New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

The ocean is an important global source of nitrous oxide (N2O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N2O, but the isotopic signatures of N2O produced by these processes are not consistent with the marine contribution to the global N2O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N2O. Natural-abundance stable isotope measurements indicate that the produced N2O had bulk δ15N and δ18O values higher than observed for ammonia-oxidizing bacteria but similar to the δ15N and δ18O values attributed to the oceanic N2O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N2O source.

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Differential photoinhibition of bacterial and archaeal ammonia oxidation

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2011.02457.x ◽

2011 ◽

Vol 327 (1) ◽

pp. 41-46 ◽

Cited By ~ 142

Author(s):

Stephanie N. Merbt ◽

David A. Stahl ◽

Emilio O. Casamayor ◽

Eugènia Martí ◽

Graeme W. Nicol ◽

...

Keyword(s):

Ammonia Oxidation ◽

Archaeal Ammonia Oxidation

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Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

Applied and Environmental Microbiology ◽

10.1128/aem.00250-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4492-4504 ◽

Cited By ~ 14

Author(s):

Manabu Nishizawa ◽

Sanae Sakai ◽

Uta Konno ◽

Nozomi Nakahara ◽

Yoshihiro Takaki ◽

...

Keyword(s):

Oxygen Isotope ◽

Ammonia Oxidation ◽

Isotope Effects ◽

Isotope Ratios ◽

Oxidation Activity ◽

Content Type ◽

Ammonia Oxidizing Archaea ◽

Nitrogen Pools ◽

Archaeal Ammonia Oxidation

ABSTRACTAmmonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in thein situquantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ15NNO2−and δ18ONO2−, respectively) are geochemical tracers for evaluating the sources and thein siturate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilicThaumarchaeotapopulations composed almost entirely of “CandidatusNitrosocaldus.” The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ18O value of nitrite produced from ammonia oxidation varied with the δ18O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilicThaumarchaeotacould be estimated using δ18ONO2−in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments.IMPORTANCEBecause ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilicThaumarchaeotaand elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation.

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Widespread of anaerobic ammonia oxidation bacteria in an eutrophic freshwater lake wetland and its impact on nitrogen cycle

Acta Ecologica Sinica ◽

10.5846/stxb201109151354 ◽

2012 ◽

Vol 32 (21) ◽

pp. 6591-6598 ◽

Cited By ~ 1

Author(s):

王衫允 WANG Shanyun ◽

祝贵兵 ZHU Guibing ◽

曲冬梅 QU Dongmei ◽

尹澄清 YIN Chengqing

Keyword(s):

Nitrogen Cycle ◽

Ammonia Oxidation ◽

Freshwater Lake ◽

Anaerobic Ammonia Oxidation

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Impact of inocula and growth mode on the molecular microbial ecology of anaerobic ammonia oxidation (anammox) bioreactor communities

Water Research ◽

10.1016/j.watres.2010.07.022 ◽

2010 ◽

Vol 44 (17) ◽

pp. 5005-5013 ◽

Cited By ~ 72

Author(s):

Hongkeun Park ◽

Alex Rosenthal ◽

Roland Jezek ◽

Krish Ramalingam ◽

John Fillos ◽

...

Keyword(s):

Microbial Ecology ◽

Ammonia Oxidation ◽

Growth Mode ◽

Anaerobic Ammonia Oxidation ◽

Molecular Microbial Ecology

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Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems

Applied and Environmental Microbiology ◽

10.1128/aem.02917-08 ◽

2009 ◽

Vol 75 (15) ◽

pp. 4993-5000 ◽

Cited By ~ 101

Author(s):

Brigitte Hai ◽

Ndeye Hélène Diallo ◽

Saidou Sall ◽

Felix Haesler ◽

Kristina Schauss ◽

...

Keyword(s):

Microbial Communities ◽

Nitrogen Cycle ◽

Plant Development ◽

Water Availability ◽

Management Practices ◽

Ammonia Oxidation ◽

Organic Fertilizers ◽

Ammonia Oxidizing Bacteria ◽

Development Stages ◽

The Impact

ABSTRACT The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.

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Different Driving Factors for Potential Activity of Ammonia-Oxidizing Archaea and Bacteria in Coastal Wetlands

10.21203/rs.3.rs-280386/v1 ◽

2021 ◽

Author(s):

Xianfang zhu ◽

Chen Wang ◽

Shuangyu Tang ◽

Guodong Ji

Keyword(s):

Nitrogen Cycle ◽

Coastal Wetlands ◽

Ammonia Oxidation ◽

Equation Model ◽

Ammonium Concentration ◽

Ammonia Oxidizing Archaea ◽

Soil Sediment ◽

Measured Activity ◽

Structure Equation Model ◽

Potential Activity

Abstract This study aimed to evaluate which environmental factors and genetic groups were important in explaining measured activity of Ammonia-oxidizing archaea (AOA) and bacteria (AOB), which play important roles in global nitrogen cycle, providing a new insight into the mechanism of archaeal and bacterial ammonia oxidation. We sampled 62 soil/sediment samples from coastal wetlands of the Bohai area of China and assessed the abundance of functional genes involved in the nitrogen cycle, soil/sediment characteristics and the potential activity of AOA (PAOA) and AOB (PAOB) using specific inhibitors. At last, we introduced the structure equation model (SEM) to infer direct and indirect effects of variables on potential activities. The results indicated that the change in AOA-amoA gene abundance may be more independent, while AOB-amoA was closely associated with the change in abundance of amx and denitrifier. PAOA was mainly defined by AOA-amoA abundance and partially influenced by the norA gene, suggesting coupling of archaeal ammonia oxidation with nitrite oxidation. PAOB was significantly defined by the abundance of amx and denitrifier, indirectly mediated by AOB-amoA. The activity of AOA seemed to be more independent of other microbial activities, while the activity of AOB varied closely with fluctuations of other microbial species. PAOA was mediated directly by the C/N ratio and indirectly by nitrite concentration and TOC value, while PAOB was mediated directly by ammonium concentration and TOC value and indirectly by C/N ratio. The activity of AOB may be determined by several other functional gene groups and had little correlation with AOB abundance while the activity of AOA was mostly controlled by itself.

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The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger

Environmental Microbiology ◽

10.1111/1462-2920.12677 ◽

2015 ◽

Vol 17 (7) ◽

pp. 2261-2274 ◽

Cited By ~ 96

Author(s):

Willm Martens-Habbena ◽

Wei Qin ◽

Rachel E. A. Horak ◽

Hidetoshi Urakawa ◽

Andrew J. Schauer ◽

...

Keyword(s):

Nitric Oxide ◽

Ammonia Oxidation ◽

Ammonia Oxidizing Archaea ◽

Archaeal Ammonia Oxidation

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The nitrogen cycle

10.1093/oso/9780198789406.003.0012 ◽

2018 ◽

Author(s):

David L. Kirchman

Keyword(s):

Nitrous Oxide ◽

Nitrogen Fixation ◽

Nitrogen Cycle ◽

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

Ammonium Nitrogen ◽

Gas Production ◽

Ammonia Oxidizing Bacteria ◽

Nitrogen Gas ◽

Chemolithoautotrophic Bacteria

Nitrogen is required for the biosynthesis of many cellular components and can take on many oxidation states, ranging from −3 to +5. Consequently, nitrogen compounds can act as either electron donors (chemolithotrophy) or electron acceptors (anaerobic respiration). The nitrogen cycle starts with nitrogen fixation, the reduction of nitrogen gas to ammonium. Nitrogen fixation is carried out only by prokaryotes, mainly some cyanobacteria and heterotrophic bacteria. The ammonium resulting from nitrogen fixation is quickly used by many organisms for biosynthesis, being preferred over nitrate as a nitrogen source. It is also oxidized aerobically by chemolithoautotrophic bacteria and archaea during the first step of nitrification. The second step, nitrite oxidation, is carried out by other bacteria not involved in ammonia oxidation, resulting in the formation of nitrate. Some bacteria are capable of carrying out both steps (“comammox”). This nitrate can then be reduced to nitrogen gas or nitrous oxide during denitrification. It can be reduced to ammonium, a process called “dissimilatory nitrate reduction to ammonium.” Nitrogen gas is also released by anaerobic oxidation of ammonium (“anammox”) which is carried out by bacteria in the Planctomycetes phylum. The theoretical contribution of anammox to total nitrogen gas release is 29%, but the actual contribution varies greatly. Another gas in the nitrogen cycle, nitrous oxide, is a greenhouse gas produced by ammonia-oxidizing bacteria and archaea. The available data indicate that the global nitrogen cycle is in balance, with losses from nitrogen gas production equaling gains via nitrogen fixation. But excess nitrogen from fertilizers is contributing to local imbalances and several environmental problems in drinking waters, reservoirs, lakes, and coastal oceans.

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