scholarly journals Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

2013 ◽  
Vol 10 (11) ◽  
pp. 7395-7410 ◽  
Author(s):  
A. E. Santoro ◽  
C. M. Sakamoto ◽  
J. M. Smith ◽  
J. N. Plant ◽  
A. L. Gehman ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
California Current ◽  
Euphotic Zone ◽  
Ammonia Oxidizing Bacteria ◽  
Central California ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
Nh3 Oxidation

Abstract. Nitrite (NO2−) is a substrate for both oxidative and reductive microbial metabolism. NO2− accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2− production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3−) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3− reduction to NO2− were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2− production in the PNM. Sensitive (< 10 nmol L−1), precise measurements of [NH4+] and [NO2−] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2− producing process, with rates of NH3 oxidation to NO2− of up to 31 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2− production from NO3− was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2− production from NO3− were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2− production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2− just below the PNM was not captured in the incubations. Residence time estimates of NO2− within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

scholarly journals Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current

2013 ◽  
Vol 10 (3) ◽  
pp. 5803-5840 ◽  
Author(s):  
A. E. Santoro ◽  
C. M. Sakamoto ◽  
J. M. Smith ◽  
J. N. Plant ◽  
A. L. Gehman ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
California Current ◽  
Euphotic Zone ◽  
Ammonia Oxidizing Bacteria ◽  
Central California ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
Nh3 Oxidation

Abstract. Nitrite (NO2–) is a substrate for both oxidative and reductive microbial metabolism. NO2– accumulates at the base of the euphotic zone in oxygenated, stratified open ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2– production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria or archaea and assimilatory nitrate (NO3–) reduction by phytoplankton or heterotrophic bacteria. Measurements of NH3 oxidation and NO3– reduction to NO2– were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2– production in the PNM. Sensitive (< 10 nmol L−1), high-resolution measurements of [NH4+] and [NO2–] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2– producing process with rates of NH3 oxidation of up to 50 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2– production from NO3– was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2– production from NO3– were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2– profiles supported direct rate measurements of a net biological sink for NO2– just below the PNM. Residence time estimates of NO2– within the PNM were similar at the mesotrophic and oligotrophic stations and ranged from 150–205 d. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

2021 ◽  
Author(s):  
Elizabeth French ◽  
Jessica A. Kozlowski ◽  
Annette Bollmann
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Natural Environments ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Batch Cultures ◽  
Freshwater Systems ◽  
Ammonia Oxidizing Archaea

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group ( Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite – can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

scholarly journals Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica

2019 ◽  
Vol 16 (20) ◽  
pp. 4113-4128 ◽  
Author(s):  
Qing Wang ◽  
Renbin Zhu ◽  
Yanling Zheng ◽  
Tao Bao ◽  
Lijun Hou
Keyword(s):  
Ammonia Oxidation ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Tundra Soils ◽  
Maritime Antarctica ◽  
Soil C ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Tundra Ecosystem

Abstract. The colonization by a large number of sea animals, including penguins and seals, plays an important role in the nitrogen cycle of the tundra ecosystem in coastal Antarctica. However, little is known about the effects of sea animal colonization on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities involved in nitrogen transformations. In this study, we chose active seal colony tundra soils (SSs), penguin colony soils (PSs), adjacent penguin-lacking tundra soils (PLs), tundra marsh soils (MSs), and background tundra soils (BSs) to investigate the effects of sea animal colonization on the abundance, activity, and diversity of AOA and AOB in maritime Antarctica. Results indicated that AOB dominated over AOA in PS, SS, and PL, whereas AOB and AOA abundances were similar in MS and BS. Penguin or seal activities increased the abundance of soil AOB amoA genes but reduced the abundance of AOA amoA genes, leading to very large ratios (1.5×102 to 3.2×104) of AOB to AOA amoA copy numbers. Potential ammonia oxidation rates (PAORs) were significantly higher (P=0.02) in SS and PS than in PL, MS, and BS and were significantly positively correlated (P<0.001) with AOB amoA gene abundance. The predominance of AOB over AOA and their correlation with PAOR suggested that AOB play a more important role in the nitrification in animal colony soils. Sequence analysis for gene clones showed that AOA and AOB in tundra soils were from the Nitrososphaera and Nitrosospira lineages, respectively. Penguin or seal activities led to a predominance of AOA phylotypes related to Nitrososphaera cluster I and AOB phylotypes related to Nitrosospira clusters I and II but very low relative abundances in AOA phylotypes related to cluster II, and AOB phylotypes related to clusters III and IV. The differences in AOB and AOA community structures were closely related to soil biogeochemical processes under the disturbance of penguin or seal activities: soil C : N alteration and sufficient input of NH4+–N and phosphorus from animal excrements. The results significantly enhanced the understanding of ammonia-oxidizing microbial communities in the tundra environment of maritime Antarctica.

scholarly journals Effects of Sea Animal Colonization on the Coupling between Dynamics and Activity of Soil Ammonia-oxidizing Bacteria and Archaea in Maritime Antarctica

2019 ◽  
Author(s):  
Qing Wang ◽  
Renbin Zhu ◽  
Yanling Zheng ◽  
Tao Bao ◽  
Lijun Hou
Keyword(s):  
Ammonia Oxidation ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Tundra Soils ◽  
Maritime Antarctica ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Tundra Ecosystem

Abstract. The colonization of a large number of sea animal, including penguins and seals, plays an important role in the nitrogen cycle of the tundra ecosystem in coastal Antarctica. However, little is known about the effects of sea animal colonization on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities involved in nitrogen transformations. In this study, we chose active seal colony tundra soils (STS), penguin colony soils (PTS), adjacent penguin-lacking tundra soils (PLS), tundra marsh soils (MS), and background tundra soils (BS), to investigate the effects of sea animal colonization on the abundance, activity, and diversity of AOA and AOB in maritime Antarctica. Results indicated that AOB dominated over AOA in PTS, STS, and PLS; whereas AOB and AOA abundances were similar in MS and BS. Penguin or seal activities increases the abundance of soil AOB amoA genes, but reduced the abundance of AOA amoA genes, leading to very large ratios (1.5 × 102 to 3.2 × 104) of AOB to AOA amoA copy numbers. Ammonia oxidation rates were significantly higher (P = 0.02) in STS and PTS than in PLS, MS, and BS, and were significantly positively correlated (P < 0.001) with AOB amoA gene abundance suggesting that AOB are more important in the nitrification in animal colony soils. Sequence analysis for gene clones showed that AOA and AOB in tundra soils were from the Nitrosospira and Nitrososphaera lineages, respectively. Seal or penguin activities led to the predominant existence of AOA phylotypes related to Nitrososphaera cluster I and AOB phylotypes related to Nitrosospira clusters I and II, but very low relative abundances in AOA phylotypes related to cluster II, and AOB phylotypes related to cluster III and IV. The differences in AOB and AOA community structures were closely related to soil biogeochemical processes under the disturbance of penguin or seal activities: soil C:N alteration and sufficient input of NH4+–N and phosphorus from animal excrements. The results provide insights into the mechanisms how microbes drive nitrification in maritime Antarctica.

Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1282-1285 ◽  
Author(s):  
Alyson E. Santoro ◽  
Carolyn Buchwald ◽  
Matthew R. McIlvin ◽  
Karen L. Casciotti
Keyword(s):  
Ammonia Oxidation ◽  
Stratospheric Ozone ◽  
Isotopic Signature ◽  
Primary Sources ◽  
Ammonia Oxidizing Bacteria ◽  
Isotopic Signatures ◽  
Ozone Destruction ◽  
Ammonia Oxidizing Archaea ◽  
Isotope Measurements ◽  
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.

scholarly journals Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields

2011 ◽  
Vol 77 (21) ◽  
pp. 7787-7796 ◽  
Author(s):  
Micol Bellucci ◽  
Irina D. Ofiţeru ◽  
David W. Graham ◽  
Ian M. Head ◽  
Thomas P. Curtis
Keyword(s):  
Wastewater Treatment ◽  
Dissolved Oxygen ◽  
Ammonia Oxidation ◽  
Rrna Gene ◽  
Airflow Rate ◽  
Ammonia Oxidizing Bacteria ◽  
Oxidation Rates ◽  
Operational Costs ◽  
Complete Nitrification ◽  
Low Do

ABSTRACTIn wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ± 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to theNitrosomonas oligotrophalineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure.

scholarly journals Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

2012 ◽  
Vol 78 (16) ◽  
pp. 5773-5780 ◽  
Author(s):  
Elizabeth French ◽  
Jessica A. Kozlowski ◽  
Maitreyee Mukherjee ◽  
George Bullerjahn ◽  
Annette Bollmann
Keyword(s):  
Growth Rates ◽  
Ammonia Oxidation ◽  
Light Exposure ◽  
Enrichment Culture ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Ammonia Oxidizing Archaea ◽  
Group I ◽  
Nitrosomonas Oligotropha

ABSTRACTAerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “CandidatusNitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from theNitrosomonas oligotrophagroup (Nitrosomonascluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

scholarly journals Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

2020 ◽  
Vol 14 (11) ◽  
pp. 2659-2674 ◽  
Author(s):  
Carolina Reyes ◽  
Logan H. Hodgskiss ◽  
Melina Kerou ◽  
Thomas Pribasnig ◽  
Sophie S. Abby ◽  
...  
Keyword(s):  
Electron Transport ◽  
Carbon Fixation ◽  
Ammonia Oxidation ◽  
Transcriptomic Analysis ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
Model Soil ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
Cu Uptake

Abstract Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.

scholarly journals Microbial N Transformations and N2O Emission after Simulated Grassland Cultivation: Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate (DMPP)

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Yun-Feng Duan ◽  
Xian-Wang Kong ◽  
Andreas Schramm ◽  
Rodrigo Labouriau ◽  
Jørgen Eriksen ◽  
...  
Keyword(s):  
Adverse Effects ◽  
Ammonia Oxidation ◽  
Nitrification Inhibitor ◽  
Transcript Abundance ◽  
N Leaching ◽  
Ammonia Oxidizing Bacteria ◽  
N Losses ◽  
Mineral N ◽  
N Transformations ◽  
Ammonia Oxidizing Archaea

ABSTRACT Grassland cultivation can mobilize large pools of N in the soil, with the potential for N leaching and N2O emissions. Spraying with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) before cultivation was simulated by use of soil columns in which the residue distribution corresponded to plowing or rotovation to study the effects of soil-residue contact on N transformations. DMPP was sprayed on aboveground parts of ryegrass and white clover plants before incorporation. During a 42-day incubation, soil mineral N dynamics, potential ammonia oxidation (PAO), denitrifying enzyme activity (DEA), nitrifier and denitrifier populations, and N2O emissions were investigated. The soil NO3 − pool was enriched with 15N to trace sources of N2O. Ammonium was rapidly released from decomposing residues, and PAO was stimulated in soil near residues. DMPP effectively reduced NH4 + transformation irrespective of residue distribution. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) were both present, but only the AOB amoA transcript abundance correlated with PAO. DMPP inhibited the transcription of AOB amoA genes. Denitrifier genes and transcripts (nirK, nirS, and clades I and II of nosZ) were recovered, and a correlation was found between nirS mRNA and DEA. DMPP showed no adverse effects on the abundance or activity of denitrifiers. The 15N enrichment of N2O showed that denitrification was responsible for 80 to 90% of emissions. With support from a control experiment without NO3 − amendment, it was concluded that DMPP will generally reduce the potential for leaching of residue-derived N, whereas the effect of DMPP on N2O emissions will be significant only when soil NO3 − availability is limiting. IMPORTANCE Residue incorporation following grassland cultivation can lead to mobilization of large pools of N and potentially to significant N losses via leaching and N2O emissions. This study proposed a mitigation strategy of applying 3,4-dimethylpyrazole phosphate (DMPP) prior to grassland cultivation and investigated its efficacy in a laboratory incubation study. DMPP inhibited the growth and activity of ammonia-oxidizing bacteria but had no adverse effects on ammonia-oxidizing archaea and denitrifiers. DMPP can effectively reduce the potential for leaching of NO3 − derived from residue decomposition, while the effect on reducing N2O emissions will be significant only when soil NO3 − availability is limiting. Our findings provide insight into how DMPP affects soil nitrifier and denitrifier populations and have direct implications for improving N use efficiency and reducing environmental impacts during grassland cultivation.

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