Ju-Pei Shen

Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam.

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). A sandy loam with pH (H(2)O) ranging from 8.3 to 8.7 was sampled in years 2006 and 2007, including seven fertilization treatments of control without fertilizers (CK), those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): NP, NK, PK and NPK, half chemical fertilizers NPK plus half organic manure (1/2OMN) and organic manure (OM). The highest bacterial amoA gene copy numbers were found in those treatments receiving N fertilizer. The archaeal amoA gene copy numbers ranging from 1.54 x 10(7) to 4.25 x 10(7) per gram of dry soil were significantly higher than those of bacterial amoA genes, ranging from 1.24 x 10(5) to 2.79 x 10(6) per gram of dry soil, which indicated a potential role of AOA in nitrification. Ammonia-oxidizing bacteria abundance had significant correlations with soil pH and potential nitrification rates. Denaturing gradient gel electrophoresis patterns revealed that the fertilization resulted in an obvious change of the AOB community, while no significant change of the AOA community was observed among different treatments. Phylogenetic analysis showed a dominance of Nitrosospira-like sequences, while three bands were affiliated with the Nitrosomonas genus. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). These results suggest that long-term fertilization had a significant impact on AOB abundance and composition, while minimal on AOA in the alkaline soil.

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. 13CO2-DNA-stable isotope probing results showed significant assimilation of 13C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO2 fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active 13CO2-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions.

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.

Ammonia‐oxidizing archaea: important players in paddy rhizosphere soil?

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase alpha-subunit (amoA) gene. Ammonia-oxidizing archaea predominated among ammonia-oxidizing prokaryotes in the paddy soil, and the AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. Ammonia-oxidizing archaea were more abundant in the rhizosphere than in bulk soil. Rice cultivation led to greater abundance of AOA than AOB amoA gene copies and to differences in AOA and AOB community composition. These results show that AOA is dominant in the rhizosphere paddy soil in this study, and we assume that AOA were influenced more by exudation from rice root (e.g. oxygen, carbon dioxide) than AOB.

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.

A review of ammonia-oxidizing bacteria and archaea in Chinese soils

Ammonia (NH3) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N2O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

PurposeDenitrification is an important biochemical process in global nitrogen cycle, with a potent greenhouse gas product N2O. Wastewater irrigation can result in the changes of soil properties and microbial communities of agricultural soils. The purpose of this study was to examine how the soil denitrification genes responded to different irrigation regimes.Materials and methodsSoil samples were collected from three rural districts of Beijing (China) with three different irrigation regimes: clean groundwater (CW), reclaimed water (RW), and wastewater (WW). The abundance and diversity of three denitrification microbial genes (nirS, nirK, and nosZ) were examined by real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) molecular approaches.Results and discussionThe abundance of nirS in the WW treatment was higher than that in the CW treatment, and no significant difference was found between the RW and CW or WW treatments. The abundance of nirK gene of the RW and WW treatments was higher than that of the CW treatment. There was no difference for nosZ gene among the three treatments. Correspondence analysis based on the DGGE profiles showed that there was no obvious difference in the nosZ gene composition, but nirS and nirK genes changed with different irrigation regimes.ConclusionsIrrigation with unclean water sources enhanced the soil NO3− content and changed the abundance and composition of soil denitrifiers, and different functional genes had different responses. Irrigation with unclean water sources increased the abundance of nirK gene and changed the community structures of nirS and nirK genes, while nosZ gene was relatively stable in the soil. These results could be helpful to explore the mechanisms of the variation of denitrification processes under long-term wastewater irrigation and partially explain the reason of more N2O output in the field with wastewater irrigation.

Frontiers in the microbial processes of ammonia oxidation in soils and sediments

PurposeTwo recent discoveries in nitrogen (N) cycling processes, i.e., archaeal ammonia oxidizers and anaerobic ammonia (ammonium) oxidation (anammox), have triggered great interest in studying microbial ammonia oxidation processes. The purpose of this review is to highlight recent progress in ammonia oxidation processes in soils and sediments and to propose future research activities in this topic.Results and discussionAerobic ammonia oxidation and anammox processes are linked through the production and consumption of nitrite, respectively, thereby removing the reactive N (NH4+, NO2−, NO3−) from soil and sediment ecosystems. Ammonia-oxidizing microorganisms are widely distributed in soils and sediments, and increasing evidence suggests that ammonia-oxidizing archaea and bacteria are functionally dominant in the ammonia oxidation of acid soils and other soils, respectively. The widespread occurrence and great variation in the abundance of anammox bacteria indicate their heterogeneous distribution and niche differentiation. Therefore, the worldwide distribution of both microbial groups in nature has stimulated researchers to investigate the physiology and metabolism of related groups, as well as appraising their contribution to N cycling.ConclusionsWe summarized the current progress and provided future perspectives in the microbiology of aerobic and anaerobic ammonia oxidation in soils and sediments. With increasing concern and interest in soil and sediment ammonia oxidation processes, studies in the microbial mechanisms underlying nitrification and anammox, as well as their interactions, are essential for understanding their contribution to the loss of N either through nitrate leaching or N-related gas emissions.

Dynamics of sulfate reduction and sulfate-reducing prokaryotes in anaerobic paddy soil amended with rice straw

Incorporation of rice straw to soil is a common agricultural practice in rice cultivation. In anaerobic paddy soil, the complete mineralization of organic matter to CH4 and CO2 is accomplished by the sequential reduction of nitrate, ferric iron, sulfate, and methanogenesis. In order to estimate the temporal changes of sulfate-reducing prokaryotes (SRP) as decomposers of organic matters, the effects of rice straw amendment on the dynamics of sulfate reduction and SRP were investigated by combining the monitoring of CH4, sulfate, and organic acids with molecular tools such as soil DNA extraction, real-time PCR, cloning, sequencing, and phylogenetic analysis. The incorporation of rice straw into paddy soil significantly increased concentrations of sulfate, formate, acetate, propionate, and lactate and CH4 production. The rate of sulfate reduction in the straw-amended slurries was significantly higher than that in the unamended slurries. The dsrAB gene copy numbers of SRP in the straw-amended soil slurries ranged from 4.26 × 106 to 1.96 × 108 per gram of dry soil, which were significantly higher than those in the unamended control ranging from 1.99 × 106 to 7.90 × 107 per gram of dry soil. Significant correlations were observed between SRP dsrAB gene copy numbers and the concentrations of sulfate and acetate. Cloning and sequencing analyses showed a clear shift of SRP community structure between treatments and time. In the straw-amended slurries, Clostridia-like SRP significantly increased, while Deltaproterobacteria-like SRP (Sytrophobacter, Desulfobacterium, Desulfovibrio, and Desulfomonile) decreased during the incubation period. Novel uncultured SRP were abundant in the straw-amended slurries and changed during the incubation period.

Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress.

The responses of activities, abundances and community structures of soil denitrifiers to mercury (Hg) stress were investigated through a short-term incubation experiment. Four soil treatments with different concentrations of Hg (CK, Hg25, Hg50, and Hg 100, denoted as 0, 25, 50, and 100 mg Hg/kg dry soil, respectively) were incubated for 28 days. Soil denitrification enzyme activity (DEA) was measured at day 3, 7 and 28. The abundances and community structures of two denitrification concerning genes, nirS (cd(1)-nitrite reductase gene) and nosZ (nitrous oxide reductase gene), were analyzed using real-time PCR and denaturing gradient gel electrophoresis (DGGE). Results showed that soil DEA was significantly stimulated in the treatments of Hg25 and Hg50 compared with others at day 7. Meanwhile, no difference in the abundances of soil nirS and nosZ was found between Hg spiked treatments and CK, except the lower abundance of nirS (P < 0.05) in the Hg added treatments compared with that in the CK at day 28. The community structures of denitrifiers based on nirS gene presented obvious change at day 7 along with the Hg additions, however, no variation was found in all treatments based on the nosZ gene. The results indicated that Hg (Hg25 and Hg50) had a strongly short-term stimulation on soil DEA, and nirS gene is more sensitive than nosZ gene to Hg stress.