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。     

不同轮作茬口土壤细菌群落及后茬小麦产量

评估不同轮作模式的生态可持续性和作物生产力,可为调整优化种植结构提供理论依据。设置7个不同轮作作物和周期茬口处理,采用实时荧光定量PCR技术测定不同轮作茬口的土壤细菌群落丰度,采用16S rRNA基因扩增子高通量测序技术分析土壤细菌群落多样性与物种组成,并测定土壤速效养分状况和后茬小麦产量。结果表明: 与夏玉米茬口相比,不同轮作周期夏花生或夏大豆茬口处理降低了土壤有机碳、无机氮和速效钾含量,显著增加了土壤有效磷含量。不同轮作周期夏花生或夏大豆茬口处理的土壤细菌16S rRNA基因拷贝数显著降低,而群落丰富度和多样性有所增加。不同轮作作物显著改变了土壤细菌群落结构和物种组成。与夏玉米茬口相比,不同轮作周期夏大豆茬口显著增加了后茬冬小麦籽粒千粒重和产量。综上,不同轮作周期夏花生或夏大豆茬口有利于增加土壤有效磷含量和细菌群落多样性,显著改变土壤细菌群落结构,其中,夏大豆茬口对后茬冬小麦产量形成具有积极作用。     

Sulfonate desulfurization in Rhodococcus from wheat rhizosphere communities

Organically bound sulfur makes up about 90% of the total sulfur in soils, with sulfonates often the dominant fraction. Actinobacteria affiliated to the genus Rhodococcus were able to desulfonate arylsulfonates in wheat rhizospheres from the Broadbalk long-term field wheat experiment, which includes plots treated with inorganic fertilizer with and without sulfate, with farmyard manure, and unfertilized plots. Direct isolation of desulfonating rhizobacteria yielded Rhodococcus strains which grew well with a range of sulfonates, and contained the asfAB genes, known to be involved in sulfonate desulfurization by bacteria. Expression of asfA in vitro increased >100-fold during growth of the Rhodococcus isolates with toluenesulfonate as sulfur source, compared with growth with sulfate. By contrast, the closely related Rhodococcus erythropolis and Rhodococcus opacus type strains had no desulfonating activity and did not contain asfA homologues. The overall actinobacterial community structure in wheat rhizospheres was influenced by the sulfur fertilization regime, as shown by specific denaturing gradient gel electrophoresis of PCR amplified 16S rRNA gene fragments, and asfAB clone library analysis identified nine different asfAB genotypes closely affiliated to the Rhodococcus isolates. However, asfAB -based multiplex restriction fragment length polymorphism (RFLP)/terminal-RFLP analysis of wheat rhizosphere communities revealed only slight differences between the fertilization regimes, suggesting that the desulfonating Rhodococcus community does not specifically respond to changes in sulfate supply.     

水仙根围细菌群落组成

【目的】探究水仙(Narcissus tazetta var.chinensis roem)土壤根围微生物组成及其与水仙生长特性的相关性。【方法】分别采集崇明水仙及漳州水仙健康植株根围土壤,抽提根围土壤中细菌总DNA并纯化,扩增16S r RNA基因并进行高通量测序分析比较不同产地植株根围细菌的组成与多样性。【结果】崇明水仙和漳州水仙根围微生物组成的主要细菌门类相同,均为12种,其中,优势菌为Proteobacteria、Chloroflexi、Bacteroidetes和Acidobacteria。根围微生物OTUs(Operational taxonomic units)分布及主成分分析(PCA)表明崇明水仙和漳州水仙根围微生物组成有较大差异,且Planctomycetales和Xanthomonadales在崇明水仙根围分布显著多于漳州水仙,而Chloroflexales和Chlorobiales在漳州水仙根围的丰度较高。【结论】根围微生物的组成,如厌氧氨氧化细菌、机会致病菌和光合细菌的多样性与丰度可能与水仙生长特性有密切的关系。     

茶园根际土壤细菌群落结构及多样性

【背景】茶园根际土壤的细菌群落结构与茶园生境土壤营养循环密切相关,其组成及多样性可以作为健康茶园的一个生物指标。【方法】采用PCR．变性梯度凝胶电泳（PCR—DGGE）分子指纹图谱技术,检测安溪铁观音种植区不同海拔茶园根际土壤样本的细菌群落结构,利用Shannon．Wiener多样性指数分析其多样性,采用非加权组平均法进行聚类分析得到其分布特征,利用蒙特卡罗检验和冗余分析分别揭示影响细菌群落分布的环境因子及细菌群落分布和环境变量之间的关系。【结果】茶园根际土壤细菌的DGGE结果显示,检测到的14种主要细菌中有11种细菌是不可培养的,3种细菌是可培养的,分别属于根瘤菌属、中华根瘤菌属和苍白杆菌属。聚类分析得到,同一海拔梯度茶园根际土壤细菌群落结构相似。Shan-non—Wiener多样性指数分析表明,400m海拔处茶园根际土壤细菌群落多样性最高。蒙特卡罗检验分析得到环境因子协同作用对茶园根际土壤细菌群落结构贡献率为59．6％。冗余分析显示,茶园根际土壤细菌群落结构与海拔密切相关。【结论与意义】茶园根际土壤细菌群落结构分布与海拔梯度密切相关,考虑不同海拔高度土壤细菌群落对茶园营养循环的影响,在铁观音的健康栽培和管理过程中具有重要意义。     

Assessment of differences in ascomycete communities in the rhizosphere of field-grown wheat and potato

To assess effects of plant crop species on rhizosphere ascomycete communities in the field, we compared a wheat monoculture and an alternating crop rotation of wheat and potato. Rhizosphere soil samples were taken at different time points during the growing season in four consecutive years (1999-2002). An ascomycete-specific primer pair (ITS5-ITS4A) was used to amplify internal transcribed spacer (ITS) sequences from total DNA extracts from rhizosphere soil. Amplified DNA was analyzed by denaturing gradient gel electrophoresis (DGGE). Individual bands from DGGE gels were sequenced and compared with known sequences from public databases. DGGE gels representing the ascomycete communities of the continuous wheat and the rotation site were compared and related to ascomycetes identified from the field. The effect of crop rotation exceeded that of the spatial heterogeneity in the field, which was evident after the first year. Significant differences between the ascomycete communities from the rhizospheres of wheat in monoculture and one year after a potato crop were found, indicating a long-term effect of potato. Sequencing of bands excised from the DGGE gels revealed the presence of ascomycetes that are common in agricultural soils.     

Evolution of wild emmer wheat and crop improvement

Allotetraploid wild emmer wheat, Triticum dicoccoides (TD) 2n = 28, the progenitor of most cultivated bread wheat, is an ecological specialist and excellent model organism for advancing evolutionary theory, wheat evolution, and wheat improvement. The center of origin and diversity of TD is northeastern Upper Galilee and the Golan. Elsewhere in the Fertile Crescent, it occurs in semi-isolated and isolated populations. The genetic structure is generally an “archipelago.” Regional and localgenetic patterns are partly or largely adaptive at the protein and DNA levels, both at coding and noncoding genomes, correlated with and predictable by environmental abiotic and biotic stresses. TD is a rich, mostly untapped, genetic resource for improving cultivated wheat, harboring drought, salt, mineral, and disease resistances, grain proteins, and with high variation in photosynthetic yield. TD was chromosomally mapped with 549 molecular markers and 70 QTLs for 11 traits of agricultural importance and domestication. Prospects include sequencing its genome; including 80% repeat elements for structural, functional, and regulatory polymorphisms, epigenetics, and genetic resources for wheat improvement. TD is affected by global warming both phenotypically (advancing flowering time) and genotypically (genetic erosion, SSR allelic turn-over, and novel drought resistant alleles). Hence, it should be conserved in situ and ex situ, to safeguard the arguably best source for wheat improvement and future food production in an exploding world population.     

不同品种酿酒葡萄根围、叶围微生物群落结构特点解析

【目的】了解不同品种酿酒葡萄根围、叶围细菌群落结构。【方法】以不同品种酿酒葡萄根围、叶围样品为分析材料,采用末端限制性片段长度多态性(T-RFLP)技术研究根围、叶围细菌群落结构,并对细菌群落多样性进行分析。【结果】不同品种葡萄根围微生物优势菌群为变形菌门,不同品种葡萄叶围微生物优势菌群为放线菌目。根围Simpson指数大小顺序为白福尔琼瑶浆白诗南赛美蓉白玉霓米勒长相思,Shannon指数与Simpson指数基本保持一致。叶围Simpson指数最大的为白诗南,最小的为米勒,与Shannon指数基本吻合。【结论】葡萄细菌群落结构综合多样性指数和品种以及定殖部位密切相关。     

轮套作对黄瓜根际土壤细菌种群的影响

以黄瓜为试材,采用PCR-DGGE技术研究了小麦、大豆、毛苕子、三叶草和苜蓿与黄瓜轮作及大蒜、毛葱与黄瓜套作对黄瓜根际土壤细菌种群的影响.结果表明:轮套作对黄瓜根际土壤细菌种群的种类、数量和黄瓜产量具有一定的影响,提高了土壤细菌种群多样性指数、均匀度指数和黄瓜产量.对DGGE条带进行测序的结果表明,它们大多与不可培养的细菌种属具有较高的同源性,大多为鞘氨醇杆菌属（Sphingobacterium）和变形细菌纲（Proteobacteria）, High bacterium G+C只在以毛葱为套作作物的黄瓜根际中出现.不同轮套作中细菌种群多样性随黄瓜生育期的变化而变化,在盛瓜期达最高值.以小麦为轮作作物和以毛葱为套作作物的黄瓜轮套作栽培模式最佳.     

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.     

Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains

Positive associations between alpine cushion plants and other species have been extensively studied. However, almost all studies have focused on the associations between macrofauna. Studies that have investigated positive associations between alpine cushion plants and rhizospheric microbes have been limited to the vegetation growing season. Here, we asked whether the positive effects that alpine cushion plants confer on rhizospheric microbe communities vary with seasons. We assessed seasonal variations in the bacterial diversity and composition in rhizosphere of two alpine cushion plants and surrounding bare ground by employing a high throughput sequencing method targeting the V3 region of bacterial 16S rRNA genes. Soil properties of the rhizosphere and the bare ground were also examined. We found that cushion rhizospheres harbored significantly more C, N, S, ammonia nitrogen, and soil moisture than the bare ground. Soil properties in cushion rhizospheres were not notably different, except for soil pH. Bacterial diversities within the same microhabitats did not vary significantly with seasons. We concluded that alpine cushion plants had positive effects on the rhizospheric bacterial communities, even though the strength of the effect varied in different cushion species. Cushion species and the soil sulfur content were probably the major factors driving the spatial distribution and structure of soil bacterial communities in the alpine communities dominated by cushion plants.     

Changes of bacterial communities in the rhizosphere of sugarcane under elevated concentration of atmospheric CO2

It is believed that climate change will influence most of interactions that sustain life on Earth. Among these, the recruitment exerted by plants in their roots vicinity can change, leading to differential assemblages of microbiomes in the rhizosphere. We approached this issue analyzing the variations in the composition of bacterial communities in the rhizosphere of sugarcane cultivated under two concentrations of atmospheric CO₂ (350 or 700 ppm). In addition to the analysis of bacterial community, the use of DNA‐SIP allowed the comparison of bacterial groups assimilating roots exudates (based on ¹³C‐labeled DNA) in both conditions, in a period of 8 days after the CO₂ pulse. The separation of ¹³C‐DNA indicated the low but increasing frequency of labeling in the rhizosphere, as averages of 0.6, 2.4 and 5.0% of total DNA were labeled after 2, 4, and 8 days after the ¹³CO₂ pulse, respectively. Based on large‐scale sequencing of the V6 region in the gene 16S rRNA, we found an increase in the bacterial diversity in the ¹³C‐DNA along the sampling period. We also describe the occurrence of distinct bacterial groups assimilating roots exudates from sugarcane cultivated under each CO₂ concentration. Bacilli, Gammaproteobacteria, and Clostridia showed high affinity for the C‐sources released by sugarcane under 350 ppm of CO₂, while under elevated concentration of CO₂, the assimilation of roots exudates was prevalently made by members of Bacilli and Betaproteobacteria. The communities became more similar along time (4 and 8 days after CO₂ pulse), in both concentrations of CO₂, electing Actinobacteria, Sphingobacteriia, and Alphaproteobacteria as the major cross‐feeders on sugarcane exudates. In summary, we described the bacterial groups with higher affinity to assimilate roots exudates in the rhizosphere of sugarcane, and also demonstrated that the rhizosphere community can be differentially assembled in a future scenario with increased contents of CO₂.     

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac

The bacterial community and diversity in healthy and diseased konjac rhizosphere soils with different ages of continuous cropping were investigated using next-generation sequencing. The results demonstrated that the number of years of continuous cropping significantly altered soil bacterial community and diversity. Soil bacterial Shannon diversity index and Chao 1 index decreased with the increasing cropping years of konjac. After 1 year of cropping, the soil exhibited the highest bacterial relative abundance and diversity. Of the 44 bacterial genera (relative abundance ratio of genera greater than 0.3%), 14 were significantly affected by the duration of continuous cropping and plant status. With increasing continuous cropping, Alicyclobacillus decreased, while Achromobacter, Lactobacillus, Kaistobacter, Rhodoplanes increased after 3 years continuous cropping. Continuous cropping altered the structure and composition of the soil bacterial community, which led to the reduction in the beneficial bacteria and multiplication of harmful bacteria. These results will improve our understanding of soil microbial community regulation and soil health maintenance in konjac farm systems.     

Field response of rice paddy crop to Azospirillum inoculation: physiology of rhizosphere bacterial communities and the genetic diversity of endophytic bacteria in different parts of the plants

The response of rice plants to the application of inoculant containing two Azospirillum brasilense strains was studied under field conditions. The experiment was performed as three treatments with four replicates in randomized complete blocks arranged as plots of 60 m² in an area on a Vertic Argiudol soil type in the province of Entre Ríos, Argentina. The bacterial rhizosphere community and also the diazotrophic isolates obtained from control and inoculated rice plants were analyzed in relation to their physiology and biological nitrogen fixation (BNF). The MPN of diazotrophs in the rhizosphere varied during the ontogenic cycle. The patterns of distribution of the microbial physiological activities obtained by principal component analysis of community-level physiological profiles (CLPP) showed differences in the utilization of carbon sources by the rhizosphere communities among treatments. Although the analyses of DGGE 16S and nifH profiles have not indicated that the inoculation influenced the genetic diversity of bacterial communities among treatments, they revealed that the banding profiles were altered in different parts of the rice plant by each Azospirillum inoculation treatment. These observations suggest that physiological responses of plant tissues to the inoculation may have occurred. According to agronomic parameters of each treatment, the Azospirillum inoculation increased aerial biomass at the tillering and grain-filling stages. Although the N content accumulated in rice plants increased by 16 and 50 kg ha^?1, the BNF contribution could not be estimated under our experimental conditions by the ¹⁵N balance technique. Based on this field inoculation experiment to rice plants, it is noteworthy that our data suggest that due to Azospirillum inoculation the increase of total N accumulated in rice plants could be a tool to help farmers to improve production and maintain high input of plant residues, providing more organic matter to the soil and guaranteeing sustainability of the system.     

Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.     

Plant genotype, micronutrient fertilization and take-all infection influence bacterial populations in the rhizosphere of wheat

The relationship between micronutrient efficiency of four wheat (Triticum aestivum L.) genotypes, tolerance to take-all disease (caused by Gaeumannomyces graminis (Sacc.) Arx and Olivier var. tritici Walker), and bacterial populations in the rhizosphere was tested in soil fertilized differentially with Zn and Mn. Plant growth was reduced by Mn or Zn deficiency and also by take-all. There was an inverse relationship between micronutrient efficiency of wheat genotypes when grown in deficient soils and the length of take-all lesions on roots (efficient genotypes had shorter lesions than inefficient ones). In comparison to the rhizosphere of control plants of genotypes Aroona and C8MM receiving sufficient Mn and Zn, the total numbers of bacterial cfu (colony forming units) were greater in the rhizosphere of Zn-efficient genotype Aroona under Zn deficiency and in Mn-efficient genotype C8MM under Mn deficiency. These effects were not observed in other genotypes. Take-all decreased the number of bacterial cfu in the rhizosphere of fully-fertilized plants but not of those subjected to either Mn or Zn deficiency. In contrast, the Zn deficiency treatment acted synergistically with take-all to increase the number of fluorescent pseudomonads in the rhizosphere. Although numbers of Mn-oxidising and Mn-reducing bacteria were generally low, take-all disease increased the number of Mn reducers in the rhizosphere of Mn-efficient genotypes Aroona and C8MM. Under Mn-deficiency conditions, the number of Mn reducers in the rhizosphere increased in Aroona but not in C8MM wheat. The results suggest that bacterial microflora may play a role in the expression of Mn and Zn efficiency and tolerance to take-all in some wheat genotypes.     

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression

The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature‐sensitive and slow‐growing bacteria have a disadvantage. The results also pointed to a potential role of slow‐growing, heat‐tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.     

健康与凋萎病杨梅树体及根围菌群的差异

凋萎病是制约杨梅产业发展的严重病害.为了有效防控凋萎病,本研究分析了杨梅健康和感染凋萎病树体各部位及根表土和根围土中细菌和真菌群落的丰富度与多样性的差异.结果 表明:与健康树相比,病树根围土、根表土、根、枝干、枝皮和叶片的细菌和真菌丰富度均发生了显著变化,其中,根表土细菌和枝皮内真菌的丰富度和多样性均显著降低,而枝皮内...     

Use of cluster and discriminant analyses to compare rhizosphere bacterial communities following biological perturbation

We present an approach to comparing the diversity and composition of bacterial communities from different habitats and for identifying which members of a community are most affected by an introduced bacterium. We use this method to explore both previously published and new data from field and growth chamber experiments in which we isolated heterotrophic bacteria from samples of root-free soil, roots of nontreated soybean seedlings, and from the roots of soybean seedlings grown from Bacillus cereus UW85nl—treated seeds. We characterize bacterial isolates for 40 physiological attributes, and grouped the isolates hierarchically using two-stage density-linkage cluster analysis. Multivariate analysis of variance and discriminant analysis of the relative frequencies of the clusters in the soil and rhizosphere habitats were then used to determine whether there were differences among the bacterial communities from the various habitats, and which of the clusters were most useful in discriminating among the communities. We used rarefied estimates of richness as a measure of community diversity in the various habitats. Introduction of UW85n 1 affected the composition and/or diversity of rhizosphere communities in three of four experiments. Present address: Department of Environmental Science, Policy and Management, 108 Hilgard Hall, University of California, Berkeley, CA 94720 Correspondence to: G.S. Gilbert.