Soil nitrification is mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which occupy different specialized ecological niches. However, little is known about the diversification of AOA and AOB communities...Soil nitrification is mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which occupy different specialized ecological niches. However, little is known about the diversification of AOA and AOB communities in a large geographical scale. Here, eight paddy soils collected from different geographic regions in China were selected to investigate the spatial distribution of AOA and AOB, and their potential nitrification activity (PNA). The result showed that the abundance of AOA was predominant over AOB, indicating that the rice fields favor the growth of AOA. PNA highly varied from 0.43 to 3.57 μg NOX-N·g·dry·soil·h-1, and was positively related with soil NH3 content, the abundance of AOA community, and negatively related with the diversity of AOB community (P amoA genes revealed remarkable differences in the compositions of AOA and AOB community. Phylogenetic analyses of amoA genes showed that Nitrosospiracluster-3-like and Nitrosomonas cluster 7-like AOB extensively dominated the AOB communities, and 54d9-like AOA within the soil group 1.1b predominated in AOA communities in paddy soils. Redundancy analysis suggested that the spatial variations of AOA community structure were influenced by soil TN content (P < 0.01), while no significant correlation between AOB community structure and soil properties was found. Findings highlight that ammonia oxidizers exhibit spatial variations in complex paddy fields due to the joint influence of soil variables associated with N availability.展开更多
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Seasonal and spatial distribution of ammonia-oxidizing archaea (AOA) and betaproteobacteria (13-AOB) in surface sediments from ...Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Seasonal and spatial distribution of ammonia-oxidizing archaea (AOA) and betaproteobacteria (13-AOB) in surface sediments from the East China Sea (ECS) were investigated using ammonia monooxygenase ct subunit (amoA) gene. In order to characterize the community of AOA and 13-AOB, real-time quantitative polymerase chain reaction (qPCR) was carried out in this study, along with environmental parameters. The abundance of 13-AOB amoA gene (2.17x 10^6-4.54x10^7 copy numbers per gram wet weight sediment) was always greater than that ofAOA amoA gene (2.18x 105-9.89x 10^6 copy numbers per gram wet weight sediment) in all sampling stations. The qPCR results were correlated with environmental parameters. AOA amoA gene copy numbers in April were positively related to temperature and nitrite concentration (p〈0.05). 13-AOB amoA gene copy numbers in August correlated negatively with salinity (p〈0.01), and correlated positively with ammonium concentration (p〈0.05). With the increase of salinity, the amoA gene copy ratio of AOB to AOA had a tendency to decrease, which suggested 13-AOB dominated in the area of high level ammonium and AOA preferred high salinity area.展开更多
Use of saline water in irrigated agriculture has become an important means for alleviating water scarcity in arid and semi-arid regions. The objective of this field experiment was to evaluate the effects of irrigation...Use of saline water in irrigated agriculture has become an important means for alleviating water scarcity in arid and semi-arid regions. The objective of this field experiment was to evaluate the effects of irrigation water salinity and N fertilization on soil physicochemical and biological properties related to nitrification and denitrification. A 3×2 factorial design was used with three levels of irrigation water salinity(0.35, 4.61 and 8.04 d S m-1) and two N rates(0 and 360 kg N ha^(-1)). The results indicated that irrigation water salinity and N fertilization had significant effects on many soil physicochemical properties including water content, salinity, p H, NH_4-N concentration, and NO_3-N concentration. The abundance(i.e., gene copy number) of ammonia-oxidizing archaea(AOA) was greater than that of ammonia-oxidizing bacteria(AOB) in all treatments. Irrigation water salinity had no significant effect on the abundance of AOA or AOB in unfertilized plots. However, saline irrigation water(i.e., the 4.61 and 8.04 d S m-1 treatments) reduced AOA abundance, AOB abundance and potential nitrification rate in N fertilized plots. Regardless of N application rate, saline irrigation water increased urease activity but reduced the activities of both nitrate reductase and nitrite reductase. Irrigation with saline irrigation water significantly reduced cotton biomass, N uptake and yield. Nitrogen application exacerbated the negative effect of saline water. These results suggest that brackish water and saline water irrigation could significantly reduce both the abundance of ammonia oxidizers and potential nitrification rates. The AOA may play a more important role than AOB in nitrification in desert soil.展开更多
The spatial distribution of ammonia-oxidizing Betaproteobacteria (βAOB) was investigated by FISH (fluorescence in situ hybridization) and DGGE (denaturing gradient get electrophoresis) techniques in the sedimen...The spatial distribution of ammonia-oxidizing Betaproteobacteria (βAOB) was investigated by FISH (fluorescence in situ hybridization) and DGGE (denaturing gradient get electrophoresis) techniques in the sediment off the Changjiang River Estuary. Sediment samples were collected from eight stations in June before the formation of hypoxia zone in 2006. The abundance of βAOB ranged from 1.87× 10^5 to 3.53×10^5 cells/g of sediment. βAOB abundance did not present a negative correlation with salinity, whereas salinity was implicated as the primary factor affecting nitrification rates. The DGGE profiles of PCR-amplified amoA gene fragments revealed that the βAOB community structure of sample S2 separated from other samples at the level of 40% similarity. The variations in composition ofβAOB were significantly correlated with the salinity, temperature, absorption ability of sediments and TOC. The statistical analysis indicates that theβAOB abundance was a main factor to influence nitrification rates with an influence ratio of 87.7% at the level of 40% biodiversity similarity. Considering the good correlation between βAOB abundance and nitrification estimates, the abundance and diversity of βAOB community could be expected as an indirect index of nitrification activity at the study sea area in summer.展开更多
The aim of the study was to find the interrelations between the activity of intracellular dehydrogenases, abundance of microorganisms, and the level of soil DNA in the Mollic Gleysol profile, with notification on the ...The aim of the study was to find the interrelations between the activity of intracellular dehydrogenases, abundance of microorganisms, and the level of soil DNA in the Mollic Gleysol profile, with notification on the dominant DNA form (extra-or intra-cellular), depending on the type of land use. Two neighbouring meadows were selected for investigations: one systematically cultivated and fertilized and the other deprived of any effect of anthropogenic activity, used as a control. We have demonstrated that dehydrogenase activity (DHA), the DNA content and microbial abundance strongly depended on the type of land use. DHA exhibited a significant correlation with the DNA content (r = 0.99^*** and r = 0.74^*, for cultivated and control sites, respectively). This relationship with such a high r value might suggest domination of the intracellular form of DNA in the cultivated meadow, which is also confirmed by the c.a. 13% increase in microorganism abundance in the cultivated soil. The optimal conditions for microbial activities were defined by the significant positive interrelationships between microbial abundance and the total organic carbon content, and a negative correlation with pH, redox potential and soil bulk density.展开更多
Tidal flats are soil resources of great significance.Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments.We determine...Tidal flats are soil resources of great significance.Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments.We determined the abundance as well as composition of ammonia-oxidizing bacteria(AOB) and ammonia-oxidizing archaea(AOA) in different soils during land reclamation process.The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction(PCR).The different abundances of AOB and AOA were negatively correlated with the salinity.The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene.Among AOB,nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process,i.e.,tidal flats,while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process,farm land and wild land.The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate.As for AOA,there was no obvious correlation with the changes in the physicochemical properties of the soil.This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.展开更多
Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as wel...Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district. To understand the abundance, diversity, and distribution of AOA in Pearl River Delta of China in response to various habitats, the archaeal amoA genes in soil, marine, river, lake, hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries. Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades, i.e., estuary sediment, marine water/sediment, soil, hot spring and Cluster 1. Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation. The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature, pH, total organic carbon, total nitrogen and dissolved oxygen variables. Assessing AOA amoA gene copy numbers, ranging from 6.84× 10^6 to 9.45 × 10^7 copies/g in dry soil/sediment, and 6.06× 10^6 to 2.41 ×10^7 copies/L in water samples, were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude. However, AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples. Overall, these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge. The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters. New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.展开更多
Soil nitrogen(N)transformation processes in the High Arctic tundra are poorly understood even though nitrogen is one of the main limiting nutrients.We analyzed soil samples collected along a High Arctic tundra transec...Soil nitrogen(N)transformation processes in the High Arctic tundra are poorly understood even though nitrogen is one of the main limiting nutrients.We analyzed soil samples collected along a High Arctic tundra transect to investigate spatial variability in key nitrogen transformation processes,functional gene abundances,ammonia-oxidizing archaea(AOA)community structures,and key nitrogen transformation regulators.The potential denitrification rates were higher than the nitrification rates in the soil samples,although nitrification may still regulate N2O emissions from tundra soil.The nutrient(total carbon,total organic carbon,total nitrogen,and NH_(4)^(+)-N)contents were important determinants of spatial variability in the potential denitrification rates of soil along the tundra transect.The total sulfurcontent was the main variable controlling potential nitrification processes,probably in association with sulfate-reducing bacteria.The nitrate content was the main variable affecting potential dissimilatory nitrate reduction to ammonium.AOA and ammonia-oxidizing bacteria amoA,nirS,and anammox 16S rRNA genes were found in all of the soil samples.AOA play more important roles than ammonia-oxidizing bacteria in soilnitrification.Anammox bacteria may utilize NO_(2)^(-)produced through nitrification.Phylogenetic analysis indicated that the AOA amoA sequences could be grouped into eight unique operational taxonomic units(OTUs)with a 97%sequence similarity and were affiliated with three group 1.1b Nitrososphaeraclusters.The results indicated that heterogeneous environmental factors(e.g.,the carbon and nitrogen contents of soil)along the High Arctic tundra transect strongly affected the nitrogen transformation rate and relevant functional gene abundances in soil.展开更多
文摘Soil nitrification is mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which occupy different specialized ecological niches. However, little is known about the diversification of AOA and AOB communities in a large geographical scale. Here, eight paddy soils collected from different geographic regions in China were selected to investigate the spatial distribution of AOA and AOB, and their potential nitrification activity (PNA). The result showed that the abundance of AOA was predominant over AOB, indicating that the rice fields favor the growth of AOA. PNA highly varied from 0.43 to 3.57 μg NOX-N·g·dry·soil·h-1, and was positively related with soil NH3 content, the abundance of AOA community, and negatively related with the diversity of AOB community (P amoA genes revealed remarkable differences in the compositions of AOA and AOB community. Phylogenetic analyses of amoA genes showed that Nitrosospiracluster-3-like and Nitrosomonas cluster 7-like AOB extensively dominated the AOB communities, and 54d9-like AOA within the soil group 1.1b predominated in AOA communities in paddy soils. Redundancy analysis suggested that the spatial variations of AOA community structure were influenced by soil TN content (P < 0.01), while no significant correlation between AOB community structure and soil properties was found. Findings highlight that ammonia oxidizers exhibit spatial variations in complex paddy fields due to the joint influence of soil variables associated with N availability.
基金The National Natural Science Foundation of China under contract No.40920164004the National Basic Research Program (973 Program) of China under contract No.2011CB403602the Foundation for Innovative Research Groups of the National Natural Science Foundation of China under contract No.41221004
文摘Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Seasonal and spatial distribution of ammonia-oxidizing archaea (AOA) and betaproteobacteria (13-AOB) in surface sediments from the East China Sea (ECS) were investigated using ammonia monooxygenase ct subunit (amoA) gene. In order to characterize the community of AOA and 13-AOB, real-time quantitative polymerase chain reaction (qPCR) was carried out in this study, along with environmental parameters. The abundance of 13-AOB amoA gene (2.17x 10^6-4.54x10^7 copy numbers per gram wet weight sediment) was always greater than that ofAOA amoA gene (2.18x 105-9.89x 10^6 copy numbers per gram wet weight sediment) in all sampling stations. The qPCR results were correlated with environmental parameters. AOA amoA gene copy numbers in April were positively related to temperature and nitrite concentration (p〈0.05). 13-AOB amoA gene copy numbers in August correlated negatively with salinity (p〈0.01), and correlated positively with ammonium concentration (p〈0.05). With the increase of salinity, the amoA gene copy ratio of AOB to AOA had a tendency to decrease, which suggested 13-AOB dominated in the area of high level ammonium and AOA preferred high salinity area.
基金funded by the National Natural Science Foundation of China (31360504)the Innovative Research Foundation for Excellent Young Scientists of Xinjiang Production and Construction Crops, China (2014CD002)
文摘Use of saline water in irrigated agriculture has become an important means for alleviating water scarcity in arid and semi-arid regions. The objective of this field experiment was to evaluate the effects of irrigation water salinity and N fertilization on soil physicochemical and biological properties related to nitrification and denitrification. A 3×2 factorial design was used with three levels of irrigation water salinity(0.35, 4.61 and 8.04 d S m-1) and two N rates(0 and 360 kg N ha^(-1)). The results indicated that irrigation water salinity and N fertilization had significant effects on many soil physicochemical properties including water content, salinity, p H, NH_4-N concentration, and NO_3-N concentration. The abundance(i.e., gene copy number) of ammonia-oxidizing archaea(AOA) was greater than that of ammonia-oxidizing bacteria(AOB) in all treatments. Irrigation water salinity had no significant effect on the abundance of AOA or AOB in unfertilized plots. However, saline irrigation water(i.e., the 4.61 and 8.04 d S m-1 treatments) reduced AOA abundance, AOB abundance and potential nitrification rate in N fertilized plots. Regardless of N application rate, saline irrigation water increased urease activity but reduced the activities of both nitrate reductase and nitrite reductase. Irrigation with saline irrigation water significantly reduced cotton biomass, N uptake and yield. Nitrogen application exacerbated the negative effect of saline water. These results suggest that brackish water and saline water irrigation could significantly reduce both the abundance of ammonia oxidizers and potential nitrification rates. The AOA may play a more important role than AOB in nitrification in desert soil.
基金The National Fundamental Project of China under grant No.2006CB400602
文摘The spatial distribution of ammonia-oxidizing Betaproteobacteria (βAOB) was investigated by FISH (fluorescence in situ hybridization) and DGGE (denaturing gradient get electrophoresis) techniques in the sediment off the Changjiang River Estuary. Sediment samples were collected from eight stations in June before the formation of hypoxia zone in 2006. The abundance of βAOB ranged from 1.87× 10^5 to 3.53×10^5 cells/g of sediment. βAOB abundance did not present a negative correlation with salinity, whereas salinity was implicated as the primary factor affecting nitrification rates. The DGGE profiles of PCR-amplified amoA gene fragments revealed that the βAOB community structure of sample S2 separated from other samples at the level of 40% similarity. The variations in composition ofβAOB were significantly correlated with the salinity, temperature, absorption ability of sediments and TOC. The statistical analysis indicates that theβAOB abundance was a main factor to influence nitrification rates with an influence ratio of 87.7% at the level of 40% biodiversity similarity. Considering the good correlation between βAOB abundance and nitrification estimates, the abundance and diversity of βAOB community could be expected as an indirect index of nitrification activity at the study sea area in summer.
文摘The aim of the study was to find the interrelations between the activity of intracellular dehydrogenases, abundance of microorganisms, and the level of soil DNA in the Mollic Gleysol profile, with notification on the dominant DNA form (extra-or intra-cellular), depending on the type of land use. Two neighbouring meadows were selected for investigations: one systematically cultivated and fertilized and the other deprived of any effect of anthropogenic activity, used as a control. We have demonstrated that dehydrogenase activity (DHA), the DNA content and microbial abundance strongly depended on the type of land use. DHA exhibited a significant correlation with the DNA content (r = 0.99^*** and r = 0.74^*, for cultivated and control sites, respectively). This relationship with such a high r value might suggest domination of the intracellular form of DNA in the cultivated meadow, which is also confirmed by the c.a. 13% increase in microorganism abundance in the cultivated soil. The optimal conditions for microbial activities were defined by the significant positive interrelationships between microbial abundance and the total organic carbon content, and a negative correlation with pH, redox potential and soil bulk density.
基金Project supported by the National Natural Science Foundation of China (Nos. 31070097 and 31011140339)the National Key Technologies R & D Program of China (Nos. 2006BAJ05A11 and2010BAK69B14)the Major Program of Science and Technology Department of Shanghai (No. 10DZ1200700),China
文摘Tidal flats are soil resources of great significance.Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments.We determined the abundance as well as composition of ammonia-oxidizing bacteria(AOB) and ammonia-oxidizing archaea(AOA) in different soils during land reclamation process.The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction(PCR).The different abundances of AOB and AOA were negatively correlated with the salinity.The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene.Among AOB,nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process,i.e.,tidal flats,while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process,farm land and wild land.The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate.As for AOA,there was no obvious correlation with the changes in the physicochemical properties of the soil.This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.
基金supported by the National Natural Science Foundation of China (No. 50978069)
文摘Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district. To understand the abundance, diversity, and distribution of AOA in Pearl River Delta of China in response to various habitats, the archaeal amoA genes in soil, marine, river, lake, hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries. Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades, i.e., estuary sediment, marine water/sediment, soil, hot spring and Cluster 1. Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation. The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature, pH, total organic carbon, total nitrogen and dissolved oxygen variables. Assessing AOA amoA gene copy numbers, ranging from 6.84× 10^6 to 9.45 × 10^7 copies/g in dry soil/sediment, and 6.06× 10^6 to 2.41 ×10^7 copies/L in water samples, were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude. However, AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples. Overall, these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge. The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters. New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.
基金This study was funded by the National Key Research and Development Program of China(Grant no.2020YFA0608501)the National Natural Science Foundation of China(Grant no.41976220)the State Key Laboratory of NBC Protection of Civilians(Grant no.SKLNBC2020-10).
文摘Soil nitrogen(N)transformation processes in the High Arctic tundra are poorly understood even though nitrogen is one of the main limiting nutrients.We analyzed soil samples collected along a High Arctic tundra transect to investigate spatial variability in key nitrogen transformation processes,functional gene abundances,ammonia-oxidizing archaea(AOA)community structures,and key nitrogen transformation regulators.The potential denitrification rates were higher than the nitrification rates in the soil samples,although nitrification may still regulate N2O emissions from tundra soil.The nutrient(total carbon,total organic carbon,total nitrogen,and NH_(4)^(+)-N)contents were important determinants of spatial variability in the potential denitrification rates of soil along the tundra transect.The total sulfurcontent was the main variable controlling potential nitrification processes,probably in association with sulfate-reducing bacteria.The nitrate content was the main variable affecting potential dissimilatory nitrate reduction to ammonium.AOA and ammonia-oxidizing bacteria amoA,nirS,and anammox 16S rRNA genes were found in all of the soil samples.AOA play more important roles than ammonia-oxidizing bacteria in soilnitrification.Anammox bacteria may utilize NO_(2)^(-)produced through nitrification.Phylogenetic analysis indicated that the AOA amoA sequences could be grouped into eight unique operational taxonomic units(OTUs)with a 97%sequence similarity and were affiliated with three group 1.1b Nitrososphaeraclusters.The results indicated that heterogeneous environmental factors(e.g.,the carbon and nitrogen contents of soil)along the High Arctic tundra transect strongly affected the nitrogen transformation rate and relevant functional gene abundances in soil.