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Shi J, Zeng Y, Wang H, Niu Y, He P, Chen H. Complete genome sequencing and analysis revealed the nitrogen utilization strategy of a novel Acuticoccus species isolated from surface water of the Indian Ocean. Mar Genomics 2022; 65:100971. [DOI: 10.1016/j.margen.2022.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022]
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Wang S, Yang Y, Jing J. A Synthesis of Viral Contribution to Marine Nitrogen Cycling. Front Microbiol 2022; 13:834581. [PMID: 35547115 PMCID: PMC9083009 DOI: 10.3389/fmicb.2022.834581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
Nitrogen is an essential component of major cellular macromolecules, such as DNA and proteins. Its bioavailability has a fundamental influence on the primary production of both terrestrial and oceanic ecosystems. Diverse marine microbes consume nitrogen, while only a limited taxon could replenish it, leaving nitrogen one of the most deficient nutrients in the ocean. A variety of microbes are involved in complex biogeochemical transformations of nitrogen compounds, and their ecological functions might be regulated by viruses in different manners. First and foremost, viruses drive marine nitrogen flow via host cell lysis, releasing abundant organic nitrogen into the surrounding environment. Secondly, viruses can also participate in the marine nitrogen cycle by expressing auxiliary metabolic genes (AMGs) to modulate host nitrogen metabolic pathways, such as nitrification, denitrification, anammox, and nitrogen transmembrane transport. Additionally, viruses also serve as a considerable reservoir of nitrogen element. The efficient turnover of viruses fundamentally promotes nitrogen flow in the oceans. In this review, we summarize viral contributions in the marine nitrogen cycling in different aspects and discuss challenges and issues based on recent discoveries of novel viruses involved in different processes of nitrogen biotransformation.
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Affiliation(s)
- Shuai Wang
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, China
| | - Yu Yang
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, China
| | - Jiaojiao Jing
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Department of Pediatric Dentistry, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, China
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Cai Y, Luo X, He X, Tang C. Primary role of increasing urea-N concentration in a novel Microcystis densa bloom: Evidence from ten years of field investigations and laboratory experiments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111713. [PMID: 33396044 DOI: 10.1016/j.ecoenv.2020.111713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
A novel Microcystis bloom caused by Microcystis densa has occurred in a typical subtropical reservoir every spring and summer since 2012, and it has caused several ecological and economic losses. To determine the environmental factors that influence the growth and physiological characteristics of M. densa, we investigated the variations in physicochemical factors and M. densa cell density from 2007 to 2017. The results showed that the urea-N concentration increased significantly (from 0.02 ± 0.00-0.20 ± 0.01 mg N l-1), whereas other factors did not vary significantly. NO3--N and urea-N concentrations were higher than the NH4+-N concentration during the M. densa bloom. The nitrogen composition changed, and urea-N and NO3--N became a major nitrogen sources in the reservoir. Water temperature and increased urea-N concentrations were the primary factors that influenced variations in M. densa cell density (45.5%, p < 0.05). Laboratory experiments demonstrated that M. densa cultured with urea-N exhibited a higher maximum cell density (9.8 ± 0.5 × 108 cells l-1), more cellular pigments for photosynthesis (chlorophyll a and phycocyanin) and photoprotection (carotenoid), and more proteins than those cultured with NH4+-N and NO3--N. These results suggested that M. densa cultured with urea-N exhibited preferable growth and physiological conditions. Moreover, M. densa exhibited an increased maximum specific uptake rate (0.93 pg N cell-1 h-1) and reduced half-saturation constant (0.03 mg N l-1) for urea-N compared with NH4+-N and NO3--N, suggesting that M. densa preferred urea-N as its major nitrogen source. These results collectively indicated that the increasing urea-N concentration was beneficial for the growth and physiological conditions of M. densa. This study provided ten years of field data and detailed physiological information supporting the critical effect of urea-N on the growth of a novel bloom species M. densa. These findings helped to reveal the mechanism of M. densa bloom formation from the perspective of dissolved organic nitrogen.
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Affiliation(s)
- Yangyang Cai
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | | | - Xiaoyuan He
- South China Sea Administration, Ministry of Natural Resources, Guangzhou, China
| | - Changyuan Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China; School of Geography and Planning, Sun Yat-sen University, Guangzhou, China.
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Watzer B, Spät P, Neumann N, Koch M, Sobotka R, Macek B, Hennrich O, Forchhammer K. The Signal Transduction Protein P II Controls Ammonium, Nitrate and Urea Uptake in Cyanobacteria. Front Microbiol 2019; 10:1428. [PMID: 31293555 PMCID: PMC6603209 DOI: 10.3389/fmicb.2019.01428] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/05/2019] [Indexed: 11/22/2022] Open
Abstract
PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite, and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homolog GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.
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Affiliation(s)
- Björn Watzer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Philipp Spät
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Quantitative Proteomics, University of Tübingen, Tübingen, Germany
| | - Niels Neumann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Moritz Koch
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Roman Sobotka
- Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, Třeboň, Czechia
| | - Boris Macek
- Interfaculty Institute for Cell Biology, Department of Quantitative Proteomics, University of Tübingen, Tübingen, Germany
| | - Oliver Hennrich
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
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Lage S, Ström L, Godhe A, Rydberg S. The effect of exogenous β-N-methylamino-l-alanine (BMAA) on the diatoms Phaeodactylum tricornutum and Thalassiosira weissflogii. HARMFUL ALGAE 2016; 58:85-92. [PMID: 28073463 DOI: 10.1016/j.hal.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 06/06/2023]
Abstract
β-N-methylamino-l-alanine (BMAA), a non-protein amino acid with neurodegenerative features, is known to be produced by cyanobacteria, diatoms and a dinoflagellate. BMAA research has intensified over the last decade, and knowledge has been gained about its bioaccumulation in aquatic and terrestrial ecosystems, toxic effects in model organisms and neurotoxicity in vivo and in vitro. Nevertheless, knowledge of the actual physiological role of BMAA in the producing species or of the ecological factors that regulate BMAA production is still lacking. A few studies propose that BMAA functions to signal nitrogen depletion in cyanobacteria. To investigate whether BMAA might have a similar role in diatoms, two diatom species - Phaeodactylum tricornutum and Thalassiosira weissflogii - were exposed to exogenous BMAA at environmental relevant concentrations, i.e. 0.005, 0.05 and 0.5μM. BMAA was taken up in a concentration dependent manner in both species in the BMAA free fraction and in the protein fraction of T. weissflogii. As a result of the treatments, the diatom cells at some of the time points and at some of the BMAA concentrations exhibited lower concentrations of chlorophyll a and protein, in comparison to controls. At the highest (0.5μM) concentration of BMAA, extracellular ammonia was found in the media of both species at all time points. These results suggest that BMAA interferes with nitrogen metabolism in diatoms, possibly by inhibiting ammonium assimilation via the GS/GOGAT pathway.
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Affiliation(s)
- Sandra Lage
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10654 Stockholm, Sweden
| | - Linnea Ström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10654 Stockholm, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sara Rydberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10654 Stockholm, Sweden.
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Alipanah L, Rohloff J, Winge P, Bones AM, Brembu T. Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6281-96. [PMID: 26163699 PMCID: PMC4588885 DOI: 10.1093/jxb/erv340] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Algal growth is strongly affected by nitrogen (N) availability. Diatoms, an ecologically important group of unicellular algae, have evolved several acclimation mechanisms to cope with N deprivation. In this study, we integrated physiological data with transcriptional and metabolite data to reveal molecular and metabolic modifications in N-deprived conditions in the marine diatom Phaeodactylum tricornutum. Physiological and metabolite measurements indicated that the photosynthetic capacity and chlorophyll content of the cells decreased, while neutral lipids increased in N-deprived cultures. Global gene expression analysis showed that P. tricornutum responded to N deprivation through an increase in N transport, assimilation, and utilization of organic N resources. Following N deprivation, reduced biosynthesis and increased recycling of N compounds like amino acids, proteins, and nucleic acids was observed at the transcript level. The majority of the genes associated with photosynthesis and chlorophyll biosynthesis were also repressed. Carbon metabolism was restructured through downregulation of the Calvin cycle and chrysolaminarin biosynthesis, and co-ordinated upregulation of glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism, leading to funnelling of carbon sources to lipid metabolism. Finally, reallocation of membrane lipids and induction of de novo triacylglycerol biosynthesis directed cells to accumulation of neutral lipids.
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Affiliation(s)
- Leila Alipanah
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Jens Rohloff
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Tore Brembu
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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Khiaosa-ard R, Metzler-Zebeli B, Ahmed S, Muro-Reyes A, Deckardt K, Chizzola R, Böhm J, Zebeli Q. Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec. J Dairy Sci 2015; 98:2611-26. [DOI: 10.3168/jds.2014-8751] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023]
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Zehr JP, Kudela RM. Nitrogen cycle of the open ocean: from genes to ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:197-225. [PMID: 21329204 DOI: 10.1146/annurev-marine-120709-142819] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The marine nitrogen (N) cycle controls the productivity of the oceans. This cycle is driven by complex biogeochemical transformations, including nitrogen fixation, denitrification, and assimilation and anaerobic ammonia oxidation, mediated by microorganisms. New processes and organisms continue to be discovered, complicating the already complex picture of oceanic N cycling. Genomics research has uncovered the diversity of nitrogen metabolism strategies in phytoplankton and bacterioplankton. The elemental ratios of nutrients in biological material are more flexible than previously believed, with implications for vertical export of carbon and associated nutrients to the deep ocean. Estimates of nitrogen fixation and denitrification continue to be modified, and anaerobic ammonia oxidation has been identified as a new process involved in denitrification in oxygen minimum zones. The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change.
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Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA.
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Collier JL, Baker KM, Bell SL. Diversity of urea-degrading microorganisms in open-ocean and estuarine planktonic communities. Environ Microbiol 2009; 11:3118-31. [PMID: 19659552 DOI: 10.1111/j.1462-2920.2009.02016.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urea is an important and dynamic natural component of marine nitrogen cycling and also a major contributor to anthropogenic eutrophication of coastal ecosystems, yet little is known about the identities or diversity of ureolytic marine microorganisms. Primers targeting the gene encoding urease were used to PCR-amplify, clone and sequence 709 urease gene fragments from 31 plankton samples collected at both estuarine and open-ocean locations. Two hundred and eighty-six amplicons belonged to 22 distinct sequence types that were closely enough related to named organisms to be identified, and included urease sequences both from typical marine planktonic organisms and from bacteria usually associated with terrestrial habitats. The remaining 423 amplicons were not closely enough related to named organisms to be identified, and belonged to 96 distinct sequence types of which 43 types were found in two or more different samples. The distributions of unidentified urease sequence types suggested that some represented truly marine microorganisms while others reflected terrestrial inputs to low-salinity estuarine areas. The urease primers revealed this great diversity of ureolytic organisms because they were able to amplify many previously unknown, environmentally relevant urease genes, and they will support new approaches for exploring the role of urea in marine ecosystems.
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Affiliation(s)
- Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
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