Ammonia-oxidizing bacteria dynamics affected by plantain under synthetic cattle urine patches

2020 ◽  
Vol 82 ◽  
pp. 97-102
Author(s):  
Priscila Simon ◽  
Cecile De Klein ◽  
Emily Gerard ◽  
Shenjing Shi
Keyword(s):  
White Clover ◽  
Rhizosphere Soil ◽  
Root Exudation ◽  
Amoa Gene ◽  
Time Frame ◽  
Bulk Soil ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers

Plantain has been suggested as a nitrous oxide (N2O) and nitrate (NO3-) leaching mitigation option as it may induce biological nitrification inhibition (BNI) via plantain root exudation, which affects the activity of ammonia-oxidizing bacteria. This preliminary study compared the abundance of the ammonia monooxygenase gene (amoA) in soils containing either plantain and white clover, or ryegrass and white clover. Plants were sown in pots and grown in a greenhouse. Two months after sowing, synthetic cattle urine was applied to half the pots, and rhizosphere and bulk soil samples were collected 30 and 90 days after urine application. The abundance of the amoA gene was measured using real time quantitative PCR. The abundance of amoA genes in rhizosphere soil around ryegrass plants and in bulk soil under ryegrass/white clover were higher in pots treated with urine than the no-urine controls. AmoA gene abundance in bulk soil under plantain/white clover was higher in pots treated with urine (P<0.05) but not in rhizosphere soil around plantain plants (P>0.05) compared with the control. Furthermore, amoA gene copy numbers in the rhizosphere soil around plantain plants were lower than for ryegrass plants (P<0.05). However, there was no difference in the abundance of amoA genes in bulk soil of either combination of plant species evaluated (P>0.05). The results suggest that, in the time frame of our experiment, plantain could induce a BNI effect in the rhizosphere soil but not in the bulk soil.

Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

2013 ◽  
Vol 59 (7) ◽  
pp. 456-464 ◽  
Author(s):  
Jie Hou ◽  
Xiuyun Cao ◽  
Chunlei Song ◽  
Yiyong Zhou
Keyword(s):  
Amoa Gene ◽  
Eutrophic Lake ◽  
Gene Copy ◽  
Nirs Gene ◽  
Bacterial Amoa Gene ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Significant Difference ◽  
Nirk Gene ◽  
Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

Abundance and composition dynamics of soil ammonia-oxidizing archaea in an alpine fir forest on the eastern Tibetan Plateau of China

2012 ◽  
Vol 58 (5) ◽  
pp. 572-580 ◽  
Author(s):  
Ao Wang ◽  
Fu-Zhong Wu ◽  
Wan-Qin Yang ◽  
Zhi-Chao Wu ◽  
Xu-Xi Wang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Soil Temperature ◽  
Coniferous Forest ◽  
Amoa Gene ◽  
Western China ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Eastern Tibetan Plateau ◽  
Dominant Group ◽  
Ammonia Oxidizing Archaea

Real-time qPCR and clone library sequencing targeting amoA genes were used to investigate the seasonal dynamics of an ammonia-oxidizing archaea (AOA) community in an alpine fir forest in western China. AOA were detected at all sampling dates, and there were significant variations in archaeal amoA gene copy numbers (7.63 × 105to 8.35 × 108per gram of dry soil) throughout the nongrowing season. Compared with ammonia-oxidizing bacteria (AOB), the AOA displayed a higher abundance on the majority of sampling dates during the freeze–thaw period. All of the AOA sequences fell within soil and sediment lineages and were affiliated with 7 clusters. Compared with the other clusters, cluster 1 was more sensitive to low temperature and was the dominant group in August. In contrast, cluster 3 dominated the AOA community in winter and probably represents a group of cold-adapted archaea. Redundancy analysis (RDA) revealed that the seasonality of the AOA community was mainly attributed to changes in soil temperature and nutrient availability (e.g., dissolved organic nitrogen and carbon). Our results indicate that AOA exist in frozen soils in the alpine coniferous forest ecosystem of the eastern Tibetan Plateau. Moreover, soil temperature may directly and (or) indirectly affect AOA abundance and composition and may further influence the soil N cycle during the winter.

scholarly journals Ammonia-oxidizing Archaea (AOA) are Winners to Survive in Oxygen-limited Habitat Compared to Ammonia-oxidizing Bacteria (AOB)

2021 ◽  
Author(s):  
Peigang Dai ◽  
Wenjing Song ◽  
Zhao Che ◽  
Lili Zhang ◽  
Zhaorong Dong
Keyword(s):  
Intertidal Zone ◽  
High Throughput Sequencing ◽  
Ammonia Oxidation ◽  
Illumina Miseq ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Niche Specialization ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Oxidation Reduction

Abstract Purpose: Both ammonia oxidizing archaea (AOA) and bacteria (AOB) perform the ammonia oxidation together. These two kinds of microbes present a convenient model for studying niche specialization. To date, few surveys concentrated on the influence of oxygen concentration on niche specialization of AOA and AOB in intertidal zones. Methods: Here, high-throughput sequencing by Illumina MiSeq and qPCR were applied to detect the change of abundance, diversity as well as community structure of both AOA and AOB with 0-60 cm sediments depth in the intertidal zone in Qingdao.Results and Conclusion: The AOA/AOB amoA gene copy numbers and AOA/AOB OTU numbers were all increased as sediment depth went deeper, which indicated that AOA were more adaptive to oxygen-limited niches compared to AOB and oxygen indeed led to the niche specialization of AOA and AOB in intertidal sediments. The dominant AOA and AOB were the Nitrosopumilus and Nitrosospira clusters, respectively, which indicated an ecological success in intertidal zone. Oxidation-reduction potential (ORP) was significantly positively correlated with AOB abundance and AOB OTU numbers (P < 0.01). In addition, both TN (P < 0.01) and pH (P < 0.05) were significantly and negatively correlated with AOB abundance. TN was also significantly and negatively correlated with AOB OTU numbers (P < 0.05).

scholarly journals Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil

2011 ◽  
Vol 77 (18) ◽  
pp. 6551-6558 ◽  
Author(s):  
John J. Kelly ◽  
Katherine Policht ◽  
Tanya Grancharova ◽  
Lakhwinder S. Hundal
Keyword(s):  
Agricultural Soil ◽  
Terrestrial Ecosystems ◽  
Gene Copy ◽  
Ecological Niches ◽  
Corn Yield ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Synthetic Fertilizer ◽  
Gene Copy Numbers

ABSTRACTThe recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1year−1) and double the agronomic rate (54 Mg hectare−1year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterialamoAgenes. In addition, only archaealamoAgene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaealamoAgenes were significantly higher than copy numbers of bacterialamoAgenes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.

scholarly journals Comparison of Different Approaches To QuantifyStaphylococcus aureus Cells by Real-Time Quantitative PCR and Application of This Technique for Examination of Cheese

2001 ◽  
Vol 67 (7) ◽  
pp. 3122-3126 ◽  
Author(s):  
Ingeborg Hein ◽  
Angelika Lehner ◽  
Petra Rieck ◽  
Kurt Klein ◽  
Ernst Brandl ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Taqman Probe ◽  
Gene Copy ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers ◽  
Gene Copies ◽  
Different Types ◽  
Pure Cultures ◽  
Gene Copy Numbers

ABSTRACT Two different real-time quantitative PCR (RTQ-PCR) approaches were applied for PCR-based quantification of Staphylococcus aureus cells by targeting the thermonuclease (nuc) gene. Purified DNA extracts from pure cultures ofS. aureus were quantified in a LightCycler system using SYBR Green I. Quantification proved to be less sensitive (60nuc gene copies/μl) than using a fluorigenic TaqMan probe (6 nuc gene copies/μl). Comparison of the LightCycler system and the well-established ABI Prism 7700 SDS with TaqMan probes revealed no statistically significant differences with respect to sensitivity and reproducibility. Application of the RTQ-PCR assay to quantify S. aureus cells in artificially contaminated cheeses of different types achieved sensitivities from 1.5 � 102 to 6.4 � 102 copies of the nuc gene/2 g, depending on the cheese matrix. The coefficients of correlation between log CFU and nuc gene copy numbers ranged from 0.979 to 0.998, thus enabling calculation of the number of CFU of S. aureus in cheese by performing RTQ-PCR.

scholarly journals Diversity and distribution of <i>amoA</i>-type nitrifying and <i>nirS</i>-type denitrifying microbial communities in the Yangtze River Estuary

2013 ◽  
Vol 10 (11) ◽  
pp. 17819-17857 ◽  
Author(s):  
Y. Zhang ◽  
X. Xie ◽  
N. Jiao ◽  
S. S.-Y. Hsiao ◽  
S.-J. Kao
Keyword(s):  
Microbial Communities ◽  
Yangtze River ◽  
Amoa Gene ◽  
Gene Copy ◽  
Yangtze River Estuary ◽  
Rarefaction Analysis ◽  
Copy Numbers ◽  
Nitrite Reductase Gene ◽  
Nitrification And Denitrification ◽  
Gene Copy Numbers

Abstract. Coupled nitrification-denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. By analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR), we investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia. The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria, suggesting that the archaea might play a dominant role in nitrification in the YRE. Compared with the amoA gene, a distinctly higher level of diversity but lower gene copy numbers were found for thenirS gene suggesting lower denitrification than nitrification potential. 15N incubation experiments indicated that nitrification rates were strongly correlated with amoA gene abundances while denitrification rates were below detection limit. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were distinctly higher in the particle-associated (> 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, analysis of correlations between the gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem.

Molecular assessment of ammonia- and nitrite-oxidizing bacteria in full-scale activated sludge wastewater treatment plants

2003 ◽  
Vol 48 (8) ◽  
pp. 119-126 ◽  
Author(s):  
K.G. Robinson ◽  
H.M. Dionisi ◽  
G. Harms ◽  
A.C. Layton ◽  
I.R. Gregory ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Activated Sludge ◽  
16S Rdna ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Amoa Gene ◽  
Full Scale ◽  
Ammonia Oxidizing Bacteria ◽  
Copy Numbers ◽  
Nitrite Oxidizing Bacteria

Nitrification was assessed in two full-scale wastewater treatment plants (WWTPs) over time using molecular methods. Both WWTPs employed a complete-mix suspended growth, aerobic activated sludge process (with biomass recycle) for combined carbon and nitrogen treatment. However, one facility treated primarily municipal wastewater while the other only industrial wastewater. Real time PCR assays were developed to determine copy numbers for total 16S rDNA (a measure of biomass content), the amoA gene (a measure of ammonia-oxidizers), and the Nitrospira 16S rDNA gene (a measure of nitrite-oxidizers) in mixed liquor samples. In both the municipal and industrial WWTP samples, total 16S rDNA values were approximately 2-9 × 1013 copies/L and Nitrospira 16S rDNA values were 2-4 × 1010 copies/L. amoA gene concentrations averaged 1.73 × 109 copies/L (municipal) and 1.06 × 1010 copies/L (industrial), however, assays for two distinct ammonia oxidizing bacteria were required.

scholarly journals Diversity and distribution of <i>amoA</i>-type nitrifying and <i>nirS</i>-type denitrifying microbial communities in the Yangtze River estuary

2014 ◽  
Vol 11 (8) ◽  
pp. 2131-2145 ◽  
Author(s):  
Y. Zhang ◽  
X. Xie ◽  
N. Jiao ◽  
S. S.-Y. Hsiao ◽  
S.-J. Kao
Keyword(s):  
Microbial Communities ◽  
Yangtze River ◽  
Amoa Gene ◽  
Gene Copy ◽  
Yangtze River Estuary ◽  
Nirs Gene ◽  
Rarefaction Analysis ◽  
Copy Numbers ◽  
Nitrification And Denitrification ◽  
Gene Copy Numbers

Abstract. Coupled nitrification–denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. We investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia, by analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR). The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria. Compared with the amoA gene, a significantly higher level of diversity but lower gene copy numbers were found for the nirS gene. Nitrification and denitrification rates based on 15N incubation experiments supported gene abundance data as denitrification rates were below detection limit, suggesting lower denitrification than nitrification potential. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were significantly higher in the particle-associated (> 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, positive correlations between the amoA and nirS gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem.

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

2012 ◽  
Vol 58 (8) ◽  
pp. 1018-1026 ◽  
Author(s):  
Jin Zeng ◽  
Da-Yong Zhao ◽  
Rui Huang ◽  
Qinglong L. Wu
Keyword(s):  
Community Composition ◽  
Gene Diversity ◽  
Lake Taihu ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Bacterial Amoa Gene ◽  
Ammonia Oxidizing Archaea ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Meiliang Bay

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91 × 105 to 8.65 × 106 copies/g dry sediment for the archaeal amoA gene and from 3.74 × 104 to 3.86 × 105 copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P < 0.05). Concentrations of ammonia (NH4+), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P < 0.05 or P < 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

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.

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