151
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Degrune F, Theodorakopoulos N, Colinet G, Hiel MP, Bodson B, Taminiau B, Daube G, Vandenbol M, Hartmann M. Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes. Front Microbiol 2017; 8:1127. [PMID: 28674527 PMCID: PMC5474472 DOI: 10.3389/fmicb.2017.01127] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/01/2017] [Indexed: 12/01/2022] Open
Abstract
Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.
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Affiliation(s)
- Florine Degrune
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- TERRA-AgricultureIsLife, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Nicolas Theodorakopoulos
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Gilles Colinet
- Exchanges Ecosystems – Atmosphere, Department of BIOSE, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Marie-Pierre Hiel
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Bernard Bodson
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | | | - Georges Daube
- Food Microbiology, University of LiègeLiège, Belgium
| | - Micheline Vandenbol
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Research Institute for Forest, Snow and Landscape Research WSLBirmensdorf, Switzerland
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152
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Ben Said S, Or D. Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia. Front Microbiol 2017; 8:1125. [PMID: 28670307 PMCID: PMC5472676 DOI: 10.3389/fmicb.2017.01125] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/01/2017] [Indexed: 11/25/2022] Open
Abstract
The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.
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Affiliation(s)
- Sami Ben Said
- Department of Environmental Systems Science, Soil and Terrestrial Environmental Physics, ETH ZürichZürich, Switzerland
| | - Dani Or
- Department of Environmental Systems Science, Soil and Terrestrial Environmental Physics, ETH ZürichZürich, Switzerland
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153
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Draft Genome Sequence of Nitrobacter vulgaris Strain Ab 1, a Nitrite-Oxidizing Bacterium. GENOME ANNOUNCEMENTS 2017; 5:5/18/e00290-17. [PMID: 28473388 PMCID: PMC5442373 DOI: 10.1128/genomea.00290-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we present the 3.9-Mb draft genome sequence of Nitrobacter vulgaris strain Ab1, which was isolated from a sewage system in Hamburg, Germany. The analysis of its genome sequence will contribute to our knowledge of nitrite-oxidizing bacteria and acyl-homoserine lactone quorum sensing in nitrifying bacteria.
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154
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Ushiki N, Jinno M, Fujitani H, Suenaga T, Terada A, Tsuneda S. Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation. J Biosci Bioeng 2017; 123:581-589. [DOI: 10.1016/j.jbiosc.2016.12.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
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155
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Liu W, Yang D, Chen W, Gu X. High-throughput sequencing-based microbial characterization of size fractionated biomass in an anoxic anammox reactor for low-strength wastewater at low temperatures. BIORESOURCE TECHNOLOGY 2017; 231:45-52. [PMID: 28192725 DOI: 10.1016/j.biortech.2017.01.050] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/23/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
The microbial characterization of three size-fractionated sludge obtained from a suspended-growth anoxic anammox reactor treating low-strength wastewater at low temperatures were investigated by using high-throughput sequencing. Particularly, the spatial variability in relative abundance of microorganisms involved in nitrogen metabolism were analyzed in detail. Results showed that population segregation did occur in the reactor. It was found, for the first time, that the genus Nitrotoga was enriched only in large granules (>400μm). Three anammox genus including Candidatus Jettenia, Brocadia and Kuenenia were detected. Among them, Candidatus Brocadia and Kuenenia preferred to grow in large-sized granules (>400μm), whereas Candidatus Jettenia dominated in small- and moderate-sized sludge (<400μm). The members of genus Candidatus Jettenia appeared to play the vital role in nitrogen removal, since sludge with diameters smaller than 400μm accounted for 81.55% of the total biomass. However, further studies are required to identify the activity of different-size sludge.
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Affiliation(s)
- Wenru Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, China.
| | - Wenjing Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Xiao Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, China
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156
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Scarascia G, Cheng H, Harb M, Hong PY. Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria. BMC Microbiol 2017; 17:85. [PMID: 28376730 PMCID: PMC5381152 DOI: 10.1186/s12866-017-0998-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 04/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. RESULTS The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. CONCLUSIONS Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.
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Affiliation(s)
- Giantommaso Scarascia
- Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Thuwal, 23955-6900, Saudi Arabia
| | - Hong Cheng
- Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Thuwal, 23955-6900, Saudi Arabia
| | - Moustapha Harb
- Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Thuwal, 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Thuwal, 23955-6900, Saudi Arabia.
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157
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Schaefer SC, Hollibaugh JT. Temperature Decouples Ammonium and Nitrite Oxidation in Coastal Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3157-3164. [PMID: 28225262 DOI: 10.1021/acs.est.6b03483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrification is a two-step process linking the reduced and oxidized sides of the nitrogen cycle. These steps are typically tightly coupled with the primary intermediate, nitrite, rarely accumulating in coastal environments. Nitrite concentrations can exceed 10 μM during summer in estuarine waters adjacent to Sapelo Island, Georgia, U.S.A. Similar peaks at other locations have been attributed to decoupling of the two steps of nitrification by hypoxia; however, the waters around Sapelo Island are aerobic and well-mixed. Experiments examining the response to temperature shifts of a nitrifying assemblage composed of the same organisms found in the field indicate that ammonia- and nitrite-oxidation become uncoupled between 20 and 30 °C, leading to nitrite accumulation. This suggests that nitrite peaks in coastal waters might be explained by differences in the responses of ammonia- and nitrite-oxidizers to increased summer temperatures. Analysis of field data from 270 stations in 29 temperate and subtropical estuaries and lagoons show transient accumulation of nitrite driven primarily by water temperatures, rather than by hypoxia. Increased climate variability and warming coastal waters may therefore increase the frequency of these nitrite peaks, with potential ecosystem consequences that include increased N2O production, NO2- toxicity, and shifts in phytoplankton community composition.
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Affiliation(s)
- Sylvia C Schaefer
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
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158
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Park MR, Park H, Chandran K. Molecular and Kinetic Characterization of Planktonic Nitrospira spp. Selectively Enriched from Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2720-2728. [PMID: 28124895 DOI: 10.1021/acs.est.6b05184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nitrospira spp. are chemolithoautotrophic nitrite-oxidizing bacteria (NOB), which are ubiquitous in natural and engineered environments. However, there exist few independent biokinetic studies on Nitrospira spp., likely because their isolation and selective enrichment from environmental consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 μm. On the basis of respirometric assays, estimated maximum specific growth rate (μmax), nitrite half saturation coefficient (KS), oxygen half saturation coefficient (KO), and biomass yield coefficient (Y) of the enriched cultures were 0.69 ± 0.10 d-1, 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O2/L, and 0.14 ± 0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and thermodynamic parameters can help toward the development and application of energy-efficient biological nutrient removal processes through effective Nitrospira out-selection.
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Affiliation(s)
- Mee-Rye Park
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
| | - Hongkeun Park
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
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159
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Simonin M, Martins JM, Le Roux X, Uzu G, Calas A, Richaume A. Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose–response relationships. Nanotoxicology 2017; 11:247-255. [DOI: 10.1080/17435390.2017.1290845] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marie Simonin
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | | | - Xavier Le Roux
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
| | - Gaëlle Uzu
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Aude Calas
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Agnès Richaume
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
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160
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Bartelme RP, McLellan SL, Newton RJ. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira. Front Microbiol 2017; 8:101. [PMID: 28194147 PMCID: PMC5276851 DOI: 10.3389/fmicb.2017.00101] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/13/2017] [Indexed: 01/04/2023] Open
Abstract
Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while supporting multiple ammonia oxidation lifestyles within the nitrifying consortium.
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Affiliation(s)
- Ryan P Bartelme
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
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161
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Cao Y, van Loosdrecht MCM, Daigger GT. Mainstream partial nitritation-anammox in municipal wastewater treatment: status, bottlenecks, and further studies. Appl Microbiol Biotechnol 2017; 101:1365-1383. [PMID: 28084538 DOI: 10.1007/s00253-016-8058-7] [Citation(s) in RCA: 397] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 11/26/2022]
Abstract
Driven by energy neutral/positive of wastewater treatment plants, significant efforts have been made on the research and development of mainstream partial nitritation and anaerobic ammonium oxidation (anammox) (PN/A) (deammonification) process since the early 2010s. To date, feasibility of mainstream PN/A process has been demonstrated and proven by experimental results at various scales although with the low loading rates and elevated nitrogen concentration in the effluent at low temperatures (15-10 °C). This review paper provides an overview of the current state of research and development of mainstream PN/A process and critically analyzes the bottlenecks for its full-scale application. The paper discusses the following: (i) the current status of research and development of mainstream PN/A process; (ii) the interactions among aerobic ammonium-oxidizing bacteria, aerobic nitrite-oxidizing bacteria, anammox bacteria, and heterotrophic bacteria; (iii) the suppression of aerobic nitrite-oxidizing bacteria; (iv) process and bioreactors; and (v) suggested further studies including efficient and robust carbon concentrating pretreatment, deepening of understanding competition between autotrophic nitrogen-converting organisms, intensification of biofilm anammox activity, reactor design, and final polishing.
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Affiliation(s)
- Yeshi Cao
- , Blk 6, 41 Tiang Jia Xian, Suzhou, 215000, Jiangsu Province, China.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Glen T Daigger
- Department of Civil and Environmental Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, MI, 48109, USA
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162
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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163
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Luo X, Han S, Lai S, Huang Q, Chen W. Long-term straw returning affectsNitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil. J Basic Microbiol 2016; 57:309-315. [DOI: 10.1002/jobm.201600400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xuesong Luo
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Songsong Lai
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
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164
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Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification. mBio 2016; 7:mBio.01753-16. [PMID: 27795404 PMCID: PMC5080386 DOI: 10.1128/mbio.01753-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi Production and consumption of NOx increased and production of N2O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable. IMPORTANCE Bacterial cell-cell signaling, or quorum sensing (QS), is a method of bacterial communication and gene regulation that is well studied in bacteria. However, little is known about the purpose of QS in many environmentally important bacteria. Here, we demonstrate quorum quenching coupled with mRNA-Seq to identify QS-controlled genes and phenotypes in Nitrobacter winogradskyi, a nitrite-oxidizing bacterium. Nitrite oxidizers play an important role in the nitrogen cycle though their participation in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite. Our quorum quenching approach revealed that QS influences production and consumption of environmentally important nitrogen oxide gases (NO, NO2, and N2O) in N. winogradskyi This study demonstrated a novel technique for studying QS in difficult-to-work-with microorganisms and showed that nitrite oxidizers might also contribute to nitrification-dependent production of nitrogen oxide gases that contribute to global warming.
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Domingo-Félez C, Pellicer-Nàcher C, Petersen MS, Jensen MM, Plósz BG, Smets BF. Heterotrophs are key contributors to nitrous oxide production in activated sludge under low C-to-N ratios during nitrification-Batch experiments and modeling. Biotechnol Bioeng 2016; 114:132-140. [DOI: 10.1002/bit.26062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/06/2016] [Accepted: 07/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
| | - Carles Pellicer-Nàcher
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
| | - Morten S. Petersen
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
| | - Marlene M. Jensen
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
| | - Benedek G. Plósz
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark; Miljøvej 113 Kongens Lyngby 2800 Denmark
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166
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Daims H, Lücker S, Wagner M. A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria. Trends Microbiol 2016; 24:699-712. [PMID: 27283264 DOI: 10.1016/j.tim.2016.05.004] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.
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Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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167
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Le Roux X, Bouskill NJ, Niboyet A, Barthes L, Dijkstra P, Field CB, Hungate BA, Lerondelle C, Pommier T, Tang J, Terada A, Tourna M, Poly F. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach. Front Microbiol 2016; 7:628. [PMID: 27242680 PMCID: PMC4868854 DOI: 10.3389/fmicb.2016.00628] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO2+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.
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Affiliation(s)
- Xavier Le Roux
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Nicholas J Bouskill
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Audrey Niboyet
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Laure Barthes
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Paul Dijkstra
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Chris B Field
- Department of Global Ecology, Carnegie Institution, Stanford University, Stanford CA, USA
| | - Bruce A Hungate
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Catherine Lerondelle
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Thomas Pommier
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Jinyun Tang
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Akihiko Terada
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Maria Tourna
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Franck Poly
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
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168
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Tangkitjawisut W, Limpiyakorn T, Powtongsook S, Pornkulwat P, Suwannasilp BB. Differences in nitrite-oxidizing communities and kinetics in a brackish environment after enrichment at low and high nitrite concentrations. J Environ Sci (China) 2016; 42:41-49. [PMID: 27090693 DOI: 10.1016/j.jes.2015.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/17/2015] [Accepted: 08/05/2015] [Indexed: 06/05/2023]
Abstract
Nitrite accumulation in shrimp ponds can pose serious adverse effects to shrimp production and the environment. This study aims to develop an effective process for the enrichment of ready-to-use nitrite-oxidizing bacteria (NOB) inocula that would be appropriate for nitrite removal in brackish shrimp ponds. To achieve this objective, the effects of nitrite concentrations on NOB communities and nitrite oxidation kinetics in a brackish environment were investigated. Moving-bed biofilm sequencing batch reactors and continuous moving-bed biofilm reactors were used for the enrichment of NOB at various nitrite concentrations, using sediment from brackish shrimp ponds as seed inoculum. The results from NOB population analysis with quantitative polymerase chain reaction (qPCR) show that only Nitrospira were detected in the sediment from the shrimp ponds. After the enrichment, both Nitrospira and Nitrobacter coexisted in the reactors controlling effluent nitrite at 0.1 and 0.5 mg-NO2(-)-N/L. On the other hand, in the reactors controlling effluent nitrite at 3, 20, and 100 mg-NO2(-)-N/L, Nitrobacter outcompeted Nitrospira in many orders of magnitude. The half saturation coefficients (Ks) for nitrite oxidation of the enrichments at low nitrite concentrations (0.1 and 0.5 mg-NO2(-)-N/L) were in the range of 0.71-0.98 mg-NO2(-)-N/L. In contrast, the K(s) values of NOB enriched at high nitrite concentrations (3, 20, and 100 mg-NO2(-)-N/L) were much higher (8.36-12.20 mg-NO2(-)-N/L). The results suggest that the selection of nitrite concentrations for the enrichment of NOB inocula can significantly influence NOB populations and kinetics, which could affect the effectiveness of their applications in brackish shrimp ponds.
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Affiliation(s)
- Wipasanee Tangkitjawisut
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
| | - Sorawit Powtongsook
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Preeyaporn Pornkulwat
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Benjaporn Boonchayaanant Suwannasilp
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand.
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169
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Shen Q, Gao J, Liu J, Liu S, Liu Z, Wang Y, Guo B, Zhuang X, Zhuang G. A New Acyl-homoserine Lactone Molecule Generated by Nitrobacter winogradskyi. Sci Rep 2016; 6:22903. [PMID: 26965192 PMCID: PMC4786786 DOI: 10.1038/srep22903] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/24/2016] [Indexed: 11/09/2022] Open
Abstract
It is crucial to reveal the regulatory mechanism of nitrification to understand nitrogen conversion in agricultural systems and wastewater treatment. In this study, the nwiI gene of Nitrobacter winogradskyi was confirmed to be a homoserine lactone synthase by heterologous expression in Escherichia coli that synthesized several acyl-homoserine lactone signals with 7 to 11 carbon acyl groups. A novel signal, 7, 8-trans-N-(decanoyl) homoserine lactone (C10:1-HSL), was identified in both N. winogradskyi and the recombined E. coli. Furthermore, this novel signal also triggered variances in the nitrification rate and the level of transcripts for the genes involved in the nitrification process. These results indicate that quorum sensing may have a potential role in regulating nitrogen metabolism.
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Affiliation(s)
- Qiuxuan Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jun Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zijun Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yinghuan Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baoyuan Guo
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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170
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A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal. ISME JOURNAL 2016; 10:2293-303. [PMID: 26894446 DOI: 10.1038/ismej.2016.8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 01/03/2016] [Accepted: 01/04/2016] [Indexed: 11/08/2022]
Abstract
The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.
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171
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Bertagnolli AD, McCalmont D, Meinhardt KA, Fransen SC, Strand S, Brown S, Stahl DA. Agricultural land usage transforms nitrifier population ecology. Environ Microbiol 2016; 18:1918-29. [DOI: 10.1111/1462-2920.13114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony D. Bertagnolli
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - Dylan McCalmont
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - Kelley A. Meinhardt
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - Steven C. Fransen
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - Stuart Strand
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - Sally Brown
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering and School of Environmental and Forest Sciences; University of Washington Seattle; Seattle WA USA
- Department of Crop and Soil Sciences; Washington State University; Prosser WA USA
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172
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Hüpeden J, Wegen S, Off S, Lücker S, Bedarf Y, Daims H, Kühn C, Spieck E. Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH. Appl Environ Microbiol 2016; 82:1838-45. [PMID: 26746710 PMCID: PMC4784051 DOI: 10.1128/aem.03163-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/31/2015] [Indexed: 12/22/2022] Open
Abstract
The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.
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Affiliation(s)
- Jennifer Hüpeden
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Simone Wegen
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sandra Off
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sebastian Lücker
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Yvonne Bedarf
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Carsten Kühn
- State Research Centre of Agriculture and Fisheries Mecklenburg-Vorpommern, Institute of Fisheries, Rostock, Germany
| | - Eva Spieck
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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173
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Fumasoli A, Etter B, Sterkele B, Morgenroth E, Udert KM. Operating a pilot-scale nitrification/distillation plant for complete nutrient recovery from urine. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:215-22. [PMID: 26744953 DOI: 10.2166/wst.2015.485] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Source-separated urine contains most of the excreted nutrients, which can be recovered by using nitrification to stabilize the urine before concentrating the nutrient solution with distillation. The aim of this study was to test this process combination at pilot scale. The nitrification process was efficient in a moving bed biofilm reactor with maximal rates of 930 mg N L(-1) d(-1). Rates decreased to 120 mg N L(-1) d(-1) after switching to more concentrated urine. At high nitrification rates (640 mg N L(-1) d(-1)) and low total ammonia concentrations (1,790 mg NH4-N L(-1) in influent) distillation caused the main primary energy demand of 71 W cap(-1) (nitrification: 13 W cap(-1)) assuming a nitrogen production of 8.8 g N cap(-1) d(-1). Possible process failures include the accumulation of the nitrification intermediate nitrite and the selection of acid-tolerant ammonia-oxidizing bacteria. Especially during reactor start-up, the process must therefore be carefully supervised. The concentrate produced by the nitrification/distillation process is low in heavy metals, but high in nutrients, suggesting a good suitability as an integral fertilizer.
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Affiliation(s)
- Alexandra Fumasoli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland E-mail:
| | - Bastian Etter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland E-mail:
| | - Bettina Sterkele
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland E-mail:
| | - Eberhard Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland E-mail: ; ETH Zürich, Institute of Environmental Engineering, 8093 Zürich, Switzerland
| | - Kai M Udert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland E-mail:
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174
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Yang Q, Shen N, Lee ZMP, Xu G, Cao Y, Kwok B, Lay W, Liu Y, Zhou Y. Simultaneous nitrification, denitrification and phosphorus removal (SNDPR) in a full-scale water reclamation plant located in warm climate. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:448-456. [PMID: 27438250 DOI: 10.2166/wst.2016.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combination of simultaneous nitrification-denitrification (SND) with enhanced biological phosphorus removal (EBPR) provides a more efficient and economically viable option for nutrient removal from municipal wastewater compared to conventional two-step nitrification-denitrification. This study analyzed the nutrients (N and P) profiles in a full-scale municipal wastewater reclamation plant (WRP) located in the tropical region, in which more than 90% of nitrogen was removed. Interestingly, average SND efficiency in aerobic zones was found to be up to 50%, whereas phosphorus profile displayed a clear cyclic release and uptake pattern with a phosphorus removal efficiency of up to 76%. The capability of sludge to perform SND and EBPR was further confirmed through a series of batch experiments. Microbial analysis revealed the presence of Accumulibacter and Tetrasphaera phosphate accumulating organisms in the plant, while few glycogen accumulating organisms (GAO) was observed. This study showed the significant occurrence of combined SND and EBPR, known as simultaneous nitrification, denitrification and phosphorus removal (SNDPR), in the studied WRP under warm climate. The possible causes behind the observed SNDPR were also discussed.
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Affiliation(s)
- Qin Yang
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Interdisciplinary Graduate School, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Nan Shen
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Zarraz M-P Lee
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail:
| | - Guangjing Xu
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail:
| | - Yeshi Cao
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Beehong Kwok
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Winson Lay
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Yu Liu
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M. Complete nitrification by Nitrospira bacteria. Nature 2015; 528:504-9. [PMID: 26610024 PMCID: PMC5152751 DOI: 10.1038/nature16461] [Citation(s) in RCA: 1139] [Impact Index Per Article: 126.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/19/2015] [Indexed: 11/11/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
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Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Elena V. Lebedeva
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Ping Han
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marton Palatinszky
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Julia Vierheilig
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Alexandr Bulaev
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Rasmus H. Kirkegaard
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Metabolomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of
Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Bernd Bendinger
- DVGW-Forschungsstelle TUHH, Hamburg University of Technology, 21073
Hamburg, Germany
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
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176
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Ngugi DK, Blom J, Stepanauskas R, Stingl U. Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. ISME JOURNAL 2015; 10:1383-99. [PMID: 26657763 PMCID: PMC5029188 DOI: 10.1038/ismej.2015.214] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 10/05/2015] [Accepted: 10/25/2015] [Indexed: 11/22/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.
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Affiliation(s)
- David Kamanda Ngugi
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | | | - Ulrich Stingl
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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177
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Wei C, He W, Wei L, Li C, Ma J. The Analysis of a Microbial Community in the UV/O3-Anaerobic/Aerobic Integrated Process for Petrochemical Nanofiltration Concentrate (NFC) Treatment by 454-Pyrosequencing. PLoS One 2015; 10:e0139991. [PMID: 26461260 PMCID: PMC4603877 DOI: 10.1371/journal.pone.0139991] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/21/2015] [Indexed: 01/24/2023] Open
Abstract
In this study, high-throughput pyrosequencing was applied on the analysis of the microbial community of activated sludge and biofilm in a lab-scale UV/O3- anaerobic/aerobic (A/O) integrated process for the treatment of petrochemical nanofiltration concentrate (NFC) wastewater. NFC is a type of saline wastewater with low biodegradability. From the anaerobic activated sludge (Sample A) and aerobic biofilm (Sample O), 59,748 and 51,231 valid sequence reads were obtained, respectively. The dominant phylotypes related to the metabolism of organic compounds, polycyclic aromatic hydrocarbon (PAH) biodegradation, assimilation of carbon from benzene, and the biodegradation of nitrogenous organic compounds were detected as genus Clostridium, genera Pseudomonas and Stenotrophomonas, class Betaproteobacteria, and genus Hyphomicrobium. Furthermore, the nitrite-oxidising bacteria Nitrospira, nitrite-reducing and sulphate-oxidising bacteria (NR-SRB) Thioalkalivibrio were also detected. In the last twenty operational days, the total Chemical Oxygen Demand (COD) and Total Organic Carbon (TOC) removal efficiencies on average were 64.93% and 62.06%, respectively. The removal efficiencies of ammonia nitrogen and Total Nitrogen (TN) on average were 90.51% and 75.11% during the entire treatment process.
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Affiliation(s)
- Chao Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
| | - Wenjie He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
- Tianjin Waterworks Group Co., Ltd., Tianjin, People's Republic of China
| | - Li Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
- * E-mail:
| | - Chunying Li
- School of Energy and Civil Engineering, Harbin University of Commerce, Harbin, Heilongjiang, People's Republic of China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
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178
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Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci U S A 2015; 112:11371-6. [PMID: 26305944 DOI: 10.1073/pnas.1506533112] [Citation(s) in RCA: 273] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.
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179
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Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers. Appl Environ Microbiol 2015; 81:5917-26. [PMID: 26092466 DOI: 10.1128/aem.01103-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/16/2015] [Indexed: 02/06/2023] Open
Abstract
Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS.
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180
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Hirsch PR, Mauchline TH. The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:45-71. [PMID: 26505688 DOI: 10.1016/bs.aambs.2015.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met.
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Affiliation(s)
- Penny R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
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