scholarly journals Phanerozoic Radiation of Ammonia Oxidizing Bacteria

2019 ◽  
Author(s):  
LM Ward ◽  
DT Johnston ◽  
PM Shih
Keyword(s):  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Deep Ocean ◽  
Nitrogen Isotope ◽  
Ammonia Oxidizing Bacteria ◽  
Crown Group ◽  
Geologic Time ◽  
Absolute Requirement ◽  
Isotope Record ◽  
Late Evolution

AbstractThe modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution – especially as it relates to the Great Oxygenation Event ~2.3 billion years ago – remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.

scholarly journals Phanerozoic radiation of ammonia oxidizing bacteria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
L. M. Ward ◽  
D. T. Johnston ◽  
P. M. Shih
Keyword(s):  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Deep Ocean ◽  
Nitrogen Isotope ◽  
Ammonia Oxidizing Bacteria ◽  
Crown Group ◽  
Geologic Time ◽  
Absolute Requirement ◽  
Isotope Record ◽  
Late Evolution

AbstractThe modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution—especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago—remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.

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

2009 ◽  
Vol 75 (15) ◽  
pp. 4993-5000 ◽  
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.

The nitrogen cycle

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.

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

scholarly journals Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Roxana T. Shafiee ◽  
Poppy J. Diver ◽  
Joseph T. Snow ◽  
Qiong Zhang ◽  
Rosalind E. M. Rickaby
Keyword(s):  
Comparative Genomics ◽  
Trace Metals ◽  
Trace Metal ◽  
Ammonia Oxidation ◽  
Testable Hypothesis ◽  
Niche Separation ◽  
Toxicity Threshold ◽  
Geologic Time ◽  
Additional Explanation ◽  
Ammonia Oxidising Archaea

AbstractAmmonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.

scholarly journals Meta-azotomics of engineered wastewater treatment processes reveals differential contributions of established and novel models of N-cycling

2020 ◽  
Author(s):  
Mee-Rye Park ◽  
Medini K. Annavajhala ◽  
Kartik Chandran
Keyword(s):  
Wastewater Treatment ◽  
Ammonia Oxidation ◽  
Carbon Sources ◽  
N Cycling ◽  
Glycerol Metabolism ◽  
Ammonia Oxidizing Bacteria ◽  
Design And Optimization ◽  
Treatment Processes ◽  
Upstream Process ◽  
Biological Nitrogen

AbstractThe application of metagenomics and metatranscriptomics to field-scale engineered biological nitrogen removal (BNR) processes revealed a complex N-cycle network (the meta-azotome) therein in terms of microbial structure, potential and extant function. Autotrophic nitrification bore the imprint of well-documented Nitrosomonas and Nitrospira in most systems. However, in select BNR processes, complete ammonia oxidizing bacteria, comammox Nitrospira, unexpectedly contributed more substantially to ammonia oxidation than canonical ammonia oxidizing bacteria, based on metatranscriptomic profiling. Methylotrophic denitrification was distinctly active in methanol-fed reactors but not in glycerol-fed reactors. Interestingly, glycerol metabolism and N-reduction transcript signatures were uncoupled, possibly suggesting the role of other carbon sources in denitrification emanating from glycerol itself or from upstream process reactors. In sum, the meta-azotome of engineered BNR processes revealed both traditional and novel mechanisms of N-cycling. Similar interrogation approaches could potentially inform better design and optimization of wastewater treatment and engineered bioprocesses in general.

Ammonia Oxidizing Bacteria (AOB) kinetic parameters estimated using the actual maximum ammonia oxidation rate

2020 ◽  
Vol 147 ◽  
pp. 104876
Author(s):  
Alberto Mannucci ◽  
Cecilia Caretti ◽  
Iacopo Ducci ◽  
Claudio Lubello ◽  
Riccardo Gori ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Oxidation Rate ◽  
Ammonia Oxidation ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidation Rate

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.

Indole degrading of ammonia oxidizing bacteria isolated from swine wastewater treatment system

2009 ◽  
Vol 59 (12) ◽  
pp. 2405-2410 ◽  
Author(s):  
Ping Li ◽  
Lei Tong ◽  
Kun Liu ◽  
Yanhong Wang ◽  
Yanxin Wang
Keyword(s):  
Wastewater Treatment ◽  
Biochemical Analysis ◽  
Ammonia Oxidation ◽  
Treatment System ◽  
Swine Wastewater ◽  
Ammonia Oxidizing Bacteria ◽  
16S Rdna Gene ◽  
Wastewater Treatment System ◽  
Nitrate And Nitrite ◽  
Physiological And Biochemical

Three new strains named LPA11, LPB11 and LPC24 were isolated to investigate the patterns of indole degradation and ammonia oxidation in swine wastewater from different parts of a swine wastewater treatment system by the direct spreading plate method. These three isolates were all identified as Pseudomonas putida based on 16S-rDNA gene sequences, main physiological and biochemical analysis. They were capable of decomposing 1.0 mM indole completely in 10, 16 and 18 days respectively. According to the results of HPLC and GC/MS, the possible pathway for the degradation was via oxindole, isatin and anthranilic acid. The three bacteria were capable of oxidizing ammonia, and the strains LPA11 and LPC24 were capable of effectively reducing nitrate and nitrite.

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.

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