1
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Zhu Y, Mulholland MR, Bernhardt PW, Neeley AR, Widner B, Tapia AM, Echevarria MA. Nitrogen uptake rates and phytoplankton composition across contrasting North Atlantic Ocean coastal regimes north and south of Cape Hatteras. Front Microbiol 2024; 15:1380179. [PMID: 38784802 PMCID: PMC11113559 DOI: 10.3389/fmicb.2024.1380179] [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: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six 15N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. Total measured N uptake rates were lowest in the Gulf Stream followed by the SAB. Notably, the MAB exhibited significantly higher N uptake rates compared to the SAB, likely due to the excess levels of pre-existing phosphorus present in the MAB. Together, urea and nitrate uptake contributed approximately 50% of the total N uptake across the study region. Although cyanate uptake rates were consistently low, they accounted for up to 11% of the total measured N uptake at some Gulf Stream stations. Phytoplankton groups were identified based on specific pigment markers, revealing a dominance of diatoms in the shelf community, while Synechococcus, Prochlorococcus, and pico-eukaryotes dominated in oligotrophic Gulf Stream waters. The reported uptake rates in this study were mostly in agreement with previous studies conducted in coastal waters of the North Atlantic Ocean. This study suggests there are distinct regional patterns of N uptake in this physically dynamic region, correlating with nutrient availability and phytoplankton community composition. These findings contribute valuable insights into the intricate interplay of biological and chemical factors shaping N dynamics in disparate marine ecosystems.
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Affiliation(s)
- Yifan Zhu
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Margaret R. Mulholland
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Peter W. Bernhardt
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | | | - Brittany Widner
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Alfonso Macías Tapia
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Office of Education, National Oceanic and Atmospheric Administration, Silver Spring, MD, United States
| | - Michael A. Echevarria
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
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2
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Mao X, Chen J, van Oosterhout C, Zhang H, Liu G, Zhuang Y, Mock T. Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. THE ISME JOURNAL 2022; 16:602-605. [PMID: 34408267 PMCID: PMC8776842 DOI: 10.1038/s41396-021-01081-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO3 by the activity of nitrifying bacteria.
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Affiliation(s)
- Xuewei Mao
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China ,grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Jianwei Chen
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China ,grid.21155.320000 0001 2034 1839Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555 China
| | - Cock van Oosterhout
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Huan Zhang
- grid.63054.340000 0001 0860 4915Department of Marine Sciences, University of Connecticut, Groton, CT 06340 USA
| | - Guangxing Liu
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yunyun Zhuang
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Thomas Mock
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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3
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Renkecz T, Scopchanova S, Hirka G, Szakonyiné IP. Development and Validation of an LC-MS-MS Method for the Quantification of Cyanate in Rat Plasma and Its Application to Toxicokinetic Bioanalysis. J Anal Toxicol 2021; 45:1028-1035. [PMID: 33044525 DOI: 10.1093/jat/bkaa163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/09/2020] [Accepted: 10/09/2020] [Indexed: 11/14/2022] Open
Abstract
Cyanate has been recognized as a uremic toxin that can adversely affect the clinical status of patients with chronic kidney disease. Besides, its toxicity has been under investigation in mammalian toxicology. If such studies are supplemented with toxicokinetic sampling and bioanalysis, additional information can be acquired about the systemic exposure. In order to serve this need, a liquid chromatography with tandem mass spectrometry (LC-MS-MS) method was elaborated and validated for the quantification of cyanate in rat plasma using its isotope-labeled analog for internal standard. Cyanate was converted to a product compatible with reverse-phase LC-MS-MS via a two-step derivatization reaction with the reagent-anthranilic acid. It was observed that this reagent solution contains the reaction products even if prepared freshly in ultrapure water. The phenomenon was interpreted as the presence of urea and its reactivity with anthranilic acid. Contrary to previous research results where fresh anthranilic acid solution was recommended to use, we have found that the aging of the reagent solution is a crucial factor to eliminate the interference. Thereafter, the optimal pH was selected for the plasma sample and processing conditions. Bioanalytical validation and incurred sample reanalysis confirmed the reliability of the method when the intermediate reaction product was used for detection. Only one freeze-thaw cycle stability could be proven, which highlighted the need to collect two sample aliquots whenever possible. Real samples were analyzed in a toxicity study to evaluate systemic exposure of potassium cyanate at three dose levels. Further on, this method might be adapted to provide additional information about the pathophysiological concentration of cyanate in patients with chronic kidney disease for therapeutic support.
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Affiliation(s)
- Tibor Renkecz
- Toxi-Coop Toxicological Research Center, Analytical Laboratory, Berlini utca 47-49, Budapest, H-1045, Hungary
| | - Sirma Scopchanova
- SCC Scientific Consulting Company Chemisch-Wissenschaftliche Beratung GmbH, Am Grenzgraben 11, Bad Kreuznach, D-55545, Germany
| | - Gábor Hirka
- Toxi-Coop Toxicological Research Center, Analytical Laboratory, Berlini utca 47-49, Budapest, H-1045, Hungary
| | - Ilona Pasics Szakonyiné
- Toxi-Coop Toxicological Research Center, Analytical Laboratory, Berlini utca 47-49, Budapest, H-1045, Hungary
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4
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Bozkurt S, Halay E, Durmaz M, Topkafa M, Ceylan Ö. A novel turn‐on fluorometric “reporter‐spacer‐receptor” chemosensor based on calix[4]arene scaffold for detection of cyanate anion. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Selahattin Bozkurt
- Scientific Analysis Technological Application and Research Center Usak University Usak Turkey
- Vocational School of Health Services Usak University Usak Turkey
| | - Erkan Halay
- Scientific Analysis Technological Application and Research Center Usak University Usak Turkey
- Department of Chemistry and Chemical Processing Technologies, Banaz Vocational School Usak University Usak Turkey
| | - Mustafa Durmaz
- Department of Chemistry Education, Ahmet Kelesoglu Education Faculty Necmettin Erbakan University Konya Turkey
| | - Mustafa Topkafa
- Department of Chemistry and Chemical Processing Technologies, Vocational School of Technical Sciences Konya Technical University Konya Turkey
| | - Özgür Ceylan
- Food Quality Control and Analysis Program, Ula Ali Kocman Vocational Scholl Mugla Sitki Kocman University Mugla Turkey
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5
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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6
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Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean. Nat Commun 2020; 11:767. [PMID: 32034151 PMCID: PMC7005884 DOI: 10.1038/s41467-020-14542-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/17/2020] [Indexed: 11/11/2022] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean. Ammonia oxidizing archaea and Nitrospinae are the main known nitrifiers in the ocean, but the much greater abundance of the former is puzzling. Here, the authors show that differences in mortality, rather than thermodynamics, cell size or biomass yield, explain the discrepancy, without the need to invoke yet undiscovered, abundant nitrite oxidizers.
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7
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Matoba Y, Uda N, Kudo M, Sugiyama M. Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis. FEBS J 2019; 287:2763-2778. [PMID: 31793174 DOI: 10.1111/febs.15163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to generate d-CS, which is accompanied by the cleavage of a bond in the urea moiety of d-OUS to remove a carbamoyl group. Although the general ATP-grasp enzymes catalyze an ATP-dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d-OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d-CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.
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Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Narutoshi Uda
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Mako Kudo
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Masanori Sugiyama
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
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8
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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9
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Kato S, Hirai M, Ohkuma M, Suzuki K. Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics. PLoS One 2019; 14:e0224888. [PMID: 31703093 PMCID: PMC6839870 DOI: 10.1371/journal.pone.0224888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/23/2019] [Indexed: 11/18/2022] Open
Abstract
Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.
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Affiliation(s)
- Shingo Kato
- Submarine Resources Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Katsuhiko Suzuki
- Submarine Resources Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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10
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Widner B, Fuchsman CA, Chang BX, Rocap G, Mulholland MR. Utilization of urea and cyanate in waters overlying and within the eastern tropical north Pacific oxygen deficient zone. FEMS Microbiol Ecol 2019; 94:5055141. [PMID: 30016420 DOI: 10.1093/femsec/fiy138] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 07/16/2018] [Indexed: 11/15/2022] Open
Abstract
In marine oxygen deficient zones (ODZs), which contribute up to half of marine N loss, microbes use nitrogen (N) for assimilatory and dissimilatory processes. Here, we examine N utilization above and within the ODZ of the Eastern Tropical North Pacific Ocean, focusing on distribution, uptake and genes for the utilization of two simple organic N compounds, urea and cyanate. Ammonium, urea and cyanate concentrations generally peaked in the oxycline while uptake rates were highest in the surface. Within the ODZ, concentrations were lower, but urea N and C and cyanate C were taken up. All identified autotrophs had an N assimilation pathway that did not require external ammonium: ODZ Prochlorococcus possessed genes to assimilate nitrate, nitrite and urea; nitrite oxidizers (Nitrospina) possessed genes to assimilate nitrite, urea and cyanate; anammox bacteria (Scalindua) possessed genes to utilize cyanate; and ammonia-oxidizing Thaumarchaeota possessed genes to utilize urea. Urease genes were present in 20% of microbes, including SAR11, suggesting the urea utilization capacity was widespread. In the ODZ core, cyanate genes were largely (∼95%) associated with Scalindua, suggesting that, within this ODZ, cyanate N is primarily used for N loss via anammox (cyanammox), and that anammox does not require ammonium for N loss.
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Affiliation(s)
- Brittany Widner
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, USA
| | - Clara A Fuchsman
- University of Washington, School of Oceanography, Seattle, USA.,Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, USA
| | - Bonnie X Chang
- Joint Institute for the Study of the Atmosphere and Ocean, University of Washington, Seattle, USA.,Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, USA
| | - Gabrielle Rocap
- University of Washington, School of Oceanography, Seattle, USA
| | - Margaret R Mulholland
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, USA
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11
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Watts MP, Spurr LP, Lê Cao KA, Wick R, Banfield JF, Moreau JW. Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium. WATER RESEARCH 2019; 158:106-117. [PMID: 31022528 DOI: 10.1016/j.watres.2019.02.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN-. Here we present results from a bioreactor experiment inoculated with SCN- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN- degradation. These microbes supported metabolically-dependent non-SCN--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.
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Affiliation(s)
- Mathew P Watts
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Liam P Spurr
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ryan Wick
- Department of Biochemistry and Molecular Biology, Bio21, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jillian F Banfield
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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12
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Selective and sensitive detection of cyanate using 3-amino-2-naphthoic acid-based turn-on fluorescence probe. Anal Bioanal Chem 2019; 411:3613-3619. [PMID: 31093695 DOI: 10.1007/s00216-019-01843-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/04/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
The cyanate anion (CNO-), formed spontaneously within cells from urea and carbamoyl phosphate, usually functions as a biomarker of some diseases such as chronic kidney disease. Therefore, accurate determination of CNO- is highly demanded. Herein, a 3-amino-2-naphthoic acid-based "turn-on" fluorescence probe was developed for specific detection of CNO-. Upon the addition of sodium cyanate, the weak-fluorescent 3-amino-2-naphthoic acid could react with CNO-, which triggered intense emission of green fluorescence. And up to 9-fold fluorescence enhancement was observed. The fluorescence enhancement ratios displayed a good linear relationship with the concentrations of CNO- in the range of 0.5-200 μM. The high selectivity and sensitivity for CNO- detection were investigated with the detection limit as low as 260 nM. The probe was further successfully applied to determine CNO- in real samples such as tap water, human urine and serum samples, which offered a promising approach in practical applications. Graphical abstract.
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13
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Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol 2019; 4:234-243. [PMID: 30531977 PMCID: PMC6825518 DOI: 10.1038/s41564-018-0316-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 10/30/2018] [Indexed: 02/01/2023]
Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4-6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7-10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.
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Affiliation(s)
- Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin Könneke
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Maria Mooshammer
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Sandra Petrov
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Laura A Bristow
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
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14
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Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol 2019; 103:177-189. [PMID: 30415428 PMCID: PMC6311188 DOI: 10.1007/s00253-018-9486-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 11/30/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.
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Affiliation(s)
- Hanna Koch
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Sebastian Lücker
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
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15
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Linder T. Cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts. World J Microbiol Biotechnol 2018; 35:3. [PMID: 30547239 PMCID: PMC6292966 DOI: 10.1007/s11274-018-2579-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/09/2018] [Indexed: 01/07/2023]
Abstract
The occurrence of putative cyanases (EC 4.2.1.104) in the genomes of yeasts belonging to the ascomycete sub-phyla Saccharomycotina (budding yeasts) and Taphrinomycotina (fission yeasts) was investigated. Predicted gene products displaying significant sequence similarity to previously characterized cyanases were identified in the genomes of the budding yeast Lipomyces starkeyi and the fission yeasts Protomyces lactucaedebilis, Saitoella complicata and Taphrina deformans. Li. starkeyi and Sai. complicata were further tested for their ability to utilize cyanate as a nitrogen source. However, neither species displayed significant growth when cyanate was provided as the sole nitrogen source. Cyanate utilization assays of 15 yeast species whose genomes lack detectable cyanase homologs unexpectedly resulted in consistently strong growth in six species as well as variable growth in an additional three species. The present study represents the first known report of cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts. Implications of cyanate utilization for the ecological niches occupied by ascomycete yeasts are discussed.
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Affiliation(s)
- Tomas Linder
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden.
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16
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Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 2018; 358:1046-1051. [PMID: 29170234 DOI: 10.1126/science.aan8260] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.
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Affiliation(s)
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria
| | - Kristin Bergauer
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | | | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA.,National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
| | - Mary Elizabeth Mathyer
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA.,Division of Dermatology, Department of Internal Medicine, Center for Pharmacogenomics, and Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Purificacion Lopez-Garcia
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.,Department of Subsurface Geobiology Analysis and Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Netherlands
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17
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Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium " Candidatus Nitrospira nitrosa". mSystems 2017; 2:mSystems00059-17. [PMID: 28905001 PMCID: PMC5596200 DOI: 10.1128/msystems.00059-17] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023] Open
Abstract
Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches. The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as “Candidatus Nitrospira nitrosa,” and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in “Ca. Nitrospira nitrosa” mainly attributed to each strain’s niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of “Ca. Nitrospira nitrosa” and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus. IMPORTANCENitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches. Author Video: An author video summary of this article is available.
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18
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Daims H, Lücker S, Wagner M. A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria. Trends Microbiol 2016; 24:699-712. [PMID: 27283264 DOI: 10.1016/j.tim.2016.05.004] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.
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Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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19
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Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, von Bergen M, Lagkouvardos I, Karst SM, Galushko A, Koch H, Berry D, Daims H, Wagner M. Cyanate as an energy source for nitrifiers. Nature 2015; 524:105-8. [PMID: 26222031 PMCID: PMC4539577 DOI: 10.1038/nature14856] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/24/2015] [Indexed: 11/18/2022]
Abstract
Ammonia- and nitrite-oxidizing microorganisms are collectively responsible for the aerobic oxidation of ammonia via nitrite to nitrate and have essential roles in the global biogeochemical nitrogen cycle. The physiology of nitrifiers has been intensively studied, and urea and ammonia are the only recognized energy sources that promote the aerobic growth of ammonia-oxidizing bacteria and archaea. Here we report the aerobic growth of a pure culture of the ammonia-oxidizing thaumarchaeote Nitrososphaera gargensis using cyanate as the sole source of energy and reductant; to our knowledge, the first organism known to do so. Cyanate, a potentially important source of reduced nitrogen in aquatic and terrestrial ecosystems, is converted to ammonium and carbon dioxide in Nitrososphaera gargensis by a cyanase enzyme that is induced upon addition of this compound. Within the cyanase gene family, this cyanase is a member of a distinct clade also containing cyanases of nitrite-oxidizing bacteria of the genus Nitrospira. We demonstrate by co-culture experiments that these nitrite oxidizers supply cyanase-lacking ammonia oxidizers with ammonium from cyanate, which is fully nitrified by this microbial consortium through reciprocal feeding. By screening a comprehensive set of more than 3,000 publically available metagenomes from environmental samples, we reveal that cyanase-encoding genes clustering with the cyanases of these nitrifiers are widespread in the environment. Our results demonstrate an unexpected metabolic versatility of nitrifying microorganisms, and suggest a previously unrecognized importance of cyanate in cycling of nitrogen compounds in the environment.
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Affiliation(s)
- Marton Palatinszky
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Mario Pogoda
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ping Han
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of Metabolomics, Permoserstr. 15, 04318 Leipzig, Germany
- Department of Chemistry and Bioscience, The Faculty of Engineering and Science, Aalborg University, Fredrik Bajers Vej 7, Building H, Room 3401., 9220 Aalborg, Denmark
| | - Ilias Lagkouvardos
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Søren M. Karst
- Department of Chemistry and Bioscience, The Faculty of Engineering and Science, Aalborg University, Fredrik Bajers Vej 7, Building H, Room 3401., 9220 Aalborg, Denmark
| | - Alexander Galushko
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Hanna Koch
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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20
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Affiliation(s)
- Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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21
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Ohe THK, da Silva AA, da Silva Rocha T, de Godoy FS, Franco DW. A Fluorescence-Based Method for Cyanate Analysis in Ethanol/Water Media: Correlation between Cyanate Presence and Ethyl Carbamate Formation in Sugar Cane Spirit. J Food Sci 2014; 79:C1950-5. [DOI: 10.1111/1750-3841.12587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Thiago Hideyuki Kobe Ohe
- Dept. de Química e Física Molecular; Inst. de Química de São Carlos; Univ. de São Paulo (USP); Avenida Trabalhador São-carlense 400, CP 780, CEP 13560-970 São Carlos - SP Brazil
| | - Alexandre Ataide da Silva
- Dept. de Química e Física Molecular; Inst. de Química de São Carlos; Univ. de São Paulo (USP); Avenida Trabalhador São-carlense 400, CP 780, CEP 13560-970 São Carlos - SP Brazil
| | - Thaís da Silva Rocha
- Dept. de Química e Física Molecular; Inst. de Química de São Carlos; Univ. de São Paulo (USP); Avenida Trabalhador São-carlense 400, CP 780, CEP 13560-970 São Carlos - SP Brazil
| | - Flávio Schutzer de Godoy
- Dept. de Química e Física Molecular; Inst. de Química de São Carlos; Univ. de São Paulo (USP); Avenida Trabalhador São-carlense 400, CP 780, CEP 13560-970 São Carlos - SP Brazil
| | - Douglas Wagner Franco
- Dept. de Química e Física Molecular; Inst. de Química de São Carlos; Univ. de São Paulo (USP); Avenida Trabalhador São-carlense 400, CP 780, CEP 13560-970 São Carlos - SP Brazil
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