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Wang Z, Yu Q, Zhao Z, Zhang Y. Ferroheme/Ferriheme Directly Involved in the Synthesis and Decomposition of Hydrazine as an Electron Carrier during Anammox. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10140-10148. [PMID: 38781353 DOI: 10.1021/acs.est.3c08525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Anammox bacteria performed the reaction of NH4+ and NO with hydrazine synthase to produce N2H4, followed by the decomposition of N2H4 with hydrazine dehydrogenase to generate N2. Ferroheme/ferriheme, which serves as the active center of both hydrazine synthase and hydrazine dehydrogenase, is thought to play a crucial role in the synthesis and decomposition of N2H4 during Anammox due to its high redox activity. However, this has yet to be proven and the exact mechanisms by which ferroheme/ferriheme is involved in the Anammox process remain unclear. In this study, abiotic and biological assays confirmed that ferroheme participated in NH4+ and NO reactions to generate N2H4 and ferriheme, and the produced N2H4 reacted with ferriheme to generate N2 and ferroheme. In other words, the ferroheme/ferriheme cycle drove the continuous reaction between NH4+ and NO. Raman, ultraviolet-visible spectroscopy, and X-ray absorption fine structure spectroscopy confirmed that ferroheme/ferriheme is involved in the synthesis and decomposition of N2H4 via the core FeII/FeIII cycle. The mechanism of ferroheme/ferriheme participation in the synthesis and decomposition of N2H4 was proposed by density functional theory calculations. These findings revealed for the first time the heme electron transfer mechanisms, which are of great significance for deepening the understanding of Anammox.
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Affiliation(s)
- Zhenxin Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, China
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Zhao R, Le Moine Bauer S, Babbin AR. " Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces. Appl Environ Microbiol 2023; 89:e0080023. [PMID: 37470485 PMCID: PMC10467342 DOI: 10.1128/aem.00800-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sven Le Moine Bauer
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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3
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Bollmeyer MM, Coleman RE, Majer SH, Ferrao SD, Lancaster KM. Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc 2023; 145:14404-14416. [PMID: 37338957 PMCID: PMC10431212 DOI: 10.1021/jacs.3c03608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli. When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c'β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.
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Affiliation(s)
- Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Rachael E. Coleman
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Sean H. Majer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Silas D. Ferrao
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
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4
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Suarez C, Hackl T, Wilen BM, Persson F, Hagelia P, Jetten MSM, Dalcin Martins P. Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel. FEMS Microbiol Lett 2023; 370:fnad049. [PMID: 37291701 PMCID: PMC10732223 DOI: 10.1093/femsle/fnad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund 221 00, Sweden
| | - Thomas Hackl
- Microbial Ecology Cluster, GELIFES, University of Groningen, Groningen 9747 AG, Netherlands
| | - Britt-Marie Wilen
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Per Hagelia
- Construction Division, The Norwegian Public Roads, Administration, Oslo 0667, Norway
| | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen 6525 AJ, Netherlands
| | - Paula Dalcin Martins
- Microbial Ecology Cluster, GELIFES, University of Groningen, Groningen 9747 AG, Netherlands
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5
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Venturin B, Rodrigues HC, Bonassa G, Hollas CE, Bolsan AC, Antes FG, De Prá MC, Fongaro G, Treichel H, Kunz A. Key enzymes involved in anammox-based processes for wastewater treatment: An applied overview. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10780. [PMID: 36058650 DOI: 10.1002/wer.10780] [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: 03/20/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The anaerobic ammonium oxidation (anammox) process has attracted significant attention as an economic, robustness, and sustainable method for the treatment of nitrogen (N)-rich wastewater. Anammox bacteria (AnAOB) coexist with other microorganisms, and particularly with ammonia-oxidizing bacteria (AOB) and/or heterotrophic bacteria (HB), in symbiosis in favor of the substrate requirement (ammonium and nitrite) of the AnAOB being supplied by these other organisms. The dynamics of these microbial communities have a significant effect on the N-removal performance, but the corresponding metabolic pathways are still not fully understood. These processes involve many common metabolites that may act as key factors to control the symbiotic interactions between these organisms, to maximize N-removal efficiency from wastewater. Therefore, this work overviews the current state of knowledge about the metabolism of these microorganisms including key enzymes and intermediate metabolites and summarizes already reported experiences based on the employment of certain metabolites for the improvement of N-removal using anammox-based processes. PRACTITIONER POINTS: Approaches knowledge about the biochemistry and metabolic pathways involved in anammox-based processes. Some molecular tools can be used to determine enzymatic activity, serving as an optimization in nitrogen removal processes. Enzymatic evaluation allied to the physical-chemical and biomolecular analysis of the nitrogen removal processes expands the application in different effluents.
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Affiliation(s)
- Bruno Venturin
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | | | - Gabriela Bonassa
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | | | | | | | | | - Gislaine Fongaro
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Helen Treichel
- Universidade Federal da Fronteira Sul, Erechim, Rio Grande do Sul, Brazil
| | - Airton Kunz
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- Universidade Federal da Fronteira Sul, Erechim, Rio Grande do Sul, Brazil
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6
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Oshiki M, Takaki Y, Hirai M, Nunoura T, Kamigaito A, Okabe S. Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures. Microbes Environ 2022; 37. [PMID: 35811137 PMCID: PMC9530715 DOI: 10.1264/jsme2.me22017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic analysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC
| | - Atsushi Kamigaito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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7
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Soares R, Costa NL, Paquete CM, Andreini C, Louro RO. A new paradigm of multiheme cytochrome evolution by grafting and pruning protein modules. Mol Biol Evol 2022; 39:6609985. [PMID: 35714268 PMCID: PMC9250108 DOI: 10.1093/molbev/msac139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multiheme cytochromes play key roles in diverse biogeochemical cycles, but understanding the origin and evolution of these proteins is a challenge due to their ancient origin and complex structure. Up until now, the evolution of multiheme cytochromes composed by multiple redox modules in a single polypeptide chain was proposed to occur by gene fusion events. In this context, the pentaheme nitrite reductase NrfA and the tetraheme cytochrome c554 were previously proposed to be at the origin of the extant octa- and nonaheme cytochrome c involved in metabolic pathways that contribute to the nitrogen, sulfur, and iron biogeochemical cycles by a gene fusion event. Here, we combine structural and character-based phylogenetic analysis with an unbiased root placement method to refine the evolutionary relationships between these multiheme cytochromes. The evidence show that NrfA and cytochrome c554 belong to different clades, which suggests that these two multiheme cytochromes are products of truncation of ancestral octaheme cytochromes related to extant octaheme nitrite reductase and MccA, respectively. From our phylogenetic analysis, the last common ancestor is predicted to be an octaheme cytochrome with nitrite reduction ability. Evolution from this octaheme framework led to the great diversity of extant multiheme cytochromes analyzed here by pruning and grafting of protein modules and hemes. By shedding light into the evolution of multiheme cytochromes that intervene in different biogeochemical cycles, this work contributes to our understanding about the interplay between biology and geochemistry across large time scales in the history of Earth.
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Affiliation(s)
- Ricardo Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal.,Instituto Nacional de Investigação Agrária e Veterinária, Portugal
| | - Nazua L Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Claudia Andreini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
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8
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Zhao R, Biddle JF, Jørgensen SL. Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments. ISME COMMUNICATIONS 2022; 2:42. [PMID: 37938673 PMCID: PMC9723696 DOI: 10.1038/s43705-022-00125-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 07/21/2023]
Abstract
Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presence of Ca. Bathyanammoxibiaceae was confined within the nitrate-ammonium transition zones with the counter gradients of nitrate and ammonium, coinciding with the predicted occurrence of the anammox process. Ca. Bathyanammoxibiaceae genomes encode the core genetic machinery for the anammox metabolism, including hydrazine synthase for converting nitric oxide and ammonium to hydrazine, and hydrazine dehydrogenase for hydrazine oxidation to dinitrogen gas, and hydroxylamine oxidoreductase for nitrite reduction to nitric oxide. Their occurrences assessed by genomes and 16S rRNA gene sequencings surveys indicate that they are present in both marine and terrestrial environments. By introducing the anammox potential of Ca. Bathyanammoxibiaceae and charactering their ideal niche in marine sediments, our findings suggest that the diversity and abundance of anammox bacteria may be higher than previously thought, and provide important insights on cultivating them in the future to not only assess their biogeochemical impacts but also constrain the emergence and evolutionary history of this functional guild on Earth.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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9
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Oshiki M, Gao L, Zhang L, Okabe S. NH 2OH Disproportionation Mediated by Anaerobic Ammonium-oxidizing (Anammox) Bacteria. Microbes Environ 2022; 37. [PMID: 35418545 PMCID: PMC9530737 DOI: 10.1264/jsme2.me21092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Anammox bacteria produce N2 gas by oxidizing NH4+ with NO2–, and hydroxylamine (NH2OH) is a potential intermediate of the anammox process. N2 gas production occurs when anammox bacteria are incubated with NH2OH only, indicating their capacity for NH2OH disproportionation with NH2OH serving as both the electron donor and acceptor. Limited information is currently available on NH2OH disproportionation by anammox bacteria; therefore, the stoichiometry of anammox bacterial NH2OH disproportionation was examined in the present study using 15N-tracing techniques. The anammox bacteria, Brocadia sinica, Jettenia caeni, and Scalindua sp. were incubated with the addition of 15NH2OH, and the production of 15N-labeled nitrogenous compounds was assessed. The anammox bacteria tested performed NH2OH disproportionation and produced 15-15N2 gas and NH4+ as reaction products. The addition of acetylene, an inhibitor of the anammox process, reduced the activity of NH2OH disproportionation, but not completely. The growth of B. sinica by NH2OH disproportionation (–240.3 kJ mol NH2OH–1 under standard conditions) was also tested in 3 up-flow column anammox reactors fed with 1) 0.7 mM NH2OH only, 2) 0.7 mM NH2OH and 0.5 mM NH4+, and 3) 0.7 mM NH2OH and 0.5 mM NO2–. NH2OH consumption activities were markedly reduced after 7 d of operation, indicating that B. sinica was unable to maintain its activity or biomass by NH2OH disproportionation.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Lin Gao
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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10
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Suarez C, Dalcin Martins P, Jetten M, Karačić S, Wilén BM, Modin O, Hagelia P, Hermansson M, Persson F. Metagenomic evidence of a novel family of anammox bacteria in a subsea environment. Environ Microbiol 2022; 24:2348-2360. [PMID: 35415863 PMCID: PMC9325076 DOI: 10.1111/1462-2920.16006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/07/2022] [Indexed: 12/02/2022]
Abstract
Bacteria in the order ‘Candidatus Brocadiales’ within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome‐assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK‐like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Paula Dalcin Martins
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
| | - Mike Jetten
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
| | - Sabina Karačić
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Britt Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Hagelia
- Construction Division, The Norwegian Public Roads Administration, Oslo, Norway
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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11
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Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins. THE ISME JOURNAL 2022; 16:1119-1129. [PMID: 34862473 PMCID: PMC8940962 DOI: 10.1038/s41396-021-01161-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/01/2022]
Abstract
Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.
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12
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Kouba V, Bachmannová C, Podzimek T, Lipovová P, van Loosdrecht MCM. Physiology of anammox adaptation to low temperatures and promising biomarkers: A review. BIORESOURCE TECHNOLOGY 2022; 349:126847. [PMID: 35167904 DOI: 10.1016/j.biortech.2022.126847] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.
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Affiliation(s)
- V Kouba
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia.
| | - Ch Bachmannová
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia
| | - T Podzimek
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - P Lipovová
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - M C M van Loosdrecht
- The Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
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Akram M, Bock J, Dietl A, Barends TR. Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation. ACS OMEGA 2021; 6:21457-21464. [PMID: 34471748 PMCID: PMC8388095 DOI: 10.1021/acsomega.1c02275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.
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Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol 2021; 6:1129-1139. [PMID: 34267357 PMCID: PMC8387239 DOI: 10.1038/s41564-021-00934-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023]
Abstract
Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein's electron transport chain, and elucidate the electron transfer pathways within the complex.
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