豆科作物间作燕麦对土壤固氮微生物丰度和群落结构的影响

利用荧光定量PCR和高通量测序的研究方法,比较了3种种植模式(燕麦单作,O;大豆/燕麦,OSO;绿豆/燕麦,OMO)对燕麦土壤固氮微生物数量和群落组成的影响.结果表明: 与大豆和绿豆间作显著改变了燕麦土壤的理化性质.燕麦土壤固氮微生物nifH基因拷贝数为每克干土1.75×10¹⁰～7.37×10¹⁰,拔节期和成熟期OSO和OMO中nifH基因拷贝数分别是O中的2.18、2.64和1.92、2.57倍,且各处理成熟期nifH基因拷贝数显著低于拔节期.样品稀释性曲线和覆盖度结果表明,各样品nifH基因测序结果可靠.与绿豆间作显著提高了燕麦土壤nifH基因的多样性.各样品固氮微生物属水平上优势类群均为Azohydromonas、固氮菌属、慢生根瘤菌属、Skermanella和在属水平上无法归类的固氮微生物,但各优势类群相对丰度存在差异.样品OTU的venn分布和主成分分析显示,拔节期和成熟期nifH基因群落结构存在差异,两个生育时期OSO和OMO具有更相似的nifH基因群落结构.表明与大豆和绿豆间作可显著提高燕麦土壤固氮微生物的数量,并影响固氮微生物的群落组成.     

用PCR-DGGE研究长期施用无机肥对种稻红壤微生物群落多样性的影响

以中国科学院红壤生态试验站的发育于第四纪红粘土的种稻红壤为研究对象,采用PCR-DGGE方法研究了长期施用无机肥对土壤微生物群落多样性的影响。在种植双季稻、连续13a施用不同无机肥后,土壤中细菌、古菌、放线菌和真菌的群落结构发生了较大的变化。未种植水稻的土壤与种稻土壤间四类微生物SSUrDNADGGE带谱相似性只有33%~66%。施磷肥的处理NP、PK、NPK之间微生物群落结构相似性较高,4类微生物的SSUrDNADGGE带谱相似性高达75%~81%。施氮钾肥(NK)、不施肥(CK)处理与施磷肥处理间土壤微生物群落结构的差异较大,其四类微生物的SSUrDNADGGE带谱相似性分别为69%~77%、55%~77%。研究的目的是深入地了解土壤中微生物群落的多样性,为科学施肥、合理利用土壤、保护微生物多样性和实现农业生态系统的可持续发展提供科学依据。     

氮添加土壤微生物群落结构影响微生物碳利用效率

尽管近年来中国氮(N)沉降水平逐渐趋于稳定,但中国东南地区N沉降相比于其他地区仍处于较高水平。N沉降对陆地生态系统碳循环过程的影响不容忽视。微生物碳利用效率(CUE)是指微生物将吸收的碳转化为生物量碳的效率,高微生物CUE意味着高土壤有机碳存储潜力。因此,探究N沉降背景下微生物CUE的变化将有助于进一步认识陆地生态系统土壤碳存储的变化。然而,目前关于N沉降下微生物群落结构的变化如何影响微生物CUE鲜有报道。在福建省泉州市戴云山国家级自然保护区的罗浮栲林通过N添加模拟N沉降。实验共包括三个N添加处理：对照(CT,+0 kg hm^-2 a^-1)、低氮(LN,+40 kg hm^-2 a^-1)和高氮(HN,+80 kg hm^-2 a^-1)。测定不同处理土壤基本理化性质、微生物生物量、酶活性和CUE,并使用高通量测序对微生物群落结构和多样性进行测定。结果表明,N添加显著影响微生物CUE,随着N添加水平的增加,CUE逐渐增加;相反,土壤pH、可提取有机碳(EOC)和微...     

玉米间作和施氮对土壤微生物代谢功能多样性的影响

微生物功能多样性是土壤健康的重要指标,在多种生物地球化学过程中发挥关键作用.本研究基于多年田间小区定位试验,设置间作和单作2种种植模式和4个施氮水平(N0,0 kg·hm-2;N125,125 kg·hm-2;N250,250 kg·hm-2;N375,375 kg·hm-2),采用 Biolog-Eco微平板法,分析...     

Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production

Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.     

土地利用驱动的土壤性状变化影响微生物群落结构和功能

微生物在调节陆地生态系统地球化学循环过程中具有重要作用。土地利用方式改变显著影响土壤微生物群落结构和功能,但对土地利用驱动的土壤性状变化与微生物群落结构和功能关系的研究相对匮乏。依托长期定位监测试验（始于1984年）,通过16S rRNA基因片段和ITS高通量测序,研究了土地利用方式（裸地、农田、草地）驱动的土壤碳氮变化对微生物群落结构和功能的影响。结果表明：对于细菌群落而言,裸地中α-多样性最高、其次是草地、农田中最低,农田和草地中细菌优势菌群变形菌（Proteobacteria）和放线菌门（Actinobacteria）相对丰度较裸地低4.5%、3.9%和5.5%、3.8%;对于真菌群落而言,裸地子囊菌门（Ascomycota）相对丰度最高、农田次之、草地最低;化能异养型、好氧化能异养型细菌相对丰度裸地显著高于农田和草地（P<0.05）,而硝化型和好氧氨氧化型细菌裸地显著低于农田和草地（P<0.05）;腐生型真菌相对丰度大小排序为：裸地>农田>草地。细菌群落变化主要与土壤容重、全氮、矿质氮、C ： N比和微生物量碳有关,而真菌群落与土壤矿质氮有关。细菌和真菌功能菌群主要受土壤容重、土壤有机碳、土壤全氮、C ： N比和微生物量碳影响。因此,土壤容重、土壤全氮、土壤有机碳、C ： N比、微生物量碳、矿质氮差异可能是影响不同土地利用方式中微生物群落和功能变化的主要因素。     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

设施蔬菜种植年限对氮素循环微生物群落结构和丰度的影响

以甘肃武威设施菜地为研究对象,采用末端限制性片段多态性分析(PCR-T-RFLP)和实时荧光定量PCR(real-time PCR)相结合的方法,研究了设施菜地种植3、9、14、17年等年限下土壤中细菌、氨氧化细菌(AOB)和nirK型反硝化细菌群落结构和丰度的变化.结果表明: 设施菜地中细菌、氨氧化细菌和nirK型反硝化细菌优势种群及丰度与大田明显不同,并随种植年限不同发生变化.随种植年限的增加,细菌和nirK型反硝化细菌的丰度呈现先增后减的趋势,分别在种植14年和9年达到最大,0～20 cm土层为每克干土9.67×10⁹、2.30×10⁷个拷贝数,是种植3年的1.51、1.52倍;而氨氧化细菌的丰度则呈现出先减后增的趋势,在种植14年的0～20 cm土层为每克干土3.28×10⁷个拷贝数,仅是种植3年土壤的45.7%,说明设施菜地中参与氮素循环的功能微生物生态适应机制存在显著差异.研究结果为进一步研究设施栽培条件下土壤微生物的适应机制等奠定了基础.     

The effects of stubble retention and tillage practices on surface soil structure and hydraulic conductivity of a loess soil

The current cropping system of excessive tillage and stubble removal in the northwestern Loess Plateau of China is clearly unsustainable. A better understanding of tillage and stubble management on surface soil structure is vital for the development of effective soil conservation practices in the long term. Changes in surface soil structure and hydraulic properties were measured after 4 years of stubble management (stubble retained vs. stubble removed) under contrasting tillage practices (no-tillage vs. conventional tillage) in a silt loam soil (Los Orthic Entisol) in Dingxi, Gansu, the northwestern Loess Plateau, China. Our results indicated that after 4 years small but significant changes in soil properties were observed amongst the different tillage and stubble treatments. Surface soil (0–5 cm) under no-tillage with stubble retention had the highest water stability of macroaggregates (>250 μm), soil organic carbon (SOC) and saturated hydraulic conductivity. Significant correlation was found between water stable macro-aggregates and soil organic carbon content, indicating the importance of the latter on soil structural stability. The improvement in soil structure and stability was confirmed by higher soil hydraulic conductivity measurements. Consistently higher K_sat was detected in the no tillage with stubble retained soil compared to other treatments. Therefore, no-tillage with stubble retention practice is an effective management technique for improving physical quality of this fragile soil in the long term.     

The effects of stubble retention and tillage practices on surface soil structure and hydraulic conductivity of a loess soil

The current cropping system of excessive tillage and stubble removal in the northwestern Loess Plateau of China is clearly unsustainable. A better understanding of tillage and stubble management on surface soil structure is vital for the development of effective soil conservation practices in the long term. Changes in surface soil structure and hydraulic properties were measured after 4 years of stubble management (stubble retained vs. stubble removed) under contrasting tillage practices (no-tillage vs. conventional tillage) in a silt loam soil (Los Orthic Entisol) in Dingxi, Gansu, the northwestern Loess Plateau, China. Our results indicated that after 4 years small but significant changes in soil properties were observed amongst the different tillage and stubble treatments. Surface soil (0–5 cm) under no-tillage with stubble retention had the highest water stability of macroaggregates (>250 μm), soil organic carbon (SOC) and saturated hydraulic conductivity. Significant correlation was found between water stable macro-aggregates and soil organic carbon content, indicating the importance of the latter on soil structural stability. The improvement in soil structure and stability was confirmed by higher soil hydraulic conductivity measurements. Consistently higher K_sat was detected in the no tillage with stubble retained soil compared to other treatments. Therefore, no-tillage with stubble retention practice is an effective management technique for improving physical quality of this fragile soil in the long term.     

Influence of the herbicide glyphosate on soil microbial community structure

The side effects of glyphosate on the soil microflora were monitored by applying a range of glyphosate concentrations (0, 2, 20, and 200 μg g⁻¹ herbicide) to incubated soil samples, and following changes in various microbial groups over 27 days. Bacterial propagule numbers were temporarily enhanced by 20 μg g⁻¹ and 200 μg g⁻¹ glyphosate, while actinomycete and fungal propagule numbers were unaffected by glyphosate. The frequency of three fungal species on organic particles in soil was temporarily enhanced by 200 μg g⁻¹ glyphosate, while one was inhibited. One species was temporily enhanced on mineral particles. However, many of these fungi were inhibited by 200 μg g⁻¹ glyphosate in pure culture. There was little agreement between species responses to glyphosate in incubated soil samples and in pure culture.     

长期施肥对黄土旱塬农田土壤微生物丰度的影响

以长武黄土高原农业生态试验站的长期定位试验为平台,通过荧光实时定量PCR (real-time PCR) 技术,研究不同施肥制度下的黄土旱塬农田土壤微生物群落丰度,揭示长期不同施肥制度对土壤微生物群落的影响规律.结果表明: 单施化肥处理细菌数量较CK裸地增加21％,古菌增加32％;化肥配施有机肥处理细菌数量增加37％,古菌数量增加36％.化肥配施有机肥处理显著增加了土壤细菌和古菌的丰度.30年长期施氮肥处理导致氨氧化细菌(AOB)的增幅达7.13倍,而氨氧化古菌(AOA)的增幅仅为0.2倍.AOB对施肥的响应程度较高,尤其是对氮肥具有较高的敏感性.与单施氮肥和氮肥混施有机肥处理相比,施磷肥处理显著增加了固氮酶铁蛋白和甲烷氧化菌含量,撂荒地的固氮酶铁蛋白、亚硝酸还原酶和甲烷氧化菌含量显著高于耕作土壤.结合土壤基本理化性质的相关性分析结果,pH、全氮和有机碳含量是影响土壤微生物群落丰度的重要因子.总之,长期施肥显著改变了黄土旱塬农田土壤各微生物丰度,不同施肥模式、耕作方式对微生物群落丰度具有显著影响.     

Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil

Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides information on the response of soil bacterial, archaeal and fungal communities during the degradation of three priority pollutants and contributes to a knowledge base that can inform the development of effective bioremediation strategies for contaminated sites.     

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.     

Varietal effects of eight paired lines of transgenic Bt maize and near-isogenic non-Bt maize on soil microbial and nematode community structure

A glasshouse experiment was undertaken to provide baseline data on the variation between conventional maize (Zea mays L.) varieties and genetically modified maize plants expressing the insecticidal Bacillus thuringiensis protein (Bt, Cry1Ab). The objective was to determine whether the variation in soil parameters under a range of conventional maize cultivars exceeded the differences between Bt and non-Bt maize cultivars. Variations in plant growth parameters (shoot and root biomass, percentage carbon, percentage nitrogen), Bt protein concentration in shoots, roots and soil, soil nematode abundance and soil microbial community structure were determined. Eight paired varieties (i.e. varieties genetically modified to express Bt protein and their near-isogenic control varieties) were investigated, together with a Bt variety for which no near-isogenic control was available (NX3622, a combined transformant expressing both Bt and herbicide tolerance) and a conventional barley (Hordeum vulgare L.) variety which was included as a positive control. The only plant parameter which showed a difference between Bt varieties and near-isogenic counterparts was the shoot carbon to nitrogen ratio; this was observed for only two of the eight varieties, and so was not attributable to the Bt trait. There were no detectable differences in the concentration of Bt protein in plant or soil with any of the Bt-expressing varieties. There were significant differences in the abundance of soil nematodes, but this was not related to the Bt trait. Differences in previously published soil nematode studies under Bt maize were smaller than these varietal effects. Soil microbial community structure, as determined by phospholipid fatty acid (PLFA) analysis, was strongly affected by plant growth stage but not by the Bt trait. The experimental addition of purified Cry1Ab protein to soil confirmed that, at ecologically relevant concentrations, there were no measurable effects on microbial community structure.     

古大湖湿地盐碱土壤微生物群落结构及多样性分析

以黑龙江省古大湖湿地原生、林地、耕地及湖岸盐碱土壤微生物为研究对象,基于高通量测序方法,分析4种生境类型条件下土壤细菌和真菌群落结构及多样性。结合土壤理化指标,进一步分析影响微生物群落多样性的环境因子。结果表明:细菌群落中变形菌门的相对丰度值最高,真菌群落中为子囊菌门。同一生境细菌群落多样性具有相似性,而真菌具有一定的差异;不同生境间两者均具有差异。耕地土壤和林地土壤的细菌群落多样性接近,但与湖岸土壤真菌的更相近。前两者中细菌群落多样性较高,其次为原生土壤,而湖岸土壤中的最低。耕地土壤与湖岸土壤真菌群落多样性较高,原生土壤较低,而林地土壤中最低。与真菌相比,细菌的群落多样性受土壤环境因子影响更大,其中pH值、含水量对土壤细菌和真菌群落多样性均具有显著影响。     

植茶年限对土壤微生物群落结构及多样性的影响

为探明植茶年限对土壤微生物群落结构及多样性的影响,以0、20、25、38和48年茶园土壤表层(0～20 cm)、亚表层(20～40 cm)土壤样品为研究对象,采用T-RFLP技术及qPCR方法对土壤细菌(B)、真菌(F)群落进行分析。结果表明: 植茶后土壤理化性质明显改变,随植茶年限的增加土壤有机碳、碱解氮及有效磷含量呈先升高后降低的趋势,表层土壤有机碳和全氮含量均显著高于亚表层土壤。不同植茶年限土壤细菌群落组分存在差异且多样性指数随植茶年限的增加呈下降趋势,而不同植茶年限土壤真菌群落组分差异不明显且多样性指数无显著差异。总体来看,土壤细菌群落对植茶年限的响应比真菌群落敏感。随植茶年限的增加,茶园土壤微生物群落有从F/B较低的“细菌型”向F/B较高的“真菌型”转变的趋势。