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1.
The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity was uncoupled to community composition.  相似文献   

2.
In this study, we investigated the impact of organic and mineral fertilizers on the community composition of arbuscular mycorrhizal (AM) fungi and bacteria in the mycorrhizosphere of maize in a field experiment established in 1956, in south-east Sweden. Roots and root-associated soil aggregates were sampled four times during the growing season in 2005, in control plots and in plots amended with calcium nitrate, ammonium sulphate, green manure, farmyard manure or sewage sludge. Fungi in roots were identified by cloning and sequencing, and bacteria in soil aggregates were analysed by terminal-restriction fragment length polymorphism, cloning and sequencing. The community composition of AM fungi and bacteria was significantly influenced by the different fertilizers. Changes in microbial community composition were mainly correlated with changes in pH induced by the fertilization regime. However, other factors, including phosphate and soil carbon content, also contributed significantly to these changes. Changes in bacterial community composition and a reduction in bacterial taxon richness throughout the growing season were also manifest. The results of this study highlight the importance and significant effects of the long-term application of different fertilizers on edaphic factors and specific groups of fungi and bacteria playing a key role in arable soils.  相似文献   

3.
In order to understand the effect of the maize rhizosphere on denitrification, the diversity and the activity of the denitrifying community were studied in soil amended with maize mucilage. Diversity of the denitrifying community was investigated by polymerase chain reaction (PCR) amplification of total community DNA extracted from soils using gene fragments, encoding the nitrate reductase (narG) and the nitrous oxide reductase (nosZ), as molecular markers. To assess the underlying diversity, PCR products were cloned and 10 gene libraries were obtained for each targeted gene. Libraries containing 738 and 713 narG and nosZ clones, respectively, were screened by restriction fragment analysis, and grouped based on their RFLP (restriction fragment length polymorphism) patterns. In all, 117 and 171 different clone families have been identified for narG and nosZ and representatives of RFLP families containing at least two clones were sequenced. Rarefaction curves of both genes did not reach a clear saturation, indicating that analysis of an increasing number of clones would have revealed further diversity. Recovered NarG sequences were related to NarG from Actinomycetales and from Proteobacteria but most of them are not related to NarG from known bacteria. In contrast, most of the NosZ sequences were related to NosZ from alpha, beta, and gammaProteobacteria. Denitrifying activity was monitored by incubating the control and amended soils anaerobically in presence of acetylene. The N2O production rates revealed denitrifying activity to be greater in amended soil than in control soil. Altogether, our results revealed that mucilage addition to the soil results in a strong impact on the activity of the denitrifying community and minor changes on its diversity.  相似文献   

4.
The potential denitrification activity and the composition of the denitrifying bacterial community in a full-scale rockwool biofilter used for treating livestock manure composting emissions were analyzed. Packing material sampled from the rockwool biofilter was anoxically batch-incubated with 15N-labeled nitrate in the presence of different electron donors (compost extract, ammonium, hydrogen sulfide, propionate, and acetate), and responses were compared with those of activated sludge from a livestock wastewater treatment facility. Overnight batch-incubation showed that potential denitrification activity for the rockwool samples was higher with added compost extract than with other potential electron donors. The number of 16S rRNA and nosZ genes in the rockwool samples were in the range of 1.64–3.27 × 109 and 0.28–2.27 × 108 copies/g dry, respectively. Denaturing gradient gel electrophoresis analysis targeting nirK, nirS, and nosZ genes indicated that the distribution of nir genes was spread in a vertical direction and the distribution of nosZ genes was spread horizontally within the biofilter. The corresponding denitrifying enzymes were mainly related to those from Phyllobacteriaceae, Bradyrhizobiaceae, and Alcaligenaceae bacteria and to environmental clones retrieved from agricultural soil, activated sludge, freshwater environments, and guts of earthworms or other invertebrates. A nosZ gene fragment having 99% nucleotide sequence identity with that of Oligotropha carboxidovorans was also detected. Some nirK fragments were related to NirK from micro-aerobic environments. Thus, denitrification in this full-scale rockwool biofilter might be achieved by a consortium of denitrifying bacteria adapted to the intensely aerated ecosystem and utilizing mainly organic matter supplied by the livestock manure composting waste-gas stream.  相似文献   

5.
陈哲  袁红朝  吴金水  魏文学 《生态学报》2009,29(11):5923-5929
以中国科学院桃源农业生态试验站长期定位施肥试验为平台,研究了3种长期施肥制度(对照不施肥-CK,化学施肥-NPK,化学施肥+有机肥-NPKOM)下土壤反硝化速率的差异.同时,以硝酸还原酶基因(narG)作为反硝化细菌的功能标志物,分析了施肥对反硝化细菌群落结构和多样性的影响.结果表明,长期施用有机肥的土壤反硝化速率,反硝化菌多样性都高于对照和施用化肥处理.从3个处理的土壤样品中共获得35个narG基因的可操作分类单元(OTU)主要分布在两个簇,与变形菌门(Proteobacteria)和放线菌门(Actinobacteria)的反硝化细菌有一定的亲缘关系,均为首次从土壤中克隆.Shannon多样性指数显示,NPKOM处理的narG基因多样性最高,CK处理次之,NPK处理最低.LUBSHUFF软件对narG基因群落组成的分析显示,施有机肥后含narG基因的细菌群落组成与CK之间有显著性差异(P<0.05),而化肥(NPK)没有产生显著影响.实验结果为进一步研究亚热带地区水稻土反硝化作用及反硝化功能菌提供了重要的依据.  相似文献   

6.
陈哲  陈春兰  秦红灵  王霞  吴敏娜  魏文学 《生态学报》2009,29(11):6142-6147
以中国科学院桃源农业生态试验站长期定位施肥试验为平台,采用聚合酶链式反应(polymerase chain reaction,PCR)和DNA序列测定技术分析研究了3种长期施肥制度(对照不施肥-CK,单施氮肥-N,氮磷钾肥-NPK)对土壤细菌群落以及硝化、反硝化微生物种群的影响.通过系统分析细菌16S rDNA、细菌的硝化基因氨单加氧酶(ammonia monooxygenase,amoA)和反硝化基因氧化亚氮还原酶(nitrous oxide reductase,nosZ)等基因文库发现,长期单施氮肥导致细菌16S rDNA和amoA的多样性明显低于CK和NPK处理,而nosZ的多样性与之相反,即单施氮肥处理明显高于CK和NPK处理.LUBSHUFF软件统计分析显示:16S rDNA和amoA基因文库在CK与N,CK与NPK,NPK与N处理间均存在显著性差异.而对于nosZ基因文库,N和NPK与CK处理相比呈现出了显著性差异,N与NPK之间的差异没有达到显著水平.上述结果表明长期施用化肥对水稻土细菌的群落结构及硝化和反硝化细菌组成产生了明显的影响,但这种影响因基因类型而异.  相似文献   

7.
Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 x 10(5) to 8.9 x 10(5) copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 x 10(3) to 2.6 x 10(4), 7.4 x 10(2) to 1.4 x 10(3), 2.5 x 10(2) to 6.4 x 10(3), and 1.2 x 10(3) to 5.5 x 10(3), respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.  相似文献   

8.
The effects of sewage sludge, used to improve fertility of replaced soil, on vegetation were studied in limestone quarry restoration. Plant community growing in the first stages after sludge application was surveyed in six quarries of NE Spain. Areas with a mixture of sewage sludge and residual soil were compared to areas where the application consisted only of residual soil (a mixture of previous top soil and mine spoils). Sewage sludge was hypothesized to increase total biomass and cover, modifying species composition and delaying the early successional recover of the community. The results showed that both biomass and plant cover increased because of sewage sludge addition. The floristic composition was dominated by ruderal species that did not show any dependence on sewage sludge application. Convergence on similarity between sludge and control plots was not detected along a 5‐year period. Although species richness was significantly lower in sludge plots, diversity and equitability indexes did not show differences between treatments. The results did not show differences in the proportion of non‐native species. The proportion of legumes was lower in sludge plots. These results show that the plant communities resulting from the addition of sewage sludge to the soil used in limestone quarry restoration have more biomass and cover, but less number of species, and they do not show a clear trend to converge to those areas restored only with non‐amended soil.  相似文献   

9.
Wang G H  Liu Junjie  Qi X N  Jin J  Wang Y  Liu X B 《农业工程》2008,28(1):220-226
Soil microbial community structure and function are commonly used as indicators for soil quality and fertility. In this paper, the bacterial community structure and function in a black soil of Dehui region influenced by fertilization were investigated by Biolog and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) methods. Biolog examination showed that substrate richness and catabolic diversities of bacterial communities were the highest in the treatment of farm yard manure, and the lowest in the chemical fertilizer treatment. DGGE fingerprint showed that the majority of bands were similar among all treatments, suggesting that microbial communities with those bands were stable, and not influenced by fertilization. In general, chemical fertilizer decreased the diversity of soil bacterial communities. The PCA (principal component analysis) plots of Biolog and DGGE revealed that the structure and function of bacterial communities were similar in the non-fertilized control and the treatment of farm yard manure alone, which inferred that the application of farm yard manure increased the quantity of soil microbes but had less effect on the changes of community structure. The catabolic function was similar, but the composition structure differed between the treatments of chemical fertilizer alone and combined application of farm yard manure with chemical fertilizer. These results suggest that the use of chemical fertilizer mainly decreased the catabolic activity of the fast growth bacteria or eutrophic bacteria.  相似文献   

10.
We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in alpha-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.  相似文献   

11.
Sewage sludge has been used as organic manure to replace chemical fertilizer. The aim of this study was to evaluate the effect of doses of sewage sludge on the soil bacterial community by DNA microarray analysis. A microarray phylochip containing 1,560 partial sequences of 16S rRNA from the most common strains of bacteria was developed for bioprospection. Soil plots from an experimental field in Brazil were assessed with or without sludge treatment containing different doses of nitrogen based on that recommended for maize cultivation. The microarray technique was useful for quickly assessing changes in the bacterial communities and a high variation was observed, mainly in soil treated with high doses of sludge. While sludge containing 25 kg N/ha favored an in crease in the number of members in various phyla, on the other hand sludge with the higher dose regarding to 200 kg N/ha caused a reduction in the number of members in almost all phyla. Proteobacteria often dominant in soils was specifically affected. This study highlights the spread of bacteria to new environments and provides direct information about bacterial composition at specific habitats. Our results have shown that bacterial community structure was greatly affected by sludge application.  相似文献   

12.
Bacterial denitrification results in the loss of fertilizer nitrogen and greenhouse gas emissions as nitrous oxides, but ecological factors in soil influencing denitrifier communities are not well understood, impeding the potential for mitigation by land management. Communities vary in the relative abundance of the alternative dissimilatory nitrite reductase genes nirK and nirS, and the nitrous oxide reductase gene nosZ; however, the significance for nitrous oxide emissions is unclear. We assessed the influence of different long-term fertilization and cultivation treatments in a 160-year-old field experiment, comparing the potential for denitrification by soil samples with the size and diversity of their denitrifier communities. Denitrification potential was much higher in soil from an area left to develop from arable into woodland than from a farmyard manure-fertilized arable treatment, which in turn was significantly higher than inorganic nitrogen-fertilized and unfertilized arable plots. This correlated with abundance of nirK but not nirS, the least abundant of the genes tested in all soils, showing an inverse relationship with nirK. Most genetic variation was seen in nirK, where sequences resolved into separate groups according to soil treatment. We conclude that bacteria containing nirK are most probably responsible for the increased denitrification potential associated with nitrogen and organic carbon in this soil.  相似文献   

13.
The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.  相似文献   

14.
The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.  相似文献   

15.
The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.  相似文献   

16.
为了探明水稻土落干过程对温室气体排放和反硝化微生物的影响,通过模拟水稻土淹水落干过程,系统监测了落干开始后24 h内N2O的释放和氧化还原电位(Eh)的变化,并利用实时PCR(qPCR)方法测定了反硝化功能基因narG和nosZ的丰度.结果表明:落干开始后4 h N2O释放量就明显增加,在24 h时N2O的释放量比淹水对照增加了5倍多;narG和nosZ基因丰度也随着落干过程的推移而快速增加;而且N2O排放通量与narG基因呈极显著相关(P<0.01).表明水稻土短期淹水落干过程中,含narG基因反硝化微生物是驱动N2O释放的主要功能微生物.  相似文献   

17.
过量施肥对设施菜田土壤菌群结构及N2O产生的影响   总被引:1,自引:0,他引:1  
【背景】N_2O是一种很强的温室气体,其温室效应强度大约是CO_2的265倍。土壤氮肥施加量是影响N_2O排放的重要因素,而厌氧条件下微生物反硝化则是N_2O产生的重要途径。【目的】研究过量施肥条件下蔬菜大棚土壤菌群结构变化及其对N_2O气体排放的影响。【方法】利用自动化培养与实时气体检测系统(Robot)监测土壤厌氧培养过程中N_2O和N_2排放通量,比较过量施肥和减氮施肥模式下土壤N_2O排放模式的差异。通过Illumina二代测序平台对这2种不同施肥处理的土壤微生物群落进行高通量测序,研究不同施肥量对土壤菌群组成的影响。【结果】过量施肥土壤中硝酸盐的含量大约是减氮施肥土壤的2倍,通过添加硝酸盐使2种土壤的硝酸盐含量均为60 mg/kg或为200 mg/kg时,过量施肥土壤在厌氧培养前期N_2O气体的产生量及产生速度都明显高于减氮施肥土壤。另外,过量施肥导致土壤菌群结构发生显著改变,并且降低了土壤微生物的多样性。相对于减氮施肥,过量施肥方式富集了Rhodanobacter属的微生物。PICRUSt预测结果显示,传统施肥没有显著改变反硝化功能基因相对丰度。【结论】长期过量氮肥施用显著增加了土壤N_2O的排放,可能原因是施肥改变了包括氮转化相关微生物在内的土壤菌群组成,从而影响了土壤N_2O气体的形成与还原过程。  相似文献   

18.
卢静  刘金波  盛荣  刘毅  陈安磊  魏文学   《生态学杂志》2014,25(10):2879-2884
为了探明水稻土落干过程对温室气体排放和反硝化微生物的影响,通过模拟水稻土淹水落干过程,系统监测了落干开始后24 h内N2O的释放和氧化还原电位(Eh)的变化,并利用实时PCR(qPCR)方法测定了反硝化功能基因narG和nosZ的丰度.结果表明:落干开始后4 h N2O释放量就明显增加,在24 h时N2O的释放量比淹水对照增加了5倍多;narG和nosZ基因丰度也随着落干过程的推移而快速增加;而且N2O排放通量与narG基因呈极显著相关(P<0.01).表明水稻土短期淹水落干过程中,含narG基因反硝化微生物是驱动N2O释放的主要功能微生物.  相似文献   

19.
In this study, microcosms were used to investigate the influence of temperature (4 and 28 degrees C) and water content (45% and 90% WHC) on microbial communities and activities in carbon-rich fen soil. Bacterial, archaeal and denitrifier community composition was assessed during incubation of microcosms for 12 weeks using terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA and nitrous oxide reductase (nosZ) genes. In addition, microbial and denitrifier abundance, potential denitrification activity and production of greenhouse gases were measured. No detectable changes were observed in prokaryote or denitrifier abundance. In general, cumulatively after 12 weeks more carbon was respired at the higher temperature (3.7 mg CO(2) g(-1) soil), irrespective of the water content, whereas nitrous oxide production was greater under wet conditions (98-336 microg N(2)O g(-1) soil). After an initial lag phase, methane emissions (963 microg CH(4) g(-1) soil) were observed only under warm and wet conditions. T-RFLP analyses of bacterial 16S rRNA and nosZ genes revealed small or undetectable community changes in response to temperature and water content, suggesting that bacterial and denitrifying microbial communities are stable and do not respond significantly to seasonal changes in soil conditions. In contrast, archaeal microbial community structure was more dynamic and was strongly influenced by temperature.  相似文献   

20.
The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.  相似文献   

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