251
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Maalcke WJ, Reimann J, de Vries S, Butt JN, Dietl A, Kip N, Mersdorf U, Barends TRM, Jetten MSM, Keltjens JT, Kartal B. Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle. J Biol Chem 2016; 291:17077-92. [PMID: 27317665 PMCID: PMC5016112 DOI: 10.1074/jbc.m116.735530] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/07/2016] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
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Affiliation(s)
- Wouter J Maalcke
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Simon de Vries
- the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Julea N Butt
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom, and
| | - Andreas Dietl
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Nardy Kip
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Ulrike Mersdorf
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Mike S M Jetten
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands, the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Jan T Keltjens
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands,
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252
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Wang X, Xu X, Liu S, Zhang Y, Zhao C, Yang F. Combination of complex adsorption and anammox for nitric oxide removal. JOURNAL OF HAZARDOUS MATERIALS 2016; 312:175-183. [PMID: 27037471 DOI: 10.1016/j.jhazmat.2016.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/27/2016] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
High-efficiency Fe(II)EDTA (approximately 80%) was selected to remove nitric oxide (NO) in a complex adsorption process; subsequently, this Fe(II)EDTA was combined with the anammox process to eliminate the NO in flue gas. The Fe(II)EDTA-NO solution negatively affected the conventional nitrite-dependent anammox bacteria when the solution concentration exceeded 0.5mM. Fe(II)EDTA-NO-cultivated anammox bacteria removed the ammonium coupled to complex NO reduction (≤3.5mM). The batch test results demonstrated that NH4(+) was eliminated through Fe(II)EDTA-NO reduction via anammox. The removal of complex NO and NH4(+) exhibited high relativity relevance, and the Fe(II)EDTA-NO/NH4(+) molar ratio was approximately 0.97. The complex NO-dependent process generates lesser nitrate than that generated by conventional anammox. Moreover, Candidatus Kuenenia stuttgartiensitiensis became the dominant anammox bacterial community when the biomass is cultivated using the inoculated bacteria, and the proportion of the former increased to 90% from the initial 38% for ribosomal intergenic spacer analysis and library construction.
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Affiliation(s)
- Xiaojing Wang
- MOE, Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Xiaochen Xu
- MOE, Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China.
| | - Sitong Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, No. 5, Yiheyuan Road, Beijing, China
| | - Yun Zhang
- MOE, Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Chuanqi Zhao
- MOE, Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Fenglin Yang
- MOE, Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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253
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Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. Sci Rep 2016; 6:28327. [PMID: 27319320 PMCID: PMC4913261 DOI: 10.1038/srep28327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 06/02/2016] [Indexed: 11/09/2022] Open
Abstract
Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all the essential transcripts for anammox metabolism. During the later stage of reactor operation, higher expression of ammonia and nitrite transport proteins and key metabolic enzymes mainly in the bottom large granules facilitated anammox bacteria activity. The high activity resulted in higher growth and multiplication of anammox bacteria and expanded the size of the granules. This conceptual model for large granule formation proposed here may assist in the future design of anammox processes for mainstream wastewater treatment.
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254
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Oshiki M, Ali M, Shinyako-Hata K, Satoh H, Okabe S. Hydroxylamine-dependent anaerobic ammonium oxidation (anammox) by “Candidatus
Brocadia sinica”. Environ Microbiol 2016; 18:3133-43. [DOI: 10.1111/1462-2920.13355] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering; National Institute of Technology, Nagaoka College; Nagaoka Niigata 940-8532 Japan
| | - Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal; 23955-6900 Saudi Arabia
| | - Kaori Shinyako-Hata
- Tokyo Engineering Consultants Co., Ltd., Kasumigaseki, Chioyadaku, Tokyo 100-0013, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
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255
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Wang Y, Hu X, Jiang B, Song Z, Ma Y. Symbiotic relationship analysis of predominant bacteria in a lab-scale anammox UASB bioreactor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7615-7626. [PMID: 26739990 DOI: 10.1007/s11356-015-6016-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
In order to provide the comprehensive insight into the key microbial groups in anaerobic ammonium oxidation (anammox) process, high-throughput sequencing analysis has been used for the investigation of the bacterial communities of a lab-scale upflow anaerobic sludge bed (UASB) anammox bioreactor. Results revealed that 109 operational taxonomic units (OTUs; out of 14,820 reads) were identified and a domination of anammox bacteria of Candidatus Kuenenia stuttgartiensis (OTU474, 35.42 %), along with heterotrophs of Limnobacter sp. MED105 (OTU951, 14.98 %), Anerolinea thermophila UNI-1 (OTU465 and OTU833, 6.60 and 3.93 %), Azoarcus sp. B72 (OTU26, 9.47 %), and Ignavibacterium sp. JCM 16511 (OTU459, 8.33 %) were detected. Metabolic pathway analysis showed that Candidatus K. stuttgartiensis encountered gene defect in synthesizing a series of metabolic cofactors for growth, implying that K. stuttgartiensis is auxotrophic. Coincidentally, the other dominant species severally showed complete metabolic pathways with full set gene encoding to corresponding cofactors presented in the surrounding environment. Furthermore, it was likely that the survival of heterotrophs in the autotrophic system indicates the existence of a symbiotic and mutual relationship in anammox system.
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Affiliation(s)
- Yujia Wang
- College of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, People's Republic of China
| | - Xiaomin Hu
- College of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, People's Republic of China.
| | - Binhui Jiang
- College of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, People's Republic of China
| | - Zhenhui Song
- College of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, People's Republic of China
| | - Yongguang Ma
- Process Equipment and Environmental Engineering Institute, Northeastern University, Shenyang, 110819, People's Republic of China
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256
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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257
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Javidpour P, Deutsch S, Mutalik VK, Hillson NJ, Petzold CJ, Keasling JD, Beller HR. Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli. PLoS One 2016; 11:e0151087. [PMID: 26975050 PMCID: PMC4790861 DOI: 10.1371/journal.pone.0151087] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/23/2016] [Indexed: 12/23/2022] Open
Abstract
Ladderanes are hydrocarbon chains with three or five linearly concatenated cyclobutane rings that are uniquely produced as membrane lipid components by anammox (anaerobic ammonia-oxidizing) bacteria. By virtue of their angle and torsional strain, ladderanes are unusually energetic compounds, and if produced biochemically by engineered microbes, could serve as renewable, high-energy-density jet fuel components. The biochemistry and genetics underlying the ladderane biosynthetic pathway are unknown, however, previous studies have identified a pool of 34 candidate genes from the anammox bacterium, Kuenenia stuttgartiensis, some or all of which may be involved with ladderane fatty acid biosynthesis. The goal of the present study was to establish a systematic means of testing the candidate genes from K. stuttgartiensis for involvement in ladderane biosynthesis through heterologous expression in E. coli under anaerobic conditions. This study describes an efficient means of assembly of synthesized, codon-optimized candidate ladderane biosynthesis genes in synthetic operons that allows for changes to regulatory element sequences, as well as modular assembly of multiple operons for simultaneous heterologous expression in E. coli (or potentially other microbial hosts). We also describe in vivo functional tests of putative anammox homologs of the phytoene desaturase CrtI, which plays an important role in the hypothesized ladderane pathway, and a method for soluble purification of one of these enzymes. This study is, to our knowledge, the first experimental effort focusing on the role of specific anammox genes in the production of ladderanes, and lays the foundation for future efforts toward determination of the ladderane biosynthetic pathway. Our substantial, but far from comprehensive, efforts at elucidating the ladderane biosynthetic pathway were not successful. We invite the scientific community to take advantage of the considerable synthetic biology resources and experimental results developed in this study to elucidate the biosynthetic pathway that produces unique and intriguing ladderane lipids.
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Affiliation(s)
- Pouya Javidpour
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States of America
| | - Samuel Deutsch
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, United States of America
| | - Vivek K. Mutalik
- Environmental Genomics and Systems Biology, LBNL, Berkeley, CA, United States of America
| | - Nathan J. Hillson
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States of America
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, United States of America
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States of America
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, United States of America
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Harry R. Beller
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA, United States of America
- Earth and Environmental Sciences, LBNL, Berkeley, CA, United States of America
- * E-mail:
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258
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Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. ISME JOURNAL 2016; 10:2106-17. [PMID: 26943628 PMCID: PMC4989316 DOI: 10.1038/ismej.2016.25] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/06/2016] [Accepted: 01/10/2016] [Indexed: 11/29/2022]
Abstract
Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.
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259
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Li G, Vilcherrez D, Carvajal-Arroyo JM, Sierra-Alvarez R, Field JA. Exogenous nitrate attenuates nitrite toxicity to anaerobic ammonium oxidizing (anammox) bacteria. CHEMOSPHERE 2016; 144:2360-2367. [PMID: 26610295 DOI: 10.1016/j.chemosphere.2015.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
Anaerobic ammonium oxidizing bacteria (anammox) can be severely inhibited by one of its main substrates, nitrite (NO2(-)). At present, there is limited information on the processes by which anammox bacteria are able to tolerate toxic NO2(-). Intracellular consumption or electrochemically driven (transmembrane proton motive force) NO2(-) export are considered the main mechanisms of NO2(-) detoxification. In this work, we evaluated the potential of exogenous nitrate (NO3(-)) on relieving NO2(-) toxicity, putatively facilitated by NarK, a NO3(-)/NO2(-) transporter encoded in the anammox genome. The relative contribution of NO3(-) to NO2(-) detoxification was found to be pH dependent. Exposure of anammox cells to NO2(-) in absence of their electron donating substrate, ammonium (NH4(+)), causes NO2(-) stress. At pH 6.7 and 7.0, the activity of NO2(-) stressed cells was respectively 0 and 27% of the non-stressed control activity (NO2(-) and NH4(+) fed simultaneously). Exogenous NO3(-) addition caused the recovery to 42% and 80% of the control activity at pH 6.7 and 7.0, respectively. The recovery of the activity of NO2(-) stressed cells improved with increasing NO3(-) concentration, the maximum recovery being achieved at 0.85 mM. The NO3(-) pre-incubation time is less significant at pH 7.0 than at pH 6.7 due to a more severe NO2(-) toxicity at lower pH. Additionally, NO3(-) caused almost complete attenuation of NO2(-) toxicity in cells exposed to the proton gradient disruptor carbonyl cyanide m-chlorophenyl hydrazone at pH 7.5, providing evidence that the NO3(-) attenuation is independent of the proton motive force. The absence of a measurable NO3(-) consumption (or NO3(-) dependent N2 production) during the batch tests leaves NO3(-) dependent active transport of NO2(-) as the only plausible explanation for the relief of NO2(-) inhibition. We suggest that anammox cells can use a secondary transport system facilitated by exogenous NO3(-) to alleviate NO2(-) toxicity.
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Affiliation(s)
- Guangbin Li
- Department of Chemical and Environmental Engineering, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ 85721-001, USA.
| | - David Vilcherrez
- Department of Chemical and Environmental Engineering, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ 85721-001, USA
| | - Jose Maria Carvajal-Arroyo
- Department of Chemical and Environmental Engineering, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ 85721-001, USA
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ 85721-001, USA
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ 85721-001, USA
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260
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Guo J, Peng Y, Fan L, Zhang L, Ni BJ, Kartal B, Feng X, Jetten MSM, Yuan Z. Metagenomic analysis of anammox communities in three different microbial aggregates. Environ Microbiol 2016; 18:2979-93. [DOI: 10.1111/1462-2920.13132] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 11/07/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Lu Fan
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Liang Zhang
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Boran Kartal
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Department of Biochemistry and Microbiology; Laboratory of Microbiology; Gent University; Gent 9000 Belgium
| | - Xin Feng
- Research Department of Microbiology; Beijing Genomics Institute (BGI)-Shenzhen; Shenzhen China
| | - Mike S. M. Jetten
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Zhiguo Yuan
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
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261
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Oshiki M, Satoh H, Okabe S. Ecology and physiology of anaerobic ammonium oxidizing bacteria. Environ Microbiol 2016; 18:2784-96. [DOI: 10.1111/1462-2920.13134] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/08/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering National Institute of Technology Nagaoka College 888 Nishikatakaimachi Nagaoka Niigata 940‐0834 Japan
| | - Hisashi Satoh
- Division of Environmental Engineering Faculty of Engineering Hokkaido University North 13, West‐8 Sapporo Hokkaido 060‐8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering Faculty of Engineering Hokkaido University North 13, West‐8 Sapporo Hokkaido 060‐8628 Japan
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262
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Yao Z, Lu P, Zhang D, Wan X, Li Y, Peng S. Stoichiometry and kinetics of the anaerobic ammonium oxidation (Anammox) with trace hydrazine addition. BIORESOURCE TECHNOLOGY 2015; 198:70-76. [PMID: 26364230 DOI: 10.1016/j.biortech.2015.08.098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/17/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
Purpose of this study is to investigate the stoichiometry and kinetics of anaerobic ammonium oxidation (Anammox) with trace hydrazine addition. The stoichiometry was established based on the electron balance of Anammox process with trace N2H4 addition. The stoichiometric coefficients were determined by the proton consumption and the changes in substrates and products. It was found that trace N2H4 addition can increase the yield of Anammox bacteria (AnAOB) and reduce NO3(-) yield, which enhances the Anammox. Subsequently, kinetic model of Anammox with trace N2H4 addition was developed, and the parameters of the anaerobic degradation model of N2H4 were obtained for the first time. The maximum specific substrate utilization rate, half-saturation constant and inhibition constant of N2H4 were 25.09mgN/g VSS/d, 10.42mgN/L and 1393.88mgN/L, respectively. These kinetic parameters might provide important information for the engineering applications of Anammox with trace N2H4 addition.
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Affiliation(s)
- Zongbao Yao
- Department of Environmental Science, Chongqing University, Chongqing 400044, PR China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; Department of Environmental Science, Chongqing University, Chongqing 400044, PR China.
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; Department of Environmental Science, Chongqing University, Chongqing 400044, PR China
| | - Xinyu Wan
- Department of Environmental Science, Chongqing University, Chongqing 400044, PR China
| | - Yulian Li
- Department of Environmental Science, Chongqing University, Chongqing 400044, PR China
| | - Shuchan Peng
- Department of Environmental Science, Chongqing University, Chongqing 400044, PR China
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263
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Ali M, Okabe S. Anammox-based technologies for nitrogen removal: Advances in process start-up and remaining issues. CHEMOSPHERE 2015. [PMID: 26196404 DOI: 10.1016/j.chemosphere.2015.06.094] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nitrogen removal from wastewater via anaerobic ammonium oxidation (anammox)-based process has been recognized as efficient, cost-effective and low energy alternative to the conventional nitrification and denitrification processes. To date, more than one hundred full-scale anammox plants have been installed and operated for treatment of NH4(+)-rich wastewater streams around the world, and the number is increasing rapidly. Since the discovery of anammox process, extensive researches have been done to develop various anammox-based technologies. However, there are still some challenges in practical application of anammox-based treatment process at full-scale, e.g., longer start-up period, limited application to mainstream municipal wastewater and poor effluent water quality. This paper aimed to summarize recent status of application of anammox process and researches on technological development for solving these remaining problems. In addition, an integrated system of anammox-based process and microbial fuel cell is proposed for sustainable and energy-positive wastewater treatment.
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Affiliation(s)
- Muhammad Ali
- 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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264
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Zhang L, Zhang S, Peng Y, Han X, Gan Y. Nitrogen removal performance and microbial distribution in pilot- and full-scale integrated fixed-biofilm activated sludge reactors based on nitritation-anammox process. BIORESOURCE TECHNOLOGY 2015; 196:448-453. [PMID: 26278191 DOI: 10.1016/j.biortech.2015.07.090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
Nitritation-anammox process was successfully established in pilot- and full-scale integrated fixed-film activated sludge (IFAS) reactors. An average nitrogen removal efficiency of 80% was achieved under ammonium loading rate of 0.7-1.3kgN/(m(3)d) in the pilot-scale reactor (12m(3)). Moreover, molecular analysis showed that ammonium oxidizing bacteria (AOB) were more abundant in the activated sludge while anammox bacteria were primarily located in the biofilm. The segregation of AOB and anammox bacteria enhanced the nitrogen removal rate and operational stability. Furthermore, a full-scale IFAS reactor of 500m(3) was set-up to treat sludge dewatering liquors. An average nitrogen removal efficiency of 85% and a nitrogen removal rate of 0.48kgN/(m(3)d) were achieved after inoculation. It was noted that high influent suspended solids would seriously affect the performance of the IFAS system. Therefore, a pre-treatment was proposed to reduce suspended solid in the full-scale application.
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Affiliation(s)
- Liang Zhang
- Key Laboratory of Beijing Water Quality Science and Water Environment Recovery Engineering, Beijing, China; Beijing Drainage Group Co. Ltd (BDG), Beijing, China
| | - Shujun Zhang
- Beijing Drainage Group Co. Ltd (BDG), Beijing, China
| | - Yongzhen Peng
- Key Laboratory of Beijing Water Quality Science and Water Environment Recovery Engineering, Beijing, China.
| | - Xiaoyu Han
- Beijing Drainage Group Co. Ltd (BDG), Beijing, China
| | - Yiping Gan
- Beijing Drainage Group Co. Ltd (BDG), Beijing, China
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265
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The inner workings of the hydrazine synthase multiprotein complex. Nature 2015; 527:394-7. [PMID: 26479033 DOI: 10.1038/nature15517] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/21/2015] [Indexed: 11/08/2022]
Abstract
Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature.
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266
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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267
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A new mathematical model for nitrogen gas production with special emphasis on the role of attached growth media in anammox hybrid reactor. Appl Microbiol Biotechnol 2015; 99:9245-54. [DOI: 10.1007/s00253-015-6793-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
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268
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Shu D, He Y, Yue H, Wang Q. Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing. BIORESOURCE TECHNOLOGY 2015; 186:163-172. [PMID: 25817026 DOI: 10.1016/j.biortech.2015.03.072] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 05/19/2023]
Abstract
The microbial communities and abundance in anaerobic sludge from 4 industrial and 2 municipal wastewater treatment plants were investigated using 454 pyrosequencing technology in this study. A total of 5482-8692 high-quality reads of 16S rRNA V3-V5 regions were obtained. Taxonomic analysis using QIIME and RDP classifier found that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were the most abundant phyla in these samples. Furthermore, real-time PCR was used to validate the absolute abundance of these 16S rRNAs and some functional genes, including total bacteria, anammox bacteria, NOB (Nitrobacter, Nitrospira), AOA amoA, AOB amoA, nosZ, nirS, nirK, narG, napA, nrfA, mcrA and dsrA. Multivariate linear regression analysis indicated that AOA might be mixotrophic. Finally, redundancy analysis was used to reveal the relationships between operation parameters and microbial communities. Results showed that the coexistence of anammox, denitrification and DNRA could be useful for the simultaneous removal of nitrogen and organic matter.
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Affiliation(s)
- Duntao Shu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, 710049 Shaanxi, China
| | - Yanling He
- School of Human Settlements & Civil Engineering, Xi'an Jiaotong University, 710049 Shaanxi, China.
| | - Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Qingyi Wang
- School of Chemical Engineering & Technology, Xi'an Jiaotong University, 710049 Shaanxi, China
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269
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Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis. J Bacteriol 2015; 197:2432-41. [PMID: 25962914 DOI: 10.1128/jb.00186-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/01/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound "prokaryotic organelle" called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacterium Kuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway. IMPORTANCE Anammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures.
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270
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Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol Rev 2015; 39:729-49. [DOI: 10.1093/femsre/fuv021] [Citation(s) in RCA: 392] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2015] [Indexed: 01/25/2023] Open
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271
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Zekker I, Rikmann E, Tenno T, Loorits L, Kroon K, Fritze H, Tuomivirta T, Vabamäe P, Raudkivi M, Mandel A, Dc Rubin SSC, Tenno T. Nitric oxide for anammox recovery in a nitrite-inhibited deammonification system. ENVIRONMENTAL TECHNOLOGY 2015; 36:2477-2487. [PMID: 25827614 DOI: 10.1080/09593330.2015.1034791] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The anaerobic ammonium oxidation (anammox) process is widely used for N-rich wastewater treatment. In the current research the deammonification reactor in a reverse order (first anammox, then the nitrifying biofilm cultivation) was started up with a high maximum N removal rate (1.4 g N m(-2) d(-1)) in a moving bed biofilm reactor. Cultivated biofilm total nitrogen removal rates were accelerated the most by anammox intermediate - nitric oxide (optimum 58 mg NO-N L(-1)) addition. Furthermore, NO was added in order to eliminate inhibition caused by nitrite concentrations (>50 mg [Formula: see text]) increasing [Formula: see text] (2/1, respectively) along with a higher ratio of [Formula: see text] (0.6/1, respectively) than stoichiometrical for this optimal NO amount added during batch tests. Planctomycetales clone P4 sequences, which was the closest (98% and 99% similarity, respectively) relative to Candidatus Brocadia fulgida sequences quantities increase to 1 × 10(6) anammox gene copies g(-1) total suspended solids to till day 650 were determined by quantitative polymerase chain reaction.
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Affiliation(s)
- Ivar Zekker
- a Institute of Chemistry, University of Tartu , 14a Ravila St., 50411 Tartu , Estonia
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272
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Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, "Candidatus Brocadia sinica". GENOME ANNOUNCEMENTS 2015; 3:3/2/e00267-15. [PMID: 25883286 PMCID: PMC4400429 DOI: 10.1128/genomea.00267-15] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A draft genome sequence of an anaerobic ammonium-oxidizing (anammox) bacterium, “Candidatus Brocadia sinica,” was determined by pyrosequencing and by screening a fosmid library. A 4.07-Mb genome sequence comprising 3 contigs was assembled, in which 3,912 gene-coding regions, 47 tRNAs, and a single rrn operon were annotated.
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273
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Hanson BT, Madsen EL. In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:252-264. [PMID: 25403415 DOI: 10.1111/1758-2229.12239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 06/04/2023]
Abstract
Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano-liquid chromatography (LC)-mass spectrometry (MS)/MS of the three protein pools generated a total of 95,725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1,270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel-slice library respectively). Remarkably, eight of the nine proteins in the nitrite-dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite-dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria.
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Affiliation(s)
- Buck T Hanson
- Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY, 14853, USA
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274
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Isanta E, Bezerra T, Fernández I, Suárez-Ojeda ME, Pérez J, Carrera J. Microbial community shifts on an anammox reactor after a temperature shock using 454-pyrosequencing analysis. BIORESOURCE TECHNOLOGY 2015; 181:207-213. [PMID: 25656864 DOI: 10.1016/j.biortech.2015.01.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
To explore the changes in the microbial community structure during the recovery process of an anammox reactor after a temperature shock, the 454-pyrosequencing technique was used. The temperature shock reduced the nitrogen removal rate up to 92% compared to that just before the temperature shock, and it took 70 days to recover a similar nitrogen removal rate to that before the temperature shock (ca. 0.30 g N L(-1) d(-1)). Pyrosequencing results indicated that microbial diversity in the reactor decreased as the reactor progressively recovered from the temperature shock. Anammox bacteria were accounted as 6%, 35% and 46% of total sequence reads in samples taken 13, 45 and 166 days after the temperature shock. These results were in agreement with N-removal performance results and anammox activity measured in the reactor during the recovery process. An anammox specific primer was used to precisely determine the anammox species in the biomass samples.
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Affiliation(s)
- Eduardo Isanta
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain
| | - Tercia Bezerra
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain
| | - Isaac Fernández
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain
| | - María Eugenia Suárez-Ojeda
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain
| | - Julio Pérez
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain
| | - Julián Carrera
- GENOCOV Research Group, Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Spain.
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275
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Welte CU, Jetten MSM. Fortunate those that are starting now. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:23-25. [PMID: 25721596 DOI: 10.1111/1758-2229.12229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Cornelia U Welte
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
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276
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Sato Y, Hori T, Ronald NR, Habe H, Ogata A. Effect of a microbiota activator on accumulated ammonium and microbial community structure in a pilot-scale membrane bioreactor. J GEN APPL MICROBIOL 2015; 61:132-8. [DOI: 10.2323/jgam.61.132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Navarro R. Ronald
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiroshi Habe
- Research Institute for Sustainable Chemistry, AIST
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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277
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Reimann J, Jetten MSM, Keltjens JT. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane. Met Ions Life Sci 2015; 15:257-313. [PMID: 25707470 DOI: 10.1007/978-3-319-12415-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.
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Affiliation(s)
- Joachim Reimann
- Department of Microbiology, Institute of Wetland and Water Research (IWWR), Radboud University of Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands,
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278
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Ali M, Oshiki M, Awata T, Isobe K, Kimura Z, Yoshikawa H, Hira D, Kindaichi T, Satoh H, Fujii T, Okabe S. Physiological characterization of anaerobic ammonium oxidizing bacterium 'Candidatus Jettenia caeni'. Environ Microbiol 2014; 17:2172-89. [PMID: 25367004 DOI: 10.1111/1462-2920.12674] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 09/25/2014] [Accepted: 10/16/2014] [Indexed: 11/26/2022]
Abstract
To date, six candidate genera of anaerobic ammonium-oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus 'Candidatus Jettenia'. Planctomycete KSU-1 was found to be a mesophilic (20-42.5°C) and neutrophilic (pH 6.5-8.5) bacterium with a maximum growth rate of 0.0020 h(-1) . Planctomycete KSU-1 cells showed typical physiological and structural features of anammox bacteria; i.e. (29) N2 gas production by coupling of (15) NH4 (+) and (14) NO2 (-) , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone-7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl-CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU-1 cells. On the basis of these experimental results, we proposed the name 'Ca. Jettenia caeni' sp. nov. for the bacterial clade of the planctomycete KSU-1.
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Affiliation(s)
- Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Mamoru Oshiki
- Department of Civil Engineering, Nagaoka National College of Technology, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takanori Awata
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Kazuo Isobe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zenichiro Kimura
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32, Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Hiroaki Yoshikawa
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Daisuke Hira
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto, 860-0082, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Takao Fujii
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto, 860-0082, 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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279
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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280
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Levipan HA, Molina V, Fernandez C. Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ∼36°S). ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:565-573. [PMID: 25756109 DOI: 10.1111/1758-2229.12158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seasonal upwelling and oxygen-deficient area off Central Chile. Analysis of 16S rRNA by tag pyrosequencing was combined with specific quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR in summer and wintertime. Nitrospina-like bacteria were the only known NOB detected by means of pyrosequencing between 30 and 80 m depth, accounting for up to 5% of total bacteria. This guild was represented by 11 and 7 operational taxonomic units (97% cut-off) in winter and summertime respectively. Nitrospina-like bacteria were phylogenetically related to sequences retrieved from coastal upwelling, oxygen minimum zones and deep-sea environments. This group was also detected by qPCR with abundances that increased with depth throughout the water column. Importantly, Nitrospina from surface layers showed low abundances but high 16S rRNA : rDNA ratios and mainly in summertime. Overall, our results highlight the seasonal variability between the structure and physiological state of this community and suggest a significant role of Nitrospina in the nitrogen cycle of seasonal upwelling areas.
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281
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Irisa T, Hira D, Furukawa K, Fujii T. Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium. J Biosci Bioeng 2014; 118:616-21. [DOI: 10.1016/j.jbiosc.2014.05.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/25/2014] [Accepted: 05/27/2014] [Indexed: 11/29/2022]
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282
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Abstract
Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.
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283
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284
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Research of Iron Reduction and the Iron Reductase Localization of Anammox Bacteria. Curr Microbiol 2014; 69:880-7. [DOI: 10.1007/s00284-014-0668-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/15/2014] [Indexed: 10/24/2022]
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285
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Ali M, Oshiki M, Okabe S. Simple, rapid and effective preservation and reactivation of anaerobic ammonium oxidizing bacterium "Candidatus Brocadia sinica". WATER RESEARCH 2014; 57:215-22. [PMID: 24726991 DOI: 10.1016/j.watres.2014.03.036] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/03/2014] [Accepted: 03/17/2014] [Indexed: 05/21/2023]
Abstract
It is still the biggest challenge to secure enough seeding biomass for rapid start-up of full-scale (anaerobic ammonium oxidation) anammox processes due to slow growth. Preservation of active anammox biomass could be one of the solutions. In this study, biomass of anammox bacterium, "Candidatus Brocadia sinica", immersed in various nutrient media were preserved at -80 °C, 4 °C and room temperature. After 45, 90 and 150 days of preservation, specific anammox activity (SAA) of the preserved anammox biomass was determined by measuring (29)N2 production rate and transcription levels of hzsA gene encoding hydrazine synthase alpha subunit. Storage in nutrient medium containing 3 mM of molybdate at room temperature with periodical (every 45 days) supply of NH4(+) and NO2(-) was proved to be the most effective storage technique for "Ca. Brocadia sinica" biomass. Using this preservation condition, 96, 92 and 65% of the initial SAA was sustained after 45, 90 and 150 days of storage, respectively. Transcription levels of hzsA gene in biomass correlated with the SAA (R(2) = 0.83), indicating it can be used as a genetic marker to evaluate the anammox activity of preserved biomass. Furthermore, the 90-day-stored biomass was successfully reactivated by immobilizing in polyvinyl alcohol (6%, w/v) and sodium alginate (2%, w/v) gel and then inoculated to up-flow column reactors. Total nitrogen removal rates rapidly increased to 7 kg-N m(-3) d(-1) within 35 days of operation. Based on these results, the room temperature preservation with molybdate addition is simple, cost-effective and feasible at a practical scale, which will accelerate the practical use of anammox process for wastewater treatment.
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Affiliation(s)
- Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Mamoru Oshiki
- 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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286
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Degli Esposti M, Chouaia B, Comandatore F, Crotti E, Sassera D, Lievens PMJ, Daffonchio D, Bandi C. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 2014; 9:e96566. [PMID: 24804722 PMCID: PMC4013037 DOI: 10.1371/journal.pone.0096566] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.
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Affiliation(s)
| | - Bessem Chouaia
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Francesco Comandatore
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | - Elena Crotti
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Davide Sassera
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Claudio Bandi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
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287
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Karlsson R, Karlsson A, Bäckman O, Johansson BR, Hulth S. Subcellular localization of an ATPase in anammox bacteria using proteomics and immunogold electron microscopy. FEMS Microbiol Lett 2014; 354:10-8. [PMID: 24635406 DOI: 10.1111/1574-6968.12425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/14/2014] [Accepted: 03/11/2014] [Indexed: 11/27/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) has received significant attention during optimization of waste-water treatment and constitutes an important pathway for the removal of bioavailable nitrogen from natural environments. Studies of key catabolic enzymes indicate that the anammox reaction takes place inside the anammoxosome, an organelle-like membranous compartment of anammox bacteria. The anammoxosome has also been suggested as a site for ATP synthesis. A lipid-based protein immobilization technique, previously used to identify proteins essential for the anammox reaction, was in this study used to select linear epitopes for antibodies specifically targeted against an identified ATPase. The approach of using proteomics and bioinformatics as tools for selecting antibody targets for immunolocalization provides an important alternative to traditional methods for selection of specific antibodies. Immunogold electron microscopy and statistical evaluations indicated that the antibodies against the ATPase were exclusively found associated with the anammoxosome membrane. This provides strong evidence for ATP synthesis by an intracellular proton motive force in anammox bacteria. Within prokaryotes, an ATP synthase associated with an intracellular compartment is a feature unique for anammox bacteria.
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288
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Villanueva L, Speth DR, van Alen T, Hoischen A, Jetten MSM. Shotgun metagenomic data reveals significant abundance but low diversity of "Candidatus Scalindua" marine anammox bacteria in the Arabian Sea oxygen minimum zone. Front Microbiol 2014; 5:31. [PMID: 24550902 PMCID: PMC3913995 DOI: 10.3389/fmicb.2014.00031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/17/2014] [Indexed: 12/02/2022] Open
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to “Candidatus Scalindua” species. Recently the genome assembly of a marine anammox enrichment culture dominated by “Candidatus Scalindua profunda” became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones (OMZs). Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the OMZ in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of “Candidatus Scalindua profunda” served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the “Candidatus Scalindua” populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA, and ACS) had a lower coverage but could still be assembled and analyzed. The results show that “Candidatus Scalindua” is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.
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Affiliation(s)
- Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands
| | - Theo van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands ; Department of Biotechnology, Delft University of Technology Delft, Netherlands
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289
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Abstract
The global biogeochemical nitrogen cycle is essential for life on Earth. Many of the underlying biotic reactions are catalyzed by a multitude of prokaryotic and eukaryotic life forms whereas others are exclusively carried out by microorganisms. The last century has seen the rise of a dramatic imbalance in the global nitrogen cycle due to human behavior that was mainly caused by the invention of the Haber-Bosch process. Its main product, ammonia, is a chemically reactive and biotically favorable form of bound nitrogen. The anthropogenic supply of reduced nitrogen to the biosphere in the form of ammonia, for example during environmental fertilization, livestock farming, and industrial processes, is mandatory in feeding an increasing world population. In this chapter, environmental ammonia pollution is linked to the activity of microbial metalloenzymes involved in respiratory energy metabolism and bioenergetics. Ammonia-producing multiheme cytochromes c are discussed as paradigm enzymes.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287, Darmstadt, Germany,
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290
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van Teeseling MCF, de Almeida NM, Klingl A, Speth DR, Op den Camp HJM, Rachel R, Jetten MSM, van Niftrik L. A new addition to the cell plan of anammox bacteria: "Candidatus Kuenenia stuttgartiensis" has a protein surface layer as the outermost layer of the cell. J Bacteriol 2014; 196:80-9. [PMID: 24142254 PMCID: PMC3911120 DOI: 10.1128/jb.00988-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/11/2013] [Indexed: 01/24/2023] Open
Abstract
Anammox bacteria perform anaerobic ammonium oxidation (anammox) and have a unique compartmentalized cell consisting of three membrane-bound compartments (from inside outwards): the anammoxosome, riboplasm, and paryphoplasm. The cell envelope of anammox bacteria has been proposed to deviate from typical bacterial cell envelopes by lacking both peptidoglycan and a typical outer membrane. However, the composition of the anammox cell envelope is presently unknown. Here, we investigated the outermost layer of the anammox cell and identified a proteinaceous surface layer (S-layer) (a crystalline array of protein subunits) as the outermost component of the cell envelope of the anammox bacterium "Candidatus Kuenenia stuttgartiensis." This is the first description of an S-layer in the phylum of the Planctomycetes and a new addition to the cell plan of anammox bacteria. This S-layer showed hexagonal symmetry with a unit cell consisting of six protein subunits. The enrichment of the S-layer from the cell led to a 160-kDa candidate protein, Kustd1514, which has no homology to any known protein. This protein is present in a glycosylated form. Antibodies were generated against the glycoprotein and used for immunogold localization. The antiserum localized Kustd1514 to the S-layer and thus verified that this protein forms the "Ca. Kuenenia stuttgartiensis" S-layer.
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Affiliation(s)
- Muriel C. F. van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Naomi M. de Almeida
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Andreas Klingl
- Centre for Electron Microscopy, Institute for Anatomy, University of Regensburg, Regensburg, Germany
| | - Daan R. Speth
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Reinhard Rachel
- Centre for Electron Microscopy, Institute for Anatomy, University of Regensburg, Regensburg, Germany
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
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291
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Brunner B, Contreras S, Lehmann MF, Matantseva O, Rollog M, Kalvelage T, Klockgether G, Lavik G, Jetten MSM, Kartal B, Kuypers MMM. Nitrogen isotope effects induced by anammox bacteria. Proc Natl Acad Sci U S A 2013; 110:18994-9. [PMID: 24191043 PMCID: PMC3839690 DOI: 10.1073/pnas.1310488110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogen (N) isotope ratios ((15)N/(14)N) provide integrative constraints on the N inventory of the modern ocean. Anaerobic ammonium oxidation (anammox), which converts ammonium and nitrite to dinitrogen gas (N2) and nitrate, is an important fixed N sink in marine ecosystems. We studied the so far unknown N isotope effects of anammox in batch culture experiments. Anammox preferentially removes (14)N from the ammonium pool with an isotope effect of +23.5‰ to +29.1‰, depending on factors controlling reversibility. The N isotope effects during the conversion of nitrite to N2 and nitrate are (i) inverse kinetic N isotope fractionation associated with the oxidation of nitrite to nitrate (-31.1 ± 3.9‰), (ii) normal kinetic N isotope fractionation during the reduction of nitrite to N2 (+16.0 ± 4.5‰), and (iii) an equilibrium N isotope effect between nitrate and nitrite (-60.5 ± 1.0‰), induced when anammox is exposed to environmental stress, leading to the superposition of N isotope exchange effects upon kinetic N isotope fractionation. Our findings indicate that anammox may be responsible for the unresolved large N isotope offsets between nitrate and nitrite in oceanic oxygen minimum zones. Irrespective of the extent of N isotope exchange between nitrate and nitrite, N removed from the combined nitrite and nitrate (NOx) pool is depleted in (15)N relative to NOx. This net N isotope effect by anammox is superimposed on the N isotope fractionation by the co-occurring reduction of nitrate to nitrite in suboxic waters, possibly enhancing the overall N isotope effect for N loss from oxygen minimum zones.
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Affiliation(s)
- Benjamin Brunner
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Sergio Contreras
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Moritz F. Lehmann
- Departement Umweltwissenschaften (Biogeochemie), Universität Basel, 4056 Basel, Switzerland; and
| | - Olga Matantseva
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Mark Rollog
- Departement Umweltwissenschaften (Biogeochemie), Universität Basel, 4056 Basel, Switzerland; and
| | - Tim Kalvelage
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Gabriele Klockgether
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Gaute Lavik
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Mike S. M. Jetten
- Department of Microbiology, Institute of Water and Wetland Research, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| | - Boran Kartal
- Department of Microbiology, Institute of Water and Wetland Research, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| | - Marcel M. M. Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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292
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Oshiki M, Awata T, Kindaichi T, Satoh H, Okabe S. Cultivation of planktonic anaerobic ammonium oxidation (anammox) bacteria using membrane bioreactor. Microbes Environ 2013; 28:436-43. [PMID: 24200833 PMCID: PMC4070702 DOI: 10.1264/jsme2.me13077] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 08/11/2013] [Indexed: 01/09/2023] Open
Abstract
Enrichment cultures of anaerobic ammonium oxidation (anammox) bacteria as planktonic cell suspensions are essential for studying their ecophysiology and biochemistry, while their cultivation is still laborious. The present study aimed to cultivate two phylogenetically distinct anammox bacteria, "Candidatus Brocadia sinica" and "Ca. Scalindua sp." in the form of planktonic cells using membrane bioreactors (MBRs). The MBRs were continuously operated for more than 250 d with nitrogen loading rates of 0.48-1.02 and 0.004-0.09 kgN m(-3) d(-1) for "Ca. Brocadia sinica" and "Ca. Scalindua sp.", respectively. Planktonic anammox bacterial cells were successfully enriched (>90%) in the MBRs, which was confirmed by fluorescence in-situ hybridization and 16S rRNA gene sequencing analysis. The decay rate and half-saturation constant for NO2(-) of "Ca. Brocadia sinica" were determined to be 0.0029-0.0081 d(-1) and 0.47 mgN L(-1), respectively, using enriched planktonic cells. The present study demonstrated that MBR enables the culture of planktonic anammox bacterial cells, which are suitable for studying their ecophysiology and biochemistry.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido 060–8628, Japan
| | - Takanori Awata
- Department of Civil and Environmental Engineering, Graduate School of Engineerging, Hiroshima University, 1–4–1 Kagamiyama, Higashihiroshima 739–8527, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineerging, Hiroshima University, 1–4–1 Kagamiyama, Higashihiroshima 739–8527, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido 060–8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido 060–8628, Japan
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293
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Dibrova DV, Cherepanov DA, Galperin MY, Skulachev VP, Mulkidjanian AY. Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1407-27. [PMID: 23871937 PMCID: PMC3839093 DOI: 10.1016/j.bbabio.2013.07.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/30/2022]
Abstract
This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On the one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Daria V Dibrova
- School of Physics, University of Osnabrueck, D-49069 Osnabrueck, Germany; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia; Institute of Mitoengineering, Lomonosov Moscow State University, Moscow 119992, Russia
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294
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Lysozyme and penicillin inhibit the growth of anaerobic ammonium-oxidizing planctomycetes. Appl Environ Microbiol 2013; 79:7763-9. [PMID: 24096424 DOI: 10.1128/aem.02467-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) planctomycetes oxidize ammonium in the absence of molecular oxygen with nitrite as the electron acceptor. Although planctomycetes are generally assumed to lack peptidoglycan in their cell walls, recent genome data imply that the anammox bacteria have the genes necessary to synthesize peptidoglycan-like cell wall structures. In this study, we investigated the effects of two antibacterial agents that target the integrity and synthesis of peptidoglycan (lysozyme and penicillin G) on the anammox bacterium Kuenenia stuttgartiensis. The effects of these compounds were determined in both short-term batch incubations and long-term (continuous-cultivation) growth experiments in membrane bioreactors. Lysozyme at 1 g/liter (20 mM EDTA) lysed anammox cells in less than 60 min, whereas penicillin G did not have any observable short-term effects on anammox activity. Penicillin G (0.5, 1, and 5 g/liter) reversibly inhibited the growth of anammox bacteria in continuous-culture experiments. Furthermore, transcriptome analyses of the penicillin G-treated reactor and the control reactor revealed that penicillin G treatment resulted in a 10-fold decrease in the ribosome levels of the cells. One of the cell division proteins (Kustd1438) was downregulated 25-fold. Our results suggested that anammox bacteria contain peptidoglycan-like components in their cell wall that can be targeted by lysozyme and penicillin G-sensitive proteins were involved in their synthesis. Finally, we showed that a continuous membrane reactor system with free-living planktonic cells was a very powerful tool to study the physiology of slow-growing microorganisms under physiological conditions.
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295
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Yao ZB, Cai Q, Zhang DJ, Xiao PY, Lu PL. The enhancement of completely autotrophic nitrogen removal over nitrite (CANON) by N2H4 addition. BIORESOURCE TECHNOLOGY 2013; 146:591-596. [PMID: 23973980 DOI: 10.1016/j.biortech.2013.07.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/22/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
The long-term addition of N2H4 to completely autotrophic nitrogen removal over nitrite (CANON) sequencing batch reactors (SBRs) recovered and enhanced their autotrophic nitrogen removal capacity while simultaneously reducing their production of NO3(-). The total nitrogen (TN) removal rate and TN removal efficiency of the process increased from 0.202±0.011 to 0.370±0.016 kg N/m(3)/d and from 65.1±3.75% to 77.4±3.8%, respectively, and the molar ratio of NO3(-) production to NH4(+) removal (MRNN) decreased to 0.058. The most effective concentration of N2H4 addition was approximately 3.99 mg/L. N2H4 could increase the specific growth rate of anaerobic ammonium-oxidizing bacteria (AnAOB) and inhibit aerobic ammonia oxidation. The electrons released from the oxidation of additional N2H4 using hydrazine dehydrogenase (HDH), which substituted the electrons from NO2(-) oxidation to NO3(-), replenished the consumption of AnAOB anabolism and significantly reduced the consequent NO3(-) production.
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Affiliation(s)
- Zong-Bao Yao
- Department of Environmental Science, Chongqing University, Chongqing 400030, PR China
| | - Qing Cai
- Department of Environmental Science, Chongqing University, Chongqing 400030, PR China; Mining and Environmental Engineering, Chongqing Vocational Institute of Engineering, Chongqing 400037, PR China
| | - Dai-Jun Zhang
- Department of Environmental Science, Chongqing University, Chongqing 400030, PR China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400030, PR China.
| | - Peng-Ying Xiao
- Department of Environmental Science, Chongqing University, Chongqing 400030, PR China
| | - Pei-Li Lu
- Department of Environmental Science, Chongqing University, Chongqing 400030, PR China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400030, PR China
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296
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Cell biology of unique anammox bacteria that contain an energy conserving prokaryotic organelle. Antonie van Leeuwenhoek 2013; 104:489-97. [PMID: 23929088 DOI: 10.1007/s10482-013-9990-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
Abstract
Anammox bacteria obtain their energy for growth from the anaerobic oxidation of ammonium with nitrite to dinitrogen gas. This property has made anammox bacteria very valuable for industry where they are applied for the removal of nitrogen compounds from industrial and domestic wastewaters. Anammox bacteria are also important in nature where they contribute significantly to oceanic nitrogen loss. Further, anammox bacteria have similarities to both Archaea and Eukarya, making them extremely interesting from a cell biological perspective. The anammox cell does not conform to the typical prokaryotic cell plan: single bilayer membranes divide the anammox cell into three distinct cellular compartments that possibly also have distinct cellular functions. The innermost and largest compartment, the anammoxosome, is the location of the energy metabolism. The middle compartment, the riboplasm, contains the nucleoid and ribosomes and thus has a genetic, information processing function. Finally, the outermost compartment, the paryphoplasm, has an as yet unknown function. In addition, anammox bacteria are proposed to have an atypical cell wall devoid of both peptidoglycan and a typical outer membrane. Here, I review the current knowledge on the cell biology of this enigmatic group of bacteria.
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297
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Nitrate-dependent ferrous iron oxidation by anaerobic ammonium oxidation (anammox) bacteria. Appl Environ Microbiol 2013; 79:4087-93. [PMID: 23624480 DOI: 10.1128/aem.00743-13] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.
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