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.     

Earthworm communities in grasslands and horticultural soils

 In a survey of 42 farm sites, comprising grassland and two types of horticultural farms (growing vegetables or flower bulbs), earthworm communities were sampled by hand-sorting and a number of soil physico-chemical characteristics recorded. For heavy metals the availability in the soil solution was estimated based on the measured absolute content. Abundance, biomass and species richness were significantly higher in grassland soils than in horticultural soils, and within the horticultural farms significantly higher in vegetable than in flower-bulb farms. No epigeic species were found in horticultural soils. The differences between the various farm types were probably related to the intensity of management practices, such as soil tillage, harvesting and crop protection measures, that result in less soil organic matter of lower quality. The data from the grassland farms were analyzed in conjunction with the physico-chemical soil characteristics, applying canonical correspondence analysis. Community parameters such as species richness and diversity apparently were not related to soil characteristics, but an appreciable part of the variation in abundance and biomass of several individual species could be explained by factors such as lutum content (particles <16 μm), pH, bio-availability of metal ions and geographical position of the sample site. It is concluded that repeated surveys of this type may become a valuable tool for monitoring soil quality. Received: 16 March 2000     

Amino acid and peptide dynamics in horticultural soils under conventional and organic management strategies

Purpose  

Free amino acids (FAAs) and peptides, and dissolved organic nitrogen (DON) comprise key pools in terrestrial soil carbon (C) and nitrogen (N) cycles. A comparative study of organic and conventional arable farming systems was conducted in Shanghai, China to determine the influence of management practices on characterization of AA and peptide dynamics.     

Trichoderma communities in soils from organic, sustainable, and conventional farms, and their relation with Southern blight of tomato

The objectives of this research were to investigate the relationship between propagule numbers and genetic diversity of Trichoderma species and Southern blight of tomato caused by soilborne plant pathogen Sclerotium rolfsii in soils with long-term organic, sustainable, and conventional farms. Dilution plating was use to quantify the propagule numbers of Trichoderma, denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis were used to identify Trichoderma species, and greenhouse assay were conducted for soil suppressiveness to Southern blight. The propagule numbers of Trichoderma tend to be higher in soils from conventional farms. There was no clear separation for the propagule numbers of Trichoderma based on different management systems using canonical correspondence analysis (CCA). However, there was general separation for total microbial communities based on organic and conventional management systems using CCA. That suggests that the difference of soil suppressiveness to disease from organic, sustainable, and conventional farms is due to the difference of the total microbial diversity but not directly due to the Trichoderma populations in each farming system. The propagule numbers of soil Trichoderma did not significantly correlate with the diseases suppressiveness, although individual species of Trichoderma harzianum was shown to be related to disease suppressiveness. Moreover, several Trichoderma species were found in the soil tested based on DGGE and DNA sequence analysis. Trichoderma hamatum, T. harzianum, Trichoderma virens, and Trichoderma erinaecem were the most abundant species in tested soil.     

Soluble organic nitrogen pools in greenhouse and open field horticultural soils under organic and conventional management: A case study

The aim of this study was to investigate the influence of four different horticultural management practices in open field and in greenhouse conditions under organic and conventional cultivation on the amount of soluble organic nitrogen (SON) present in the soil. Soils used in greenhouses and open field cultivation were sampled in Shanghai, China, where organic farming has been conducted for 3 years or conventional faming has been continued in the same area. The amounts of SON, nitrate (NO₃^?) and ammonium (NH₄⁺) were greater in the greenhouse soils than those under open field cultivation, which indicated a higher degree of soil management was imposed under greenhouse conditions. Greenhouse cultivation is also known to accelerate the turnover of SON in the soils, which may explain the significantly higher amounts of SON present in these soils. Organic farming, which does not use artificial fertilizers and pesticides, also resulted in significantly higher amounts of SON (average 42.10 mg kg^?1) compared with soils under conventional faming (24.59 mg kg^?1). The reasons for the observed differences in pool sizes of soluble inorganic nitrogen (SIN) and NO₃^? in the greenhouse soils and the open fields include (a) the heavy application of both complex fertilizer and organic fertilizer that exceeded crop requirements and (b) warmer temperatures and moist soils in the greenhouses, which are likely to lead to greater rates of N cycling compared with the open field soils. These results suggest that SON may be an important source of N in all horticultural systems, representing a pool of labile N readily available for plant growth. However, its concentration is less sensitive to different management practices than SIN. In contrast to SON, the total soluble nitrogen and inorganic N (SIN) pools varied widely with the different management practices although they were dominated by NO₃^? in all treatments. Soil organic N was positively related to dissolved organic carbon and NO₃^? contents. This relationship indicates that NO₃^? and dissolved organic matter play a key role in the retention of SON in soil.     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

Dried soil samples from many sources have been stored in archives world-wide over the years, but there has been little research on their value for studying microbial populations. Samples collected since 1843 from the Broadbalk field experiment on crop nutrition at Rothamsted have been used to document changes in the structure and composition of soils as agricultural practices evolve, also offering an invaluable record of environmental changes from the pre- to post-industrial era in the UK. To date, the microbial communities of these soils have not been studied, in part due to the well-documented drop in bacterial culturability in dried soils. However, modern molecular methods based on PCR amplification of DNA extracted directly from soil do not require bacterial cells to be viable or intact and may allow investigations into the legacy of bacteria that were present at the time of sample collection.

In a preliminary study, to establish if dried soils can provide a historical record of bacterial communities, samples from the Broadbalk soil archive dating back to 1868 were investigated and plots treated with either farmyard manure (FYM) or inorganic fertilizer (NPK) were compared. As anticipated, the processes of air-drying and milling greatly reduced bacterial viability whilst DNA yields declined less and may be preserved by desiccation. A higher proportion of culturable bacteria survived the archiving process in the FYM soil, possibly protected by the increased soil organic matter. The majority of surviving bacteria were firmicutes, whether collected in 2003 or in 1914, but a wide range of genera was detected in DNA extracted from the samples using PCR and DGGE of 16S rRNA genes. Analysis of DGGE band profiles indicated that the two plots maintained divergent populations. Sequence analysis of bands excised from DGGE gels, from a sample collected in 1914, revealed DNA from - and β-proteobacteria as well as firmicutes. PCR using primers specific for ammonia oxidizing bacteria showed similar band profiles across the two treatments in recently collected samples, however older samples from the NPK plot showed greater divergence. Primers specific for the genus Pseudomonas were designed and used in real-time quantitative PCR to indicate that archived soil collected in 1868 contained 10-fold less pseudomonad DNA than fresh soil, representing around 10⁵ genomes g⁻¹ soil. Prior to milling, dramatically less pseudomonad DNA was extracted from recently collected air-dried soil from the NPK compared to the FYM plot; otherwise, the two plots followed similar trends. Overall bacterial abundance, diversity and survival during the archiving process differed in the two soils, possibly due to differences in clay and soil organic matter content. Nevertheless, the results demonstrate that air-dried soils can protect microbial DNA for more than 150 years and offer an invaluable resource for future research.     

黄土高原不同植物群落土壤团聚体中有机碳和酶活性研究

以黄土高原延河流域森林区3种典型植物群落为研究对象,研究了3种植物群落土壤团聚体中有机碳的含量、组分及土壤酶活性,分析了有机碳与酶活性的关系。结果表明:(1)3种植物群落,土壤团聚体各种形态有机碳和酶活性均表现为0~10 cm土层含量高于10~20 cm土层,辽东栎群落0~10 cm土层土壤多酚氧化酶活性却低于10~20 cm土层。(2)土壤团聚体有机碳含量在植物群落间表现为:辽东栎群落人工刺槐群落狼牙刺群落,酶活性在植被群落间的高低表现则不一致。土壤有机碳含量和酶活性在团聚体间均表现为随团聚体粒级的增大而增大,或先增大再减小的趋势。(3)蔗糖酶、纤维素酶以及β-D葡糖苷酶活性与各种形态有机碳均呈显著的正相关关系,多酚氧化酶和过氧化物酶与有机碳含量相关性不显著。(4)辽东栎群落和狼牙刺群落土壤团聚体蔗糖酶、纤维素酶、以及β-D葡糖苷酶活性在团聚体中表现为:|0.25 mm团聚体||2~0.25 mm团聚体||5~2 mm团聚体||5 mm团聚体|,其多酚氧化酶和过氧化物酶以及人工刺槐群落各种土壤酶活性均表现为2~0.25 mm粒级团聚体中最大。(5)β-D葡糖苷酶活性增大,能促进土壤各种有机碳含量增加;土壤蔗糖酶活性和β-D葡糖苷酶活性的提高有助于土壤活性有机碳含量增加;土壤多酚氧化酶活性的增大,有利于土壤腐殖质碳的积累。     

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

Abstract

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity.     

Rhizosphere effects on functional stability of microbial communities in conventional and organic soils following elevated temperature treatment

The resistance and resilience of soil function may be increased through selection of crops and organic matter inputs. Soil from paired organic or conventional plots was left unplanted or used to grow barley. Substrate induced respiration (SIR) and community level physiological profiles (CLPP) were significantly different in both planted and unplanted systems and in conventional and organically-managed farming systems with no interaction; planted and organic systems had higher SIR. Following heat treatment (30 min at 70 °C), CLPP of planted and unplanted soils in both farming systems changed; a small short-lived decline in SIR only occurred in the planted soils. Differences in the response of these microbial communities to stress may be related to the relative proportions of active and dormant organisms; an increase in functional diversity did not necessarily reflect changed soil function.     

Chemical properties,microbial biomass,and activity differ between soils of organic and conventional horticultural systems under greenhouse and open field management: a case study

Purpose  

Increasing soil organic matter content is important in improving soil fertility; however, conventional farming practices generally lead to a reduction in such organic material. A comparative study of organic and conventional arable farming systems was conducted in Shanghai, China, to determine the influence of management practices on soil chemistry, microbial activity, and biomass. Soils used in greenhouses and open field cultivation were obtained from plots subjected to organic farming methods for 3 years or from conventionally farmed fields in the same area.     

A DGGE analysis shows that crop rotation systems influence the bacterial and fungal communities in soils

A better understanding of the relationships among different cropping systems, their effects on soil microbial ecology, and their effects on crop health and productivity is necessary for the development of more efficient, sustainable crop production systems. We used denaturing gradient gel electrophoresis (DGGE) to determine the impacts of crop rotations and crop types on bacterial and fungal communities in the soil. The communities of bacterial 16S rRNA genes and fungal 18S rRNA genes were analyzed in experimental field plots that were kept under 4 different crop rotation systems from 1999 to 2008 (continuous cabbage (Brassica oleracea var. capitata L.), cabbage–lettuce (Lactuca sativa L.) rotation, cabbage–radish (Raphanus sativus L. var. longipinnatus L.H. Bailey) rotation, and a 3-year crop rotation). A principal component analysis (PCA) and a canonical correspondence analysis (CCA) revealed that both the bacterial and fungal communities in bulk soils were influenced by the crop rotation systems. However, the primary factors influencing each community differed: bacterial communities were most affected by soil properties (especially carbon content), while fungal communities were influenced most strongly by rotation times. To elucidate factors that may cause differences in crop rhizosphere microbial communities, the microbial communities in the harvested cabbage rhizospheres were also analyzed. The results suggest that the fungal communities in bulk soil are related to the rhizosphere fungal communities. Our present study indicates that the microbial communities in bulk and rhizosphere soils could be managed by crop rotation systems.     

Comparative study of the microbial diversity of bulk paddy soil of two rice fields subjected to organic and conventional farming

Two adjacent paddies of an experimental rice field, subjected to organic and conventional farming, were characterized aiming the comparative assessment of microbiological variations occurring in the bulk paddy soil over the rice cycle. This study comprehended the simultaneous characterization of general physicochemical soil properties [total carbon and nitrogen, pH (H₂O and KCl), C:N ratio and water content], biochemical properties [enzymatic activities and Community Level Physiological Profiles (CLPP)], the estimation of cultivable organisms (enumeration of fast growing heterotrophic bacteria, actinomycetes and fungi) and the assessment of bacterial diversity using a culture-independent method (PCR-DGGE fingerprinting). The linkage of the parameters measured was analysed by canonical correspondence analysis (CCA).CCA ordination plots of the CLPP showed a similar pattern of microbial functional activity in both agronomic management systems, except in June. Enzymatic activity, water content and fungi counts were the main factors affecting the observed CLPP time variation. Such a variation was not expressed by the Shannon and evenness indices, which did not evidence significant differences in the bacterial and functional diversity between or within farming type over the analysed period. The cluster and CCA analyses of the DGGE profiles allowed the distinction of the bacterial communities of both paddies, with temporal variations being observed in the organically managed field but not in the conventional paddy. Enzymatic activity, pH and molinate content were the factors which most contributed to the observed variations. Altogether these results underline the functional redundancy of the rice paddy soil and evidence the temporal variations on the metabolic activity of soil, irrespective of farming type.     

长期施肥对黑土农田土壤微生物群落的影响

基于中国科学院海伦农业生态试验站长期定位试验区,应用实时荧光定量PCR(Real-time PCR)和变性梯度凝胶电泳(DGGE)技术研究了无施肥(NF)、单施N、P化肥(NP)以及化肥配施有机猪粪肥(NPM)等3种长期施肥措施对黑土区玉米田土壤微生物群落密度和结构的影响.Real-time PCR方法定量NF、NP及NPM措施土壤细菌群落基因组DNA质量分别为381、1 351和1 773 ng g-1干土,真菌群落基因组DNA质量分别113.3、127.3和20.6 ng g-1干土,真菌与细菌的比率分别为0.31、0.09和0.01,NPM措施显著低于另两种施肥方式(p＜0.05).DGGE方法研究表明,NP和NPM措施不能改善土壤细菌和真菌群落的多样性、均匀性及优势菌优势程度;但主成分分析结果显示NP和NPM措施均可改变土壤细菌和真菌群落的构成,且真菌群落的变化更为显著;聚类分析结果显示NP和NPM措施下细菌群落结构较相近,其相似系数为0.89,真菌群落中NP措施与NF措施相近,相似系数为0.63,高于NP与NPM措施的相似系数0.51.上述结果表明有机猪粪肥的长期施用可以显著降低黑土农田土壤真菌与细菌的比率,且明显地改变土壤细菌和真菌群落的结构.     

Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes

We studied the effects of the application of organic (OM) and inorganic fertilizer (CF) on soil protease activity and proteolytic bacterial communities in rhizosphere and bulk soil on an experimental lettuce field in Hokkaido, Japan. The protease activity always was higher in soils of the OM than with the CF treatment, and also higher in the rhizosphere than in the bulk soil. We analyzed proteolytic bacterial communities by denaturing gradient gel electrophoresis (DGGE) of the alkaline metalloprotease (apr) and neutral metalloprotease (npr) genes. Most apr forms detected were closely related to apr of Pseudomonas fluorescens, and all npr variants closely resembled the gene of Bacillus megaterium. These results were consistent with findings from tests using cultured bacterial communities, indicating a high specificity of our PCR-DGGE for amplifying apr and npr genes. The community compositions of proteolytic bacteria were assessed by principal component analysis of the DGGE profiles. There were significant differences in the effects of CF and OM on the community compositions of apr- and npr-expressing bacteria, and the communities of the two types of bacteria played different roles in rhizosphere and bulk soil. We found significant correlations between the protease activity and the communities of the two types of bacteria. The results indicate that different proteolytic bacteria release different amounts or activities of protease, and that the composition of proteolytic bacterial communities may play a major role in determining overall soil protease activity.     

Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle

Overwintering cattle outdoors causes soil surface disturbance, substantial increases of soil N_tot, C_org, and P and a shift in pH to alkaline levels. Since fungi predominate in unfertilized soils with acidic pH and have filamentous hyphae, we hypothesized that changes caused by overwintering cattle outdoors (trampling, excreta returns, and changes in soil chemistry) will lead to suppressed species richness, lower biomass, and alter the structure of fungal communities. The research was conducted on an upland pasture used more than 10 years for cattle overwintering. Both culture-dependent and -independent methods were used for the determination of either fungal species composition (cultivation; DGGE) or biomass (numbers of CFU; concentration of fungal PLFA marker 18:2ω6,9). Soils under three different levels of cattle disturbance (S - severe, M - moderate, C - no disturbance/control) were investigated during three subsequent years. In addition, the DGGE analysis of soils was completed by comparison with analysis of fresh cattle excrements (Ex). The composition of fungal communities showed significantly higher richness and a substantial shift in species composition in cattle-disturbed soils (S, M) in comparison to the non-disturbed soil (C). The number of separated DGGE bands was significantly higher in S (30.67 ± 1.63; mean ± SD) and M (25.50 ± 1.64) soils than in the C soil (19.33 ± 1.75). Sequencing of typical bands revealed common fungal genera - Alternaria, Penicillium, Fusarium, Rhizopus, Isaria, and Metarhizium. Profiles of the S soil were enriched by bands of rumen-born anaerobic fungi (Neocallimastix, Cyllamyces) occurring mainly in profiles of excrements, where relatively low band richness (14.33 ± 1.15) was observed. The increasing level of cattle disturbance induced an increase in the biomass of complex fungal community over the three-year experimental period from 3.39 ± 2.11 (mean ± SD) nmol of fungal PLFA per gram of the C soil to 5.87 ± 3.16 in the M soil and 9.21 ± 4.69 in the S soil. Concentrations of soil N_tot and C_org were evaluated as the parameters significantly correlating with biomass as well as composition of the fungal community.     

Effect of organic and mineral fertilizers on soil respiration and enzyme activities of two Mediterranean horticultural soils

The effects of municipal food waste compost addition and mineral fertilization on selected soil microbiological activities were investigated during 3 years of reiterated treatments on two Mediterranean agricultural soils with different organic carbon content. Compost at 15, 30 and 45 t ha⁻¹ (dry matter), mineral (NPK) fertilizers and combined fertilizers with 15 t ha⁻¹ of compost plus two reduced doses of mineral N were applied to both soils. At both sites, organic amendment increased soil respiration, fluorescein diacetate hydrolysis, phosphatase and arylsulphatase activities. The differences in soil microbial activities among treatments, found after 3 years of repeated treatments, were attributable to the variations of soil organic C content and to the impact of soil tillage. Our results show that, in Mediterranean intensively cultivated agroecosystems, annual organic amendments improve the microbial activity of soil and produce cumulative effects, suggesting the usefulness of repeated high-rate compost applications.