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Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A. Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO 2, but strongly affected by drought. THE ISME JOURNAL 2020; 14:3038-3053. [PMID: 32770119 PMCID: PMC7784676 DOI: 10.1038/s41396-020-00735-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.
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Affiliation(s)
- Joana Séneca
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christos Zioutis
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Eva Simon
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Altirdning 11, 8952, Irdning, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Wolfgang Wanek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
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52
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Reyes C, Hodgskiss LH, Kerou M, Pribasnig T, Abby SS, Bayer B, Kraemer SM, Schleper C. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. THE ISME JOURNAL 2020; 14:2659-2674. [PMID: 32665710 PMCID: PMC7785015 DOI: 10.1038/s41396-020-0715-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/09/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
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Affiliation(s)
- Carolina Reyes
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Sophie S Abby
- University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Barbara Bayer
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Department of Limnology and Oceanography, Division of Bio-oceanography, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106-9620, USA
| | - Stephan M Kraemer
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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53
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Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Williams TA, Gubry-Rangin C. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Commun 2020; 11:5494. [PMID: 33127895 PMCID: PMC7603488 DOI: 10.1038/s41467-020-19132-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
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Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Christopher Quince
- Warwick Medical School, University of Warwick, Coventry, UK
- Organisms and Ecosystems, Earlham Institute, Norwich, UK
- Gut Microbes and Health, Quadram Institute, Norwich, UK
| | - Jennifer Holden
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Lihong Zhang
- European Centre for Environment and Human Health, Medical School, University of Exeter, Exeter, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
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54
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Mącik M, Gryta A, Sas-Paszt L, Frąc M. The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. Int J Mol Sci 2020; 21:E8003. [PMID: 33121206 PMCID: PMC7663420 DOI: 10.3390/ijms21218003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.
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Affiliation(s)
- Mateusz Mącik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Lidia Sas-Paszt
- Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100 Skierniewice, Poland;
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
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55
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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. mBio 2020; 11:mBio.02371-20. [PMID: 33051370 PMCID: PMC7554672 DOI: 10.1128/mbio.02371-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
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56
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Frąc M, Lipiec J, Usowicz B, Oszust K, Brzezińska M. Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 2020; 8:e9501. [PMID: 32953254 PMCID: PMC7474522 DOI: 10.7717/peerj.9501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Bogusław Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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57
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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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58
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Mooshammer M, Alves RJE, Bayer B, Melcher M, Stieglmeier M, Jochum L, Rittmann SKMR, Watzka M, Schleper C, Herndl GJ, Wanek W. Nitrogen Isotope Fractionation During Archaeal Ammonia Oxidation: Coupled Estimates From Measurements of Residual Ammonium and Accumulated Nitrite. Front Microbiol 2020; 11:1710. [PMID: 32849360 PMCID: PMC7399158 DOI: 10.3389/fmicb.2020.01710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2 -), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or ε A M O , has been typically determined based on isotope kinetics during product formation (cumulative product, NO2 -) alone, which may have overestimated ε A M O due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4 +). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4 +) and cumulative product (CP, NO2 -) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76 and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained ε A M O values of 31.9-33.1‰ for both strains based on RS (δ15NH4 +) and showed that estimates based on CP (δ15NO2 -) give larger isotope fractionation factors by 6-8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (-38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4 + assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between ε A M O estimates based on RS and CP might have derived from the incorporation of 15N-enriched residual NH4 + after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly.
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Affiliation(s)
- Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Ricardo J. E. Alves
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michaela Stieglmeier
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Lara Jochum
- LMU – Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Utrecht, Netherlands
| | - Wolfgang Wanek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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59
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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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Abstract
The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations.IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.
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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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Zhao H, Yu L, Yu M, Afzal M, Dai Z, Brookes P, Xu J. Nitrogen combined with biochar changed the feedback mechanism between soil nitrification and Cd availability in an acidic soil. JOURNAL OF HAZARDOUS MATERIALS 2020; 390:121631. [PMID: 31776087 DOI: 10.1016/j.jhazmat.2019.121631] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/21/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Inorganic nitrogen (N) inputs increase soil nitrification, acidification and trace metal toxicity e.g. cadmium (Cd). Biochar (B) has been widely used for metal immobilization. However, little is known about how the combination of N fertilizers with biochar (N-B) changes soil Cd availability through altering nitrification process. Here, (NH4)2SO4 or CO(NH2)2 was applied in combination with biochar to an acidic, artificially enriched Cd contaminated soil. Not as we expected, available Cd did not increase following (NH4)2SO4 or CO(NH2)2 addition. Nitrification and acidification of Cd contaminated soils were greatly inhibited, accompanied by elimination of ammonia-oxidizing bacteria (AOB). Exchangeable H+ of Cd contaminated soils was significantly lower than that of uncontaminated soils, thus inhibiting Cd itself from mobilization. N-B addition nearly halved soil available Cd and significantly increased nitrification by promoting AOB recovery. However, the restored nitrification did not cause soil acidification, due to the high buffering and slow liming effects of biochar. Available Cd continuously decreased with decreasing soil acidity and exchangeable Al. This study firstly demonstrated a feedback between soil nitrification and Cd after N application, and how biochar modified the feedback. Biochar, therefore, provides a feasible strategy for eliminating potential Cd toxicity on both soil biological and chemical processes.
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Affiliation(s)
- Haochun Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Lu Yu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mengjie Yu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Muhammad Afzal
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zhongming Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Philip Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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63
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Reji L, Francis CA. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME JOURNAL 2020; 14:2105-2115. [PMID: 32405026 DOI: 10.1038/s41396-020-0675-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022]
Abstract
Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO2 assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.
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Affiliation(s)
- Linta Reji
- Earth System Science, Stanford University, Stanford, CA, USA
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64
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Wu L, Peng L, Wei W, Wang D, Ni BJ. Nitrous oxide production from wastewater treatment: The potential as energy resource rather than potent greenhouse gas. JOURNAL OF HAZARDOUS MATERIALS 2020; 387:121694. [PMID: 31776086 DOI: 10.1016/j.jhazmat.2019.121694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Nitrous oxide (N2O), produced from wastewater treatment, is a potent greenhouse gas and has become a global concern in recent years. However, N2O has also been commonly used as a powerful oxidant for energy generation. As such, an increasing effort has been devoted to explore the energy potential of N2O from wastewater treatment processes recently. Nevertheless, the holistic knowledge on energy recovery from nitrogen in wastewater is still lacking for facilitating its further development. Striving for sustainable wastewater treatment, this review paper aimed to give the up-to-date status on several essential aspects regarding the N2O recovery as an energy resource rather than emission as a greenhouse gas, including energy production via N2O decomposition, main biotic N2O production sources, the potential bioprocesses used for N2O recovery, and the possible N2O harvesting strategies. We then put forward perspectives for N2O recovery and future challenges to improve our understanding of the energy generation, microbial processes involved and harvesting approaches in order to potentially achieve sustainable wastewater treatment via N2O recovery.
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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, NSW 2007, Australia
| | - Lai Peng
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 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, NSW 2007, Australia.
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65
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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Herber J, Klotz F, Frommeyer B, Weis S, Straile D, Kolar A, Sikorski J, Egert M, Dannenmann M, Pester M. A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 2019; 22:212-228. [PMID: 31657089 DOI: 10.1111/1462-2920.14840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.
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Affiliation(s)
- Janina Herber
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Dietmar Straile
- Limnological Institute, University of Konstanz, Mainaustraße 252, Constance, 78464, Germany
| | - Allison Kolar
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Johannes Sikorski
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany.,Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, Braunschweig, 38106, Germany
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68
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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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69
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Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK. Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. ISME JOURNAL 2019; 14:335-346. [PMID: 31624348 PMCID: PMC6976641 DOI: 10.1038/s41396-019-0538-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 01/08/2023]
Abstract
Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.
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Affiliation(s)
- Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Man-Young Jung
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea.
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70
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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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71
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Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances. Sci Rep 2019; 9:13506. [PMID: 31534180 PMCID: PMC6751160 DOI: 10.1038/s41598-019-49832-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/24/2019] [Indexed: 11/08/2022] Open
Abstract
Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community composition. Strikingly, we found that in comparison to the drying phase, water return (as sporadic storms and rewetting) led to larger shifts in the surface microbial community composition and diversity. In addition, microhabitat characteristics, such as the greater capacity of the hyporheic zone to maintain/conserve moisture, tended to modulate the ability of certain microbes (e.g., bacteria) to cope with severe hydrological disturbances.
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72
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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73
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Lehtovirta-Morley LE. Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together. FEMS Microbiol Lett 2019; 365:4931719. [PMID: 29668934 DOI: 10.1093/femsle/fny058] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022] Open
Abstract
Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.
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Affiliation(s)
- Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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74
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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75
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & 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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76
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Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
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77
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Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front Microbiol 2019; 10:1571. [PMID: 31379764 PMCID: PMC6657660 DOI: 10.3389/fmicb.2019.01571] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Romana Bittner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sophie S Abby
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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78
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Abstract
Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous Nitrosopumilus strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ∼28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the "Thaspiviridae." Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.
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79
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Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. mSystems 2019; 4:4/4/e00181-19. [PMID: 31239395 PMCID: PMC6593220 DOI: 10.1128/msystems.00181-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms. Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments. IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.
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80
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Liu L, Li S, Han J, Lin W, Luo J. A Two-Step Strategy for the Rapid Enrichment of Nitrosocosmicus-Like Ammonia-Oxidizing Thaumarchaea. Front Microbiol 2019; 10:875. [PMID: 31105671 PMCID: PMC6491936 DOI: 10.3389/fmicb.2019.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
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Affiliation(s)
- Liangting Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Surong Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiamin Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Weitie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianfei Luo
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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81
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Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold C, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H. Low yield and abiotic origin of N 2O formed by the complete nitrifier Nitrospira inopinata. Nat Commun 2019; 10:1836. [PMID: 31015413 PMCID: PMC6478695 DOI: 10.1038/s41467-019-09790-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 03/27/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.
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Affiliation(s)
- K Dimitri Kits
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Julia Vierheilig
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Division of Water Quality and Health, Krems, 3500, Austria
- Interuniversity Cooperation Centre for Water and Health, Krems, 3500, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Shurong Liu
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Craig Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - Andreas Richter
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Holger Wissel
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
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82
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Insights into the physiology of ammonia-oxidizing microorganisms. Curr Opin Chem Biol 2019; 49:9-15. [DOI: 10.1016/j.cbpa.2018.09.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 11/17/2022]
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83
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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84
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Wang Y, Huang JM, Cui GJ, Nunoura T, Takaki Y, Li WL, Li J, Gao ZM, Takai K, Zhang AQ, Stepanauskas R. Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean. Environ Microbiol 2019; 21:716-729. [PMID: 30592124 DOI: 10.1111/1462-2920.14518] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/18/2018] [Accepted: 12/26/2018] [Indexed: 02/05/2023]
Abstract
Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12 -independent MetE and B12 -dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.
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Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Guo-Jie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - 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
| | - 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 Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Wen-Li Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Ai-Qun Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
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85
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Abstract
Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
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Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
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86
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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87
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Kumar A, Ng DHP, Wu Y, Cao B. Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes. MICROBIAL ECOLOGY 2019; 77:1-11. [PMID: 29808411 DOI: 10.1007/s00248-018-1204-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/09/2018] [Indexed: 05/13/2023]
Abstract
Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.
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Affiliation(s)
- Amit Kumar
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, N1-01C-69, Singapore, 639798, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Daphne H P Ng
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, N1-01C-69, Singapore, 639798, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Yichao Wu
- College of Resources and Environment, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, 430070, China
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, N1-01C-69, Singapore, 639798, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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88
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Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns. Int J Mol Sci 2018; 19:ijms19123772. [PMID: 30486439 PMCID: PMC6321513 DOI: 10.3390/ijms19123772] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/21/2023] Open
Abstract
Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.
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89
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Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers. Emerg Top Life Sci 2018; 2:619-628. [PMID: 33525821 DOI: 10.1042/etls20180018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.
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90
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Arce MI, von Schiller D, Bengtsson MM, Hinze C, Jung H, Alves RJE, Urich T, Singer G. Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments. Front Microbiol 2018; 9:2794. [PMID: 30519221 PMCID: PMC6250940 DOI: 10.3389/fmicb.2018.02794] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4 +) pool size decreased, nitrate (NO3 -) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases - a hydrological scenario expected to become more important in the future.
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Affiliation(s)
- Maria Isabel Arce
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Daniel von Schiller
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Mia M. Bengtsson
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Hoseung Jung
- Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys), Humboldt University of Berlin, Berlin, Germany
| | - Ricardo J. Eloy Alves
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Gabriel Singer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
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91
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Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China). SUSTAINABILITY 2018. [DOI: 10.3390/su10103825] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Agricultural practices have significant impacts on soil properties and microbial communities; however, little is known about their responses to open field and plastic tunnels under organic and conventional farming. We therefore investigated the responses of soil chemical variables and microbial communities to different agricultural management and cultivation types, including organic management in open field (OF), organic management in plastic tunnels (OP), conventional management in open field (CF) and conventional management in plastic tunnels (CP), by using a pyrosequencing approach of 16S rRNA gene amplicon. Both factors had significant influences on the soil properties and microbial communities. Organic farming increased the nutrient-related soil variables compared to conventional farming regardless of cultivation type, especially for the available N and P, which were increased by 137% and 711%, respectively, in OP compared to CP. Additionally, OP had the highest microbial abundance and diversity among treatments, whereas no difference was found between OF, CF and CP. Furthermore, OP possessed diverse differential bacteria which were mainly related to the organic material turnover (e.g., Roseiflexus, Planctomyces and Butyrivibrio) and plant growth promotion (e.g., Nostoc, Glycomyces and Bacillus). Redundancy analysis (RDA) showed that pH, electrical conductivity (EC), nutrient levels (e.g., available N and available P) and total Zn content were significantly correlated to the structure of the microbial community. Overall, our results showed that the long-term organic farming with high fertilizer input increased soil nutrient levels and microbial abundance and diversity under plastic-tunnel condition compared to other cultivation systems.
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92
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Kobayashi S, Hira D, Yoshida K, Toyofuku M, Shida Y, Ogasawara W, Yamaguchi T, Araki N, Oshiki M. Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, Nitrososphaera viennensis. Microbes Environ 2018; 33:428-434. [PMID: 30318500 PMCID: PMC6308003 DOI: 10.1264/jsme2.me18058] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15NO2− to 15NO, the oxidation of hydroxylamine (15NH2OH) to 15NO, and the production of 14–15N2O from 15NH2OH and 14NO2−. To the best of our knowledge, the present study is the first to document the enzymatic properties of AOA NirK.
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Affiliation(s)
- Shun Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Daisuke Hira
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University
| | - Keitaro Yoshida
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology
| | | | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
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93
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Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME JOURNAL 2018; 12:2389-2402. [PMID: 29899515 DOI: 10.1038/s41396-018-0191-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 01/17/2023]
Abstract
Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.
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94
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Zorz JK, Kozlowski JA, Stein LY, Strous M, Kleiner M. Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria. Front Microbiol 2018; 9:938. [PMID: 29867847 PMCID: PMC5960693 DOI: 10.3389/fmicb.2018.00938] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.
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Affiliation(s)
- Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jessica A Kozlowski
- Department of Ecogenomics and Systems Biology, Division Archaea Biology and Ecogenomics, University of Vienna, Vienna, Austria
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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95
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Carini P, Dupont CL, Santoro AE. Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environ Microbiol 2018; 20:2112-2124. [PMID: 29626379 DOI: 10.1111/1462-2920.14107] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.
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Affiliation(s)
- Paul Carini
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
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96
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Kato S, Sakai S, Hirai M, Tasumi E, Nishizawa M, Suzuki K, Takai K. Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle. Microbes Environ 2018; 33:107-110. [PMID: 29459499 PMCID: PMC5877337 DOI: 10.1264/jsme2.me17165] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.
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Affiliation(s)
- Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Research and Development Center for Submarine Resources, JAMSTEC
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, JAMSTEC
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC
| | - Katsuhiko Suzuki
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Research and Development Center for Submarine Resources, JAMSTEC
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC
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97
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Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, Kirkegaard RH, de la Torre JR, Daims H, Wagner M. Cultivation and Genomic Analysis of " Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland. Front Microbiol 2018; 9:193. [PMID: 29491853 PMCID: PMC5817080 DOI: 10.3389/fmicb.2018.00193] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as "Candidatus Nitrosocaldus islandicus," is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. "Ca. N. islandicus" encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as "Ca. N. islandicus" is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that "Ca. N. islandicus" has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.
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Affiliation(s)
- Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Craig W. Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Julia Vierheilig
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Christopher J. Sedlacek
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus H. Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - José R. de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
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98
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Beeckman F, Motte H, Beeckman T. Nitrification in agricultural soils: impact, actors and mitigation. Curr Opin Biotechnol 2018; 50:166-173. [PMID: 29414056 DOI: 10.1016/j.copbio.2018.01.014] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/11/2018] [Indexed: 12/22/2022]
Abstract
Nitrogen is one of the most important nutrients for plant growth and hence heavily applied in agricultural systems via fertilization. Nitrification, that is, the conversion of ammonium via nitrite to nitrate by soil microorganisms, however, leads to nitrate leaching and gaseous nitrous oxide production and as such to an up to 50% loss of nitrogen availability for the plant. Nitrate leaching also results in eutrophication of groundwater, drinking water and recreational waters, toxic algal blooms and biodiversity loss, while nitrous oxide is a greenhouse gas with a global warming potential 300× greater than carbon dioxide. Logically, inhibition of nitrification is an important strategy used in agriculture to reduce nitrogen losses, and contributes to a more environmental-friendly practice. However, recently identified and crucial players in nitrification, that is, ammonia-oxidizing archaea and comammox bacteria, seem to be under-investigated in this respect. In this review, we give an update on the different pathways in ammonia oxidation, the relevance for agriculture and the interaction with nitrification inhibitors. As such, we hope to pinpoint possible strategies to optimize the efficiency of nitrification inhibition.
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Affiliation(s)
- Fabian Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium.
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
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99
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Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. Front Microbiol 2018; 9:28. [PMID: 29434576 PMCID: PMC5797428 DOI: 10.3389/fmicb.2018.00028] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.
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Affiliation(s)
- Sophie S Abby
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Centre National de la Recherche Scientifique, Université Grenoble Alpes, Grenoble, France
| | - Michael Melcher
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Michaela Stieglmeier
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Claudia Rossel
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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100
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Rodrigues-Oliveira T, Belmok A, Vasconcellos D, Schuster B, Kyaw CM. Archaeal S-Layers: Overview and Current State of the Art. Front Microbiol 2017; 8:2597. [PMID: 29312266 PMCID: PMC5744192 DOI: 10.3389/fmicb.2017.02597] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 01/01/2023] Open
Abstract
In contrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S-layers, few reports have employed archaea as a study model. As such, archaeal S-layers represent an area for exploration in both basic and applied research.
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Affiliation(s)
- Thiago Rodrigues-Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Aline Belmok
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Deborah Vasconcellos
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Bernhard Schuster
- Department of NanoBiotechnology, Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cynthia M. Kyaw
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
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