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Kong L, Wang Y, Cui D, He W, Zhang C, Zheng C. Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics. CHEMOSPHERE 2024:142500. [PMID: 38852635 DOI: 10.1016/j.chemosphere.2024.142500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6∼800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1 including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.
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Affiliation(s)
- Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; EIT Institute for Advanced Study, Ningbo, Zhejiang 315200, China
| | - Yi Wang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; EIT Institute for Advanced Study, Ningbo, Zhejiang 315200, China.
| | - Dongyu Cui
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chunmiao Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; EIT Institute for Advanced Study, Ningbo, Zhejiang 315200, China
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Beeckman F, Annetta L, Corrochano-Monsalve M, Beeckman T, Motte H. Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition. Trends Microbiol 2024; 32:590-601. [PMID: 37973432 DOI: 10.1016/j.tim.2023.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Laure Annetta
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain; Instituto Multidisciplinar Para el Estudio del Medio 'Ramon Margalef', Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Spain
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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Cyphert EL, Nand S, Franco G, Hajkowski M, Soto L, Lee DM, Ferner M, Zabin C, Blumenthal J, Deck A, Boyer K, Burrus K, Hernandez CJ, Anand A. Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594453. [PMID: 38798377 PMCID: PMC11118425 DOI: 10.1101/2024.05.15.594453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Heron's Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.
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Affiliation(s)
| | | | | | | | | | | | - Matt Ferner
- San Francisco Bay National Estuarine Research Reserve
| | | | | | - Anna Deck
- San Francisco Bay National Estuarine Research Reserve
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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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Shaaban M. Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120393. [PMID: 38364533 DOI: 10.1016/j.jenvman.2024.120393] [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: 11/10/2023] [Revised: 01/07/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.
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Affiliation(s)
- Muhammad Shaaban
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.
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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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Martocello DE, Wankel SD. Physiological Influence of Fe and Cu Availability on Nitrogen Isotope Fractionation during Ammonia Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:421-431. [PMID: 38147309 DOI: 10.1021/acs.est.3c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Microbially mediated cycling processes play central roles in regulating the speciation and availability of nitrogen, a vital nutrient with wide implications for agriculture, water quality, wastewater treatment, ecosystem health, and climate change. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by bacteria (AOB) and archaea (AOA) that require the trace metal micronutrients copper (Cu) and iron (Fe) for growth and metabolic catalysis. While stable isotope analyses for constraining nitrogen cycling are commonly used, it is unclear whether metal availability may modulate expression of stable isotope fractionation during ammonia oxidation, by varying growth or through regulation of metabolic metalloenzymes. We present the first study examining the influence of Fe and Cu availability on the kinetic nitrogen isotope effect in ammonia oxidation (15εAO). We report a general independence of 15εAO from the growth rate in AOB, except at a low temperature (10 °C). With AOA Nitrosopumilus maritimus SCM1, however, 15εAO decreases nonlinearly at lower oxidation rates. We examine assumptions involved in the interpretation of 15εAO values and suggest these dynamics may arise from physiological constraints that push the system toward isotopic equilibrium. These results suggest important links between isotope fractionation and environmental constraints on physiology in these key N cycling microorganisms.
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Affiliation(s)
- Donald E Martocello
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Scott D Wankel
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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Jia C, Zhou G, Ma L, Qiu X, Zhang J, Wang J, Zhang C, Chen L, Ma D, Zhao Z, Xue Z. The addition of discrimination inhibitors stimulations discrimination potential and N 2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems. Front Microbiol 2024; 14:1337507. [PMID: 38264480 PMCID: PMC10803610 DOI: 10.3389/fmicb.2023.1337507] [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: 11/13/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level. Methods In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation. Results The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA. Conclusion The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.
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Affiliation(s)
- Chunhua Jia
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guixiang Zhou
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ling Ma
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiuwen Qiu
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Jiabao Zhang
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jingkuan Wang
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Congzhi Zhang
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lin Chen
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Donghao Ma
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhanhui Zhao
- School of Geomatics and Urban Spatial Informatics, Henan University of Urban Construction, Pingdingshan, Henan, China
| | - Zaiqi Xue
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Beeckman F, Drozdzecki A, De Knijf A, Audenaert D, Beeckman T, Motte H. High-throughput assays to identify archaea-targeting nitrification inhibitors. FRONTIERS IN PLANT SCIENCE 2024; 14:1283047. [PMID: 38259951 PMCID: PMC10800436 DOI: 10.3389/fpls.2023.1283047] [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: 08/25/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 -) and then to nitrate (NO3 -). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 - leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Andrzej Drozdzecki
- Screening Core, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Dominique Audenaert
- Screening Core, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
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10
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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [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: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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11
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Ding F, He T, Qi X, Zhang H, An L, Xu S, Zhang X. Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167653. [PMID: 37806577 DOI: 10.1016/j.scitotenv.2023.167653] [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: 08/03/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.
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Affiliation(s)
- Fan Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Tianjiao He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xing'e Qi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hui Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China; The College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Shijian Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xinfang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China.
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12
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [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: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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13
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Beeckman F, Drozdzecki A, De Knijf A, Corrochano-Monsalve M, Bodé S, Blom P, Goeminne G, González-Murua C, Lücker S, Boeckx P, Stevens CV, Audenaert D, Beeckman T, Motte H. Drug discovery-based approach identifies new nitrification inhibitors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118996. [PMID: 37725864 DOI: 10.1016/j.jenvman.2023.118996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Andrzej Drozdzecki
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Samuel Bodé
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Pascal Boeckx
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian V Stevens
- Synthesis, Bioresources and Bioorganic Chemistry Research Group (SynBioC), Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dominique Audenaert
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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14
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Ros-Rocher N, Brunet T. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Anim Cogn 2023; 26:1767-1782. [PMID: 37067637 PMCID: PMC10770216 DOI: 10.1007/s10071-023-01776-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: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process.
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Affiliation(s)
- Núria Ros-Rocher
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Thibaut Brunet
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France.
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15
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Gwak JH, Awala SI, Kim SJ, Lee SH, Yang EJ, Park J, Jung J, Rhee SK. Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica. J Microbiol 2023; 61:967-980. [PMID: 38062325 DOI: 10.1007/s12275-023-00090-0] [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: 08/12/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Sang-Hoon Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eun-Jin Yang
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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16
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Sharpe G, Zhao L, Meyer MG, Gong W, Burns SM, Tagliabue A, Buck KN, Santoro AE, Graff JR, Marchetti A, Gifford S. Synechococcus nitrogen gene loss in iron-limited ocean regions. ISME COMMUNICATIONS 2023; 3:107. [PMID: 37783796 PMCID: PMC10545762 DOI: 10.1038/s43705-023-00314-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptations to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose that nitrate and nitrite assimilation gene loss in Synechococcus may represent an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export.
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Affiliation(s)
- Garrett Sharpe
- Environment Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liang Zhao
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meredith G Meyer
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Weida Gong
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M Burns
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | | | - Kristen N Buck
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Jason R Graff
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Adrian Marchetti
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Gifford
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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17
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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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18
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Choi E, Chaudhry SI, Martens-Habbena W. Role of Nitric Oxide in Hydroxylamine Oxidation by Ammonia-Oxidizing Bacteria. Appl Environ Microbiol 2023; 89:e0217322. [PMID: 37439697 PMCID: PMC10467338 DOI: 10.1128/aem.02173-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2- production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2- production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions.
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Affiliation(s)
- Eunkyung Choi
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
| | - Sana I. Chaudhry
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
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19
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Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P. Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasit Vectors 2023; 16:226. [PMID: 37415204 DOI: 10.1186/s13071-023-05842-w] [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: 03/13/2023] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial. METHODS In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions. RESULTS First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release. CONCLUSION These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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20
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Kumar A, Matsuoka M, Matsuyama A, Yoshida M, Zhang KYJ. Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5172-5184. [PMID: 36967599 DOI: 10.1021/acs.jafc.3c00896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The usage of nitrification inhibitors is one of the strategies that reduce or slow down the denitrification process to prevent nitrogen loss to the atmosphere in the form of N2O. Directly targeting microbial denitrification could be one of the mitigation strategies; however, until now little efforts have been devoted toward the development of denitrification inhibitors. Here, we have identified small-molecule inhibitors of one of the proteins involved in the fungal denitrification pathway. Specifically, virtual screening was employed to identify the inhibitors of copper-containing nitrite reductase (FoNirK) of the filamentous fungus Fusarium oxysporum. Three series of chemical compounds were identified, out of which compounds belonging to two chemical scaffolds inhibited FoNirK enzymatic activity in low micromolar ranges. Several compounds also displayed moderate inhibition of fungal denitrification activity in vivo. Evaluation of in vitro activity against NirK from denitrifying bacterium Achromobacter xylosoxidans (AxNirK) and in vivo bacterial denitrification revealed a similar inhibitory profile.
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Affiliation(s)
- Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Matsuoka
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihisa Matsuyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, and Collaboerative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, and Collaboerative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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21
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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22
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Gong JC, Jin H, Li BH, Tian Y, Liu CY, Li PF, Liu Q, Ingeniero RCO, Yang GP. Emissions of Nitric Oxide from Photochemical and Microbial Processes in Coastal Waters of the Yellow and East China Seas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4039-4049. [PMID: 36808991 DOI: 10.1021/acs.est.2c08978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nitric oxide (NO) is an atmospheric pollutant and climate forcer as well as a key intermediary in the marine nitrogen cycle, but the ocean's NO contribution and production mechanisms remain unclear. Here, high-resolution NO observations were conducted simultaneously in the surface ocean and the lower atmosphere of the Yellow Sea and the East China Sea; moreover, NO production from photolysis and microbial processes was analyzed. The NO sea-air exchange showed uneven distributions (RSD = 349.1%) with an average flux of 5.3 ± 18.5 × 10-17 mol cm-2 s-1. In coastal waters where nitrite photolysis was the predominant source (89.0%), NO concentrations were remarkably higher (84.7%) than the overall average of the study area. The NO from archaeal nitrification accounted for 52.8% of all microbial production (11.0%). We also examined the relationship between gaseous NO and ozone which helped identify sources of atmospheric NO. The sea-to-air flux of NO in coastal waters was narrowed by contaminated air with elevated NO concentrations. These findings indicate that the emissions of NO from coastal waters, mainly controlled by reactive nitrogen inputs, will increase with the reduced terrestrial NO discharge.
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Affiliation(s)
- Jiang-Chen Gong
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hong Jin
- Shandong Qingdao Ecological Environment Monitoring Center, Qingdao 266003, China
| | - Bing-Han Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Ye Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Chun-Ying Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Pei-Feng Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Qian Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | | | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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23
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Oudova-Rivera B, Wright CL, Crombie AT, Murrell JC, Lehtovirta-Morley LE. The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. Environ Microbiol 2023; 25:948-961. [PMID: 36598494 DOI: 10.1111/1462-2920.16316] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023]
Abstract
The ammonia monooxygenase (AMO) is a key enzyme in ammonia-oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia-oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one-carbon (C1) compounds in ammonia-oxidizing archaea.
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Affiliation(s)
| | - Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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24
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González-Castillo A, Carballo JL, Bautista-Guerrero E. Genomics, Phylogeny, and in Silico Phenotyping of Nitrosopumilus Genus. Curr Microbiol 2022; 80:3. [PMID: 36427110 DOI: 10.1007/s00284-022-03121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
The present study reports the first genome of Nitrosopumilus extracted from the marine sponge Thoosa mismalolli. The genomic study of Nitrosopumilus genus using seven genomes type strains (N. maritimus, N. piranensis, N. zosterae, N. ureiphilus, N. adriaticus, N. oxyclinae and N. cobalaminigenes), four genomes Candidatus species (Ca. N. koreensis, Ca. N. sp. AR2, Ca. N. salaria BD31, and SZUA-335), and six reference genomes (SI075, SI0036, SI0060, SI0034, SI0048, and bin36o) isolated from marine sponge, a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, near-surface sediment, and MAG N. sp NMAG03 isolated from Thoosa mismalolli was performed. These genomes were characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA) of 139 single-copy genes (SCG), core-pangenome, ANI, and in silico phenotypic characterization. We found that the genomes of the Nitrosopumilus genus formed three separate clusters (A, B, and C) based in 139 SCG sequence similarity. The genomes showed values between 75.2 and 99.5% for ANI, the core genome consisted of 168 gene families and the pangenome of 6,011 gene families. Based on the genomic analyses performed, the cluster A may contain a potential new species (NMAG03), and the cluster C could be represented by three new species of the genus. Finally, based on the results shown in this polyphasic approach, we support the use of the integrated approach for genomic analysis of poorly studied genera.
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Affiliation(s)
- Adrián González-Castillo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.
| | - José Luis Carballo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.,Departamento de Zoología, Laboratorio de Biología Marina, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012, Seville, Spain
| | - Eric Bautista-Guerrero
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de La Costa, Universidad de Guadalajara, Puerto Vallarta, México
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25
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Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proc Natl Acad Sci U S A 2022; 119:e2200014119. [PMID: 36067300 PMCID: PMC9477243 DOI: 10.1073/pnas.2200014119] [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: 11/18/2022] Open
Abstract
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
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26
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Insights into Prokaryotic Community and Its Potential Functions in Nitrogen Metabolism in the Bay of Bengal, a Pronounced Oxygen Minimum Zone. Microbiol Spectr 2022; 10:e0089221. [PMID: 35579458 PMCID: PMC9241787 DOI: 10.1128/spectrum.00892-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (≤1 μM O2) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 μM O2). We found the sinking of Trichodesmium into deep water was far more efficient than that of Prochlorococcus, suggesting Trichodesmium blooms might be an essential carbon and nitrogen source for the maintenance of the BoB OMZ. In addition to the shift in the prokaryotic community composition, the abundance of some functional genes also changed with the change of oxygen concentration. Compared to oxic (>60 μM O2) Tara Ocean and high-hypoxic (>20 to ≤60 μM O2) BoB samples, we found more SAR11-nar sequences (responsible for reducing nitrate to nitrite) in low-hypoxic (>5 to ≤20 μM O2) BoB waters. This suggested SAR11-nar genes would be more widespread due to the expansion of OMZs. It seems that the nitrite-N was not further reduced to nitrogen through denitrification but likely oxidized to nitrate by Nitrospinae in the BoB OMZ and then accumulated in the form of nitrate-N. However, the lack of N2 production in the BoB would change if the BoB OMZ became anoxic. Together, these results suggested that reduction of oxygen concentration and OMZ expansion may increase the use of nitrate by SAR11 and N2 production in the BoB. IMPORTANCE Recognizing the prokaryotic community and its functions in hypoxic (>5 to ≤60 μM O2) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level. This study highlighted that Trichodesmium might be an essential carbon and nitrogen source in the maintenance of the BoB OMZ. Additionally, we suggest that the lack of N2 production in the BoB would change if the BoB OMZ became anoxic, and the expansion of OMZs in the global ocean may potentially increase the use of nitrate by SAR11.
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27
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Temporal and Spatial Patterns of Sediment Microbial Communities and Driving Environment Variables in a Shallow Temperate Mountain River. Microorganisms 2022; 10:microorganisms10040816. [PMID: 35456866 PMCID: PMC9028755 DOI: 10.3390/microorganisms10040816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial communities in sediment play an important role in the circulation of nutrients in aquatic ecosystems. In this study, the main environmental factors and sediment microbial communities were investigated bimonthly from August 2018 to June 2020 at River Taizicheng, a shallow temperate mountain river at the core area of the 2022 Winter Olympics. Microbial community structure was analyzed using 16S rRNA genes (bacteria 16S V3 + V4 and archaea 16S V4 + V5) and high-throughput sequencing technologies. Structure equation model (SEM) and canonical correspondence analysis (CCA) were used to explore the driving environmental factors of the microbial community. Our results showed that the diversity indices of the microbial community were positively influenced by sediment nutrients but negatively affected by water nutrients. Bacteroidetes and Proteobacteria were the most dominant phyla. The best-fitted SEM model indicated that environmental variables not only affected community abundance directly, but also indirectly through influencing their diversity. Flavobacterium, Arenimonas and Terrimonas were the dominant genera as a result of enriched nutrients. The microbial community had high spatial–temporal autocorrelation. CCA showed that DO, WT and various forms of phosphorus were the main variables affecting the temporal and spatial patterns of the microbial community in the river. The results will be helpful in understanding the driving factors of microbial communities in temperate monsoon areas.
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28
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Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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29
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Lin YP, Ansari A, Wunderlich RF, Lur HS, Ngoc-Dan Cao T, Mukhtar H. Assessing the influence of environmental niche segregation in ammonia oxidizers on N 2O fluxes from soil and sediments. CHEMOSPHERE 2022; 289:133049. [PMID: 34838835 DOI: 10.1016/j.chemosphere.2021.133049] [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: 07/21/2021] [Revised: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N2O) production is essential for predicting N2O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N2O fluxes over pH (4.0-9.0) and temperature (10-45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N2O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N2O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N2O fluxes decreased with increasing pH. Consequently, net N2O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R2 = 0.45, p < 0.01) between PAO and N2O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N2O fluxes, highlighting the potential for mitigating N2O emissions via pH manipulation.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taiwan
| | - Thanh Ngoc-Dan Cao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taiwan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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30
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Kraft B, Jehmlich N, Larsen M, Bristow LA, Könneke M, Thamdrup B, Canfield DE. Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 2022; 375:97-100. [PMID: 34990242 DOI: 10.1126/science.abe6733] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the world’s oceans and are key players in the nitrogen cycle. Their energy metabolism—the oxidation of ammonia to nitrite—requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. By carrying out incubations for which oxygen concentrations were resolved to the nanomolar range, we show that after oxygen depletion, Nitrosopumilus maritimus produces dinitrogen and oxygen, which is used for ammonia oxidation. The pathway is not completely resolved but likely has nitric oxide and nitrous oxide as key intermediates. N. maritimus joins a handful of organisms known to produce oxygen in the dark. On the basis of this ability, we reevaluate the role of N. maritimus in oxygen-depleted marine environments.
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Affiliation(s)
- Beate Kraft
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research UFZ GmbH, Leipzig, Germany
| | - Morten Larsen
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Martin Könneke
- Marine Archaea Group, Center for Marine Environmental Sciences (MARUM), and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Bo Thamdrup
- 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, China.,Danish Institute of Advanced Study, University of Southern Denmark, Odense, Denmark
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31
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Rodriguez J, Chakrabarti S, Choi E, Shehadeh N, Sierra-Martinez S, Zhao J, Martens-Habbena W. Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB. Front Microbiol 2021; 12:671480. [PMID: 34322099 PMCID: PMC8312096 DOI: 10.3389/fmicb.2021.671480] [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: 02/23/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.
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Affiliation(s)
| | | | | | | | | | | | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, United States
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Huang L, Chakrabarti S, Cooper J, Perez A, John SM, Daroub SH, Martens-Habbena W. Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil. ISME COMMUNICATIONS 2021; 1:19. [PMID: 37938645 PMCID: PMC9723749 DOI: 10.1038/s43705-021-00020-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/14/2021] [Indexed: 12/21/2022]
Abstract
Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.
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Affiliation(s)
- Laibin Huang
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences, University of Florida, Belle Glade, FL, USA
| | - Ana Perez
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Sophia M John
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences, University of Florida, Belle Glade, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA.
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Zhang Q, Zhang X, Duan P, Jiang X, Shen H, Yan X, Xiong Z. The effect of long-term biochar amendment on N 2O emissions: Experiments with N 15-O 18 isotopes combined with specific inhibition approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144533. [PMID: 33482542 DOI: 10.1016/j.scitotenv.2020.144533] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Numerous studies reporting a transient decrease in soil nitrous oxide (N2O) emissions after biochar amendment have mainly used short-term experiments. Thus, long-term field trials are needed to clarify the actual impact of biochar on N2O emissions and the underlying mechanisms. To address this, both a 15N18O labeling technique and gene analyses were applied to investigate how N2O production pathways and microbial mediation were affected by long term biochar amendment in field. Then, 1-octyne and 2-phenyl l-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) were used in combination with potassium chlorate to evaluate the relative contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to potential ammonia oxidation (PAO) and the associated N2O production. Acidic and alkaline greenhouse vegetable soils that had each received two separate treatments were collected (control, no biochar amendment; biochar, biochar amended in the field after 2 or 7 years). The results showed that biochar decreased N2O emissions by 48% in acidic soils and by 22% in alkaline soils compared to those in control. These results were explained by decreases in nitrifier denitrification- (by 74%) and heterotrophic denitrification-derived N2O production (by 58%), as further evidenced by a decrease in NO2- (by 87%) and the (nirK+nirS+fungal nirK):(nosZ-I + nosZ-II) ratio (by 5%) in both greenhouse vegetable soils. However, biochar increased nitrifier nitrification-derived N2O in both soils because of increases in pH and PAO, which were attributed to an increased abundance of AOB rather than AOA. The contribution of AOB to PAO (or N2O) exceeded 69% (or 68%) of the total in acidic soil and 88% (or 85%) of the total in alkaline soil after biochar amendment. Our findings demonstrated that the mitigation of N2O by biochar is linked to specific N2O production pathways.
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Affiliation(s)
- Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Georg-August University of Göttingen, Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, Büsgenweg 2, 37077 Göttingen, Germany
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengpeng Duan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Xueyang Jiang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Haojie Shen
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyuan Yan
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Ma H, Tecimen HB, Pei G, Imran S, Gao R, Yin Y. Effects of co-addition of ammonium, nitrite, and glucose with methionine on soil nitrogen. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:332. [PMID: 33966117 DOI: 10.1007/s10661-021-09109-8] [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: 01/06/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
Methionine is one of the many amino acids in the soil. In order to study the role of methionine in acidic forest soil, the effect of methionine (Met) was compared with control together with addition of ammonium (Met + A), nitrite (Met + N), and glucose (Met + C) under 60% or 90% water holding capacity (WHC), because ammonium and nitrite are important factors in nitrification, and glucose affect the heterotrophic nitrification and nitrogen immobilization. We found that methionine addition significantly reduced NO3- concentration in acidic forest soil. Compared to Met, Met + A and Met + N treatments non-significantly enhanced nitrification; however, Met + C treatment decreased NH4+ concentration which suggested that soil autotrophic and heterotrophic nitrification were limited in the presence of methionine at 60% WHC. Further, our findings of 15N-labeled treatment showed the impact and priming effect of methionine was negative for NO3- concentration and positive for N2O emission, which were observed mainly from the soil N source rather than methionine. At 90% WHC, Met + C treatment significantly lessened concentrations of NH4+ and NO3-, nonetheless improved N2O compared to Met treatment. Therefore, besides the denitrification and dissimilatory NO3- reduction to ammonia, the immobilization might be the key factor to explain this decrease in NO3- concentration at 90% WHC, while these processes were induced with the C addition. This study indicated that the positive role of amino acids in soil N cycling might be overrated.
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Affiliation(s)
- Hongliang Ma
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian, 350007, Fuzhou, China.
- School of Geographical Science, Fujian Normal University, Fujian, 350007, Fuzhou, China.
| | - Hüseyin Barış Tecimen
- Soil Science and Ecology Dept, Faculty of Forestry, Istanbul University-Cerrahpasa, 34473, Istanbul, Turkey
| | - Guangting Pei
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian, 350007, Fuzhou, China
- School of Geographical Science, Fujian Normal University, Fujian, 350007, Fuzhou, China
| | - Shakeel Imran
- University of Agriculture Faisalabad Sub-Campus Burewala, Vehari, 61100, Pakistan
| | - Ren Gao
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian, 350007, Fuzhou, China
- School of Geographical Science, Fujian Normal University, Fujian, 350007, Fuzhou, China
| | - Yunfeng Yin
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian, 350007, Fuzhou, China
- School of Geographical Science, Fujian Normal University, Fujian, 350007, Fuzhou, China
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35
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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Coupled nitrification and N 2 gas production as a cryptic process in oxic riverbeds. Nat Commun 2021; 12:1217. [PMID: 33619247 PMCID: PMC7900231 DOI: 10.1038/s41467-021-21400-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 01/22/2021] [Indexed: 11/08/2022] Open
Abstract
The coupling between nitrification and N2 gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N2 gas. Here we show, in oxic riverbeds, that the pattern of N2 gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N2 gas that 20 years’ research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle. The N cycle involves complex, microbially-mediated shuttling between ammonium, nitrite and nitrate, with climatically important greenhouse gas byproducts. Here the authors use isotope labeling experiments in river sediments and find a cryptic new step in the N cycle between nitrification and the removal of fixed N through N2 gas production.
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Kowal P, Ciesielski S, Godzieba M, Fitobór K, Gajewska M, Kołecka K. Assessment of diversity and composition of bacterial community in sludge treatment reed bed systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:144060. [PMID: 33317898 DOI: 10.1016/j.scitotenv.2020.144060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
Due to their low emission of odours and lack of the need to apply additional chemical agents, sludge treatment reed beds (STRBs) constitute an economically feasible and eco-friendly approach to sewage sludge management. Correctly designed and operated STRBs ensure effective reduction of the dry matter content coupled with the mineralisation of organic compounds. Successful operation of STRBs relies on complex interactions between the plants and microorganisms responsible for the decomposition of organic matter and nutrient cycling. While the biocenoses of wetland systems dedicated to wastewater treatment have been intensively investigated, in the case of sludge treatment applications, there is a deficit of available microbial data. The aim of this study was to explore the diversity and spatial distribution of the bacteria in three distinct STRBs which differ in maturation and feeding patterns. Analyses of the dry mass and organic matter content showed the general trend of the sludge stabilisation processes advancing through the bed depth, with the best performance in the Matured Continuous Feed (MCF) bed being noted. Samples from the MCF bed showed the statistically greatest biodiversity in relation to the other beds. Moreover, increased biodiversity of microorganisms was observed on the surface of the STRBs and the bottom zone of the MCF equipped with a passive aeration system, which proves the application of such solutions in order to enhance the performance of the process. The results of 16S rRNA gene sequencing revealed that Bacteroidetes, Proteobacteria and Firmicutes contributed approximately 80% of all identified sequences read. Network analysis revealed dominant role of Bacteroidetes in the formation of interspecies co-existence patterns. Nitrospira was the most abundant organism responsible for nitrogen metabolism in the STRBs.
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Affiliation(s)
- Przemysław Kowal
- Dept. of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Slawomir Ciesielski
- Dept. of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Michała Oczapowskiego 2, 10-719 Olsztyn, Poland
| | - Martyna Godzieba
- Dept. of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Michała Oczapowskiego 2, 10-719 Olsztyn, Poland
| | - Karolina Fitobór
- Dept. of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Magdalena Gajewska
- Dept. of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Katarzyna Kołecka
- Dept. of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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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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39
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Walker AM, Leigh MB, Mincks SL. Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope. Front Microbiol 2021; 12:581124. [PMID: 33584606 PMCID: PMC7876419 DOI: 10.3389/fmicb.2021.581124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
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Affiliation(s)
- Alexis M Walker
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Sarah L Mincks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
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40
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Wu L, Wei W, Ni BJ. Response to Comment on "A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea". ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:799-800. [PMID: 33325686 DOI: 10.1021/acs.est.0c08136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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Abstract
Ammonia-oxidizing bacteria (AOB) convert ammonia (NH3) to nitrite (NO2-) as their primary metabolism and thus provide a blueprint for the use of NH3 as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH2OH) to NO2-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH2OH and were both originally reported to produce NO2-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH2OH oxidation. Under aerobic conditions substoichiometric production of NO2- was observed along with production of nitrous oxide (N2O). Under anaerobic conditions, however, N2O was the exclusive product of NH2OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O2, thus producing NO2- abiotically. Because N2O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO2- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO2- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH2OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH2OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.
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Affiliation(s)
- Rachael E. Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M. Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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Papadopoulou ES, Bachtsevani E, Lampronikou E, Adamou E, Katsaouni A, Vasileiadis S, Thion C, Menkissoglu-Spiroudi U, Nicol GW, Karpouzas DG. Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates. Front Microbiol 2020; 11:581283. [PMID: 33250872 PMCID: PMC7672009 DOI: 10.3389/fmicb.2020.581283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Adamou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Katsaouni
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Cécile Thion
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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43
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Stahl DA. The path leading to the discovery of the ammoniaoxidizing archaea. Environ Microbiol 2020; 22:4507-4519. [PMID: 32955155 DOI: 10.1111/1462-2920.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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44
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Fuchsman CA, Stüeken EE. Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans. Environ Microbiol 2020; 23:2801-2822. [PMID: 32869502 DOI: 10.1111/1462-2920.15220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N2 production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N2 O and N2 production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N2 production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, KY16 9AL, Scotland, UK
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45
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Wu L, Chen X, Wei W, Liu Y, Wang D, Ni BJ. A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9175-9190. [PMID: 32657581 DOI: 10.1021/acs.est.0c03948] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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46
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Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, Nielsen JL, Mori K, Takahashi R, Virginia Armbrust E, Winkler MKH, DeLong EF, Li M, Lee PH, Zhou J, Zhang C, Zhang T, Stahl DA, Ingalls AE. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME JOURNAL 2020; 14:2595-2609. [PMID: 32636492 PMCID: PMC7490402 DOI: 10.1038/s41396-020-0710-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
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Affiliation(s)
- Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA.
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USA
| | - Haodong Liu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Xiaowu Huang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | | | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China.,Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Environment, Tsinghua University, Beijing, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA.
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47
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Stein LY. The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases. Trends Microbiol 2020; 28:500-511. [DOI: 10.1016/j.tim.2020.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
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48
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He X, Ji G. Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:15233-15244. [PMID: 32072408 DOI: 10.1007/s11356-020-07952-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.
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Affiliation(s)
- Xiangjun He
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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49
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Zhang S, Qin W, Xia X, Xia L, Li S, Zhang L, Bai Y, Wang G. Ammonia oxidizers in river sediments of the Qinghai-Tibet Plateau and their adaptations to high-elevation conditions. WATER RESEARCH 2020; 173:115589. [PMID: 32058148 DOI: 10.1016/j.watres.2020.115589] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/27/2020] [Accepted: 02/02/2020] [Indexed: 06/10/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as complete ammonia oxidizers (comammox) aerobically catalyze ammonia oxidation which plays essential roles in riverine nitrogen cycle. However, performances of these ammonia oxidizers in high-elevation river sediments have rarely been documented. This study investigated the abundance, community, and activity of ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau (QTP). Comammox were dominant ammonia oxidizers in 23% of studied samples and the clade B was principal comammox type. amoA gene abundances of AOA and AOB in these high-elevation rivers were comparable to those in low-elevation rivers. However, in contrast to most studied low-elevation rivers, AOB amoA gene abundance outnumbered AOA in 92% samples, which might be caused by the lower temperature and more intense solar radiation of the QTP. Potential nitrification rates (PNRs) ranged from 0.02 to 2.95 nmol-N h-1 g-1 dry sediment. Ammonia concentration was the limiting factor to PNRs at some sites, and when ammonia was not limiting, the PNR: ammonia ratio was greater at higher temperatures. There was no apparent variation in ammonia oxidizer community compositions along the elevation gradient due to the high elevation (2687 to 4223 m) of our entire study area. However, compared with low-elevation rivers, the lower temperature, huge diurnal temperature change, and lower nutrient conditions in the QTP rivers shaped distinctive communities for ammonia oxidizers; the unique community characteristics were significantly correlated to PNRs. These results suggest that ammonia oxidizers in the five high-elevation rivers have adapted to high-elevation conditions; more research should be conducted to study their adaptation mechanisms and their roles in riverine nitrogen cycle.
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Affiliation(s)
- Sibo Zhang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Lingzi Xia
- School of Civil and Environmental Engineering, Cornell University, USA
| | - Siling Li
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Liwei Zhang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Yubei Bai
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Gongqin Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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50
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Taylor HB, Kurtz HD. Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach. Microbiologyopen 2020; 9:e1011. [PMID: 32126588 PMCID: PMC7221436 DOI: 10.1002/mbo3.1011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 01/22/2023] Open
Abstract
Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.
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Affiliation(s)
- Harrison B Taylor
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States
| | - Harry D Kurtz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States
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