Microbial community analysis of field-grown soybeans with different nodulation phenotypes

Microorganisms associated with the stems and roots of nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod(+) soybean roots. Fusarium solani was stably associated with nodulated (Nod(+) and Nod(++)) roots and less abundant in Nod(-) soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod(-), Nod(+), or Nod(++)). The analysis of root samples indicated that the microbial community in Nod(-) soybeans was more similar to that in Nod(++) soybeans than to that in Nod(+) soybeans.     

Competition between strains ofBradyrhizobium japonicum for nodulation of soybeans at different nitrogen fertilizer levels

Competitive abilities of 3 strains ofBradyrhizobium japonicum (E104, E109, E110) for nodulation of soybean (Glycine max) at increasing nitrogen fertilizer levels were studied. Dry weight of plants nodulated by strain E110 were depressed at 10 g N·m^–2, the highest fertilizer level, even when mixed with strain E109. Strain E104 alone or mixed with E109 increased dry matter production. Strain E110 formed many dually infected nodules with strain E104 present but not with strain E109. However, strain E104 formed nodules containing strain E109. Neither strain E110 or E109 produced bacteriocin, so the incompatibility of these two strains had to be due to another reason. Strain E104 successfully competes with strain E109 but not with E110 at 10 g N·m^–2. It is concluded that strain E110 dominates the symbiotic relationships even if other strains are also present in the nodules. However, at a high N-fertilizer level strain E110 decreases the plant yield in contrast to E104, which could be recommended as inoculant at increased levels of soluble soil-N.     

Early autoregulation of symbiotic root nodulation in soybeans

Autoregulation of symbiotic root nodulation in soybean seedlings (Glycine max L. Merrill cv Pride 216) was studied following double inoculation of primary roots with Bradyrhizobium japonicum 110. When the second inoculation was given 10 or 17 hours after the first, the nodulation in the first-inoculated region of the root was suppressed. The effect was eliminated if B. japonicum 110 containing Tn5 insertions in the `common' nod ABC genes was used for the second inoculation, indicating the requirement for changes in the root mediated by these bacterial genes. When the root cortex in the suppressed basal region was examined 3 days after inoculation, cell division centers were present in numbers not significantly different from the numbers in control roots given a sham second inoculation; their size distribution, however, showed a failure of enlargement compared with controls.     

Suppression of nodulation in soybeans by superoptimal inoculation with Bradyrhizobium japonicum

Symbiotic nodulation of the primary roots of soybeans ( Glycine max L. Merrill cv. Pride 216) is regulated by the plant, and is suppressed in response to a high inoculum dose of Bradyrhizobium japonicum USDA strain I–110 (ARS)⁺ applied at one time to the root. If an optimal dose is followed 10 h later by a superoptimal dose, nodules from the first inoculum near the base of the primary root are suppressed in a dose-dependent way similar to that observed after single inoculations. The nodules which appear are probably derived from infections initiated by the bacteria in both inocula.     

Relationship between autoregulation and nitrate inhibition of nodulation in soybeans

Ten of 11 supernodulating mutants of soybean [ Glycine max (L.) Merr.] cv. Bragg, in which nodulation was far in excess of that in the wild type, showed pronounced tolerance of nodulation to applied nitrate. Mutant nts (nitrate-tolerant symbiosis) 1116 had an intermediate nodulation response and also showed some inhibition by nitrate. Mutant 1029, a revertant of nts382 (an extreme supernodulator), showed a wild-type nodulation pattern and was equally sensitive to nitrate as cv. Bragg. Grafting experiments with cv. Bragg and nts382 indicated that both supernodulation and tolerance of nodulation to nitrate were dependent on shoot factors. Total leaf nitrate reductase (EC 1.6.6.1 and EC 1.6.6.2) activity of the supernodulating mutants was similar to that in cv. Bragg. We conclude from these results that the inhibitory effect of nitrate on nodule initiation and development in soybean depends on an interaction between nitrate and the autoregulation singal. In the supernodulating mutants, the autoregulation signal is either altered or absent and cosequently nodulation in these mutants is not sensitive to nitrate.     

Changing nitrogen source on the yield and nitrogen content of soybeans

Summary Soybean plants were grown in nutrient culture solutions containing 150 ppm of N either as an equal concentration of NH₄ ⁺ or NO₃ ^–, or all NO₃ ^–. At the R2 stage of growth for some plants, the N form was changed to either all NO₃ ^– or all NH₄ ⁺, but at the same total N concentration as before. Highest seed yield was obtained with all NO₃ ^– over the entire growth period, the poorest when the N form was switched from an equal ratio of NH₄ ⁺ and NO₃ ^– to all NH₄ ⁺ at the R2 stage. Kjeldahl N concentrations in the plant leaves and seed were highest when NH₄ ⁺ was part or all of the N source in the nutrient solution. These results may partially explain why the literature is inconsistent on the effect of added fertilizer N on soybean seed yield, and may pose a problem in using leaf Kjeldahl N concentration to determine plant N sufficiency.     

Phosphorus fertilization and tillage effect on dinitrogen fixation in soybeans

Summary Tillage has been shown to affect the uptake of phosphorus (P) and yield of soybeans, [Glycine max (L.) Merr.], but there is little information concerning the effects of P fertilization on nitrogen (N₂) fixation in soybeans under no-tillage. Two field experiments were conducted in 1980 and 1981 to determine the effects of soil P on N₂ fixation under no-tillage and to study the interaction of P fertilization and tillage of N₂ fixation, nutrient uptake, and yield of soybeans. In Exp. I, P was applied in 1977 at five rates up to 384 kg P ha⁻¹ and the effects of residual soil P were evaluated in 1980 and 1981 under no-tillage management. Nitrogen fixation rates, as measured by acetylene reduction assay, were significantly affected by soil P in Exp. I, but the assay proved to be a poor technique for estimating total plant N in these tests. Acetylene reduction rates and plant P increased rapidly as soil P increased from 2 to 20 mg kg⁻¹, with little additional increase above 20 mg P kg⁻¹. In Exp. II, rates (0, 32, 64, and 128 kg P ha⁻¹) and time (fall, spring and fall plus spring) of P application were compared under conventional tillage and no tillage. However, plant P increased with increasing levels of applied P. Applied P had no affect on acetylene reduction rates but rates were greater for no-tillage than conventional tillage at the V9 and R5 stages of growth in 1981. Plant uptake of P was more efficient under no-tillage than under conventional tillage in 1980 and 1981. Application of 64 kg P ha⁻¹ under no-tillage resulted in equivalent plant P levels as the 128 kg P ha⁻¹ applied under conventional tillage.     

长期磷肥处理农田黑土细菌群落特征

研究了公主岭国家黑土长期定位站不同施肥处理（对照、磷、氮 磷、氮 磷 钾、有机肥-磷、有机肥-氮-磷、有机肥-氮-磷-钾等）土壤基本理化性质及细菌群落特征.结果表明：有机肥处理土壤有机质（OM）、总氮（TN）、有效磷（AP）、碱解氮（AN）、速效钾（AK）等养分含量显著增加,而单施化肥各处理OM、AN含量无明显变化.与未施肥对照处理相比,有机肥-氮-磷配施与有机肥-氮-磷-钾配施处理总细菌磷脂脂肪酸分别增加34%和62%,G⁺菌磷脂脂肪酸分别增加58%和74%,G^-菌磷脂脂肪酸分别增加64%和69%.各化肥处理细菌脂肪酸含量均有所下降,以磷处理最低.除G⁺菌磷脂脂肪酸外（有机肥-磷配施显著大于氮-磷-钾肥配施）,氮-磷肥配施、氮-磷-钾肥配施与有机肥-磷肥配施三者间细菌脂肪酸含量无显著差异.相关分析表明,各细菌磷脂脂肪酸与OM、AP、AN、AK、NO₃^--N含量呈极显著相关.     

The effect of nitrogen fertilization on the phenology of roots in a barrier island sand dune community

Little work has been done on the phenology of root growth and senescence largely due to methodological difficulties. The application of minirhizotron technology has enabled the tracking of individual roots through an entire growing season. As a result, direct measures of mortality, root growth, and an analysis of cohorts can be obtained. This study examined the belowground response of vegetation in a nutrient limited system to nitrogen addition. Small plots on a 36 year old dune on Hog Island, a barrier island in the Virginia Coast Reserve Long Term Ecological Research Site, were fertilized with nitrogen. Minirhizotron tubes were installed in each fertilized and control plot. Each tube was sampled monthly for nine months, March through October of 1992. Root length density increased throughout the growing season with the greatest root length density in the top 20 cm of the soil profile. The fertilized plots had greater root length densities (14.1 mm cm^-2) than the unfertilized plots (2.9 mm cm^-2). There was no significant depth × treatment interaction. Root mortality did not significantly change with fertilization. The largest loss of roots for a cohort occurred within the first month. The dune grassland community did not respond to fertilization with large changes in root distribution or increases in mortality in this study.     

耕作和施肥对不同深度黑土中细菌群落结构的影响

【目的】为探讨耕作和施加有机肥、化肥对黑土表层(0-30cm)、中层(100-130cm)及深层(200-230cm)细菌群落结构的影响,【方法】应用DGGE技术对相应土层中细菌群落结构进行了解析。【结果】结果表明,与对照相比,耕作和施加有机肥、化肥对表层黑土细菌群落结构影响较大,二者差异度为4%;而对中层和深层细菌群落结构影响较小,二者差异度为2%。对于细菌群落结构的垂向变化,中层和深层中细菌群落结构的相似性远远高于同表层的相似性。【结论】可见,耕作和施加有机肥、化肥仅对黑土表层土壤(0-30cm)具有一定的影响,而对100cm以下土壤细菌群落影响较小,细菌群落随土壤深度不同的垂向变化要远高于土壤管理措施造成的影响。     

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity was uncoupled to community composition.     

Electrophoresis time impacts the denaturing gradient gel electrophoresis-based assessment of bacterial community structure

We investigated the impact of denaturing gradient gel electrophoresis (DGGE) run time on the assessment of bacterial community structure. Results indicated that increased electrophoresis run time (while maintaining 1000 volt-hours) resulted in dissimilar profiles, likely due to instability of the denaturing gradient. We recommend that DGGE run times be minimized to provide optimal band resolution, as extended electrophoresis times can greatly impact subsequent band-based analyses.     

长期施肥制度对稻田土壤反硝化细菌群落活性和结构的影响

以中国科学院桃源农业生态试验站长期定位施肥试验为平台,研究了3种长期施肥制度(对照不施肥-CK,化学施肥-NPK,化学施肥+有机肥-NPKOM)下土壤反硝化速率的差异.同时,以硝酸还原酶基因(narG)作为反硝化细菌的功能标志物,分析了施肥对反硝化细菌群落结构和多样性的影响.结果表明,长期施用有机肥的土壤反硝化速率,反硝化菌多样性都高于对照和施用化肥处理.从3个处理的土壤样品中共获得35个narG基因的可操作分类单元(OTU)主要分布在两个簇,与变形菌门(Proteobacteria)和放线菌门(Actinobacteria)的反硝化细菌有一定的亲缘关系,均为首次从土壤中克隆.Shannon多样性指数显示,NPKOM处理的narG基因多样性最高,CK处理次之,NPK处理最低.LUBSHUFF软件对narG基因群落组成的分析显示,施有机肥后含narG基因的细菌群落组成与CK之间有显著性差异(P<0.05),而化肥(NPK)没有产生显著影响.实验结果为进一步研究亚热带地区水稻土反硝化作用及反硝化功能菌提供了重要的依据.     

Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities

Plant and Soil - Soil microbiomes and their interactions with crop plants are important drivers of agricultural health and productivity. Our objective was to examine short-term responses of soil...     

Effects of N-serve on soybeans and soil nitrogen transformations

Summary Plant dry weight, total N, and total Ca was increased at 0.1 and 1 ppm N-serve. At greater 10 ppm the plants showed visual symptoms of a stunted growth, stem elongation, flowers, and pods failed to form or were aborted, young leaves were curled, and roots were club shaped with many branches. These symptoms were increasingly evident with increasing N-serve application rates. The reason was attributed to an auxin effect. Dry wt and total N in the plant was less than the control at the higher N-serve applications. There was little effect on nitrogenase activity at less than 10 ppm N-serve. Nodulation tended to increase at 0.1 and 1 ppm N-serve.Nitrification was inhibited up to 104 days at 20 ppm N-serve. The soil pH of the high N-serve rates was decreased at 104 days probably due to nitrification. Generally there were little detectable differences among treatments in soil organic N. The average soil organic N from 0 to 104 days decreased by 0.01%. Average increase in total N within each pot at harvest was equivalent to about 138 kg N/ha.     

Response of a weed community to nitrogen fertilization: a multivariate analysis

The effect of nitrogen fertilizers on the composition of a weed community was investigated in a barley field. Two doses (70 and 140 kg N/ha) of three fertilizers (ammonium sulphate, calcium-ammonium nitrate, and liquid urea) were used. The results were evaluated using the canonical correspondence analysis. Hybrid analyses and various combinations of environmental variables and co variables were used to separate the influence of the dose and the type of fertilizer and to separate the direct and indirect effects of fertilization. The results reveal that both the dose and type of fertilizer have a significant effect on the composition of the weed community. The results suggest that both the direct effect of fertilizer and an indirect effect, through increased competition of the crop, are important determinants of weed community composition.     

Assessing life cycle environmental impacts of inoculating soybeans in Argentina with Bradyrhizobium japonicum

The International Journal of Life Cycle Assessment - To estimate life cycle impacts from introducing the yield-enhancing inoculant containing the nitrogen-fixing bacterium Bradyrhizobium japonicum...     

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession

Successful microbial invasions are determined by a species’ ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre‐invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.