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Leone F, Imfeld A, Mirzaei Y, Gélinas Y. Using 13C enriched acetate in isotope labelling incubation experiments: a note of caution. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024; 60:66-73. [PMID: 38097918 DOI: 10.1080/10256016.2023.2291460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/09/2023] [Indexed: 02/01/2024]
Abstract
Vapour-phase fumigation with HCl is routinely used to remove inorganic carbon in preparation for the measurement of the concentration and δ13C value of organic carbon in a sample using elemental analysis coupled to an isotope ratio mass spectrometer. Acidification of the sample to be analyzed can lead to the loss of low molecular weight conjugate bases as volatile organic acids during the acidification and/or the drying steps following fumigation, through protonation of the conjugate base and volatilization. Such loss could lead to a severe bias in incubation experiments where 13C-enriched compounds such as acetate are used to trace reaction pathways or metabolites in a cultivation medium or a mesocosm for example. In this work, we enriched a carbonate-free freshwater sediment with 1-13C sodium acetate by 5, 10 and 20 ‰ relative to the δ13C value of the natural organic carbon of the sediment, and then tested the effects of HCl fumigation, drying at 50 °C and drying at room temperature, alone or in combination, on the measured δ13C values. We found that fumigation and drying at 50 °C, alone or in combination, both lead to the loss of the majority of the 13C-enriched acetate spike.
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Affiliation(s)
- Frédéric Leone
- Geotop and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Anic Imfeld
- Geotop and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Yeganeh Mirzaei
- Geotop and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Yves Gélinas
- Geotop and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
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2
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Dietl A, Wellach K, Mahadevan P, Mertes N, Winter S, Kutsch T, Walz C, Schlichting I, Fabritz S, Barends TM. Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference. J Biol Chem 2023; 299:104602. [PMID: 36907440 PMCID: PMC10139942 DOI: 10.1016/j.jbc.2023.104602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
The genomes of anaerobic ammonium-oxidizing (anammox) bacteria contain a gene cluster comprising genes of unusual fatty acid biosynthesis enzymes that were suggested to be involved in the synthesis of the unique "ladderane" lipids produced by these organisms. This cluster encodes an acyl carrier protein (denoted as "amxACP") and a variant of FabZ, an ACP-3-hydroxyacyl dehydratase. In this study, we characterize this enzyme, which we call anammox-specific FabZ ("amxFabZ"), to investigate the unresolved biosynthetic pathway of ladderane lipids. We find that amxFabZ displays distinct sequence differences to "canonical" FabZ, such as a bulky, apolar residue on the inside of the substrate binding tunnel, where the canonical enzyme has a glycine. Additionally, substrate screens suggest that amxFabZ efficiently converts substrates with acyl chain lengths of up to eight carbons, whereas longer substrates are converted much more slowly under the conditions used. We also present crystal structures of amxFabZs, mutational studies and the structure of a complex between amxFabZ and amxACP, which show that the structures alone cannot explain the apparent differences from canonical FabZ. Moreover, we find that while amxFabZ does dehydrate substrates bound to amxACP, it does not convert substrates bound to canonical ACP of the same anammox organism. We discuss the possible functional relevance of these observations in the light of proposals for the mechanism for ladderane biosynthesis.
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Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| | - Kathrin Wellach
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Pavithra Mahadevan
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Nicole Mertes
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - SophieL Winter
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Tobias Kutsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Carlo Walz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Mass Spectrometry Core Facility, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - ThomasR M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
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3
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Wang H, Zou Y, Li M, Tang Z, Wang J, Tian Z, Strassner N, Yang Q, Zheng Q, Guo Y, Liu W, Pan L, Houk KN. A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions. Nat Chem 2023; 15:177-184. [PMID: 36690833 DOI: 10.1038/s41557-022-01104-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/01/2022] [Indexed: 01/24/2023]
Abstract
Cycloaddition reactions are among the most widely used reactions in chemical synthesis. Nature achieves these cyclization reactions with a variety of enzymes, including Diels-Alderases that catalyse concerted 4 + 2 cycloadditions, but biosynthetic enzymes with 2 + 2 cyclase activity have yet to be discovered. Here we report that PloI4, a β-barrel-fold protein homologous to the exo-selective 4 + 2 cyclase that functions in the biosynthesis of pyrroindomycins, catalyses competitive 2 + 2 and 4 + 2 cycloaddition reactions. PloI4 is believed to catalyse an endo-4 + 2 cycloaddition in the biosynthesis of pyrrolosporin A; however, when the substrate precursor of pyrroindomycins was treated with PloI4, an exo-2 + 2 adduct was produced in addition to the exo- and endo-4 + 2 adducts. Biochemical characterizations, computational analyses, (co)crystal structures and mutagenesis outcomes have allowed the catalytic versatility of PloI4 to be rationalized. Mechanistic studies involved the directed engineering of PloI4 to variants that produced the exo-4 + 2, endo-4 + 2 or exo-2 + 2 product preferentially. This work illustrates an enzymatic thermal 2 + 2 cycloaddition and provides evidence of a process through which an enzyme evolves along with its substrate for specialization and activity improvement.
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Affiliation(s)
- Hongbo Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiabao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry, Shanghai Normal University, Shanghai, China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.,Abiochem Biotechnology Co., Ltd, Shanghai, China
| | - Nina Strassner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Yujiao Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Department of Chemistry, Shanghai Normal University, Shanghai, China.
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
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4
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Dietl A, Barends TRM. Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism. Proteins 2021; 90:73-82. [PMID: 34310758 DOI: 10.1002/prot.26187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 07/16/2021] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria express a distinct acyl carrier protein implicated in the biosynthesis of the highly unusual "ladderane" lipids these organisms produce. This "anammox-specific" ACP, or amxACP, shows several unique features such as a conserved FF motif and an unusual sequence in the functionally important helix III. Investigation of the protein's structure and dynamics, both in the crystal by ensemble refinement and by MD simulations, reveals that helix III adopts a rare six-residue-long 310 -helical conformation that confers a large degree of conformational and positional variability on this part of the protein. This way of introducing structural flexibility by using the inherent properties of 310 -helices appears unique among ACPs. Moreover, the structure suggests a role for the FF motif in shielding the thioester linkage between the protein's prosthetic group and its acyl cargo from hydrolysis.
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Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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5
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Raghavan V, Johnson JL, Stec DF, Song B, Zajac G, Baranska M, Harris CM, Schley ND, Polavarapu PL, Harris TM. Absolute Configurations of Naturally Occurring [5]- and [3]-Ladderanoic Acids: Isolation, Chiroptical Spectroscopy, and Crystallography. JOURNAL OF NATURAL PRODUCTS 2018; 81:2654-2666. [PMID: 30562024 DOI: 10.1021/acs.jnatprod.8b00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have isolated mixtures of [5]- and [3]-ladderanoic acids 1a and 2a from the biomass of an anammox bioreactor and have separated the acids and their phenacyl esters for the first time by HPLC. The absolute configurations of the naturally occurring acids and their phenacyl esters are assigned as R at the site of side-chain attachment by comparison of experimental specific rotations with corresponding values predicted using quantum chemical (QC) methods. The absolute configurations for 1a and 2a were independently verified by comparison of experimental Raman optical activity spectra with corresponding spectra predicted using QC methods. The configurational assignments of 1a and 2a and of the phenacyl ester of 1a were also confirmed by X-ray crystallography.
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Affiliation(s)
- Vijay Raghavan
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Jordan L Johnson
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Donald F Stec
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Bongkeun Song
- Department of Biological Sciences , Virginia Institute of Marine Science , Gloucester Point , Virginia 23062 , United States
| | - Grzegorz Zajac
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | - Malgorzata Baranska
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET) , Jagiellonian University , Bobrzynskiego 14 , 30-348 Krakow , Poland
| | - Constance M Harris
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Nathan D Schley
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Prasad L Polavarapu
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Thomas M Harris
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
- Department of Biological Sciences , Virginia Institute of Marine Science , Gloucester Point , Virginia 23062 , United States
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6
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Meng Y, Yin C, Zhou Z, Meng F. Increased salinity triggers significant changes in the functional proteins of ANAMMOX bacteria within a biofilm community. CHEMOSPHERE 2018; 207:655-664. [PMID: 29852465 DOI: 10.1016/j.chemosphere.2018.05.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/21/2018] [Accepted: 05/13/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic ammonium oxidation (ANAMMOX) processes can potentially be influenced by salinity related to variable salinity in water environment. Here, we used 16S rRNA sequencing analysis combining with iTRAQ-based quantitative proteomic approach to reveal the response of microbial community and functional proteins to salinity, which was increased from 0 to 20 g L-1 with a step of 5 g L-1 (designed as S5, S10, S15 and S20) compared to control reactor (without salinity stress desined as S0). The 16S rRNA sequencing analysis showed that a high salinity (20 g L-1, S20) decreased the abundance of genus Candidatus Jettenia but increased that of Candidatus Kuenenia. A total of 1609 differentially expressed proteins were acquired in the three comparison groups (S5:S0, S20:S0 and S20:S5). Of these, 39 proteins co-occurred in the three salt-exposed samples. Hydrazine dehydrogenase (HDH; Q1PW30) and nitrate reductase (Q1PZD8) were up-regulated more than 3-folds in the exposure of 20 g-NaCl/L. The functional enrichment analysis further showed that some proteins responsible for ion binding, catalysis and oxidation-reduction reaction were up-regulated, which explained the physiological resilience of ANAMMOX bacteria under salinity stress. Additionally, ANAMMOX bacteria responded to salinity by modulating the electron transport systems, indicating that the cells retained a high potential for proton pumping, as well as the ATP production. Furthermore, the over-expression of HDH which associated with ANAMMOX metabolism, was potentially related to the increased abundance of halophilic Candidatus Kuenenia. These findings provide a comprehensive baseline for understanding the roles of salinity stresses in shaping the functional proteins of ANAMMOX bacteria.
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Affiliation(s)
- Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control, Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China
| | - Cuiqin Yin
- Hefei Water Supply Group Co., Ltd, Anhui 230011, China
| | - Zhongbo Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control, Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control, Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China.
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7
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Zhang Q, Gu C, Zhou H, Liang Y, Zhao Y, Di H. Alterations in anaerobic ammonium oxidation of paddy soil following organic carbon treatment estimated using 13C-DNA stable isotope probing. Appl Microbiol Biotechnol 2017; 102:1407-1416. [PMID: 29274059 DOI: 10.1007/s00253-017-8689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Abstract
In this study, soil samples from the typical rice-wheat cropping system in Jiangsu Province, China, subjected to different fertilizer application treatments-no carbon (CK), urea (UR), straw (SR), pig manure (PM), starch (ST), and glucose (GL)-were used to determine potential anaerobic ammonium oxidation (anammox) rate and its association with bacterial abundance, diversity, and activity by using DNA stable isotope probing combined with 15N isotope tracing and molecular techniques. The effects of different organic carbon sources on anammox were significant, in the following order: GL > ST, SR > UR > PM; anammox activity differed significantly across treatments; however, the 13C active anammox bacteria were only closely related to Ca. Brocadia. The anammox hydrazine synthase β subunit functional gene sequences were highly associated with the Candidatus genus Brocadia in PM and CK treatments. The different organic carbon sources had different inhibitory effects with anammox rate, which dropped from 3.19 to 1.04 nmol dinitrogen gas g-1 dry soil h-1 among treatments. About 4.2-22.3% of dinitrogen gas emissions were attributed to anammox and indicated that a specific population of anammox bacteria was present and varied with the addition of exogenous organic compounds in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox.
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Affiliation(s)
- Qichun Zhang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, China.
| | - Chao Gu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Huifang Zhou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Yongchao Liang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
| | - Yuhua Zhao
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
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8
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Gu C, Zhou H, Zhang Q, Zhao Y, Di H, Liang Y. Effects of various fertilization regimes on abundance and activity of anaerobic ammonium oxidation bacteria in rice-wheat cropping systems in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:1064-1072. [PMID: 28511351 DOI: 10.1016/j.scitotenv.2017.04.240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/30/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is an important process in many marine and paddy ecosystems. However, few studies have reported on the contribution to the nitrogen cycle of anammox and its dynamics in rice-wheat cropping systems with different fertilization regimes. Here, isotope tracing and molecular techniques were used to determine the potential rates of anammox and their association with bacterial abundance, diversity, and activity. Rice-wheat cropping systems at two sites in Jiangsu Province, China were selected and the treatments at each site were: 1) no fertilization (CK), 2) 100% chemical fertilization (CF), 3) pig manure compost plus 50% chemical fertilization (PMCF), and 4) straw plus 100% chemical fertilization (SRCF). The results revealed that anammox bacteria with high abundance were detected in both the wheat and rice seasons. The abundance of anammox in PMCF treatment was higher than that in SRCF treatment in both Changshu and Jintan. Moreover, the abundance of anammox bacteria in CF treatment was significantly higher than that in CK in Changshu. Analysis of anammox hydrazine synthase β subunit (hzs-β) gene sequences showed that in the rice season, the anammox bacteria Ca. Brocadia, Ca. Scalindua, and Ca. Jettenia were present. In contrast, all of the anammox hydrazine oxidase (hzo) genes were affiliated with Ca. Brocadia, suggesting that hzs genes are more representative of anammox biological diversity compared to hzo. Sequences from the PMCF treatment where affiliated with both Ca. Jettenia and Ca. Brocadia, and showed the highest diversity. Anammox activity was detected in both the wheat and rice seasons, but there were significant differences between seasons. The anammox rates were in the range 0.34 to 1.04nmol dinitrogen gas∙g-1 dry soil∙h-1, and 3.15 to 9.62% of dinitrogen gas emissions were attributed to anammox. However, no significant difference among the fertilizer treatments for anammox activity was found in the study.
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Affiliation(s)
- Chao Gu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Huifang Zhou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Qichun Zhang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Yuhua Zhao
- College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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9
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Wegener G, Kellermann MY, Elvert M. Tracking activity and function of microorganisms by stable isotope probing of membrane lipids. Curr Opin Biotechnol 2016; 41:43-52. [PMID: 27179643 DOI: 10.1016/j.copbio.2016.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Microorganisms in soils and sediments are highly abundant and phylogenetically diverse, but their specific metabolic activity and function in the environment is often not well constrained. To address this critical aspect in environmental biogeochemistry, different methods involving stable isotope probing (SIP) and detection of the isotope label in a variety of molecular compounds have been developed. Here we review recent progress in lipid-SIP, a technique that combines the assimilation of specific 13C-labeled metabolic substrates such as inorganic carbon, methane, glucose and amino acids into diagnostic membrane lipid compounds. Using the structural characteristics of certain lipid types in combination with genetic molecular techniques, the SIP approach reveals the activity and function of distinct microbial groups in the environment. More recently, deuterium labeling in the form of deuterated water (D2O) extended the lipid-SIP portfolio. Since lipid biosynthetic pathways involve hydrogen (H+) uptake from water, lipid production can be inferred from the detection of D-assimilation into these compounds. Furthermore, by combining D2O and 13C-inorganic carbon (IC) labeling in a dual-SIP approach, rates of auto- and heterotrophic carbon fixation can be estimated. We discuss the design, analytical prerequisites, data processing and interpretation of single and dual-SIP experiments and highlight a case study on anaerobic methanotrophic communities inhabiting hydrothermally heated marine sediments.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany.
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany
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10
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Wagner JP, Schreiner PR. Nature Utilizes Unusual High London Dispersion Interactions for Compact Membranes Composed of Molecular Ladders. J Chem Theory Comput 2014; 10:1353-8. [DOI: 10.1021/ct5000499] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Philipp Wagner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
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11
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van Niftrik L, Jetten MSM. Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev 2012; 76:585-96. [PMID: 22933561 PMCID: PMC3429623 DOI: 10.1128/mmbr.05025-11] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called "prokaryotic organelle" analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya.
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Affiliation(s)
- Laura van Niftrik
- Department of Microbiology, Institute for Water & Wetland Research, Faculty of Science, Radboud University Nijmegen, The Netherlands.
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12
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Nouri DH, Tantillo DJ. Attack of radicals and protons on ladderane lipids: quantum chemical calculations and biological implications. Org Biomol Chem 2012; 10:5514-7. [DOI: 10.1039/c2ob25717c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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