Quantification of Archaea-Driven Freshwater Nitrification
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Microbial Community and Geochemical Analyses of Trans-Trench Sediments for Understanding the Roles of Hadal Environments
The ISME Journal (2020) 14:740–756 https://doi.org/10.1038/s41396-019-0564-z ARTICLE Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments 1 2 3,4,9 2 2,10 2 Satoshi Hiraoka ● Miho Hirai ● Yohei Matsui ● Akiko Makabe ● Hiroaki Minegishi ● Miwako Tsuda ● 3 5 5,6 7 8 2 Juliarni ● Eugenio Rastelli ● Roberto Danovaro ● Cinzia Corinaldesi ● Tomo Kitahashi ● Eiji Tasumi ● 2 2 2 1 Manabu Nishizawa ● Ken Takai ● Hidetaka Nomaki ● Takuro Nunoura Received: 9 August 2019 / Revised: 20 November 2019 / Accepted: 28 November 2019 / Published online: 11 December 2019 © The Author(s) 2019. This article is published with open access Abstract Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and fi 1234567890();,: 1234567890();,: Mariana Trenches. Tag-sequencing analyses showed speci c distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. -
Human Alteration of the Global Nitrogen Cycle
What is Nitrogen? Human Alteration of the Nitrogen is the most abundant element in Global Nitrogen Cycle the Earth’s atmosphere. Nitrogen makes up 78% of the troposphere. Nitrogen cannot be absorbed directly by the plants and animals until it is converted into compounds they can use. This process is called the Nitrogen Cycle. Heather McGraw, Mandy Williams, Suzanne Heinzel, and Cristen Whorl, Give SIUE Permission to Put Our Presentation on E-reserve at Lovejoy Library. The Nitrogen Cycle How does the nitrogen cycle work? Step 1- Nitrogen Fixation- Special bacteria convert the nitrogen gas (N2 ) to ammonia (NH3) which the plants can use. Step 2- Nitrification- Nitrification is the process which converts the ammonia into nitrite ions which the plants can take in as nutrients. Step 3- Ammonification- After all of the living organisms have used the nitrogen, decomposer bacteria convert the nitrogen-rich waste compounds into simpler ones. Step 4- Denitrification- Denitrification is the final step in which other bacteria convert the simple nitrogen compounds back into nitrogen gas (N2 ), which is then released back into the atmosphere to begin the cycle again. How does human intervention affect the nitrogen cycle? Nitric Oxide (NO) is released into the atmosphere when any type of fuel is burned. This includes byproducts of internal combustion engines. Production and Use of Nitrous Oxide (N2O) is released into the atmosphere through Nitrogen Fertilizers bacteria in livestock waste and commercial fertilizers applied to the soil. Removing nitrogen from the Earth’s crust and soil when we mine nitrogen-rich mineral deposits. Discharge of municipal sewage adds nitrogen compounds to aquatic ecosystems which disrupts the ecosystem and kills fish. -
Nitrogen Removal Training Program
Nitrogen Removal Training Program Module 1 Nitrogen in the Aquatic Environment • Forms of Nitrogen and Nitrogen Transformations • Nitrogen in Surface Waters • Water Quality Impacts of Nitrogen Discharges • Nitrogen in Wastewater Module 1 Transparency 1 Nitrogen Removal Training Program Module 1 Forms of Nitrogen and Nitrogen Transformations Module 1 Transparency 2 Forms of Nitrogen in the Environment Unoxidized Forms Oxidized Forms of Nitrogen of Nitrogen Nitrite (NO -) • Nitrogen Gas (N2) • 2 + Nitrate (NO -) • Ammonia (NH4 , NH3) • 3 • Organic Nitrogen (urea, • Nitrous Oxide (N2O) amino acids, peptides, proteins, etc...) • Nitric Oxide (NO) • Nitrogen Dioxide (NO2) Module 1 Transparency 3 Nitrogen Fixation • Biological Fixation - Use of atmospheric nitrogen by certain photosynthetic blue-green algae and bacteria for growth. Nitrogen Gas Organic Nitrogen (N2) • Lightning Fixation - Conversion of atmospheric nitrogen to nitrate by lightning. lightning Nitrogen Gas + Ozone Nitrate - (N2) (O3)(NO3 ) • Industrial Fixation - Conversion of nitrogen gas to ammonia and nitrate-nitrogen (used in the manufacture of fertilizers and explosives). Module 1 Transparency 4 Biological Nitrogen Fixation Nitrogen Gas (N2) Bacteria Blue-green Algae Organic N Organic N Certain blue-green algae and bacteria use atmospheric nitrogen to produce organic nitrogen compounds. Module 1 Transparency 5 Atmospheric Fixation Lightning converts Nitrogen Gas and Ozone to Nitrate. Nitrogen Gas Nitrate Module 1 Transparency 6 Industrial Fixation N2 Nitrogen gas is converted to ammonia and nitrate in the production of fertilizer and explosives. NH3 - NO3 Module 1 Transparency 7 Ammonification and Assimilation Ammonification - Conversion of organic nitrogen to ammonia-nitrogen resulting from the biological decomposition of dead plant and animal tissue and animal fecal matter. -
Novel Insights Into the Thaumarchaeota in the Deepest Oceans: Their Metabolism and Potential Adaptation Mechanisms
Zhong et al. Microbiome (2020) 8:78 https://doi.org/10.1186/s40168-020-00849-2 RESEARCH Open Access Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms Haohui Zhong1,2, Laura Lehtovirta-Morley3, Jiwen Liu1,2, Yanfen Zheng1, Heyu Lin1, Delei Song1, Jonathan D. Todd3, Jiwei Tian4 and Xiao-Hua Zhang1,2,5* Abstract Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. -
Coursework Declaration and Feedback Form
Coursework Declaration and Feedback Form The Student should complete and sign this part Student Student Number: Name: Programme of Study (e.g. MSc in Electronics and Electrical Engineering): Course Code: ENG5059P Course Name: MSc Project Name of Name of First Supervisor: Second Supervisor: Title of Project: Declaration of Originality and Submission Information I affirm that this submission is all my own work in accordance with the University of Glasgow Regulations and the School of Engineering E N G 5 0 5 9 P requirements Signed (Student) : Date of Submission : Feedback from Lecturer to Student – to be completed by Lecturer or Demonstrator Grade Awarded: Feedback (as appropriate to the coursework which was assessed): Lecturer/Demonstrator: Date returned to the Teaching Office: Whole Genome Analysis of Nitrifying Bacteria in Construction and the Built Environment Student Name: Kaung Sett Student ID: 2603933 Supervisor Name: Dr Umer Zeeshan Ijaz Co-supervisor Name: Dr Ciara Keating August 2021 A thesis submitted in partial FulFilment oF the requirements For the degree oF MASTER OF SCIENCE IN CIVIL ENGINEERING ACKNOWLEDGEMENT First and foremost, the author would like to acknowledge his supervisors, Dr. Umer Zeeshan Ijaz and Dr Ciara Keating, for giving him this opportunity and their invaluable technological ideas, thoroughly bioinformatics and environmental concepts for this project during its preparation, analysis and giving their supervision on his project. Next, the author desires to express his deepest gratitude to University of Glasgow for providing this opportunity to improve his knowledge and skills. Then, the author deeply appreciated to his parents for their continuous love, financial support, and encouragement throughout his entire life. -
Alternative Strategies of Nutrient Acquisition and Energy Conservation Map to the Biogeography of Marine Ammonia- Oxidizing Archaea
The ISME Journal (2020) 14:2595–2609 https://doi.org/10.1038/s41396-020-0710-7 ARTICLE Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia- oxidizing archaea 1 2,3 2,3 4 5 6 Wei Qin ● Yue Zheng ● Feng Zhao ● Yulin Wang ● Hidetoshi Urakawa ● Willm Martens-Habbena ● 7 8 9 10 11 12 Haodong Liu ● Xiaowu Huang ● Xinxu Zhang ● Tatsunori Nakagawa ● Daniel R. Mende ● Annette Bollmann ● 13 14 15 16 17 10 Baozhan Wang ● Yao Zhang ● Shady A. Amin ● Jeppe L. Nielsen ● Koji Mori ● Reiji Takahashi ● 1 18 11 9 19,8 E. Virginia Armbrust ● Mari-K.H. Winkler ● Edward F. DeLong ● Meng Li ● Po-Heng Lee ● 20,21,22 7 4 18 1 Jizhong Zhou ● Chuanlun Zhang ● Tong Zhang ● David A. Stahl ● Anitra E. Ingalls Received: 15 February 2020 / Revised: 16 June 2020 / Accepted: 25 June 2020 / Published online: 7 July 2020 © The Author(s) 2020. This article is published with open access 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 1234567890();,: 1234567890();,: 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. -
Archaea and the Origin of Eukaryotes
REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative. -
Effects of Phosphorus on Nitrification Process in a Fertile Soil Amended
agriculture Article Effects of Phosphorus on Nitrification Process in a Fertile Soil Amended with Urea Jianfeng Ning 1,2,*, Yuji Arai 2 , Jian Shen 1, Ronghui Wang 1 and Shaoying Ai 1,* 1 Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou 510640, China; [email protected] (J.S.); [email protected] (R.W.) 2 Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; [email protected] * Correspondence: [email protected] (J.N.); [email protected] (S.A.) Abstract: While the effects of carbon on soil nitrogen (N) cycle have been extensively studied, it is not clearly understood how co-existing macronutrients, such as phosphorus (P), affect the N cycle in agroecosystems. In this study, P amendment effects on nitrification in a fertile agricultural soil were investigated under a typical N-P amendment rate. In a laboratory incubation study, soils were amended with urea, monopotassium phosphate and a mixture of urea and monopotassium phosphate at the same rate. In soils that received no amendments (control), P only, urea only, and urea plus P amendment, nitrification occurred within the first five days, with an average net nitrification rate of 5.30, 5.77, 16.66 and 9.00 mg N kg−1d−1, respectively. Interestingly, nitrification in urea-treated soils was retarded by P addition where a N:P ratio seemed to be a key factor impeding nitrification. -
Downloaded from Mage and Compared
bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta Florian U. Moeller1, Nicole S. Webster2,3, Craig W. Herbold1, Faris Behnam1, Daryl Domman1, 5 Mads Albertsen4, Maria Mooshammer1, Stephanie Markert5,8, Dmitrij Turaev6, Dörte Becher7, Thomas Rattei6, Thomas Schweder5,8, Andreas Richter9, Margarete Watzka9, Per Halkjaer Nielsen4, and Michael Wagner1,* 1Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, 10 Austria. 2Australian Institute of Marine Science, Townsville, Queensland, Australia. 3 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of 15 Queensland, St Lucia, QLD, Australia 4Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark. 20 5Institute of Marine Biotechnology e.V., Greifswald, Germany 6Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Austria. 25 7Institute of Microbiology, Microbial Proteomics, University of Greifswald, Greifswald, Germany 8Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany 9Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, 30 University of Vienna, Austria. *Corresponding author: Michael Wagner, Department of Microbiology and Ecosystem Science, Althanstrasse 14, University of Vienna, 1090 Vienna, Austria. Email: wagner@microbial- ecology.net 1 bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Marine Ammonia-Oxidizing Archaeal Isolates Display Obligate Mixotrophy and Wide Ecotypic Variation
Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation Wei Qina, Shady A. Aminb, Willm Martens-Habbenaa, Christopher B. Walkera, Hidetoshi Urakawac, Allan H. Devolb, Anitra E. Ingallsb, James W. Moffettd, E. Virginia Armbrustb, and David A. Stahla,1 aDepartment of Civil and Environmental Engineering and bSchool of Oceanography, University of Washington, Seattle, WA 98195; cDepartment of Marine and Ecological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965; and dDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089 Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved July 11, 2014 (received for review December 30, 2013) Ammonia-oxidizing archaea (AOA) are now implicated in exerting other abundant marine plankton (including Pelagibacter and significant control over the form and availability of reactive nitrogen Prochlorococcus) was made possible by genomic and biochemical species in marine environments. Detailed studies of specific meta- characterization of SCM1 (13, 14). More recent physiological bolic traits and physicochemical factors controlling their activities studies examining the copper requirements of SCM1 provided and distribution have not been well constrained in part due to the a framework to evaluate the significance of copper in controlling scarcity of isolated AOA strains. Here, we report the isolation of two the environmental distribution and activity of marine AOA (12). new coastal marine AOA, strains PS0 and HCA1. Comparison of the The capture of a greater representation of AOA environ- new strains to Nitrosopumilus maritimus strain SCM1, the only ma- mental diversity in pure culture should therefore serve to expand rine AOA in pure culture thus far, demonstrated distinct adaptations understanding of traits influencing their activity patterns in to pH, salinity, organic carbon, temperature, and light. -
Enigmatic, Ultrasmall, Uncultivated Archaea
Enigmatic, ultrasmall, uncultivated Archaea Brett J. Bakera, Luis R. Comollib, Gregory J. Dicka,1, Loren J. Hauserc, Doug Hyattc, Brian D. Dilld, Miriam L. Landc, Nathan C. VerBerkmoesd, Robert L. Hettichd, and Jillian F. Banfielda,e,2 aDepartment of Earth and Planetary Science and eEnvironmental Science, Policy, and Management, University of California, Berkeley, CA 94720; bLawrence Berkeley National Laboratories, Berkeley, CA 94720; and cBiosciences and dChemical Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831 Edited by Norman R. Pace, University of Colorado, Boulder, CO, and approved March 30, 2010 (received for review December 16, 2009) Metagenomics has provided access to genomes of as yet unculti- diversity of microbial life (15), it is likely that other unusual rela- vated microorganisms in natural environments, yet there are gaps tionships critical to survival of organisms and communities remain in our knowledge—particularly for Archaea—that occur at rela- to be discovered. In the present study, we explored the biology of tively low abundance and in extreme environments. Ultrasmall cells three unique, uncultivated lineages of ultrasmall Archaea by com- (<500 nm in diameter) from lineages without cultivated represen- bining metagenomics, community proteomics, and 3D tomographic tatives that branch near the crenarchaeal/euryarchaeal divide have analysis of cells and cell-to-cell interactions in natural biofilms. been detected in a variety of acidic ecosystems. We reconstructed Using these complementary cultivation-independent methods, we composite, near-complete ∼1-Mb genomes for three lineages, re- report several unexpected metabolic features that illustrate unique ferred to as ARMAN (archaeal Richmond Mine acidophilic nanoor- facets of microbial biology and ecology. -
Nitrification 31
NITROGEN IN SOILS/Nitrification 31 See also: Eutrophication; Greenhouse Gas Emis- Powlson DS (1993) Understanding the soil nitrogen cycle. sions; Isotopes in Soil and Plant Investigations; Soil Use and Management 9: 86–94. Nitrogen in Soils: Cycle; Nitrification; Plant Uptake; Powlson DS (1999) Fate of nitrogen from manufactured Symbiotic Fixation; Pollution: Groundwater fertilizers in agriculture. In: Wilson WS, Ball AS, and Hinton RH (eds) Managing Risks of Nitrates to Humans Further Reading and the Environment, pp. 42–57. Cambridge: Royal Society of Chemistry. Addiscott TM, Whitmore AP, and Powlson DS (1991) Powlson DS (1997) Integrating agricultural nutrient man- Farming, Fertilizers and the Nitrate Problem. Wallingford: agement with environmental objectives – current state CAB International. and future prospects. Proceedings No. 402. York: The Benjamin N (2000) Nitrates in the human diet – good or Fertiliser Society. bad? Annales de Zootechnologie 49: 207–216. Powlson DS, Hart PBS, Poulton PR, Johnston AE, and Catt JA et al. (1998) Strategies to decrease nitrate leaching Jenkinson DS (1986) Recovery of 15N-labelled fertilizer in the Brimstone Farm experiment, Oxfordshire, UK, applied in autumn to winter wheat at four sites in eastern 1988–1993: the effects of winter cover crops and England. Journal of Agricultural Science, Cambridge unfertilized grass leys. Plant and Soil 203: 57–69. 107: 611–620. Cheney K (1990) Effect of nitrogen fertilizer rate on soil Recous S, Fresnau C, Faurie G, and Mary B (1988) The fate nitrate nitrogen content after harvesting winter wheat. of labelled 15N urea and ammonium nitrate applied to a Journal of Agricultural Science, Cambridge 114: winter wheat crop.