutant phenotypes, were investigated via forward and backward mutations by using various cloning techniques. The results of this study provide report-like information that will contribute to understanding the relationship between glucose sensing/ signalling and oxidative stress response components.
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Versantvoort W, Pol A, Jetten MSM, van Niftrik L, Reimann J, Kartal B, Op den Camp HJM. Multiheme hydroxylamine oxidoreductases produce NO during ammonia oxidation in methanotrophs. Proc Natl Acad Sci U S A 2020; 117:24459-24463. [PMID: 32913059 PMCID: PMC7533708 DOI: 10.1073/pnas.2011299117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.
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Ferousi C, Lindhoud S, Baymann F, Hester ER, Reimann J, Kartal B. Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome. J Biol Chem 2019; 294:16953-16965. [PMID: 31582564 DOI: 10.1074/jbc.ra119.010568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys-Lys-Cys-His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.
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Akram M, Reimann J, Dietl A, Menzel A, Versantvoort W, Kartal B, Jetten MSM, Barends TRM. A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase. J Biol Chem 2019; 294:16712-16728. [PMID: 31548310 DOI: 10.1074/jbc.ra119.008788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/17/2019] [Indexed: 01/17/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.
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Russ L, van Alen TA, Jetten MSM, Op den Camp HJM, Kartal B. Interactions of anaerobic ammonium oxidizers and sulfide-oxidizing bacteria in a substrate-limited model system mimicking the marine environment. FEMS Microbiol Ecol 2019; 95:5555569. [DOI: 10.1093/femsec/fiz137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/26/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTIn nature anaerobic ammonium oxidation (anammox) and denitrification processes convert fixed nitrogen to gaseous nitrogen compounds, which are then released to the atmosphere. While anammox bacteria produce N2 from ammonium and nitrite, in the denitrification process nitrate and nitrite are converted to N2 and the greenhouse gas nitrous oxide (N2O). Furthermore, nitrite needed by the anammox bacteria can be supplied by nitrate reduction to nitrite. Consequently, the interplay between nitrogen-transforming microorganisms control the amount of harmless N2 or the greenhouse gas N2O released to the atmosphere. Therefore, it is important to understand the interactions of these microorganisms in the natural environment, where dynamic conditions result in fluctuating substrate concentrations. Here, we studied the interactions between the sulfide-oxidizing denitrifier Sedimenticola selenatireducens and the anammox bacterium Scalindua brodae in a bioreactor mimicking the marine environment by creating sulfide, ammonium and nitrate limitation in distinct operational phases. Through a microbial interaction, Se. selenatireducens reduced nitrate to nitrite, which together with the supplied ammonium was converted to N2 by Sc. Brodae. Using comparative transcriptomics, we determined that Sc. Brodae and Se. selenatireducens had significant responses to ammonium and nitrate limitation, respectively, indicating that the activities of these microorganisms are regulated by different nitrogen compounds.
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Versantvoort W, Guerrero-Castillo S, Wessels HJCT, van Niftrik L, Jetten MSM, Brandt U, Reimann J, Kartal B. Complexome analysis of the nitrite-dependent methanotroph Methylomirabilis lanthanidiphila. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:734-744. [PMID: 31376363 DOI: 10.1016/j.bbabio.2019.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 01/31/2023]
Abstract
The atmospheric concentration of the potent greenhouse gases methane and nitrous oxide (N2O) has increased drastically during the last century. Methylomirabilis bacteria can play an important role in controlling the emission of these two gases from natural ecosystems, by oxidizing methane to CO2 and reducing nitrite to N2 without producing N2O. These bacteria have an anaerobic metabolism, but are proposed to possess an oxygen-dependent pathway for methane activation. Methylomirabilis bacteria reduce nitrite to NO, and are proposed to dismutate NO into O2 and N2 by a putative NO dismutase (NO-D). The O2 produced in the cell can then be used to activate methane by a particulate methane monooxygenase. So far, the metabolic model of Methylomirabilis bacteria was based mainly on (meta)genomics and physiological experiments. Here we applied a complexome profiling approach to determine which of the proposed enzymes are actually expressed in Methylomirabilis lanthanidiphila. To validate the proposed metabolic model, we focused on enzymes involved in respiration, as well as nitrogen and carbon transformation. All complexes suggested to be involved in nitrite-dependent methane oxidation, were identified in M. lanthanidiphila, including the putative NO-D. Furthermore, several complexes involved in nitrate reduction/nitrite oxidation and NO reduction were detected, which likely play a role in detoxification and redox homeostasis. In conclusion, complexome profiling validated the expression and composition of enzymes hypothesized to be involved in the energy, methane and nitrogen metabolism of M. lanthanidiphila, thereby further corroborating their unique metabolism involved in the environmentally relevant process of nitrite-dependent methane oxidation.
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Stultiens K, Cruz SG, van Kessel MAHJ, Jetten MSM, Kartal B, Op den Camp HJM. Interactions between anaerobic ammonium- and methane-oxidizing microorganisms in a laboratory-scale sequencing batch reactor. Appl Microbiol Biotechnol 2019; 103:6783-6795. [PMID: 31227868 PMCID: PMC6667409 DOI: 10.1007/s00253-019-09976-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
Abstract
The reject water of anaerobic digestors still contains high levels of methane and ammonium that need to be treated before these effluents can be discharged to surface waters. Simultaneous anaerobic methane and ammonium oxidation performed by nitrate/nitrite-dependent anaerobic methane-oxidizing(N-damo) microorganisms and anaerobic ammonium-oxidizing(anammox) bacteria is considered a potential solution to this challenge. Here, a stable coculture of N-damo archaea, N-damo bacteria, and anammox bacteria was obtained in a sequencing batch reactor fed with methane, ammonium, and nitrite. Nitrite and ammonium removal rates of up to 455 mg N-NO2- L-1 day-1 and 228 mg N-NH4+ L-1 were reached. All nitrate produced by anammox bacteria (57 mg N-NO3- L-1 day-1) was consumed, leading to a nitrogen removal efficiency of 97.5%. In the nitrite and ammonium limited state, N-damo and anammox bacteria each constituted about 30-40% of the culture and were separated as granules and flocs in later stages of the reactor operation. The N-damo archaea increased up to 20% and mainly resided in the granular biomass with their N-damo bacterial counterparts. About 70% of the nitrite in the reactor was removed via the anammox process, and batch assays confirmed that anammox activity in the reactor was close to its maximal potential activity. In contrast, activity of N-damo bacteria was much higher in batch, indicating that these bacteria were performing suboptimally in the sequencing batch reactor, and would probably be outcompeted by anammox bacteria if ammonium was supplied in excess. Together these results indicate that the combination of N-damo and anammox can be implemented for the removal of methane at the expense of nitrite and nitrate in future wastewater treatment systems.
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Hu Z, Wessels HJCT, van Alen T, Jetten MSM, Kartal B. Publisher Correction: Nitric oxide-dependent anaerobic ammonium oxidation. Nat Commun 2019; 10:1910. [PMID: 31000740 PMCID: PMC6472394 DOI: 10.1038/s41467-019-09797-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
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Akram M, Dietl A, Mersdorf U, Prinz S, Maalcke W, Keltjens J, Ferousi C, de Almeida NM, Reimann J, Kartal B, Jetten MSM, Parey K, Barends TRM. A 192-heme electron transfer network in the hydrazine dehydrogenase complex. SCIENCE ADVANCES 2019; 5:eaav4310. [PMID: 31001586 PMCID: PMC6469936 DOI: 10.1126/sciadv.aav4310] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/28/2019] [Indexed: 05/21/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
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Dietl A, Maalcke WJ, Ferousi C, Jetten MSM, Kartal B, Barends TRM. A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:333-341. [DOI: 10.1107/s2059798318017473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 11/10/2022]
Abstract
The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.
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Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, van Alen T, Jetten MSM, Kartal B, Op den Camp HJM, Reimann J. Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila. Front Microbiol 2018; 9:1672. [PMID: 30140258 PMCID: PMC6094997 DOI: 10.3389/fmicb.2018.01672] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/04/2018] [Indexed: 11/18/2022] Open
Abstract
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ‘Candidatus Methylomirabilis oxyfera,’ a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of ‘Ca. M. oxyfera’ with cerium added as trace element and without nitrate resulted in the shift of the dominant species. Here, we present a high quality draft genome of the new species ‘Candidatus Methylomirabilis lanthanidiphila’ and use comparative genomics to analyze its metabolic potential in both nitrogen and carbon cycling. To distinguish between gene content specific for the ‘Ca. Methylomirabilis’ genus and the NC10 phylum, the genome of a distantly related NC10 phylum member, CSP1-5, an aerobic methylotroph, is included in the analysis. All genes for the conversion of nitrite to N2 identified in ‘Ca. M. oxyfera’ are conserved in ‘Ca. M. lanthanidiphila,’ including the two putative genes for NO dismutase. In addition both species have several heme-copper oxidases potentially involved in NO and O2 respiration. For the oxidation of methane ‘Ca. Methylomirabilis’ species encode a membrane bound methane monooxygenase. CSP1-5 can act as a methylotroph, but lacks the ability to activate methane. In contrast to ‘Ca. M. oxyfera,’ which harbors three methanol dehydrogenases (MDH), both CSP1-5 and ‘Ca. M. lanthanidiphila’ only encode a lanthanide-dependent XoxF-type MDH, once more underlining the importance of rare earth elements for methylotrophic bacteria. The pathways for the subsequent oxidation of formaldehyde to carbon dioxide and for the Calvin–Benson–Bassham cycle are conserved in all species. Furthermore, CSP1-5 can only interconvert nitrate and nitrite, but lacks subsequent nitrite or NO reductases. Thus, it appears that although the conversion of methanol to carbon dioxide is present in several NC10 phylum bacteria, the coupling of nitrite reduction to the oxidation of methane is a trait so far unique to the genus ‘Ca. Methylomirabilis.’
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van Kessel MA, Stultiens K, Slegers MF, Guerrero Cruz S, Jetten MS, Kartal B, Op den Camp HJ. Current perspectives on the application of N-damo and anammox in wastewater treatment. Curr Opin Biotechnol 2018; 50:222-227. [PMID: 29477927 DOI: 10.1016/j.copbio.2018.01.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
The efficient treatment of wastewater for the removal of nitrogen is of key importance to prevent eutrophication and deoxygenation of receiving water bodies. In addition, ineffective wastewater treatment can be a source of greenhouse gasses. The application of newly discovered microbial processes, such as nitrite/nitrate-dependent methane oxidation (N-damo), can make wastewater treatment systems more sustainable; especially when they are combined with anaerobic ammonium oxidation (anammox). A treatment system based on these microbial processes will need oxygen supply for the production of nitrite. This oxygen may inhibit N-damo and anammox and careful regulation of the oxygen supply is of key importance for the success of the application of N-damo in wastewater treatment.
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Ferousi C, Lindhoud S, Baymann F, Kartal B, Jetten MSM, Reimann J. Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria. Curr Opin Chem Biol 2017; 37:129-136. [DOI: 10.1016/j.cbpa.2017.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023]
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Kartal B, Keltjens JT. Anammox Biochemistry: a Tale of Heme c Proteins. Trends Biochem Sci 2016; 41:998-1011. [DOI: 10.1016/j.tibs.2016.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
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