接种溶磷真菌对玉米和大豆根际细菌群落结构多样性的影响

Application of phosphate-solubilizing microorganisms （PSMs） has been reported to increase P uptake and plant growth. However, no information is available regarding the ecological consequences of the inoculation with PSMs. The effect of inoculation with phosphate-solubilizing fungal （PSF） isolates Aspergillus niger P39 and Penicillium oxalicum P66 on the bacterial communities in the rhizospheres of maize （Zea mays L. ‘Haiyu 6＇） and soybean （Glycine max Merr. ‘Heinong 35＇） was examined using culture-dependent methods as well as a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. Compared with the control, the number of culturable microbes for soybean was significantly greater with P39, whereas for maize, the same was significantly greater with P66. In addition, a greater number of microbes were found in the rhizosphere of maize compared with soybean. The fingerprint of DGGE for 16S rDNA indicated that inoculation with PSF also increased bacterial communities, with the P66 treatment having higher numbers of DGGE bands and a higher Shannon-Weaver diversity index compared with P39; the composition of the microbial community was also more complex with the P66 treatment. Overall, complex interactions between plant species and exotic PSMs affected the structure of the bacterial community in the rhizosphere, but plant species were more important in determining the bacterial community structure than the introduction of exotic microorganisms.     

Morphological and molecular diversity at a regional scale: A step closer to understanding Antarctic nematode biogeography

Antarctica is one of the harshest environments on earth and yet life has managed to persist on the continent for millions of years. While most of the continent is covered by snow and ice, in some coastal and mountain regions that do not have permanent cover terrestrial invertebrate fauna dominate. Nematodes are one of the most common taxa present in these environments, but despite their abundance very little work on diversity and distribution has been performed for the Phylum across the Antarctic continent. We examined nematodes from 123 limno-terrestrial samples from the vicinity of the Australian Antarctic Stations (62.8°E–110.5°E) using the mitochondrial cytochrome c oxidase subunit I (COI) gene, and morphological analyses. We identified the nematodes Plectus murrayi, Pl.cf. frigophilus, Scottnema cf. lindsayae, Halomonhystera cf. halophila, H. cf. continentalis and Eudorylaimus spp. The distribution of these species appears to be determined by habitat type and salinity. We also made comparisons using the COI gene with nematodes from localised sampling from Dronning Maud Land, Francis Island (Antarctic Peninsula), and Tierra del Fuego (TF), and also with COI sequences from other worldwide locations. Contrasting levels of COI sequence divergence were identified among genera and species, ranging from low levels for Pl. murrayi (≤0.5%), medium levels for S. cf. lindsayae (≤2.1%) and Halomonhystera (≤4.3%), and high within Pl.cf. frigophilus (≤8.4%). Distribution ranges varied according to the species, with widespread ranges within Antarctica for Pl. murrayi and Scottnema cf. lindsayae (a range of over 2000 km); and distribution beyond Antarctica to TF for Pl.cf. frigophilus. Our results reveal the presence of cryptic species even when conservative approaches are applied in species delimitation.     

Primary environmental factors controlling gully distribution at the local and regional scale:An example from Northeastern China

Gully erosion is the main cause of global land degradation.The factors controlling gully erosion at watershed scale have been extensively studied,but the spatia...     

Molecular diversity of bacterial chitinases in arable soils and the effects of environmental factors on the chitinolytic bacterial community

The molecular diversity of bacterial chitinases in the bulk soils of arable land was investigated using culture-independent methods. The results demonstrate that bacterial chitinases in arable soils are highly diverse and comprise unique groups when their sequences were compared to those in public databases. The diversity of bacterial chitinases in arable soil was further evaluated using conventional phylogenetic analysis, the UniFrac analysis of the phylogenetic data, and the multidimensional scaling (MDS) analysis of T-RFLP profiles to elucidate the relationship between the diversity of bacterial chitinases and soil characteristics. These analyses indicate that environmental factors such as soil type and pH are responsible for shaping the composition of bacterial chitinases.     

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients

Purpose

Rhizosphere soil bacterial communities are crucial to plant growth, health, and stress resistance. In order to detect how bacterial communities associated with the rhizosphere of phylogenetically related plant species vary in terms of composition, function, and diversity, we investigated the rhizosphere bacterial community structure of two perennial shrub species, Caragana jubata and Caragana roborovskyi, under natural field conditions in northwest China and analyzed the influence of soil properties and environmental factors.

Materials and methods

Eighteen root samples, eight for C. jubata, and ten for C. roborovskyi, along with any adherent soil particles, were collected from multiple sites in northwest China. The rhizosphere soil was washed from the roots, and bacterial communities were analyzed using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Then, α-diversity and β-diversity were calculated using QIIME.

Results and discussion

Across species, Proteobacteria (29 %), Actinobacteria (15 %), Chloroflexi (10 %), Acidobacteria (10 %), Bacteroidetes (8 %), Firmicutes (8 %), Planctomycetes (7 %), Gemmatimonadetes (4 %), and Verrucomicrobia (3 %) were the most abundant phyla in the rhizosphere of C. jubata and C. roborovskyi. However, principal co-ordinates analysis indicated strong interspecific patterns of bacterial rhizosphere communities. Further, the richness of Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, and Nitrospirae was significantly higher in the rhizosphere of C. jubata compared with C. roborovskyi, while the opposite was found for Actinobacteria and Cyanobacteria. However, the Shannon index showed no significant difference in α-diversity between C. jubata and C. roborovskyi. Distance-based redundancy analysis indicated that soil properties and environmental factors exerted strong influences on the structure of the rhizosphere bacterial community and explained 47 and 46 % of community variances between samples, respectively.

Conclusions

Our results showed strong interspecific clustering of the bacterial rhizosphere communities of C. roborovskyi and C. jubata. Altitude explained most of the variation in the composition of bacterial rhizosphere communities of C. roborovskyi and C. jubata, followed by soil pH, water content, organic matter content, total nitrogen content, and mean annual rainfall.

     

Airborne radiometric survey data and a DTM as covariates for regional scale mapping of soil organic carbon across Northern Ireland

Soil scientists require cost-effective methods to make accurate regional predictions of soil organic carbon (SOC) content. We assess the suitability of airborne radiometric data and digital elevation data as covariates to improve the precision of predictions of SOC from an intensive survey in Northern Ireland. Radiometric data (K band) and, to a lesser extent, altitude are shown to increase the precision of SOC predictions when they are included in linear mixed models of SOC variation. However the statistical distribution of SOC in Northern Ireland is bimodal and therefore unsuitable for geostatistical analysis unless the two peaks can be accounted for by the fixed effects in the linear mixed models. The upper peak in the distribution is due to areas of peat soils. This problem may be partly countered if soil maps are used to classify areas of Northern Ireland according to their expected SOC content and then different models are fitted to each of these classes. Here we divide the soil in Northern Ireland into three classes, namely mineral, organo-mineral and peat. This leads to a further increase in the precision of SOC predictions and the median square error is 2.2 %². However a substantial number of our observations appear to be mis-classified and therefore the mean squared error in the predictions is larger (30.6 %²) since it is dominated by large errors due to mis-classification. Further improvement in SOC prediction may therefore be possible if better delineation between areas of large SOC (peat) and small SOC (non-peat) could be achieved.     

Bias in bacterial diversity as a result of Nycodenz extraction from bulk soil

Nycodenz density centrifugation (NDC) is an isolation method that allows extraction of both culturable and unculturable bacterial cells from soil, to be used in further downstream analysis; however, to date there has been a lack of information concerning the efficiency of this method. The aim of this study was therefore to investigate the overall efficiency of NDC extractions from soil and to identify sampling bias, if any.Bacterial cells were extracted from three soil plots from the Danish CRUCIAL field trial using an already established NDC protocol. To evaluate all aspects of the NDC procedure, DNA was extracted directly from soil, from NDC-extracted cells, and from the soil pellets left after NDC. Bacterial diversity was assessed by PCR amplification of the V4-V6 regions of the 16S rRNA from the extracted DNA followed by sample-tagged amplicon-pyrosequencing using the 454 Genome Sequencer FLX system. Sequences were processed and analyzed using the Ribosomal Database Project’s (RDP) Pyrosequencing Pipeline tools.In this study, we show that extraction of bacteria from soil using NDC can result in significant biases in the form of either over- or underrepresentation of specific bacterial phyla commonly found in soil. Furthermore, rarefaction analysis, analysis of similarity, multidimensional scaling plots and analysis of variance showed that the diversity in the NDC-extracted sample was reduced significantly compared to both the original soil sample and the remaining NDC-pellet. To further study the soil diversity a mathematical model was employed to estimate how many sequences would be required in order to find 95% of all operational taxonomic units (OTUs) in the soil. The model estimated that the soil contains approximately 29,400 OTUs and that just 351,500 sequences are needed to cover 95% of the bacterial biodiversity, the equivalent of one full standard GS FLX run.     

Evaluation of models to upscale the small scale variability of Cd sorption in a case study

Cadmium sorption, basic soil properties and water retention were jointly analyzed in an acidic sandy podzol under pine forest in the North of Germany. Samples were taken along a 10 m transect at a depth of 0.15 m with a sample-support of 0.15 m. The small-scale Cd sorption variability was upscaled in two steps. Firstly, it was simplified and, secondly, aggregated from the sample to the pedon scale. We evaluated different models to simplify Cd sorption variability at different levels of spatial aggregation. Our evaluation method was the numerical simulation of Cd transport in the topsoil where the variability of Cd sorption is the key input.We described Cd sorption with the Freundlich parameterization and tested three models to simplify its spatial variability. The reference model (model 1) had two and the simplified models only one spatially variable sorption parameter. Model 2 varied the parameter K_f of the Freundlich parameterization and set the exponent constant. Model 3 expressed only the linear variability of sorption. Each sample had a scaling factor that related to a constant sorption reference function. The Freundlich parameter K_f of the third simplification model (model 4), was derived by a local pedotransfer function. Its variability was, therefore, filtered by the available variation of a limited number of basic soil properties.The average sorption was at all aggregation levels not significantly different between the models. However, the corresponding uncertainty was smallest for model 3, intermediate for model 4 and largest for model 2. We evaluated the different sorption variability models with the simulation of Cd transport. The mean Cd concentrations in the topsoil predicted by the different models were statistically not different. However, at all support scales, the uncertainties of the predicted mean Cd concentrations and the RMSE's were smallest when model 3 was used, where the error was about 20% at the sample scale and decreased to below 10% at the pedon scale. Therefore, if measurements of sorption isotherms are available, we recommend to use model 3 to derive the mean sorption behavior with minimal uncertainty.     

Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil

Previous research has shown that soil structure can influence the distribution of bacteria in aggregates and, thereby, influence microbiological processes and diversity at small spatial scales. Here, we studied the microbial community structure of inner and outer fractions of microaggregates of a desert agricultural soil from the Imperial Valley of Southern California. To study the distribution of soil bacteria, 1,536 clones were identified using phylogenetic taxon probes to classify arrays of 16S rRNA genes. Among the predominant taxonomic groups were the α-Proteobacteria, Planctomycetes, and Acidobacteria. When compared across all phyla, the taxonomic compositions and distributions of bacterial taxa associated with the inner and outer fractions were nearly identical. Our results suggest that the ephemeral nature of soil aggregates in desert agricultural soils may reduce differences in the spatial distribution of bacterial populations as compared to that which occur in soils with more stable aggregates.     

Additions of maize root mucilage to soil changed the structure of the bacterial community

The organic compounds released from roots (rhizodeposits) stimulate the growth of the rhizosphere microbial community. They may be responsible for the differences in the structure of the microbial communities commonly observed between the rhizosphere and the bulk soil. Rhizodeposits consists of a broad range of compounds including root mucilage. The aim of this study was to investigate if additions of maize root mucilage, at a rate of 70 μg C g⁻¹ day⁻¹ for 15 days, to an agricultural soil could affect the structure of the bacterial community. Mucilage additions moderately increased microbial C (+23% increase relative to control), which suggests that the turnover rate of microorganisms consuming this substrate was high. Consistent with this, the number of cultivable bacteria was enhanced by +450%. Catabolic (Biolog^® GN2) and 16S-23S intergenic spacer fingerprints exhibited significant differences between control and mucilage treatments. These data indicate that mucilage can affect both the metabolic and genetic structure of the bacterial community as shown by a greater catabolic potential for carbohydrates. We concluded that mucilage is likely to significantly contribute to differences in the structure of the bacterial communities present in the rhizosphere compared to the bulk soil.     

Estimation of the bacterial community diversity of soybean-nodulating bradyrhizobia isolated from Rj-genotype soybeans

Abstract

The diversities of communities of soybean-nodulating indigenous bradyrhizobia in Japan were estimated using mathematical ecology methods based on the results of polymerase chain reaction–restriction fragment length polymorphism analysis of the 16S–23S rDNA internal-transcribed spacer region. Polar ordination analysis indicated a significant correlation between the compositions of bradyrhizobial communities and northern latitudes in Japan. This result suggests that the composition and the geographical distribution of indigenous soybean-nodulating bradyrhizobia might be affected by soil temperature and the associated diversity of the host plants acclimatized to a particular climate. Furthermore, for estimation of the compositional difference in bacterial communities among three different Rj-genotype soybean cultivars, an analysis of the diversity indexes was conducted and this analysis indicated differences in the composition of the communities isolated from the Rj ₂ Rj ₃-genotype compared with those from the non-Rj- and Rj ₄-genotype cultivars. This result suggests that Rj ₂ Rj ₃-genotype soybeans might affect not only compatibility with particular bradyrhizobia, but also preference to bradyrhizobia for nodulation.     

Differences in the composition and diversity of bacterial communities from agricultural and forest soils

Differences in the bacterial communities of soils caused by disturbances and land management were identified in rRNA gene libraries prepared from conventional tilled (CT) and no tilled (NT) cropland, a successional forest after 30 y of regrowth (NF) and an old forest of >65 y (OF) at Horseshoe Bend, in the southern Piedmont of Georgia (USA). Libraries were also prepared from forests after 80 y of regrowth at the Coweeta Long Term Ecological Research site (CWT) in the Southern Appalachians of western North Carolina (USA). The composition of the bacterial communities in cropland soils differed from those of the Horseshoe Bend OF and CWT forest soils, and many of the most abundant OTUs were different. Likewise, the diversity of bacterial communities from forest was less than that from cropland. The lower diversity in forest soils was attributed to the presence of a few, very abundant taxa in forest soils that were of reduced abundance or absent in cropland soils. After 30 y of regrowth, the composition of the bacterial soil community of the NF was similar to that of the OF, but the diversity was greater. These results suggested that the bacterial community of soil changes slowly within the time scale of these studies. In contrast, the composition and diversity of the bacterial communities in the Horseshoe Bend OF and Coweeta soils were very similar. Thus, this forest soil bacterial community was widely distributed in spite of the differences in soil properties, vegetation, and climate as well as resilient to disturbances of the above ground vegetation.     

高产水稻土细菌多样性的培养法与非培养法比较研究

利用细菌的通用引物扩增江西余江县高产水稻土红壤细菌总DNA和平板培养细菌混合总DNA的16S rDNA基因片段,在此基础上分别建立两种16S rDNA文库(文库a和文库b)。从两个文库中各随机挑选100个克隆,扩增出阳性克隆中的插入片段后选用HhaⅠ和RsaⅠ两种四碱基酶进行ARDRA(amplified rDNA restriction analysis)分析。统计比较分析发现,文库a的Shannon-Wienner指数、Simpson指数、丰富度、均一度分别为4.432、0.987、18.885和0.973,均高于文库b中相应的多样性参数(分别为2.271、0.758、5.736和0.501),即平板培养方法所展现的细菌群落结构多样性低于土壤中原始的多样性。结果表明,传统培养方法存在着很大的局限性,必须结合新的分子生物学技术手段才能更全面完善地认识土壤微生物群落结构多样性,以期充分利用其中丰富的微生物资源。     

Extreme variability of steroid profiles in cow feces and pig slurries at the regional scale: implications for the use of steroids to specify fecal pollution sources in waters

Thirty-five samples of cow feces (cowpat and cow manure) and pig slurries subjected to different treatment processes and different storage times before land spreading were extracted and analyzed by gas chromatography-mass spectrometry to determine their fecal stanol profiles. The fresh pig slurry data presented here increase considerably the classical range of values obtained for steroid ratios, resulting in an overlap with the range for cow feces. These results lead to the inability to distinguish species source of feces on the basis of steroid ratios alone. The cause of these differences is not known, although it appears likely to be related to differences in the metabolism of animals in relation to their age and/or variations in diet, rather than to secondary mechanisms of steroid degradation during storage or/and treatment of the feces. Nevertheless, the specificity of steroids to serve as a tool to differentiate cow feces from pig slurries is restored by considering the fecal stanol profile, notably, the six most diagnostic stanol compounds, which are 5β-cholestan-3β-ol (coprostanol), 5β-cholestan-3α-ol (epicoprostanol), 24-methyl-5α-cholestan-3β-ol (campestanol), 24-ethyl-5α-cholestan-3β-ol (sitostanol), 24-ethyl-5β-cholestan-3β-ol (24-ethylcoprostanol), and 24-ethyl-5β-cholestan-3α-ol (24-ethylepicoprostanol). In this study, chemometric analysis of the fingerprint of these six stanols using principal components analysis (PCA) distinguished pig slurries from cow feces. The application of PCA to the stanol profiles, as developed in this study, could be a promising tool for identifying the animal source in fecal contamination of waters.     

Effect of the landscape context on the density and persistence of a predator population in a protected area subject to environmental variability

Protected areas are the most important tool for the conservation of biodiversity. However, many species are area-demanding and their populations seldom meet their space requirements in reserves. In this context, the unprotected exterior becomes an important part of their home range, and variations in habitat quality of the surroundings of a protected area might affect the dynamics of populations. Using a spatially explicit simulation model, we studied the effect of the surrounding landscape of a protected area on the density and persistence of a predator population inhabiting inside the reserve in different conditions of environmental variability. We simulated individuals of a predator population, their herbivorous prey and a vegetative substrate in a landscape comprised of a square protected area and different types of habitat quality outside the reserve. We studied the combination of three substrate qualities of protected area (inside) with three of the landscape context and three levels of variability of productivity. Our results showed that there were strong effects of both the relative quality of the surrounding landscape and of the environmental variability on the density and persistence of the simulated population inside the protected area. More importantly, we showed that complex patterns emerge when spatial heterogeneity and temporal variability interact with population dynamics. Specifically, under high environmental variability, when the protected area had a high habitat quality, the highest population persistence was not attained when the exterior was also of high quality, but when the surroundings had an intermediate quality. The latter result suggests that, under the mentioned conditions, small enhancements in the quality of the matrix may have, for some species, better effects on increasing persistence in small reserves than large and costly enhancements.     

接种自生固氮菌对玉米根际土壤酶活性和细菌群落功能多样性的影响

为了探索玉米根际土壤微生态特征对接种自生固氮菌的响应机理,在盆栽实验条件下,研究了3株自生固氮菌褐球固氮菌（Azotobacter chroococcum YCYS）、芸苔叶杆菌（Phyllobacterium brasssicacearum QL54）和类芽孢杆菌（Paenibacillus sabinae MX31）接种盆栽玉米（Zea mays L.）之后,玉米根际土壤酶活性和细菌群落功能多样性的变化。结果表明,接种自生固氮菌对玉米根际土壤酶活性和细菌群落功能多样性产生了一定的影响,而且不同自生固氮菌之间的接种效果有一定的差异。接种褐球固氮菌（A. chroococcum YCYS）和类芽孢杆菌（P. sabinae MX31）玉米根际土壤脲酶活性分别比对照高20.55%和9.58%。然而接种处理对玉米根际土壤碱性磷酸酶活性的影响差异不显著（P0.05）。BIOLOG结果显示,接种自生固氮菌可以提高细菌总代谢活性,其中接种褐球固氮菌（A. chroococcum YCYS）处理的AWCD是对照的1.8倍,并且细菌群落丰富度指数（R）显著高于对照（P0.01）。不同接种处理土壤根际细菌生理碳代谢优势群落结构不同。主成分分析（PCA）表明接种自生固氮菌可以调控根际土壤细菌群落功能多样性。     

长期施肥对黄棕壤性水稻土氨氧化细菌多样性的影响

以湖北省农科院长期施肥试验站的黄棕壤性水稻土为研究对象,采用PCR-DGGE方法,研究了氮肥（N）、氮磷（NP）、氮磷钾（NPK）、有机肥（M）、有机肥+氮磷钾（MNPK） 长期施用对土壤氨氧化细菌遗传多样性的影响。结果表明,与长期不施肥处理（CK）相比,长期施肥提高了黄棕壤性水稻土有机质、全氮、微生物量碳氮（SMB-C、SMB-N）含量,并改变了氨氧化细菌的群落结构。其中有机肥与化肥长期配施下氨氧化细菌的多样性高于化肥处理。氨氧化细菌聚类分析表明,稻麦收获后土壤氨氧化细菌DGGE图谱分别聚为一个族群;同一作物收获后,M和MNPK聚为一类,N、NP、NPK和CK聚为一类,后者内部分类在两季作物间有差别。DGGE指纹图谱条带序列分析表明,供试土壤的优势氨氧化细菌为-变形菌纲的亚硝化单胞菌和亚硝化螺旋菌。     

小尺度下茶园土壤有效态微量元素空间变异特征及其影响因素分析

  【目的】  开展小尺度下茶园土壤有效态微量元素空间变异及影响因素研究,以指导茶园养分管理和土壤培肥。  【方法】  于2020年,在四川雅安名山区中峰镇面积约2 km2的生态茶园,采用随机布点法布设94个采样点,每个采样点取 0—30 cm 表层土壤,分析土壤pH、有机质以及有效铁、有效锰、有效铜和有效锌4种微量元素含量,用阈值法(平均值±3倍标准差)对分析数据进行异常值处理。采用地统计学与GIS空间分析技术相结合的方法,探讨了小尺度下茶园土壤有效铁、有效锰、有效铜和有效锌4种有效态微量元素的空间异质性,并运用相关性分析和回归分析方法探究其影响因素。  【结果】  研究区土壤有效铁、有效锰、有效铜和有效锌平均含量分别为56.0、28.0、1.2和1.8 mg/kg,变异系数分别为52.59%、89.95%、38.81%和32.90%,属于中等程度变异。有效铁、有效铜和有效锌含量均服从正态分布,而有效锰含量服从对数正态分布。土壤有效铜呈纯块金效应,全局Moran’s I指数为负值;有效铁、有效锰以指数模型为最优拟合模型,有效锌以球面模型为最佳,块基比在36.57%～61.85%,均呈中等空间相关性,全局Moran’s I指数均为正值,且有效铁含量具有极显著空间自相关性。4种土壤有效态微量元素空间分布格局差异较大,有效铁含量呈现南高北低的趋势,有效锰含量随地面坡度的增加呈现降低趋势,有效铜含量斑块状分布明显,有效锌含量则呈现出从研究区两端向中部递减的分布特征。有效铁含量与有机质、pH显著正相关,有效锌含量则与有机质呈极显著正相关,有效锰含量与坡度之间存在显著相关性,有效铜含量则与各因子均无显著相关性。  【结论】  中锋生态茶园土壤有效铁、有效锰、有效铜和有效锌含量总体上均较丰富,均属中等变异强度。土壤有效铜存在空间孤立现象,有效铁、有效锰和有效锌表现为空间聚集特征。茶园土壤有效铁和有效锌含量主要受土壤有机质含量的影响,有效锰含量则主要受坡度的影响。