scholarly journals Effects of Zeolite and Biochar Addition on Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea Communities during Agricultural Waste Composting

2020 ◽  
Vol 12 (16) ◽  
pp. 6336 ◽  
Author(s):  
Xin Wu ◽  
Liheng Ren ◽  
Jiachao Zhang ◽  
Hui Peng
Keyword(s):  
Enzyme Activity ◽  
Ammonia Oxidation ◽  
Agricultural Waste ◽  
Amoa Gene ◽  
Enzyme Linked Immunosorbent Assay ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Monooxygenase ◽  
Gene Abundance ◽  
Ammonia Oxidizing Archaea ◽  
The Relationship

The effects of zeolite and biochar addition on ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities during agricultural waste composting were determined in this study. Four treatments were conducted as follows: Treatment A as the control with no additive, Treatment B with 5% of zeolite, Treatment C with 5% of biochar, and Treatment D with 5% of zeolite and 5% biochar, respectively. The AOB and AOA amoA gene abundance as well as the ammonia monooxygenase (AMO) activity were estimated by quantitative PCR and enzyme-linked immunosorbent assay, respectively. The relationship between gene abundance and AMO enzyme activity was determined by regression analysis. Results indicated that the AOB was more abundant than that of AOA throughout the composting process. Addition of biochar and its integrated application with zeolite promoted the AOB community abundance and AMO enzyme activity. Significant positive relationships were obtained between AMO enzyme activity and AOB community abundance (r2 = 0.792; P < 0.01) and AOA community abundance (r2 = 0.772; P < 0.01), indicating that both bacteria and archaea played significant roles in microbial ammonia oxidation during composting. Using biochar and zeolite might promote the nitrification activity by altering the sample properties during agricultural waste composting.

Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic Orbal processes

2002 ◽  
Vol 46 (1-2) ◽  
pp. 273-280 ◽  
Author(s):  
H.-D. Park ◽  
J.M. Regan ◽  
D.R. Noguera
Keyword(s):  
Fragment Length Polymorphism ◽  
Ammonia Oxidation ◽  
Wastewater Treatment Plants ◽  
Phylogenetic Analyses ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Monooxygenase ◽  
Anoxic Zone ◽  
Bacterial Populations ◽  
Nitrosomonas Oligotropha

Aerated-anoxic processes operate under the principle that small additions of oxygen to an anoxic reactor induce simultaneous nitrification and denitrification. In these systems, ammonia oxidation in the anoxic zone can easily account for 30–50% of the total nitrification in the reactor, even though the dissolved oxygen concentration is usually below detection limit. To investigate whether the nitrification efficiency in aerated-anoxic processes was due to the presence of specialized ammonia-oxidizing bacteria (AOB), an analysis of the AOB population in an aerated-anoxic Orbal process and a conventional nitrogen removal process was carried out using phylogenetic analyses based on the ammonia monooxygenase A (amoA) gene. Terminal restriction fragment length polymorphism (TRFLP) analyses revealed that Nitrosospira-like organisms were one of the major contributors to ammonia oxidation in a full-scale aerated-anoxic Orbal reactor. However, the relative populations of Nitrosospira-like and Nitrosomonas-like AOB were not constant and appeared to have seasonal variability. Cloning and sequence comparison of amoA gene fragments demonstrated that most of the AOB in the aerated-anoxic Orbal process belonged to the Nitrosospira sp. and Nitrosomonas oligotropha lineages. The abundance of Nitrosospira-like organisms in aerated-anoxic reactors is significant, since this group of AOB has not been usually associated with nitrification in wastewater treatment plants.

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.

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.

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 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 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.

scholarly journals Evidence for Different Contributions of Archaea and Bacteria to the Ammonia-Oxidizing Potential of Diverse Oregon Soils

2010 ◽  
Vol 76 (23) ◽  
pp. 7691-7698 ◽  
Author(s):  
Anne E. Taylor ◽  
Lydia H. Zeglin ◽  
Sandra Dooley ◽  
David D. Myrold ◽  
Peter J. Bottomley
Keyword(s):  
Protein Synthesis ◽  
Protein Synthesis Inhibitor ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Monooxygenase ◽  
Bacterial Protein ◽  
Protein Synthesis Inhibitors ◽  
Synthesis Inhibitor ◽  
Ammonia Oxidizing Archaea ◽  
Pasture Soil ◽  
Bacterial Protein Synthesis

ABSTRACT A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 μg/ml), whereas a combination of kanamycin plus gentamicin (800 μg/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30�C and 40�C and without supplemental NH4 + (≤10 μM NH4 + in solution), and pasture soil RNP demonstrated ∼50% insensitivity to 100 μM allyl thiourea (ATU). In addition, fallowed and pasture soil RNPs were insensitive to the fungal inhibitors nystatin and azoxystrobin. This combination of properties suggests that neither fungi nor AOB contributed to pasture soil RNP and that AOA were responsible for the RNP of the pasture soils. Both AOA and AOB may contribute to RNP in fallowed soil, while RNP in cropped soils was dominated by AOB.

Quantification of amoA gene abundance and their amoA mRNA levels in activated sludge by real-time PCR

2004 ◽  
Vol 50 (8) ◽  
pp. 1-8 ◽  
Author(s):  
N. Araki ◽  
T. Yamaguchi ◽  
S. Yamazaki ◽  
H. Harada
Keyword(s):  
16S Rrna ◽  
Dissolved Oxygen ◽  
Real Time ◽  
Real Time Pcr ◽  
Ammonia Oxidation ◽  
Amoa Gene ◽  
Ammonia Concentration ◽  
Ammonia Oxidizing Bacteria ◽  
Mrna Levels ◽  
Transcription Level

The transcription level of amoA mRNA encoding a subunit of ammonia monooxygenase (AMO) in ammonia-oxidizing bacteria (AOB) was quantified by reverse transcription-polymerase chain reaction (RT-PCR) methods in combination with real-time PCR technology. The effects of ammonia concentration and dissolved oxygen (DO) on the transcription levels of amoA mRNA and 16S rRNA in AOB were evaluated in batch experiments with nitrifying sludge taken from a lab-scale reactor treating artificial wastewater. A batch incubation without ammonia resulted in a rapid decrease, within four hours, in the transcription level of amoA mRNA to as low as 1/10 of that at the beginning of the experiment, while the 16S rRNA level in AOB was almost constant. After subsequent incubation with 3 mM ammonia for eight hours, a small increase in the transcription level of amoA mRNA occurred, but ammonia oxidation proceeded in the interim. Copy numbers of amoA mRNA showed an almost fixed value for over eight hours in the absence of dissolved oxygen.

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