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Zhao R, Zhang IH, Jayakumar A, Ward BB, Babbin AR. Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones. ISME COMMUNICATIONS 2024; 4:ycae060. [PMID: 38770059 PMCID: PMC11104535 DOI: 10.1093/ismeco/ycae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the Scalindua genus, which represent most, if not all, of the anammox bacteria in the global ODZs. Metagenomic read-recruiting and comparison with historical data show that they are ubiquitously present in all three major ODZs. Beyond the core anammox metabolism, both organisms contain cyanase, and the more dominant one encodes a urease, indicating most ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. Molecular clock analysis suggests that the evolutionary radiation of these bacteria into ODZs occurred no earlier than 310 million years ago, ~1 billion years after the emergence of the earliest modern-type ODZs. Different strains of the ODZ Scalindua species are also found in benthic sediments, and the first ODZ Scalindua is likely derived from the benthos. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encodes genes for urea utilization but has lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to thrive in the global ODZ waters. Our findings expand the known metabolisms and evolutionary history of the bacteria controlling the global nitrogen budget.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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2
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Zhao R, Babbin AR, Roerdink DL, Thorseth IH, Jørgensen SL. Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments. ISME COMMUNICATIONS 2023; 3:26. [PMID: 36991114 PMCID: PMC10060263 DOI: 10.1038/s43705-023-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Desiree L Roerdink
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Ingunn H Thorseth
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway.
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Vijayan J, Nathan VK, Ammini P, Ammanamveetil AMH. Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28383-28406. [PMID: 36680718 PMCID: PMC9862233 DOI: 10.1007/s11356-023-25195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/04/2023] [Indexed: 04/16/2023]
Abstract
Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.
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Affiliation(s)
- Jasna Vijayan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India.
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamilnadu, India
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, Kerala, India
| | - Abdulla Mohamed Hatha Ammanamveetil
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India
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4
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Long AM, Jurgensen SK, Petchel AR, Savoie ER, Brum JR. Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation. Front Microbiol 2021; 12:748961. [PMID: 34777296 PMCID: PMC8578717 DOI: 10.3389/fmicb.2021.748961] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 01/05/2023] Open
Abstract
Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.
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Affiliation(s)
- Andrew M. Long
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | | | | | | | - Jennifer R. Brum
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
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Yang Y, Li M, Li H, Li XY, Lin JG, Denecke M, Gu JD. Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139387. [PMID: 32460079 DOI: 10.1016/j.scitotenv.2020.139387] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N2). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.
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Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.
| | - Hui Li
- School of Resource and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
| | - Xiao-Yan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City 30010, Taiwan
| | - Martin Denecke
- Department of Urban Water- and Waste Management, University of Duisburg-Essen, Universitätsstraße 15, 45141 Essen, Germany
| | - Ji-Dong Gu
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, Guangdong 510300, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China.
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Li J, Feng L, Biswal BK, Chen GH, Wu D. Bioaugmentation of marine anammox bacteria (MAB)-based anaerobic ammonia oxidation by adding Fe(III) in saline wastewater treatment under low temperature. BIORESOURCE TECHNOLOGY 2020; 295:122292. [PMID: 31655251 DOI: 10.1016/j.biortech.2019.122292] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
This work investigated a new method of using Fe(III) to enhance the reactor performance enriched with marine anammox bacteria (MAB). The experiments were conducted in a sequencing batch reactor at low temperature (15 °C), high salinity (35 g/L) and varying Fe(III) concentrations (0-250 mg/l). The results of this study showed that at low Fe(III) (6 mg Fe/L), the rate of ammonium removal, nitrite removal and specific anammox activity remarkably increased to 0.42 kg/(m3·d), 0.53 kg/(m3·d), 0.56 kg/(kg·d), respectively. However, Fe(III) at above 120 mg Fe/L, the reaction time was significantly shortened from 5 to 2 h. MAB-based nitrite removal could be predicated based on the change of pH (ΔpH) and oxidation-reduction potential (ΔORP). Kinetics analysis demonstrated, the "Remodified Logistic Model" could simulate the Fe(III) enhanced anammox process. Overall, this research shed the light of designing a new high-rate anaerobic nitrogen removal technology for carbon insufficient, nitrogen-laden saline wastewater.
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Affiliation(s)
- Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China; Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Li Feng
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Basanta Kumar Biswal
- Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Di Wu
- Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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7
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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Abstract
In the ocean's major oxygen minimum zones (OMZs), oxygen is effectively absent from sea water and life is dominated by microorganisms that use chemicals other than oxygen for respiration. Recent studies that combine advanced genomic and chemical detection methods are delineating the different metabolic niches that microorganisms can occupy in OMZs. Understanding these niches, the microorganisms that inhabit them, and their influence on marine biogeochemical cycles is crucial as OMZs expand with increasing seawater temperatures.
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Affiliation(s)
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY, Zhang T. Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. MICROBIOME 2019; 7:122. [PMID: 31462278 PMCID: PMC6714388 DOI: 10.1186/s40168-019-0730-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation anammox (PNA) reactors have received considerable attention for their crucial roles in energy-efficient nitrogen removal from wastewater. However, a comprehensive understanding of how abiotic and biotic factors shape bacterial community assembly in PNA reactors is not well reported. RESULTS Here, we used integrated multi-omics (i.e., high-throughput 16S rRNA gene, metagenomic, metatranscriptomic, and metaproteomic sequencing) to reveal how abiotic and biotic factors shape the bacterial community assembly in a lab-scale one-stage PNA reactor treating synthetic wastewater. Analysis results of amplicon sequences (16S rRNA gene) from a time-series revealed distinct relative abundance patterns of the key autotrophic bacteria, i.e., anammox bacteria and ammonia-oxidizing bacteria (AOB), and the associated heterotrophic populations in the seed sludge and the sludge at the new stable state after deterioration. Using shotgun metagenomic sequences of anammox sludge, we recovered 58 metagenome-assembled genomes (MAGs), including 3 MAGs of anammox bacteria and 3 MAGs of AOB. The integrated metagenomic, metatranscriptomic, and metaproteomic data revealed that nitrogen metabolism is the most active process in the studied PNA reactor. The abundant heterotrophs contribute to the reduction of nitrate to nitrite/ammonium for autotrophic bacteria (anammox bacteria and AOB). Genomic and transcriptomic data revealed that the preference for electron donors of the dominant heterotrophs in different bacterial assemblages (seed and new stable state) varied along with the shift in anammox bacteria that have different metabolic features in terms of EPS composition. Notably, the most abundant heterotrophic bacteria in the reactor were more auxotrophic than the less abundant heterotrophs, regarding the syntheses of amino acids and vitamins. In addition, one of the abundant bacteria observed in the bacterial community exhibited highly transcribed secretion systems (type VI). CONCLUSIONS These findings provide the first insight that the bacterial communities in the PNA reactor are defined by not only abiotic factors (operating mode) but also metabolic interactions, such as nitrogen metabolism, exchange of electron donors, and auxotrophies.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Qigui Niu
- School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, 266237 Shandong Province People’s Republic of China
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Mishty Negi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579 Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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10
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Ali M, Shaw DR, Zhang L, Haroon MF, Narita Y, Emwas AH, Saikaly PE, Okabe S. Aggregation ability of three phylogenetically distant anammox bacterial species. WATER RESEARCH 2018; 143:10-18. [PMID: 29933181 DOI: 10.1016/j.watres.2018.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/30/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are well known for their aggregation ability. However, very little is known about cell surface physicochemical properties of anammox bacteria and thus their aggregation abilities have not been quantitatively evaluated yet. Here, we investigated the aggregation abilities of three different anammox bacterial species: "Candidatus Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Brocadia sapporoensis". Planktonic free-living enrichment cultures of these three anammox species were harvested from the membrane bioreactors (MBRs). The physicochemical properties (e.g., contact angle, zeta potential, and surface thermodynamics) were analyzed for these anammox bacterial species and used in the extended DLVO theory to understand the force-distance relationship. In addition, their extracellular polymeric substances (EPSs) were characterized by X-ray photoelectron spectroscopy and nuclear magnetic resonance. The results revealed that the "Ca. B. sinica" cells have the most hydrophobic surface and less hydrophilic functional groups in EPS than other anammox strains, suggesting better aggregation capability. Furthermore, aggregate formation and anammox bacterial populations were monitored when planktonic free-living cells were cultured in up-flow column reactors under the same conditions. Rapid development of microbial aggregates was observed with the anammox bacterial population shifts to a dominance of "Ca. B. sinica" in all three reactors. The dominance of "Ca. B. sinica" could be explained by its better aggregation ability and the superior growth kinetic properties (higher growth rate and affinity to nitrite). The superior aggregation ability of "Ca. B. sinica" indicates significant advantages (efficient and rapid start-up of anammox reactors due to better biomass retention as granules and consequently stable performance) in wastewater treatment application.
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Affiliation(s)
- Muhammad Ali
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia; Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Dario Rangel Shaw
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia
| | - Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Mohamed Fauzi Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yuko Narita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology, Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Pascal E Saikaly
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia.
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan.
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11
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Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME JOURNAL 2018; 12:2706-2722. [PMID: 29991764 DOI: 10.1038/s41396-018-0223-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.
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Affiliation(s)
- Sangita Ganesh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.,Radiant Genomics, Emeryville, 94608, CA, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Laura A Bristow
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Nigel Blackwood
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, Faculty of Natural Sciences and Oceanography, University of Concepción, Casilla 160-C, Concepción, Chile.,Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | - Annie Bourbonnais
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Mark A Altabet
- School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | | | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.
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12
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Zhang L, Narita Y, Gao L, Ali M, Oshiki M, Ishii S, Okabe S. Microbial competition among anammox bacteria in nitrite-limited bioreactors. WATER RESEARCH 2017; 125:249-258. [PMID: 28865374 DOI: 10.1016/j.watres.2017.08.052] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 05/05/2023]
Abstract
Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. "Candidatus Brocadia sinica", "Candidatus Jettenia caeni" and "Candidatus Kuenenia stuttgartiensis") were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that "Ca. J. caeni" could proliferate only at low NLRs, whereas "Ca. B. sinica" outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that "Ca. J. caeni" was mainly present as spherical microclusters at the inner part (low NO2- environment), whereas "Ca. B. sinica" was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of "Ca. J. caeni" at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (Ks) for nitrite and a difference in the maintenance rate (m). In addition, the growth of "Ca. K. stuttgartiensis" could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of "Ca. B. sinica" and "Ca. J. caeni".
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Affiliation(s)
- Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Yuko Narita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Lin Gao
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan; Water Desalination and Reuse Center (WDRC), Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mamoru Oshiki
- Department of Civil Engineering, Nagaoka National College of Technology, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Satoshi Ishii
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan; Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory of BioChemistry, 1479 Gortner Avenue, St. Paul, MN 55108-6106, USA
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan.
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13
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Jasmin C, Anas A, Tharakan B, Jaleel A, Puthiyaveettil V, Narayanane S, Lincy J, Nair S. Diversity of sediment-associated Planctomycetes in the Arabian Sea oxygen minimum zone. J Basic Microbiol 2017; 57:1010-1017. [DOI: 10.1002/jobm.201600750] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 08/23/2017] [Accepted: 08/30/2017] [Indexed: 11/12/2022]
Affiliation(s)
| | - Abdulaziz Anas
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Balu Tharakan
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Abdul Jaleel
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | | | - Saravanane Narayanane
- Centre for Marine Living Resource and Ecology; Ministry of Earth Sciences; Kakkanad, Kochi, Kerala India
| | - Jovitha Lincy
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Shanta Nair
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
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14
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Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One 2017; 12:e0174930. [PMID: 28384184 PMCID: PMC5383146 DOI: 10.1371/journal.pone.0174930] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/18/2017] [Indexed: 12/12/2022] Open
Abstract
Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
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Affiliation(s)
- William B. Ludington
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
- * E-mail:
| | - Thaddeus D. Seher
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
| | - Olin Applegate
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Xunde Li
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Joseph I. Kliegman
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Charles Langelier
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Edward R. Atwill
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Thomas Harter
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Joseph L. DeRisi
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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15
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Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. Sci Rep 2016; 6:28327. [PMID: 27319320 PMCID: PMC4913261 DOI: 10.1038/srep28327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 06/02/2016] [Indexed: 11/09/2022] Open
Abstract
Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all the essential transcripts for anammox metabolism. During the later stage of reactor operation, higher expression of ammonia and nitrite transport proteins and key metabolic enzymes mainly in the bottom large granules facilitated anammox bacteria activity. The high activity resulted in higher growth and multiplication of anammox bacteria and expanded the size of the granules. This conceptual model for large granule formation proposed here may assist in the future design of anammox processes for mainstream wastewater treatment.
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16
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Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM. Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ 2016; 4:e1924. [PMID: 27077014 PMCID: PMC4830246 DOI: 10.7717/peerj.1924] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/21/2016] [Indexed: 01/24/2023] Open
Abstract
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria.
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Affiliation(s)
- Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), 't Horntje (Texel), Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
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17
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Raes EJ, Bodrossy L, Van de Kamp J, Holmes B, Hardman-Mountford N, Thompson PA, McInnes AS, Waite AM. Reduction of the Powerful Greenhouse Gas N2O in the South-Eastern Indian Ocean. PLoS One 2016; 11:e0145996. [PMID: 26800249 PMCID: PMC4723335 DOI: 10.1371/journal.pone.0145996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/29/2015] [Indexed: 11/22/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and a key catalyst of stratospheric ozone depletion. Yet, little data exist about the sink and source terms of the production and reduction of N2O outside the well-known oxygen minimum zones (OMZ). Here we show the presence of functional marker genes for the reduction of N2O in the last step of the denitrification process (nitrous oxide reductase genes; nosZ) in oxygenated surface waters (180–250 O2 μmol.kg-1) in the south-eastern Indian Ocean. Overall copy numbers indicated that nosZ genes represented a significant proportion of the microbial community, which is unexpected in these oxygenated waters. Our data show strong temperature sensitivity for nosZ genes and reaction rates along a vast latitudinal gradient (32°S-12°S). These data suggest a large N2O sink in the warmer Tropical waters of the south-eastern Indian Ocean. Clone sequencing from PCR products revealed that most denitrification genes belonged to Rhodobacteraceae. Our work highlights the need to investigate the feedback and tight linkages between nitrification and denitrification (both sources of N2O, but the latter also a source of bioavailable N losses) in the understudied yet strategic Indian Ocean and other oligotrophic systems.
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Affiliation(s)
- Eric J. Raes
- The Oceans Institute, University of Western Australia, M047 35 Stirling Hwy Crawley, 6009 WA, Australia
- CSIRO Oceans and Atmosphere Flagship, Private Bag 5, Wembley, 6913 WA, Australia
- * E-mail:
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Jodie Van de Kamp
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Bronwyn Holmes
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Nick Hardman-Mountford
- The Oceans Institute, University of Western Australia, M047 35 Stirling Hwy Crawley, 6009 WA, Australia
- CSIRO Oceans and Atmosphere Flagship, Private Bag 5, Wembley, 6913 WA, Australia
| | - Peter A. Thompson
- CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, 7001 TAS, Australia
| | - Allison S. McInnes
- University of Technology, Sydney, Plant Functional Biology & Climate Change, City campus 15 Broadway Ultimo NSW 2007, Australia
| | - Anya M. Waite
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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18
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Chu J, Zhang J, Zhou X, Liu B, Li Y. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments. Curr Microbiol 2015; 71:421-7. [DOI: 10.1007/s00284-015-0851-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/28/2015] [Indexed: 11/28/2022]
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19
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Sonthiphand P, Hall MW, Neufeld JD. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Front Microbiol 2014; 5:399. [PMID: 25147546 PMCID: PMC4123730 DOI: 10.3389/fmicb.2014.00399] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 02/01/2023] Open
Abstract
Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.
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Affiliation(s)
| | - Michael W Hall
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
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20
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Smedile F, Messina E, La Cono V, Yakimov MM. Comparative analysis of deep-sea bacterioplankton OMICS revealed the occurrence of habitat-specific genomic attributes. Mar Genomics 2014; 17:1-8. [PMID: 24937756 DOI: 10.1016/j.margen.2014.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/23/2014] [Accepted: 06/03/2014] [Indexed: 01/20/2023]
Abstract
Bathyal aphotic ocean represents the largest biotope on our planet, which sustains highly diverse but low-density microbial communities, with yet untapped genomic attributes, potentially useful for discovery of new biomolecules, industrial enzymes and pathways. In the last two decades, culture-independent approaches of high-throughput sequencing have provided new insights into structure and function of marine bacterioplankton, leading to unprecedented opportunities to accurately characterize microbial communities and their interactions with the environments. In the present review we focused on the analysis of relatively few deep-sea OMICS studies, completed thus far, to find the specific genomic patterns determining the lifeway and adaptation mechanisms of prokaryotes thriving in the dark deep ocean below the depth of 1000m. Phylogenomic and omic studies provided clear evidence that the bathyal microbial communities are distinct from the epipelagic counterparts and, along with generally larger genomes, possess their own habitat-specific genomic attributes. The high abundance in the deep ocean OMICS of the systems for environmental sensing, signal transduction and metabolic versatility as compared to the epipelagic counterparts is thought to enable the deep-sea bacterioplankton to rapidly adapt to changing environmental conditions associated with resource scarcity and high diversity of energy and carbon substrates in the bathyal biotopes. Together with a versatile heterotrophy, mixotrophy and anaplerosis are thought to enable the deep-sea bacterioplankton to cope with these environmental conditions.
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Affiliation(s)
- Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy.
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