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Liao T, Wang S, Zhang H, Stüeken EE, Luo H. Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils. Mol Biol Evol 2024; 41:msae096. [PMID: 38776415 PMCID: PMC11135946 DOI: 10.1093/molbev/msae096] [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: 01/09/2024] [Revised: 04/21/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Queen's Terrace, KY16 9TS, UK
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Earth and Environmental Sciences Programme, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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2
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Palomo A, Dechesne A, Smets BF, Zheng Y. Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters. WATER RESEARCH 2023; 245:120655. [PMID: 37748347 DOI: 10.1016/j.watres.2023.120655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.
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Affiliation(s)
- Alejandro Palomo
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yan Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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3
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Krüger M, Chaudhari N, Thamdrup B, Overholt WA, Bristow LA, Taubert M, Küsel K, Jehmlich N, von Bergen M, Herrmann M. Differential contribution of nitrifying prokaryotes to groundwater nitrification. THE ISME JOURNAL 2023; 17:1601-1611. [PMID: 37422599 PMCID: PMC10504367 DOI: 10.1038/s41396-023-01471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.
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Affiliation(s)
- Markus Krüger
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Narendrakumar Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bo Thamdrup
- Department of Biology, Nordcee-University of Southern Denmark, Odense, Denmark
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Laura A Bristow
- Department of Biology, Nordcee-University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Ishizaki Y, Kurisu F, Furumai H, Kasuga I. Autotrophic growth activity of complete ammonia oxidizers in an upflow biological contact filter for drinking water treatment. Lett Appl Microbiol 2023; 76:ovad105. [PMID: 37679291 DOI: 10.1093/lambio/ovad105] [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: 07/30/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Biological filters effectively remove ammonium from drinking water via nitrification. In a pilot-scale upflow biological contact filter (U-BCF), complete ammonia oxidizers (comammox), which are capable of oxidizing ammonia to nitrate in one cell, were more abundant than ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, little information is available on the contribution of comammox to nitrification. In this study, we evaluated the autotrophic growth activity of comammox associated with biological activated carbon (BAC) in a U-BCF by DNA-stable isotope probing (DNA-SIP). BAC samples collected from the U-BCF were continuously fed mineral medium containing 0.14 mg N L-1 ammonium and 12C- or 13C-labeled bicarbonate for 20 days. DNA-SIP analysis revealed that comammox (clades A and B) as well as AOA assimilated bicarbonate after 10 days of incubation, proving that dominant comammox could contribute to nitrification. Contrarily, AOB remained inactive throughout the observation period. Amplicon sequencing of the 13C-labeled DNA fractions of comammox revealed that specific genotypes other than the most dominant genotype in the original sample were more enriched under the incubation condition for the DNA-SIP experiment. Thus, dominant genotypes of comammox in a U-BCF might utilize organic nitrogen to fuel nitrification in ammonia-limited environments.
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Affiliation(s)
- Yuta Ishizaki
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research and Development Initiative, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
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5
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Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, Xiao X, Li J, Jia K, Greening C, Shao Z, Hubert CRJ. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun 2023; 14:1127. [PMID: 36854684 PMCID: PMC9974965 DOI: 10.1038/s41467-023-36877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Muhua Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Laura Woods
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Wenxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510075, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Keithley AE, Ryu H, Gomez-Alvarez V, Harmon S, Bennett-Stamper C, Williams D, Lytle DA. Comprehensive characterization of aerobic groundwater biotreatment media. WATER RESEARCH 2023; 230:119587. [PMID: 36638728 PMCID: PMC10119871 DOI: 10.1016/j.watres.2023.119587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Aerobic biotreatment systems can treat multiple reduced inorganic contaminants in groundwater, including ammonia (NH3), arsenic (As), iron (Fe), and manganese (Mn). While individual systems treating multiple contaminants simultaneously have been characterized and several systems treating one contaminant have been compared, a comparison of systems treating co-occurring contaminants is lacking. This study assessed the treatment performance and microbial communities within 7 pilot- and full-scale groundwater biotreatment systems in the United States that treated waters with pH 5.6-7.8, 0.1-2.0 mg/L dissolved oxygen, 75-376 mg CaCO3/L alkalinity, < 0.03-3.79 mg NH3-N/L, < 4-31 µg As/L, < 0.01-9.37 mg Fe/L, 2-1220 µg Mn/L, and 0.1-5.6 mg/L total organic carbon (TOC). Different reactor configurations and media types were represented, allowing for a broad assessment of linkages between water quality and microbial communities via microscopy, biofilm quantification, and molecular methods. Influent NH3, TOC, and pH contributed to differences in the microbial communities. Mn oxidase gene copy numbers were slightly negatively correlated with the influent Mn concentration, but no significant relationships between gene copy number and influent concentration were observed for the other contaminants. Extracellular enzyme activities, community composition, and carbon transformation pathways suggested heterotrophic bacteria may be important in nitrifying biofilters. Aerobic groundwater biofilters are complex, and improved understanding could lead to engineering enhancements.
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Affiliation(s)
- Asher E Keithley
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States.
| | - Hodon Ryu
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Vicente Gomez-Alvarez
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Stephen Harmon
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Christina Bennett-Stamper
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Daniel Williams
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Darren A Lytle
- ORD, CESER, WID, Drinking Water Management Branch, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
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Cotto I, Vilardi KJ, Huo L, Fogarty EC, Khunjar W, Wilson C, De Clippeleir H, Gilmore K, Bailey E, Lücker S, Pinto AJ. Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster. WATER RESEARCH 2023; 229:119497. [PMID: 36563511 DOI: 10.1016/j.watres.2022.119497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare the species-level diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether this comparison is consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that Nitrosomonas-like bacteria exhibited higher species-level diversity in comparison with other nitrifying bacteria, while the strain-level diversity (also called microdiversity) of most Nitrospira-like bacteria were higher than Nitrosomonas-like bacteria with few exceptions (one Nitrospira lineage II population). Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between principal comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73% ± 8), the Nitrospira_A-like nitrite oxidizer (85% ± 4), and the Nitrospira_D-like nitrite oxidizer (83% ± 1). This demonstrated the low species-level diversity of comammox bacteria compared with strict nitrifiers and further suggests that the same comammox population was detected in all systems. Comammox bacteria (Nitrospira lineage II), Nitrosomonas and, Nitrospira_D (Nitrospira lineage II) MAGs were significantly less microdiverse than the Nitrospira_A (lineage I) MAGs. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.
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Affiliation(s)
- Irmarie Cotto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Linxuan Huo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Emily C Fogarty
- Committee on Microbiology, The University of Chicago, Chicago, IL, United States
| | | | | | | | - Kevin Gilmore
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, United States
| | - Erika Bailey
- City of Raleigh Public Utilities, Raleigh, NC, United States
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Ameet J Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States.
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Palomo A, Dechesne A, Pedersen AG, Smets BF. Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira. MICROBIOME 2022; 10:204. [PMID: 36451244 PMCID: PMC9714041 DOI: 10.1186/s40168-022-01411-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders G. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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Liu S, Cai H, Zhao X, Wu Z, Chen Q, Xu X, Zhong S, Sun W, Ni J. Comammox biogeography subject to anthropogenic interferences along a high-altitude river. WATER RESEARCH 2022; 226:119225. [PMID: 36272199 DOI: 10.1016/j.watres.2022.119225] [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: 05/08/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (> 2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.
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Affiliation(s)
- Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China.
| | - Hetong Cai
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China
| | - Xiaohui Zhao
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China; College of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an, China
| | - Zongzhi Wu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China
| | - Sining Zhong
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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