Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein.     

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO₃⁻-N g⁻¹ dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in ¹³C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of ¹³CO₂ by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the ¹³C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The ¹³C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter. A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.     

Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China

The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.     

Autotrophic growth of nitrifying community in an agricultural soil

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by ¹³CO₂ after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the ¹³C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the ¹³C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that ¹³CO₂ assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.     

轮作模式对冬小麦土壤氨氧化微生物群落多样性和组成的影响

农田温室气体减排已成为农业绿色发展的重要内容,驱动温室气体氧化亚氮(N₂O)产生的氨氧化微生物受到了研究者们的广泛关注。为探究轮作模式对土壤氨氧化微生物群落的影响,基于田间定位试验,研究了夏红小豆-冬小麦、夏绿豆-冬小麦、夏花生-冬小麦、夏大豆-冬小麦和夏玉米-冬小麦5种轮作模式中冬小麦根际和非根际土壤氨氧化古菌(AOA)和氨氧化细菌(AOB)的群落组成和多样性变化特征。结果表明:与夏玉米-冬小麦模式相比,豆禾轮作模式增加了根际土中有机碳和硝态氮含量,以及非根际土中全氮和铵态氮含量。豆禾轮作模式降低了非根际土壤中AOA群落的ACE指数和Chao1指数,并显著降低根际土中AOB群落的ACE指数和Chao1指数(P<0.05)。豆禾轮作显著增加AOA群落中泉古菌门(Crenarchaeota)和AOB群落中变形菌门(Proteobacteria)某些类群的相对丰度(P<0.05)。根际土中豆禾轮作模式与麦玉模式的AOA群落结构发生明显分离,而非根际土中豆禾轮作模式与麦玉模式的AOB群落发生分离(P<0.05)。研究结果表明:豆禾轮作种植改变了AOA和AOB的群落结构和多样性,土壤pH值和速效氮含量是驱动AOA和AOB群落结构变化的重要因子,且根际与非根际土壤中氨氧化微生物存在生态位分离。     

Soil phosphorus does not keep pace with soil carbon and nitrogen accumulation following woody encroachment

Soil carbon, nitrogen, and phosphorus cycles are strongly interlinked and controlled through biological processes, and the phosphorus cycle is further controlled through geochemical processes. In dryland ecosystems, woody encroachment often modifies soil carbon, nitrogen, and phosphorus stores, although it remains unknown if these three elements change proportionally in response to this vegetation change. We evaluated proportional changes and spatial patterns of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) concentrations following woody encroachment by taking spatially explicit soil cores to a depth of 1.2 m across a subtropical savanna landscape which has undergone encroachment by Prosopis glandulosa (an N₂ fixer) and other woody species during the past century in southern Texas, USA. SOC and TN were coupled with respect to increasing magnitudes and spatial patterns throughout the soil profile following woody encroachment, while TP increased slower than SOC and TN in topmost surface soils (0–5 cm) but faster in subsurface soils (15–120 cm). Spatial patterns of TP strongly resembled those of vegetation cover throughout the soil profile, but differed from those of SOC and TN, especially in subsurface soils. The encroachment of woody species dominated by N₂‐fixing trees into this P‐limited ecosystem resulted in the accumulation of proportionally less soil P compared to C and N in surface soils; however, proportionally more P accrued in deeper portions of the soil profile beneath woody patches where alkaline soil pH and high carbonate concentrations would favor precipitation of P as relatively insoluble calcium phosphates. This imbalanced relationship highlights that the relative importance of biotic vs. abiotic mechanisms controlling C and N vs. P accumulation following vegetation change may vary with depth. Our findings suggest that efforts to incorporate effects of land cover changes into coupled climate–biogeochemical models should attempt to represent C‐N‐P imbalances that may arise following vegetation change.     

N2O emission rates in a California meadow soil are influenced by fertilizer level, soil moisture and the community structure of ammonia-oxidizing bacteria

The response of nitrous oxide (N₂O) emission rates and β‐proteobacterial ammonia‐oxidizing (AOB) communities to manipulations of temperature, soil moisture and nitrogenous fertilizer concentration were studied for 16–20 weeks in a multifactorial laboratory experiment using a California meadow soil. Interactions among these three environmental factors influenced the N₂O emission rates, and two patterns of N₂O emission rates due to nitrification (NitN₂O) were observed. First, in soils receiving low or moderate amounts of fertilizer, the rates decreased sharply in response to increasing soil moisture and temperature. Second, in soils receiving high amounts of fertilizer, the rates were influenced by an interaction between soil moisture and temperature, such that at 20 °C increasing soil moisture resulted in an increase in the rates, and at 30 °C the highest rate was observed at moderate soil moisture. We used path analysis to identify the interrelationships that best explain these two patterns. Path analysis revealed that in the high fertilizer (HF) treatment, the major path by which ammonia influenced NitN₂O rates was indirect through an influence on the abundance of one particular phylogenetic group (AOB ‘cluster 10’). In contrast, in the low and moderate fertilizer treatments soil moisture influenced the rates both directly (the major path) and indirectly through AOB community structure. Although terminal restriction fragment length polymorphism (T‐RFLP) analysis revealed shifts in the community structure of AOB in all treatments, the shifts at HF concentrations were particularly striking, with dominance by three different phylogenetic groups under different combinations of the three environmental factors. The high emission rates observed at the lowest soil moistures suggest that bacterial nitrifiers may use denitrification as a stress response.     

Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes

The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (S_Chao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, S_Chao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (S_Chao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil.     

Recovery of Soil Ammonia Oxidation After Long-Term Zinc Exposure Is Not Related to the Richness of the Bacterial Nitrifying Community

A soil sterilization–reinoculation approach was used to manipulate soil microbial diversity and to assess the effect of the diversity of the ammonia-oxidizing bacteria (AOB) on the recovery of the nitrifying community to metal stress (zinc). Gamma-irradiated soil was inoculated with 13 different combinations of up to 22 different soils collected worldwide to create varying degrees of AOB diversity. Two months after inoculation, AOB amoA DGGE based diversity (weighted richness) varied more than 10-fold among the 13 treatments, the largest value observed where the number of inocula had been largest. Subsequently, the 13 treatments were either or not amended with ZnCl₂. Initially, Zn amendment completely inhibited nitrification. After 6 months of Zn exposure, recovery of the potential nitrification activity in the Zn amended soils ranged from <10 % to >100 % of the potential nitrification activity in the corresponding non-amended soils. This recovery was neither related to DGGE-based indices of AOB diversity nor to the AOB abundance assessed 2 months after inoculation (p?>?0.05). However, recovery was significantly related (r?=?0.75) to the potential nitrification rate before Zn amendment and only weakly to the number of soil inocula used in the treatments (r?=?0.46). The lack of clear effects of AOB diversity on recovery may be related to an inherently sufficient diversity and functional redundancy of AOB communities in soil. Our data indicate that potential microbial activity can be a significant factor in recovery.     

Characterization of N<Subscript>2</Subscript>O emissions and associated microbial communities from the ant mounds in soils of a humid tropical rainforest

Tropical rainforest soils harbor a considerable diversity of soil fauna that contributes to emissions of N₂O. Despite their ecological dominance, there is limited information available about the contribution of epigeal ant mounds to N₂O emissions in these tropical soils. This study aimed to determine whether ant mounds contribute to local soil N emissions in the tropical humid rainforest. N₂O emission was determined in vitro from individual live ants, ant-processed mound soils, and surrounding reference soils for two trophically distinct and abundant ant species: the leaf-cutting Atta mexicana and omnivorous Solenopsis geminata. The abundance of total bacteria, nitrifiers (AOA and AOB), and denitrifiers (nirK, nirS, and nosZ) was estimated in these soils using quantitative PCR, and their respective mineral N contents determined. There was negligible N₂O emission detected from live ant individuals. However, the mound soils of both species emitted significantly greater (3-fold) amount of N₂O than their respective surrounding reference soils. This emission increased significantly up to 6-fold in the presence of acetylene, indicating that, in addition to N₂O, dinitrogen (N₂) is also produced from these mound soils at an equivalent rate (N₂O/N₂?=?0.57). Functional gene abundance (nitrifiers and denitrifiers) and mineral N pools (ammonium and nitrate) were significantly greater in mound soils than in their respective reference soils. Furthermore, in the light of the measured parameters and their correlation trends, nitrification and denitrification appeared to represent the major N₂O-producing microbial processes in ant mound soils. The ant mounds were estimated to contribute from 0.1 to 3.7% of the total N₂O emissions of tropical rainforest soils.     

Nitrification inhibitors effectively target N2O-producing Nitrosospira spp. in tropical soil

The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N₂O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N₂O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N₂O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N₂O-producing AOB Nitrosospira with N₂O, NO₃⁻, NH₄⁺, water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO₃⁻, NH₄⁺ and pH; and AOA Nitrososphaera and NOB Nitrospira with NH₄⁺, which suggests different drivers. These results support the co-occurrence of non-N₂O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N₂O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.     

Suppression of nitrification and nitrous oxide emission by the tropical grass Brachiaria humidicola

Nitrification by soil nitrifiers may result in substantial losses of applied nitrogen through NO₃ ^– leaching and N₂O emission. The biological inhibition of nitrification by crop plants or pasture species is not well known. This study was conducted to evaluate the ability of three pasture species, Brachiaria humidicola, B. decumbens and Melinis minutiflora to inhibit nitrification. Plants were grown in a growth chamber for sixty days, fertilized with (NH₄)₂SO₄. After harvesting, the soil was incubated with (NH₄)₂SO₄ for 24 days. Ammonium oxidizing bacteria (AOB), NH₄-N levels, and N₂O emission were monitored at 4 d intervals. Among the species studied, B. humidicola inhibited nitrification and maintained NH₄-N in soil to a much greater extent than the other two species. This nitrification inhibition lasted for 12 days after initiation of soil incubation study (i.e. from 60 DAS when the plants were harvested). The AOB populations and N₂O emission from the soil were significantly lower in the soils where B. humidicola has been grown compared to the other two species. Root exudates and soil extracts of B. humidicola suppressed AOB populations, whereas those of B. decumbens and M. minutiflora did not. The results are in consistence with the hypothesis that B. humidicola suppressed nitrification and N₂O emissions through an inhibitory effect on the AOB population.     

攀枝花不同海拔高度烤烟农田红壤中氨氧化细菌与氨氧化古菌的群落结构分析

为探究攀枝花干热河谷区农田土壤氨氧化古菌（Ammonia oxidizing archaea,AOA）与氨氧化细菌（Ammonia oxidizing bacteria,AOB）群落对海拔高度的响应特征,深入认识该区域的氮素循环过程。以攀枝花米易县不同海拔（1600 m、1800 m和2000 m）农田红壤为研究对象,运用化学分析和末端限制性片段长度多态性（Terminal restriction fragment length polymorphism,T-RFLP）分别测定土壤理化性质、AOA和AOB群落组成及多样性,研究不同海拔农田土壤中AOA和AOB群落变异及其驱动因子。研究结果显示,不同海拔农田土壤pH均小于7,土壤有机碳（SOC）、全氮（TN）、速效钾（AK）和铵态氮（NH₄⁺-N）含量随海拔升高而降低,碱解氮（AN）、有效磷（AP）和硝态氮（NO₃^--N）含量随海拔升高先增加后降低;随海拔升高,AOA群落多样性指数增加,而AOB群落多样性指数先增加后降低;AOA以亚硝基球菌属（Nitrososphaera）为优势菌群,AOB以亚硝化螺菌属（Nitrosospira）为优势菌群;土壤有机碳（SOC）、速效钾（AK）和硝态氮（NO₃^--N）是影响该区域农田土壤AOA和AOB群落发育的主要因子。总体而言,攀枝花干热河谷区不同海拔农田土壤AOA和AOB群落结构变化明显,土壤硝态氮、速效钾和有机碳是影响AOA和AOB群落结构变异的主要因子;研究结果可为揭示干热河谷区农田红壤氮循环相关微生物的海拔分布格局提供理论依据。     

Impact of carbon source amendment on ammonia-oxidizing microorganisms in reservoir riparian soil

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be key players in ammonia biotransformation in the environment. Soil organic matter can affect the distribution of soil AOA and AOB. However, the link between organic matter and AOA and AOB communities remain largely unclear. The current study investigated the impact of organic carbon amendment on the abundance and composition of ammonia-oxidating microorganisms in reed-planted soil in a riparian zone of the Miyun Reservoir (Beijing). The results indicated that AOB outnumbered AOA in riparian wetland soil both before and after glucose application. Glucose application significantly increased the abundance of AOA , but had only a slight impact on the abundance of AOB. The addition of glucose had a strong impact on the community structures of both AOA and AOB. Moreover, phylogenetic analysis indicated that the obtained archaeal amoA gene sequences showed no close relationship with cultivated AOA species. Few Nitrosospira-like AOB sequences were detected in glucose-amended soil. This study may provide some new insight regarding soil ammonia-oxidizing microorganisms.     

The effect of cattle and sheep grazing on salt-marsh vegetation at Skallingen,Denmark

The aggregated effect of cattle and sheep grazing on Puccinellion maritimae and other salt-marsh vegetation has been studied together with changes in species composition, the percentage cover of each species, total cover and the percentage of bare ground, six years after grazing had been prevented by construction of experimental exclosures. The results of these experiments are discussed in relation to the natural development of the vegetation that occurred in a permanent plot in the ungrazed part of the salt marsh. Six years without grazing caused a marked increase in total cover and a dramatic reduction in the amount of bare ground. The species composition of the Puccinellia maritima community did not change during these six years, but all species increased in cover. Whereas Artemisia maritima migrated into the Festuca rubra community and only two species Festuca and Halimione portulacoides, increased in cover, all other species showed reduced cover and Salicornia europaea disappeared from the plot after six years without grazing. During the same period of time, three species, Salicornia europaea, Suaeda maritima, and Glaux maritima, disappeared from the plot in the ungrazed marsh as a result of natural development. During thirty-five years the vegetation originally dominated by Puccinellia maritima and Salicornia europaea has changed into a community dominated by Halimione portulacoides, whereas the grazed salt marsh is still dominated by Puccinellia maritima and Salicornia europaea. These results are discussed in relation to the literature on the effect of cattle and sheep grazing on salt-marsh vegetation.     

Soil C:N:P stoichiometry responds to vegetation change from grassland to woodland

Woody encroachment has been a major land cover change in dryland ecosystems during the past century. While numerous studies have demonstrated strong effects of woody encroachment on soil carbon (C), nitrogen (N), and phosphorus (P) storage, far less is known about the plasticity of soil C:N:P stoichiometry in response to woody encroachment. We assessed landscape-scale patterns of spatial heterogeneity in soil C:N:P ratios throughout a 1.2 m soil profile in a region where grassland is being replaced by a diverse assemblage of subtropical woody plants dominated by Prosopis glandulosa, an N₂-fixing tree. Woody species had leaf and fine root C:N:P ratios significantly different from grasses. Variation in soil C:N ratios in both horizontal and vertical planes was remarkably smaller than that of soil N:P and C:P ratios. Spatial patterns of soil C:N ratio throughout the profile were not strongly related to vegetation cover. In contrast, spatial patterns of soil N:P and C:P ratios displayed a strong resemblance to that of vegetation cover throughout the soil profile. Within the uppermost soil layer (0–5 cm), soil N:P and C:P ratios were higher underneath woody patches while lower within the grassland; however, this pattern was reversed in subsurface soils (15–120 cm). These results indicate a complex response of soil C:N:P stoichiometry to vegetation change, which could have important implications for understanding C, N, and P interactions and nutrient limitations in dryland ecosystems.     

Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the alpha-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein.     

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils

Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson’s correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.     

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P⩽0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH₄⁺-availability that exist in the field.