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Chen Z, Wu Y, Dolfing J, Zhuang S, Wang B, Li D, Huang S, Rittmann BE. Complex ammonium oxidation demands visualized resolution. Sci Bull (Beijing) 2024; 69:2478-2482. [PMID: 38604937 DOI: 10.1016/j.scib.2024.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China.
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Dan Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton NJ 08540, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe AZ 85287-5701, USA
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2
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Baker BJ, Hyde E, Leão P. Nature should be the model for microbial sciences. J Bacteriol 2024:e0022824. [PMID: 39158294 DOI: 10.1128/jb.00228-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.
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Affiliation(s)
- Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Emily Hyde
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Pedro Leão
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
- Department of Microbiology-RIBES, Radboud University, Nijmegen, the Netherlands
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3
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Palatinszky M, Herbold CW, Sedlacek CJ, Pühringer D, Kitzinger K, Giguere AT, Wasmund K, Nielsen PH, Dueholm MKD, Jehmlich N, Gruseck R, Legin A, Kostan J, Krasnici N, Schreiner C, Palmetzhofer J, Hofmann T, Zumstein M, Djinović-Carugo K, Daims H, Wagner M. Growth of complete ammonia oxidizers on guanidine. Nature 2024:10.1038/s41586-024-07832-z. [PMID: 39143220 DOI: 10.1038/s41586-024-07832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry1-3. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.
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Affiliation(s)
- Marton Palatinszky
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora (School of Biological Sciences), Te Whare Wānanga o Waitaha (University of Canterbury), Ōtautahi (Christchurch), Aotearoa New Zealand
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dominic Pühringer
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andrew T Giguere
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Kenneth Wasmund
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten K D Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research-UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Richard Gruseck
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Julius Kostan
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Nesrete Krasnici
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Johanna Palmetzhofer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Thilo Hofmann
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Zumstein
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- The Comammox Research Platform, University of Vienna, Vienna, Austria.
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4
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Zhao Z, Amano C, Reinthaler T, Baltar F, Orellana MV, Herndl GJ. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat Commun 2024; 15:6411. [PMID: 39080340 PMCID: PMC11289388 DOI: 10.1038/s41467-024-50867-z] [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: 07/14/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.
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Affiliation(s)
- Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Mónica V Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands.
- Environmental & Climate Research Hub, University of Vienna, Vienna, Austria.
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5
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Zhou Y, Yan A, Yang J, He W, Guo S, Li Y, Wu J, Dai Y, Pan X, Cui D, Pereira O, Teng W, Bi R, Chen S, Fan L, Wang P, Liao Y, Qin W, Sui SF, Zhu Y, Zhang C, Liu Z. Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans. Front Microbiol 2024; 15:1367658. [PMID: 38737410 PMCID: PMC11082331 DOI: 10.3389/fmicb.2024.1367658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions. Methods In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria. Results and Discussion Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.
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Affiliation(s)
- Yangkai Zhou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - An Yan
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jiawen Yang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuai Guo
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yifan Li
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jing Wu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yanchao Dai
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Xijiang Pan
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Dongyu Cui
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Olivier Pereira
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, China
| | - Wenkai Teng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ran Bi
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Peiyi Wang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yan Liao
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Wei Qin
- School of Biological Sciences and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Sen-Fang Sui
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
- Advanced Institute for Ocean Research, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zheng Liu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Wang J, Wen X, Fang Z, Gao P, Wu P, Li X, Zeng G. Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:24099-24112. [PMID: 38436843 DOI: 10.1007/s11356-024-32707-1] [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: 10/23/2023] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Studies published recently proposed that ammonia-oxidizing archaea (AOA) may be beneficial for hypersaline (salinity > 50 g NaCl L-1) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L-1 in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance to the challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.
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Affiliation(s)
- Jiale Wang
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China.
| | - Xin Wen
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China
| | - Zhuoan Fang
- Chongqing International Investment Consultation Group Co., Ltd., Chongqing, 400000, People's Republic of China
| | - Pei Gao
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China
| | - Pei Wu
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China
| | - Xiang Li
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China
| | - Guoming Zeng
- School of Civil Engineering and Architecture, Chongqing University of Science and Technology, Chongqing, 401331, People's Republic of China
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7
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Lu N, Wang L, Zheng TF, Peng Y, Liu SJ, Wen HR. A dinuclear Cd II cluster-based stable luminescent metal-organic framework for the consecutive and visual detection of H 2PO 4- and OCN . Dalton Trans 2024; 53:5160-5166. [PMID: 38380950 DOI: 10.1039/d3dt03523a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Due to their hazard to biological systems, it is urgent to develop materials that can rapidly and sensitively detect the concentration of H2PO4- and OCN- ions. In this work, a new CdII-based luminescent metal-organic framework with the formula [Cd(BTDB)(2,6-BBIP)]n (JXUST-47, H2BTDB = (benzo[c][1,2,5]thiadiazole-4,7-diyl)dibenzoic acid, 2,6-BBIP = 2,6-bis(benzimidazol-1-yl)pyridine) and sql topology was successfully synthesized using a mixed-ligand strategy. JXUST-47 shows good chemical and thermal stability. It also exhibits weak quenching and fluorescence blue shift for H2PO4- and red shift for OCN-, with the detection limits of 0.106 and 0.128 mM, respectively. In addition, considering the demand for H2PO4- and OCN- ion detection, by combining this with the functions of a smartphone, the chroma of photographs have been used to realize the consecutive visual detection of the concentration of these ions.
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Affiliation(s)
- Na Lu
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
| | - Li Wang
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
| | - Teng-Fei Zheng
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
| | - Yan Peng
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
| | - Sui-Jun Liu
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
| | - He-Rui Wen
- School of Chemistry and Chemical Engineering, Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi Province, P.R. China.
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8
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Li C, Liao H, Xu L, Wang C, Yao M, Wang J, Li X. Comparative genomics reveals the adaptation of ammonia-oxidising Thaumarchaeota to arid soils. Environ Microbiol 2024; 26:e16601. [PMID: 38454574 DOI: 10.1111/1462-2920.16601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Thaumarchaeota are predominant in oligotrophic habitats such as deserts and arid soils, but their adaptations to these arid conditions are not well understood. In this study, we assembled 23 Thaumarchaeota genomes from arid and semi-arid soils collected from the Inner Mongolia Steppe and the Qinghai-Tibet Plateau. Using a comparative genomics approach, integrated with 614 Thaumarchaeota genomes from public databases, we identified the traits and evolutionary forces that contribute to their adaptations to aridity. Our results showed that the newly assembled genomes represent an early diverging group within the lineage of ammonia-oxidising Thaumarchaeota. While the genomic functions previously identified in arid soil lineages were conserved across terrestrial, shallow-ocean and deep-ocean lineages, several traits likely contribute to Thaumarchaeota's adaptation to aridity. These include chlorite dismutase, arsenate reductase, V-type ATPase and genes dealing with oxidative stresses. The acquisition and loss of traits at the last common ancestor of arid soil lineages may have facilitated the specialisation of Thaumarchaeota in arid soils. Additionally, the acquisition of unique adaptive traits, such as a urea transporter, Ca2+ :H+ antiporter, mannosyl-3-phosphoglycerate synthase and phosphatase, DNA end-binding protein Ku and phage shock protein A, further distinguishes arid soil Thaumarchaeota. This study provides evidence for the adaptations of Thaumarchaeota to arid soil, enhancing our understanding of the nitrogen and carbon cycling driven by Thaumarchaeota in drylands.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Haijun Liao
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Changting Wang
- Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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9
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Qin W, Wei SP, Zheng Y, Choi E, Li X, Johnston J, Wan X, Abrahamson B, Flinkstrom Z, Wang B, Li H, Hou L, Tao Q, Chlouber WW, Sun X, Wells M, Ngo L, Hunt KA, Urakawa H, Tao X, Wang D, Yan X, Wang D, Pan C, Weber PK, Jiang J, Zhou J, Zhang Y, Stahl DA, Ward BB, Mayali X, Martens-Habbena W, Winkler MKH. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat Microbiol 2024; 9:524-536. [PMID: 38297167 DOI: 10.1038/s41564-023-01593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.
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Affiliation(s)
- Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Stephany P Wei
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Eunkyung Choi
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - Xiangpeng Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | | | - Xianhui Wan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Baozhan Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hanyan Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Lei Hou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wyatt W Chlouber
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xin Sun
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Michael Wells
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Long Ngo
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Xuanyu Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Dongyu Wang
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Chongle Pan
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
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10
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Rasmussen AN, Francis CA. Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. THE ISME JOURNAL 2024; 18:wrae148. [PMID: 39077992 PMCID: PMC11334935 DOI: 10.1093/ismejo/wrae148] [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: 01/15/2024] [Revised: 05/24/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]
Abstract
Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
- Oceans Department, Stanford University, Stanford, CA 94305, United States
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11
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Oggerin M, Viver T, Brüwer J, Voß D, García-Llorca M, Zielinski O, Orellana LH, Fuchs BM. Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre. THE ISME JOURNAL 2024; 18:wrae155. [PMID: 39096506 PMCID: PMC11366302 DOI: 10.1093/ismejo/wrae155] [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: 12/21/2023] [Revised: 05/17/2024] [Accepted: 08/02/2024] [Indexed: 08/05/2024]
Abstract
One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.
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Affiliation(s)
- Monike Oggerin
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Tomeu Viver
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Jan Brüwer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Daniela Voß
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshafen, Germany
| | - Marina García-Llorca
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Oliver Zielinski
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshafen, Germany
- Leibniz Institute for Baltic Sea Research Warnemünde, D-18119 Rostock, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
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12
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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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13
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Tang X, Li Y, Liu M, Hou L, Han P. Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:167333. [PMID: 37748616 DOI: 10.1016/j.scitotenv.2023.167333] [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: 06/25/2023] [Revised: 09/01/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L-1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.
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Affiliation(s)
- Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ye Li
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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14
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Liu Q, Chen Y, Xu XW. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Front Microbiol 2023; 14:1273211. [PMID: 38156017 PMCID: PMC10753782 DOI: 10.3389/fmicb.2023.1273211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.
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Affiliation(s)
- Qian Liu
- Donghai Laboratory, Zhoushan, Zhejiang, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuhao Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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15
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Bender SF, Schulz S, Martínez-Cuesta R, Laughlin RJ, Kublik S, Pfeiffer-Zakharova K, Vestergaard G, Hartman K, Parladé E, Römbke J, Watson CJ, Schloter M, van der Heijden MGA. Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses. THE NEW PHYTOLOGIST 2023; 240:2020-2034. [PMID: 37700504 DOI: 10.1111/nph.19252] [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: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.
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Affiliation(s)
- S Franz Bender
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Rubén Martínez-Cuesta
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ronald J Laughlin
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Kristina Pfeiffer-Zakharova
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kyle Hartman
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jörg Römbke
- ECT Ökotoxikologie GmbH, Böttgerstr. 2-14, D-65439, Flörsheim, Germany
| | - Catherine J Watson
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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16
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Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li DD, Tu Q. Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front Microbiol 2023; 14:1291242. [PMID: 38053549 PMCID: PMC10694361 DOI: 10.3389/fmicb.2023.1291242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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17
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Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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18
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [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: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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19
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Liu H, Jing H, Wang F. Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Front Microbiol 2023; 14:1268790. [PMID: 37840747 PMCID: PMC10568479 DOI: 10.3389/fmicb.2023.1268790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.
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Affiliation(s)
- Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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20
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [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: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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21
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Su Z, Liu T, Guo J, Zheng M. Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12557-12570. [PMID: 37589598 PMCID: PMC10470456 DOI: 10.1021/acs.est.3c00636] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing bacteria (NOB). Since NOB were first isolated 130 years ago, the understanding of the phylogenetical and physiological diversities of NOB has been gradually deepened. In recent endeavors of advanced biological nitrogen removal, NOB have been more considered as a troublesome disruptor, and strategies on NOB suppression often fail in practice after long-term operation due to the growth of specific NOB that are able to adapt to even harsh conditions. In line with a review of the history of currently known NOB genera, a phylogenetic tree is constructed to exhibit a wide range of NOB in different phyla. In addition, the growth behavior and metabolic performance of different NOB strains are summarized. These specific features of various NOB (e.g., high oxygen affinity of Nitrospira, tolerance to chemical inhibitors of Nitrobacter and Candidatus Nitrotoga, and preference to high temperature of Nitrolancea) highlight the differentiation of the NOB ecological niche in biological nitrogen processes and potentially support their adaptation to different suppression strategies (e.g., low dissolved oxygen, chemical treatment, and high temperature). This review implicates the acquired physiological characteristics of NOB to their emergence from a genomic and ecological perspective and emphasizes the importance of understanding physiological characterization and genomic information in future wastewater treatment studies.
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Affiliation(s)
- Zicheng Su
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Tao Liu
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Min Zheng
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
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22
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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. THE ISME JOURNAL 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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23
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Wang C, Zhu WJ, Ding HT, Liu NH, Cao HY, Suo CL, Liu ZK, Zhang Y, Sun ML, Fu HH, Li CY, Chen XL, Zhang YZ, Wang P. Structural and molecular basis for urea recognition by Prochlorococcus. J Biol Chem 2023; 299:104958. [PMID: 37380083 PMCID: PMC10392092 DOI: 10.1016/j.jbc.2023.104958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Nitrogen (N) is an essential element for microbial growth and metabolism. The growth and reproduction of microorganisms in more than 75% of areas of the ocean are limited by N. Prochlorococcus is numerically the most abundant photosynthetic organism on the planet. Urea is an important and efficient N source for Prochlorococcus. However, how Prochlorococcus recognizes and absorbs urea still remains unclear. Prochlorococcus marinus MIT 9313, a typical Cyanobacteria, contains an ABC-type transporter, UrtABCDE, which may account for the transport of urea. Here, we heterologously expressed and purified UrtA, the substrate-binding protein of UrtABCDE, detected its binding affinity toward urea, and further determined the crystal structure of the UrtA/urea complex. Molecular dynamics simulations indicated that UrtA can alternate between "open" and "closed" states for urea binding. Based on structural and biochemical analyses, the molecular mechanism for urea recognition and binding was proposed. When a urea molecule is bound, UrtA undergoes a state change from open to closed surrounding the urea molecule, and the urea molecule is further stabilized by the hydrogen bonds supported by the conserved residues around it. Moreover, bioinformatics analysis showed that ABC-type urea transporters are widespread in bacteria and probably share similar urea recognition and binding mechanisms as UrtA from P. marinus MIT 9313. Our study provides a better understanding of urea absorption and utilization in marine bacteria.
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Affiliation(s)
- Chen Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wen-Jing Zhu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Tao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hai-Yan Cao
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chuan-Lei Suo
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ze-Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yi Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Mei-Ling Sun
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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24
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Zhang Y, Liu T, Li MM, Hua ZS, Evans P, Qu Y, Tan S, Zheng M, Lu H, Jiao JY, Lücker S, Daims H, Li WJ, Guo J. Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira. THE ISME JOURNAL 2023:10.1038/s41396-023-01409-w. [PMID: 37069235 DOI: 10.1038/s41396-023-01409-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.
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Affiliation(s)
- Yan Zhang
- School of Environmental and Chemical Engineering, Foshan University, Foshan, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
| | - Paul Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Yanni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia.
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25
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Parada AE, Mayali X, Weber PK, Wollard J, Santoro AE, Fuhrman JA, Pett-Ridge J, Dekas AE. Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota. Environ Microbiol 2023; 25:689-704. [PMID: 36478085 DOI: 10.1111/1462-2920.16299] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
Marine Group I (MGI) Thaumarchaeota were originally described as chemoautotrophic nitrifiers, but molecular and isotopic evidence suggests heterotrophic and/or mixotrophic capabilities. Here, we investigated the quantity and composition of organic matter assimilated by individual, uncultured MGI cells from the Pacific Ocean to constrain their potential for mixotrophy and heterotrophy. We observed that most MGI cells did not assimilate carbon from any organic substrate provided (glucose, pyruvate, oxaloacetate, protein, urea, and amino acids). The minority of MGI cells that did assimilate it did so exclusively from nitrogenous substrates (urea, 15% of MGI and amino acids, 36% of MGI), and only as an auxiliary carbon source (<20% of that subset's total cellular carbon was derived from those substrates). At the population level, MGI assimilation of organic carbon comprised just 0.5%-11% of total biomass carbon. We observed extensive assimilation of inorganic carbon and urea- and amino acid-derived nitrogen (equal to that from ammonium), consistent with metagenomic and metatranscriptomic analyses performed here and previously showing a widespread potential for MGI to perform autotrophy and transport and degrade organic nitrogen. Our results constrain the quantity and composition of organic matter used by MGI and suggest they use it primarily to meet nitrogen demands for anabolism and nitrification.
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Affiliation(s)
- Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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26
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Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
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27
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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28
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Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs. Mar Genomics 2022; 66:100994. [DOI: 10.1016/j.margen.2022.100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
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Qi H, Huang D, Wang F, Ye M, Jiang X. Spatial dynamics of prokaryotic microbial communities in sediments of the Yellow Sea: Assembly process, co-occurrence relationships, and environmental implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115645. [PMID: 35797911 DOI: 10.1016/j.jenvman.2022.115645] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Marine sediment microorganisms play an important role in the biogeochemical cycle of elements and the transformation of exogenous pollutants; therefore, it is important to study the microbial assembly process and inter taxa associations. In this study, we investigated the profiles and assembly processes of microbial communities of sediments collected from 19 points in the Yellow Sea. As revealed by 16S rRNA sequencing, Proteobacteria (43.11%-65.54%) was the dominant phylum in marine sediment. Further, the physicochemical properties of sediments were significantly influenced by depth (P < 0.05), and the effects of homogeneous selection became greater with increasing depth. The microbial species located in marine sediment at 35°N had a significantly higher co-occurrence relationship (82.76%) than those at 34°N (57.99%) and 36°N (54.07%). Additionally, the microbial community structure of the sediments changed significantly at the genus level with strong fluctuations in the physicochemical properties. By contrast, the carbon, nitrogen, and sulfur associated functional gene diversity and abundance showed no clear variation among different locations, indicating the probable functional redundancy and a potential functional gene pool of the microbes in marine sediments. This study could provide new insights into the composition of microorganisms in sediments in the Yellow Sea, the driving force of microbial diversity, the assembly process, the modes of species' co-occurrence, and their ecological functions.
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Affiliation(s)
- Huiyuan Qi
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Fenghe Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
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30
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Kraft B, Canfield DE. Microbe Profile: Nitrosopumilus maritimus. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35852832 DOI: 10.1099/mic.0.001207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nitrosopumilus maritimus is a marine ammonia-oxidizing archaeon with a high affinity for ammonia. It fixes carbon via a modified hydroxypropionate/hydroxybutyrate cycle and shows weak utilization of cyanate as a supplementary energy and nitrogen source. When oxygen is depleted, N. maritimus produces its own oxygen, which may explain its regular occurrence in anoxic waters. Several enzymes of the ammonia oxidation and oxygen production pathways remain to be identified.
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Affiliation(s)
- Beate Kraft
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Donald E Canfield
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.,Key Laboratory of Petroleum Geochemistry, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, PR China.,Danish Institute of Advanced Study, 5230 Odense, Denmark
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31
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Klotz F, Kitzinger K, Ngugi DK, Büsing P, Littmann S, Kuypers MMM, Schink B, Pester M. Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels. THE ISME JOURNAL 2022; 16:1647-1656. [PMID: 35260828 PMCID: PMC9122916 DOI: 10.1038/s41396-022-01216-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 05/09/2023]
Abstract
Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1, corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell-1 d-1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 109 g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.
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Affiliation(s)
- Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - David Kamanda Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany.
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany.
- Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, D-38106, Braunschweig, Germany.
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32
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Zarlenga D, Thompson P, Mitreva M, Rosa BA, Hoberg E. Horizontal gene transfer provides insights into the deep evolutionary history and biology of Trichinella. Food Waterborne Parasitol 2022; 27:e00155. [PMID: 35542181 PMCID: PMC9079694 DOI: 10.1016/j.fawpar.2022.e00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
Evolution involves temporal changes in the characteristics of a species that are subsequently propagated or rejected through natural selection. In the case of parasites, host switching also plays a prominent role in the evolutionary process. These changes are rooted in genetic variation and gene flow where genes may be deleted, mutated (sequence), duplicated, rearranged and/or translocated and then transmitted through vertical gene transfer. However, the introduction of new genes is not driven only by Mendelian inheritance and mutation but also by the introduction of DNA from outside a lineage in the form of horizontal gene transfer between donor and recipient organisms. Once introduced and integrated into the biology of the recipient, vertical inheritance then perpetuates the newly acquired genetic factor, where further functionality may involve co-option of what has become a pre-existing physiological capacity. Upon sequencing the Trichinella spiralis (Clade I) genome, a cyanate hydratase (cyanase) gene was identified that is common among bacteria, fungi, and plants, but rarely observed among other eukaryotes. The sequence of the Trichinella cyanase gene clusters with those derived from the Kingdom Plantae in contrast to the genes found in some Clade III and IV nematodes that cluster with cyanases of bacterial origin. Phylogenetic analyses suggest that the Trichinella cyanase was acquired during the Devonian period and independently from those of other nematodes. These data may help inform us of the deep evolutionary history and ecological connectivity of early ancestors within the lineage of contemporary Trichinella. Further, in many extant organisms, cyanate detoxification has been largely superseded by energy requirements for metabolism. Thus, deciphering the function of Trichinella cyanase may provide new avenues for treatment and control.
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Affiliation(s)
- Dante Zarlenga
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Peter Thompson
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Bruce A. Rosa
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eric Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
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33
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Ren M, Wang J. Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems. THE ISME JOURNAL 2022; 16:1491-1501. [PMID: 35091647 PMCID: PMC9123079 DOI: 10.1038/s41396-022-01199-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 01/05/2022] [Accepted: 01/17/2022] [Indexed: 04/29/2023]
Abstract
Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.
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Affiliation(s)
- Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). THE ISME JOURNAL 2022; 16:1348-1362. [PMID: 34987183 PMCID: PMC9038741 DOI: 10.1038/s41396-021-01177-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 01/22/2023]
Abstract
Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.
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Reji L, Cardarelli EL, Boye K, Bargar JR, Francis CA. Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. THE ISME JOURNAL 2022; 16:1140-1152. [PMID: 34873295 PMCID: PMC8940955 DOI: 10.1038/s41396-021-01167-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 02/03/2023]
Abstract
The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.
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Affiliation(s)
- Linta Reji
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.16750.350000 0001 2097 5006Present Address: Department of Geosciences, Princeton University, Princeton, NJ USA
| | - Emily L. Cardarelli
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.20861.3d0000000107068890Present Address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Kristin Boye
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - John R. Bargar
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Christopher A. Francis
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA
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High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China. Microorganisms 2022; 10:microorganisms10030542. [PMID: 35336118 PMCID: PMC8950554 DOI: 10.3390/microorganisms10030542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Members of the Thaumarchaeota phylum play a key role in nitrogen cycling and are prevalent in a variety of environments including soil, sediment, and seawater. However, few studies have shown the presence of Thaumarchaeota in the terrestrial deep subsurface. Using high-throughput 16S rRNA gene sequencing, this study presents evidence for the high relative abundance of Thaumarchaeota in a biofilm sample collected from the well of Chinese Continental Scientific Drilling at a depth of 2000 m. Phylogenetic analysis showed a close relationship of these thaumarchaeotal sequences with known ammonia-oxidizing archaea (AOA) isolates, suggesting the presence of AOA in the deep metamorphic environment of eastern China which is believed to be oxic. Based on fluid geochemistry and FAProTax functional prediction, a pathway of nitrogen cycling is proposed. Firstly, heterotrophic nitrogen fixation is executed by diazotrophic bacteria coupled with methane oxidation. Then, ammonia is oxidized to nitrite by AOA, and nitrite is further oxidized to nitrate by bacteria within the phylum Nitrospirae. Denitrification and anaerobic ammonia oxidation occur slowly, leading to nitrate accumulation in the subsurface. With respect to biogeochemistry, the reaction between downward diffusing O2 and upward diffusing CH4 potentially fuels the ecosystem with a high relative abundance of Thaumarchaeota.
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37
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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Mao X, Chen J, van Oosterhout C, Zhang H, Liu G, Zhuang Y, Mock T. Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. THE ISME JOURNAL 2022; 16:602-605. [PMID: 34408267 PMCID: PMC8776842 DOI: 10.1038/s41396-021-01081-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO3 by the activity of nitrifying bacteria.
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Affiliation(s)
- Xuewei Mao
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China ,grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Jianwei Chen
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China ,grid.21155.320000 0001 2034 1839Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555 China
| | - Cock van Oosterhout
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Huan Zhang
- grid.63054.340000 0001 0860 4915Department of Marine Sciences, University of Connecticut, Groton, CT 06340 USA
| | - Guangxing Liu
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yunyun Zhuang
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Thomas Mock
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 2022; 7:e0127021. [PMID: 35076275 PMCID: PMC8788347 DOI: 10.1128/msystems.01270-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.
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Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517451. [PMID: 35094062 PMCID: PMC9075580 DOI: 10.1093/femsre/fuac006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022] Open
Abstract
Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.
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Affiliation(s)
- Jasmine S Berg
- Corrresponding author: Géopolis, Quartier Unil-Mouline, Université de Lausanne, 1015 Lausanne, Switzerland. E-mail:
| | - Soeren Ahmerkamp
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1090, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
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Han Y, Zhang M, Chen X, Zhai W, Tan E, Tang K. Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea. ENVIRONMENT INTERNATIONAL 2022; 158:106889. [PMID: 34619534 DOI: 10.1016/j.envint.2021.106889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Eutrophication-induced water deoxygenation occurs continually in coastal oceans, and alters community structure, metabolic processes, and the energy shunt, resulting in a major threat to the ecological environment. Seasonal deoxygenation events have occurred in the Bohai Sea (China), however, how these affect the functional activity of microorganisms remains unclear. Here, through the use of absolute quantification of 16S rRNA genes amplicon sequencing and metatranscriptomics approaches, we investigated the structure of the microbial community and the patterns of transcriptional activity in deoxygenated seawaters. The dominant phyla were Proteobacteria (average value, 1.4 × 106 copies ml-1), Cyanobacteria (3.7 × 105 copies ml-1), Bacteroidetes (2.7 × 105 copies ml-1), and the ammonia-oxidizing archaea Thaumarchaeota (1.9 × 105 copies ml-1). Among the various environmental factors, dissolved oxygen, pH and temperature displayed the most significant correlation with microbial community composition and functional activity. Metatranscriptomic data showed high transcriptional activity of Thaumarchaeota in the deoxygenated waters, with a significant increase in the expression of core genes representing ammonia oxidation, ammonia transport, and carbon fixation (3-hydroxypropionic acid/4-hydroxybutyric acid cycle) pathways. The transcripts of Cyanobacteria involved in photosynthesis and carbon fixation (Calvin-Benson-Bassham cycle) significantly decreased in low oxygen waters. Meanwhile, the transcripts for the ribulose bisphosphate carboxylase-encoding gene shifted from being assigned to photoautotrophic to chemoautotrophic organisms in surface and bottom waters, respectively. Moreover, the transcription profile indicated that heterotrophs play a critical role in transforming low-molecular-weight dissolved organic nitrogen. Elevated abundances of transcripts related to microbial antioxidant activity corresponded to an enhanced aerobic metabolism of Thaumarchaeota in the low oxygen seawater. In general, our transcriptional evidences showed a population increase of Thaumarchaeota, especially the coastal ecotype of ammonia oxidizers, in low oxygen aquatic environments, and indicated an enhanced contribution of chemolithoautotrophic carbon fixation to carbon flow.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Weidong Zhai
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, Shandong, PR China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, Hainan, PR China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China.
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Vázquez-Campos X, Kinsela AS, Bligh MW, Payne TE, Wilkins MR, Waite TD. Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. Front Microbiol 2021; 12:732575. [PMID: 34737728 PMCID: PMC8561730 DOI: 10.3389/fmicb.2021.732575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
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Affiliation(s)
- Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew S. Kinsela
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Mark W. Bligh
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Timothy E. Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, Australia
| | - Marc R. Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - T. David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
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Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments. ISME JOURNAL 2021; 15:3657-3667. [PMID: 34158628 PMCID: PMC8630020 DOI: 10.1038/s41396-021-01041-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/08/2022]
Abstract
Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10-19-10-17 W cell-1, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.
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Wang Y, Zhao R, Liu L, Li B, Zhang T. Selective enrichment of comammox from activated sludge using antibiotics. WATER RESEARCH 2021; 197:117087. [PMID: 33819658 DOI: 10.1016/j.watres.2021.117087] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 05/04/2023]
Abstract
While the ubiquitous presence of comammox in engineered systems provides the foundation of developing a novel biological nitrogen removal process, factors contributing to the comammox dynamics in engineered systems have not been well resolved. Here, we investigate the long-term effects of ten different antibiotics on microbial community dynamics in activated sludge and the results show that both types and concentrations of antibiotics affect the taxonomic composition of nitrifiers, including comammox, ammonia-oxidizing bacteria, and canonical nitrite-oxidizing bacteria. Specifically, phylogenetically different comammox Nitrospira were selectively enriched by four types of antibiotics (i.e., ampicillin, kanamycin, lincomycin, and trimethoprim). Comparative genomic analysis of the four newly identified comammox clade A Nitrospira revealed that the comammox enriched by antibiotics shared the conserved key metabolic potentials, such as carbon fixation, complete ammonia oxidation, and utilization of hydrogen as alternative electron donors, among the known comammox organisms. Comammox strains enriched in this study also encoded genes involved in formate and cyanate metabolism that were recently reported in comammox clade A organisms from wastewater treatment systems. Our findings highlight that the comammox in activated sludge ecosystems possess high metabolic versatility than previously recognized and could be selectively enriched by some antibiotics.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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46
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Cheng YX, Chen J, Wu D, Liu YS, Yang YQ, He LX, Ye P, Zhao JL, Liu SS, Yang B, Ying GG. Highly enhanced biodegradation of pharmaceutical and personal care products in a novel tidal flow constructed wetland with baffle and plants. WATER RESEARCH 2021; 193:116870. [PMID: 33545438 DOI: 10.1016/j.watres.2021.116870] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 05/18/2023]
Abstract
Research on decentralized wastewaters deserves special focus due to the potential abundance of emerging organic pollutants including pharmaceutical and personal care products (PPCPs), which might pose serious threats to the local water bodies and even to human health. Constructed wetland (CW) is a common decentralized wastewater treatment technology, with a certain ability to eliminate PPCPs. Nonetheless, PPCPs removal in common CWs is frequently challenging, besides, the removal mechanism remains elusive. Based on our previous study, tidal flow constructed wetlands (TFCWs) is effective in nitrogen removal. Here, 3 TFCWs with different modifications (baffle, plants, both baffle and plants) were constructed to treat raw domestic sewage and specifically to evaluate the removal efficiencies and mechanism of PPCPs. 24 PPCPs including 7 antibiotics, 8 steroid hormones and 9 biocides were detected in the level of 1.10 ± 0.29 ng/L-799 ± 10.6 ng/L in the influents. Consequently, we found that modification with both baffle and plants significantly influenced the removal of PPCPs. Moreover, the highest removal rates of biocides (97.1 ± 0.29%), steroid hormones (99.8 ± 0.02%), and antibiotics (90.2 ± 1.60%) were achieved via both baffles and plants in TFCWs. Based on the mass balance analysis, microbial degradation dominated the removal of PPCPs with a percentage higher than 85.7%, followed by substrate adsorption (5.22 × 10-2-14.3%) and plant uptake (1.66 × 10-3-0.44%). Further, 16S rDNA sequencing analysis revealed that the presence of baffle and plants improve the removal efficiency of PPCPs by means of enhancing microbial diversity and changing dominant microorganisms. Moreover, Thaumarchaeota was potentially the key microorganism in the phylum level for PPCPs elimination by TFCWs through LEfSe (linear discriminant analysis (LDA) effect size) analysis. These findings provide new insights into the removal of PPCPs in CWs.
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Affiliation(s)
- Yu-Xiao Cheng
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Jun Chen
- Guangdong Provincial Engineering Technology Research Center for Life and Health of River&Lake, Pearl River Hydraulic Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510611, China
| | - Dan Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China.
| | - Yong-Qiang Yang
- CAS Key Laboratory of Mineralogy and Metallogeny/Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Pu Ye
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Shuang-Shuang Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Bin Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
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Li J, Hua ZS, Liu T, Wang C, Li J, Bai G, Lücker S, Jetten MSM, Zheng M, Guo J. Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor. ISME COMMUNICATIONS 2021; 1:7. [PMID: 37938245 PMCID: PMC9723585 DOI: 10.1038/s43705-021-00005-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.
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Affiliation(s)
- Jiyun Li
- School of Environment, Tsinghua University, Beijing, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Tao Liu
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing, China.
| | - Jie Li
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Ge Bai
- School of Environment, Tsinghua University, Beijing, China
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Min Zheng
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| | - Jianhua Guo
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
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Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD. Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. WATER RESEARCH 2021; 191:116798. [PMID: 33444853 DOI: 10.1016/j.watres.2020.116798] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 05/04/2023]
Abstract
Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.
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Affiliation(s)
- Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Craig W Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Man-Young Jung
- Division of Biology Education, Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, South Korea; Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Faculty of Science Education, Jeju National University, Jeju 6324, South Korea
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, Washington, United States; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Du
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Xiaoyan Li
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China; Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, China.
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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Anoxic chlorophyll maximum enhances local organic matter remineralization and nitrogen loss in Lake Tanganyika. Nat Commun 2021; 12:830. [PMID: 33547297 PMCID: PMC7864930 DOI: 10.1038/s41467-021-21115-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023] Open
Abstract
In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone. Enigmatic blooms of phytoplankton in aquatic oxygen-deficient zones could exacerbate depletion of nitrogen. Here the authors perform stable isotope experiments on the oxygen-deficient waters of Lake Tanganyika in Africa, finding that blooms drive down fixed nitrogen and could expand as a result of climate change.
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