红壤稻田不同生育期土壤氨氧化微生物群落结构

以福建省红壤稻田土壤为对象,通过提取土壤总DNA,利用特异引物进行PCR(聚合酶链反应)扩增和DGGE(变性梯度凝胶电泳)并结合DNA克隆测序,研究了水稻生长过程中稻田土壤氨氧化细菌和氨氧化古菌群落结构的变化。结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌资源。水稻生长过程中土壤氨氧化细菌群落组成较为稳定,只表现出水稻生长前期(苗期、分蘖期)和中后期(孕穗期、成熟期)间存在一定差异。而土壤氨氧化古菌群落组成变化较大,在水稻生长的苗期、分蘖期、孕穗期和成熟期4个时期间均存在一定差异。在水稻生长过程中,土壤氨氧化细菌群落多样性指数无显著性变化,但氨氧化古菌群落多样性指数随水稻生长明显提高,孕穗期后才达到平稳。水稻生长前期土壤硝化势也具有显著上升趋势,孕穗期时达到最高,而后有所下降。土壤硝化势与氨氧化古菌群落多样性指数具有显著正相关性,与氨氧化细菌没有相关性。研究表明,氨氧化古菌对红壤稻田土壤硝化作用的影响程度较大,证实了氨氧化微生物尤其是氨氧化古菌在稻田土壤微生物组成及其生态系统功能中的重要性。     

渭北旱塬长期施肥试验中氨氧化细菌的多样性及群落结构分析

以中国科学院长武黄土高原农业生态试验站23 a长期施肥定位试验的土壤样品为研究对象,通过构建氨氧化细菌的amoA基因克隆文库,采用PCR-RFLP方法分析了裸地（LD）、种植不施肥（CK）、单施氮肥（N）、单施磷肥（P）和氮磷共施（NP）这5个处理条件下土壤中氨氧化细菌的多样性及其群落结构。结果表明,N处理的土壤中氨氧化细菌的Shannon-Wiene（rH′）和Margalef（dM）a指数均最高,其次是CK、NP、P,而LD处理中最低,表明长期单施氮肥后增加了土壤中氨氧化细菌的多样性和丰富度,长期种植作物后也同样会增加土壤中氨氧化细菌的多样性和丰富度,但单施磷肥和氮磷共施后土壤中氨氧化细菌的多样性和丰富度都有所降低。基于amoA基因建立的系统进化树显示,所有来自于各处理条件下土壤中氨氧化细菌的优势种群都是属于Nitrosospira和Nitrosospira-like,与Nitrosospira cluster 3聚为一组,但优势菌种在克隆文库中所占的比例不同,表明不同的施肥处理下土壤中氨氧化细菌的群落结构发生了改变。     

不同栽培条件下蔬菜塑料大棚土壤氮磷生物转化特征

为了从土壤生物学角度评价太湖地区不同栽培条件下蔬菜塑料大棚土壤肥力与质量,该研究调查了江苏省宜兴市不同蔬菜品种、不同栽培年限、不同栽培方式及不同土壤深度的蔬菜塑料大棚土壤氮磷生物学特性.结果显示,土壤脲酶活性受不同蔬菜品种影响,栽种黄瓜的土壤脲酶活性显著小于栽种茄子的土壤.随着栽培年限的增加,土壤脲酶活性与氨氧化细菌数量明显增加.在种植同一种蔬菜(黄瓜)条件下,基质槽培下理化性状与部分生物学指标优于土壤栽培.蔬菜塑料大棚土壤脲酶活性与氨氧化细菌数量随着土壤深度的增加总体呈缓慢降低的趋势,中性磷酸酶活性随土壤深度增加先升高而后降低;与相同土层的露地土壤相比,蔬菜塑料大棚土壤理化性状逐渐恶化,土壤脲酶活性和氨氧化细菌数量相对较高.这些结果可以为该地区蔬菜塑料大棚土壤的可持续利用提供初步的土壤生物学依据.     

Community composition of ammonia-oxidizing bacteria in the rhizosphere of intercropped wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.), maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.), and faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L.)

Cereal/cereal and cereal/legume intercropping systems are popular in the north, northwest, and southwest of China and often result in yield increases compared to monocropping. Rhizosphere interactions may play a significant role in the yield increases, particularly with respect to nutrient availability. The aim of this study was to investigate the effects of intercropping on N availability and community composition of ammonia-oxidizing bacteria in the rhizosphere of wheat, maize, and faba bean at different growth stages. Denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes was used to analyze the community composition of bacterial ammonia oxidizers belonging to β-proteobacteria. The results showed that intercropping with faba bean significantly increased nitrate concentrations in the rhizosphere of wheat and maize at the second sampling time (20 June) compared to monocropping or intercropping between maize and wheat. Intercropping significantly affected the community composition of ammonia-oxidizing bacteria in the rhizosphere compared to monocropping, and the effects were most pronounced in the maize/faba bean and wheat/maize intercropping systems when faba bean and wheat were at anthesis and maize was in seedling stage. In wheat/faba bean intercropping, the effects of intercropping on community composition of ammonia-oxidizing bacteria were less pronounced at the seedling stage of the two species but were significant at anthesis.     

Bacterial diversity and occurrence of ammonia-oxidizing bacteria in the Atacama Desert soil during a “desert bloom” event

The Atacama Desert, located in northern Chile, is one of the driest deserts on the Earth. However, in some years, short and sporadic rainfall in the southern end of this desert has increased the soil moisture that produces ephemeral “desert bloom”. Our goal was to assess the composition of the bacterial community and determine variations in the ammonia-oxidizing bacteria guild diversity from soils collected during the course of the “desert bloom” event. The bacterial composition from this arid soil was determined by cloning and sequencing the 16S rRNA gene. A relatively high diversity of clones belonging to 14 bacterial groups was detected. The ammonia-oxidizers showed a significantly higher diversity of amoA gene clones after the “desert bloom” than during or at the beginning of this event. All sequences obtained were related to Nitrosospira genera and environmental clones. These results suggest that the diversity of ammonia-oxidizing bacteria in this arid soil can be affected by the occurrence of “desert bloom”.     

脱氮功能菌去除市政废水中氮素的研究

为了探讨实验室筛选获得的氨氧化细菌CM-NR014和反硝化细菌CM-NRD3联合去除市政废水中氮素的应用价值,采用了两级A／O工艺进行菌株去除废水中氮素的小试实验,最后将菌株用于废水脱氮工程中。结果表明,脱氮功能菌实现了短程硝化-反硝化,氨氮去除率在98％以上,总氮去除率在75％以上,COD（化学需氧量）去除率大于90％,出水各项指标均低于城镇污水处理厂污染物排放一级（A）标准。脱氮功能菌在去除市政废水中氮素方面有很高的应用价值,可用于城镇污水处理厂提标改造等。     

海藻酸钠固定化包埋对氨氧化细菌除氨效果的影响

以海藻酸钠作为氨氧化细菌的包埋固定载体,以固定化氨氧化细菌对氨氮的去除率为主要指标,研究氨氧化细菌的最佳包埋条件,并比较了未固定细胞与固定化细胞两种处理对水中氨氮去除效果的影响。结果表明,当海藻酸钠浓度为4%、CaC l2浓度为3%、包菌量为3.0 g L-1时,氨气去除率均超过80%,达到最佳包埋条件。与未固定细胞的处理相比,固定化细胞对温度、pH的变化以及有机物、有毒物质污染等环境变化表现出更强的适应能力。     

不同品种水稻土壤氨氧化细菌和氨氧化古菌群落结构组成

本研究通过提取土壤总DNA,利用特异引物进行PCR扩增和变性梯度凝胶电泳(DGGE),研究了不同品种水稻对稻田土壤氨氧化细菌和氨氧化古菌群落结构组成的影响.结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌,且氨氧化古菌种类更多;不同品种水稻氨氧化细菌群落结构组成差异较大,其中以"天A/Km71"、"闽优1027"和"Km62/1027"3个品种相似性较高,且明显不同于其余3个品种:而氨氧化古菌群落结构组成在不同土层间表现出较大差异,其中以"天A/Km71"和"Km62/1027"的表土与根际土氨氧化古菌群落组成差异最大.研究表明不同水稻品种及土壤层次对氨氧化微生物群落结构组成具有一定影响,证明氨氧化微生物尤其是氨氧化古菌在稻田土壤生态系统中占有重要地位.     

Balanced Fertilization along with Farmyard Manures Enhances Abundance of Microbial Groups and Their Resistance and Resilience against Heat Stress in a Semi-arid Inceptisol

The impact of long-term (36-year) application of balanced fertilizers and farmyard manures (FYM) on the abundance of microbial groups (bacteria, fungi, actinomycetes, Pseudomonas, Azotobacter, ammonia-oxidizing bacteria) and their resistance and resilience against heat stress was investigated in a semi-arid Inceptisol at New Delhi, India. Surface soils from selected treatments [control, nitrogen (N), N and phosphorus (P), NP and potassium (K), NPK + FYM] under a maize crop were assessed immediately after sampling (0-day) and at 1, 14, 28, and 56 day(s) after heat stress (48 °C for 24 h). The heat stress significantly reduced the microbial groups by 20 to 80%. Recovery after stress was 60 to 100% within 56 days. Resistance and resilience of fungi and actinomycetes were greater than other groups of organisms. Ammonia-oxidizing bacteria (AOB) were found to be most sensitive with the lowest resistance index. Application of NPK + FYM was most effective in enhancing the resistance and resilience of soil microorganisms against heat stress.     

硝化抑制作用机理研究进展

总结了氨氧化细菌(AOB)和氨单加氧酶(AMO)的特性及氨(NH3)的催化氧化过程,综述了烷烃、烯烃、炔烃、芳烃、含硫(S)化合物、氮(N)杂环化合物和双氰胺(DCD)的硝化抑制作用机理。     

Effects of Silver Nanoparticles on Soil Ammonia-Oxidizing Microorganisms Under Temperatures of 25 and 5℃

The excellent bactericidal performance of silver nanoparticles (Ag NPs) has led to their wide applications, resulting in increasing concerns about their potential environmental impacts. This study evaluated the influences of different concentrations of Ag NPs (0, 1, 10, and 100 μg g^-1 dry soil) on the ammonia-oxidizing microorganisms in soil at cultivation temperatures of 25 and 5℃ for 37 d. The results showed that 1 μg g^-1 dry soil of Ag NPs had no acute effects on the ammonia-oxidizing microorganisms. However, 10 and 100 μg g^-1 dry soil of Ag NPs levels were found to significantly inhibit the activities of soil nitrification, with a decrease of 69.89% and 94.55%, respectively, at 25℃ and 61.65% and 83.79%, respectively, at 5℃ compared to the control (0 μg g^-1 dry soil of Ag NPs). These levels of Ag NPs also obviously decreased soil urease activity from about 380.47 ±0.07 (at 5℃) and 529.76 ±13.44 (at 25℃) mg N g^-1 dry soil d^-1 to 61.70 ±2.97 and 68.29 ±8.22 mg N g^-1 dry soil d^-1, respectively, after 37 d of cultivation. Quantitative polymerase chain reaction showed the abundance of ammonia-oxidizing archaea and bacteria. For the same exposure time, the effects of Ag NPs on the activities of ammonia-oxidizing microorganisms and urease decreased with decreasing temperature. The threshold concentration of Ag NPs that induced negative effects on ammonia-oxidizing microorganisms was higher at 5℃ than at 25℃. Therefore, the temperature has a major impact on the toxicity of Ag NPs to ammonia-oxidizing microorganisms and on the urease activity, with toxicity being reduced with decreasing temperature.     

Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils

Recent studies of ammonia-oxidizing archaea (AOA) suggested their significant contributions to global nitrogen cycling, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota. AOA are ubiquitous in terrestrial ecosystems, have unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirements compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers have been dramatically challenged, and the dominant nitrifying groups urgently called for re-assessment. Controversially, the relative contributions of AOA and AOB to autotrophic ammonia oxidation have been reported to vary in different soils, but ammonia substrate availability, which was largely restricted under acidic conditions, seemed to be the key driver. Theoretically predicted ammonia concentrations in acidic soils below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in ammonia-limited acidic environments. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeon, Nitrosotalea devanaterra. Here, we review the currently available knowledge concerning the history and progress in our understanding of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms of nitrification in nutrient-depleted acidic soils, present the possible mechanisms shaping the distinct niches of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in ammonia oxidation of acidic soils.     

污泥反硝化除磷-诱导磷结晶工艺中硝化池内的微生物特性

为了探究双污泥系统下反硝化除磷-诱导磷结晶工艺中硝化池内微生物特性,该文利用原位荧光杂交（fluorescence in situ hybridization,FISH）技术、电子显微镜扫描（scanning electron micrograph,SEM）方法和Image-Pro Plus（IPP）软件考察了该工艺中硝化细菌的种群结构、形态和硝化污泥微观三维结构图。结果表明：该工艺中硝化池内氨氧化细菌（ammonia-oxidizing bacteria,AOB）数量要多于亚硝酸盐氧化细菌（nitrite-oxidizing bacteria,NOB）,占总细菌的比例分别为46.2%,28.5%,且AOB处于污泥颗粒外层而NOB处于污泥颗粒内层,可能由于NOB利用AOB的代谢产物所致;工艺中硝化细菌多以球形或短杆菌为主,NOB生长时多以几个细胞形成小团聚体,而AOB生长时则形成大的团聚体;通过硝化污泥微观三维结构发现,污泥外层呈密实状而内层较疏松且有空洞存在,可能由于污泥外层和内层微生物的丰度差异、营养物质和溶解氧的浓度差异所致。此外,与传统的单污泥污水处理工艺相比,双污泥工艺明显地增强了硝化细菌的生长和富集能力。     

Improvement of media for thermophilic ammonia-oxidizing bacteria in compost

Thermophilic ammonia-oxidizing bacteria (AOB) have the potential to reduce ammonium emissions from commercial-scale animal waste composting operations. Two new media have been designed to culture and enumerate thermophilic AOB species. C-1 medium was designed to reflect compost composition. C-2 medium and CQ-2 medium were modified synthetic organic wastewater for the cultivation and enumeration of AOB, respectively. These new media have several advantages over the conventional medium. C-2 medium is effective for nitrification at 50°C, and C-1 and C-2 media support reasonable growth of thermophilic AOB. Furthermore, C-1 and CQ-2 media allow enumeration of thermophilic AOB during the composting process. This is the first report of the successful cultivation and enumeration of thermophilic AOB in compost. These results suggest the possibility of isolation and manipulation of novel thermophilic AOB species for environmental bioremediation.     

Classification of chemoautotrophic ammonia-oxidizing bacteria using pyruvate kinase genes as high resolution phylogenetic markers

Abstract

The phylogenetic relationship of β-proteobacterial ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of the genes encoding the 16S rRNA (16S rDNA) and the active site polypeptide of the ammonia monooxygenase (AmoA). However, classification of AOB with different morphotypes is not possible based solely on these markers. Pyruvate kinase (PYK), which is a key enzyme in the glycolytic pathway, functions at a primary metabolic intersection. The gene sequence of PYK is known to be a phylogenetic marker for bacteria and has been used for this purpose. The phylogenetic relationships of closely related AOB, ‘Nitrosolobus’, ‘Nitrosovibrio’ and Nitrosospira, were estimated based on pyk (PYK), a housekeeping and protein-coding gene. As a result, the pyk phylogenetic tree of the AOB showed a high resolution compared with the tree based on 16S rDNA sequences. Therefore, we conclude that analysis of the PYK gene sequences could play an important role in the in-depth classification and identification of AOB at a rank below the genus level.     

Effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on abundance and activity of ammonia oxidizers in soil

Biology and Fertility of Soils - Recent evidence from several environments suggest that besides autotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) are also able to...     

Balanced fertilization improved soil ammonia-oxidizing bacterial community in latosolic red soil

Abstract

We investigated the impact of nitrogen (N), phosphorus (P), potassium (K) (NPK) and NPK plus glucose-balanced fertilization compared with N-only fertilization on the soil pH, NH₄ ⁺, NO₃ ^?, ammonia-oxidizing bacterial community, bacterial community and function during microcosm incubation. The NPK and NPK plus glucose treatments resulted in significantly reducing soil acidification and NO₃ ^? accumulation compared with the N-only fertilization. The terminal restriction fragment size measuring 283 (Nitrosospira) and 54 bp (unidentified) were predominant in the soil ammonia-oxidizing bacterial composition for all treatments. The N-only fertilization did not change the ammonia-oxidizing bacterial community, the bacterial community composition based on terminal restriction fragment length polymorphism analysis, and the bacterial functional diversity based on Biolog EcoPlate^TM incubation. The NPK and NPK plus glucose treatments resulted in a shift in the soil ammonia-oxidizing bacterial community and bacterial community composition, and significantly increased the bacterial functional diversity (average well colour development, Richness and Shannon index). Nitrosomonas species were detected in the soil upon NPK and NPK plus glucose treatment on incubation day 9 but not on days 1 and 31. The effect of NPK treatment on the bacterial community composition was transient; a new 116 bp fragment was present on incubation day 9, but the data returned to their original values by day 31. In contrast, treatment with NPK plus glucose resulted in the appearance of a new 116 bp fragment that remained until incubation day 31. These results demonstrated that the balanced fertilization of N, P, K and glucose, plays an important role in regulating ammonia-oxidizing bacterial community quickly, and promoting nitrification functions. The results also showed the importance of balanced fertilization in reducing acidification, improving bacterial community structure and function in latosolic red soil. Therefore, optimizing the ammonia oxidation process by balanced fertilization may be helpful to reduce the loss of soil nitrogen.     

The apoplast-habitat of endophytic dinitrogen-fixing bacteria and their significance for the nitrogen nutrition of nonleguminous plants

Recent attention has been drawn to plant-growth-promoting bacteria which colonize not only the rhizosphere and the surface of roots but also the interior of roots and shoots of higher plants. The bacteria are found in the apoplast i.e. intercellular spaces and xylem vessels. These so-called endophytic bacteria are considered to be more effective in providing the host plant with nitrogen than associative rhizosphere bacteria on the root surface and appear to play an important role in biological nitrogen fixation (BNF) in nonleguminous plants. This is discussed in detail. Bacteria which have been found in the apoplast of nonleguminous plants include Azospirillum spp., Pantoea agglomerans, Acetobacter diazotrophicus, Herbaspirillum spp., Azoarcus spp. and Rhizobium spp. The significance of the apoplastic colonization of these bacteria for the nitrogen nutrition of tropical non-legumes is discussed.     

阿特拉津降解菌FM326（Arthrobacter sp.）的分离筛选、鉴定和生物学特性

采集除草剂阿特拉津污染的土壤,通过直接涂布法和富集驯化培养分离法,分别获得6株和5株能够降解阿特拉津的细菌。通过降解效率和降解动态试验,筛选到1株高效降解阿特拉津的菌株FM326,该菌株能以阿特拉津为唯一的碳源和氮源生长,培养96h后对1000mg·L-1阿特拉津降解效率达到97%。通过生理生化鉴定和16SrDNA序列分析,菌株FM326鉴定为节杆菌属（Arthrobacter sp.）细菌。该菌株表现出最适生长温度30～35℃,最适生长pH值5～9,好氧生长的生长特性。     

岩溶地貌部位对土壤微生物丰度与酶活性的影响

以中国地质科学院岩溶地质研究所桂林丫吉岩溶试验场为研究区,单氨加氧酶的编码基因amoA的部分序列作为氨氧化细菌(AOB)指示基因,利用荧光定量PCR技术,结合平板菌落计数法和土壤酶活性测定,探讨了岩溶地貌部位及土壤成因对微生物群落丰度和酶活性的影响。结果发现,受岩溶地貌部位和土壤成因的影响,土壤酶活性、土壤微生物总数在垭口、坡地、洼地呈增加的趋势,而氨氧化细菌丰度则呈现降低的趋势。结果表明,土壤氨氧化细菌丰度与真菌数呈极其显著的正相关,而与蔗糖酶活性呈极其显著负相关。