Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods

Several biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizosphere–microbial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.     

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.     

Effects of Arbuscular Mycorrhizal Colonization on Microbial Community in Rhizosphere Soil and Fusarium Wilt Disease in Tomato

Fusarium wilt is caused by soil-borne pathogen Fusarium oxysporum. Tomato (Lycopersicon esculentum Mill.) is susceptible to Fusarium oxysporum f. sp. lycopersici race 1 and was infected with wilt disease. A pot experiment was conducted to investigate effects of inoculating arbuscular mycorrhizal (AM) fungus (Glomus etunicatium) on the microbial community in the rhizosphere soil and Fusarium wilt in tomato (cv. Oogatafukuju). The results indicated that AM fungal inoculation suppressed the Fusarium number in the rhizosphere soil of tomato and decreased the Fusarium wilt disease index. Compared to the control, AM fungal inoculation increased the actinomycete number but increased bacterial number. Bacterial and fungal numbers were high but actinomycetes number was low when tomato basal stems became discolored brown. Fusarium inoculation significantly suppressed development of AM colonization and decreased polyphenol oxidase (PPO) activity in leaves and roots of tomato. Inoculation with AM fungi and Fusarium maintained high PPO activity in leaves and roots. The AM colonization increased root growth of tomato, whereas Fusarium inoculation had no significant effect on tomato growth. These findings suggest that because AM fungal inoculation changes microbial communities and enhances PPO activity, it should suppress occurrence of Fusarium wilt in tomato.     

Do water regimes affect iron‐plaque formation and microbial communities in the rhizosphere of paddy rice?

Pot experiments were conducted to investigate the effect of soil water regimes on the formation of iron (Fe) plaque on the root surface of rice seedlings (Oryza sativa L.) and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes (submergence, 100%, and 60% water‐holding capacity [WHC]), and were grown for 5 and 11 weeks. Aerobic lithotrophic Fe(II)‐oxidizing (FeOB) and acetate‐utilizing Fe(III)‐reducing bacteria (FeRB) in the rhizosphere and non‐rhizosphere soil were determined at 5 weeks using the most probable number (MPN) method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non‐rhizosphere soil samples were determined at 11 weeks using Biolog‐GN2 plates. The amount of Fe plaque (per unit dry root weight) was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times (r = 0.98 and 0.92, respectively, n = 12). Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non‐rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe‐oxidizing/reducing bacteria, while increasing the Fe‐plaque formation.     

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana <Emphasis Type="Italic">Fusarium</Emphasis> wilt disease by reshaping the soil microbiome

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p?<?0.05) increased the soil pH and content of soil total C and available P and K, and this probably reshaped soil microbial community as revealed by redundancy analysis and variance partitioning analysis. The observed disease suppression due to biofertilizer application after soil fumigation can be attributed to the reduced abundance of F. oxysporum by general suppression resulting from manipulated soil properties and recovered soil microbiome.     

Microbiological Features Associated with the Suppression of Fusarium Wilt of Lettuce Studied by Applying a Single Selected Compost

The effect of compost suppressiveness towards Fusarium oxysporum f. sp. lactucae has been studied using a combined approach. Bioassays have been carried out in controlled conditions to obtain standardization of the environment in order to minimize the disturbances and variability of the soil microbial communities. Compost addition has demonstrated significant efficacy in controlling the disease. The microbial activities and the bacterial and fungal concentrations have been quantified and correlated in a principal component analysis in order to clarify the correlation between the original variables. The samples were clearly distinguished between the substrates in which the plants were grown and the rhizosphere samples. Denaturing Gradient Gel Electrophoresis (DGGE) has been used to track the microbial communities throughout the bioassays. The approach has shown to be useful in detecting both bacterial and fungal species that preferentially associate with the roots of seedlings. Detected microorganisms assumed to be involved in compost-mediated suppression had a high probability of being vital because they were not detected in the substrate where the plants were grown at the start of the experiment.     

Soil Microbial Community Composition and Diversity in the Rhizosphere of a Chinese Medicinal Plant

Rehmannia glutinosa is an important medicinal plant, but there is a serious problem of decreasing productivity with its continuous cropping on the same land. We hypothesize some relationships between this problem and the disturbed soil ecosystem. In this work, two community‐based microbiological measurements, community‐level physiological profiling (CLPP) using Biolog sole carbon (C) source utilization tests and phospholipid ester–linked fatty acid (PLFA) profiles, were used to evaluate soil microbial community function and composition of different R. glutinosa cropping soils. Field investigation showed that the problems with continuous cropping occurred not only in 2‐year continuous fields but also in 5‐year rotation fields. Soil basal respiration and metabolic quotient were significantly greater in R. glutinosa cropping soils than in the noncropping controls. In contrast, the Shannon index from the Biolog data set was lower in R. glutinosa cropping soils. Both CLPP‐ and PLFA‐based principal component analyses (PCA) showed distinct groupings of soil microbial communities in R. glutinosa rhizosphere, and 11 PLFAs representing different microbes were identified from the principal component scores of PLFAs. Among these, an abundance of PLFA 18:2ω6,9, which is a biomarker of soil fungi, was significantly higher in R. glutinosa cropping soils than control soils. These results suggest an alteration of soil microbial community following R. glutinosa cropping, and this might be an important reason for the constraints associated with continuous cropping.     

Apatite Control of Phosphorus Release to Runoff from Soils of Phosphate Mine Reclamation Areas

This study was initiated to explore the effects of ozone (O₃) exposure on potted wheat roots and soil microbial community function. Three treatments were performed: (1) Air with daily averaged O₃ concentration of 4–10 ppb (control situation, CK), (2) Air plus 8 h averaged O₃ concentration of 76.1 ppb (O₃-1), and (3) Air plus 8 h averaged O₃ concentration of 118.8 ppb (O₃-2). In treatments with elevated O₃ concentration (O₃-1 and O₃-2), the root and shoot biomass were reduced by 25% and 18%, respectively, compared to the control treatment (CK). On the other hand, root activity was significantly reduced by 58% and 90.8% in the O₃-1 and O₃-2 treatments, respectively, compared to CK. The soil microbial biomass was significantly reduced only in the highest O₃ concentration (O₃-2 treatment) in the rhizosphere soil. Soil microbial community composition was assessed under O₃ stress based on the changes in the sole carbon source utilization profiles of soil microbial communities using the Biolog? system. Principal component analysis showed that there was significant discrimination in the sole-carbon source utilization pattern of soil microbial communities among the O₃ treatments in rhizosphere soil; however, there was none in the bulk soil. In rhizosphere soil, the functional richness of the soil microbial community was reduced by 27% and 38% in O₃-1 and O₃-2 treatments, respectively, compared to CK. O₃-2 treatment remarkably decreased the Shannon diversity index of soil microbial community function in rhizosphere soil, but the O₃-1 treatment did not. In the dominant microorganisms using carbon sources of carbohydrates and amino acids groups were significantly reduced by an elevated O₃ concentration in the rhizosphere soil. Our study shows that the elevated ozone levels may alter microbial community function in rhizosphere soil but not in the bulk soil. Hence, this suggests that O₃ effects on soil microbes are caused by O₃ detriments on the plant, but not by the O₃ direct effects on the soil microbes.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Effects of glyphosate on rhizosphere soil microbial communities under two different plant compositions by cultivation-dependent and -independent methodologies

We studied, under two different plant compositions, the short-term effects of glyphosate on rhizosphere soil microbial communities through the utilization of cultivation-dependent and -independent techniques. A short-term pot study was carried out using factorial treatments that included two different compositions of forage plant species (triticale versus a mixture of triticale and pea) and two concentrations of glyphosate (50 and 500 mg active ingredient kg⁻¹ soil, as a commercial formulation, Roundup Plus) arranged in a completely randomized design experiment with four replicates. Control plants (no glyphosate added) were clipped in an attempt to compare two methods of weed control (manual = clipping; chemical = herbicide treatment). Rhizosphere soil was sampled 15 and 30 days after glyphosate treatment and the following soil components were determined: potentially mineralizable nitrogen, ammonium content, community-level physiological profiles using Biolog Ecoplates™, DNA microbial biomass and genotype diversity by means of PCR-DGGE. Fifteen days after herbicide treatment, a glyphosate-induced stimulation of the activity and functional diversity of the cultivable portion of the heterotrophic soil microbial community was observed, most likely due to glyphosate acting as an available source of C, N and P. On the other hand, 30 days after herbicide treatment, both the activity and diversity of the rhizosphere soil microbial communities showed an inconsistent response to glyphosate addition. Apart from its intended effect on plants, glyphosate had non-target effects on the rhizosphere soil microbial community which were, interestingly, more enhanced in triticale than in “triticale + pea” pots. Biolog™ was more sensitive than PCR-DGGE to detect changes in soil microbial communities induced by glyphosate and plant composition.     

Identification and quantification of Fusarium oxysporum in planta and soil by means of an improved specific and quantitative PCR assay

The proper identification and quantification of F. oxysporum populations inhabiting soil and plant rhizosphere niches are of importance for soil microbial ecology and plant pathology. In this study, we report the improvement of a PCR protocol for the specific identification of the F. oxysporum species complex and its conversion into a real-time qPCR assay for the quantification up to 1 pg of the fungus DNA in soil and different plant tissues. The amplification efficiency, sensibility and reproducibility of qPCR assays were not influenced by presence of non-target DNA from either plant or soil. The applicability of the newly developed qPCR protocol for F. oxysporum population studies was demonstrated using the technique for quantifying the fungus in different complex environmental samples. The use of the qPCR protocol allowed to accurately quantify up to 25 pg of F. oxysporum/g of naturally infested field soil, as well as to identify significant differences in the amount of F. oxysporum DNA in roots of different chickpea cultivars grown in a field soil infested with diverse pathogenic and nonpathogenic F. oxysporum populations. This qPCR protocol may be especially important for studies on soil microbial ecology and plant pathology since it provides a new opportunity for analyzing F. oxysporum populations and their interactions with the soil microflora, environment and plant host genotypes.     

Effect of Capsicum annuum cultivated in sub-alkaline soil on bacterial community and activities of cultivable plant growth promoting bacteria under field conditions

In literature, it remains little explored the soil–plant relationships within Capsicum agroecosystem. We studied how chili peppers plants contribute to influence microbial diversity. Across the bulk and rhizosphere soils of three genotypes of Capsicum annuum, the structure, the diversity and the abundance of bacteria was evaluated by means of DNA-based culture-independent approach. Furthermore, 515 bacterial strains isolated from the bulk and rhizosphere soil, were used to investigate the effect of C. annuum on four plant growth promoting bacteria (PGPB) abilities. Our results indicated that the three genotypes influence differently the physical-chemical and microbial properties of soil around the roots. Bacterial abundance resulted in increasing with different trend rhizospheres to bulk soil ratio; however, bacterial diversity was significantly higher only in the rhizosphere of one genotype. Only the indolic compounds production was stimulated in the rhizosphere of the three cultivars. Inhibition of Fusarium oxysporum was stimulated just with one genotype, where 53 of rhizosphere isolates showed more than 10% of inhibition. 165 of isolates produced siderophores and the major part belonged to the high production level. Interactions between PGPB features revealed that anti-phytopathogenic activity was not associated with the others characteristics; however, phosphate solubilization was associated with both siderophores and indolic compounds productions.     

生物复混肥对土壤微生物群落功能多样性和微生物量的影响

在温室盆栽条件下,采用Biolog微平板法和氯仿熏蒸浸提法,研究了玉米施用等养分量的无机肥、有机无机复混肥和生物复混肥后土壤微生物群落功能多样性及土壤微生物量的变化。结果表明:生物复混肥处理的土壤微生物平均颜色变化率(AWCD)、微生物群落Shannon指数(H)和微生物群落丰富度指数(S)均最高;施用生物复混肥可明显提高土壤微生物对碳源的利用率,尤其是多酚化合物类和糖类;不同处理土壤微生物碳源利用特征有一定差异,生物复混肥在第1主成分上的得分值为正值,其他各处理在第1主成分上的得分值基本上为负值,起分异作用的主要碳源是糖类和羧酸类。在玉米生长期间各处理土壤微生物量大致呈先升高后逐渐平稳的趋势,且土壤微生物量碳、氮、磷的含量均以生物复混肥处理最高,最高值分别为333.21mg.kg 1、53.02 mg.kg 1和22.20 mg.kg 1。研究表明,生物复混肥的施用比等养分量的有机无机复混肥处理能显著提高土壤微生物群落碳源利用率、微生物群落丰富度和功能多样性,显著增加土壤微生物量碳、氮、磷的含量,有利于维持良好的土壤微生态环境。     

Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum J. H. Owen, results in considerable yield losses for cucumber plants. A bio-organic fertilizer (BIO), which was a combination of manure composts with antagonistic microorganisms, and an organic fertilizer (OF) were evaluated for their efficiencies in controlling Fusarium wilt. Application of the BIO suppressed the disease incidence by 83% and reduced yield losses threefold compared with the application of OF. Analysis of microbial communities in rhizosphere soils by high-throughput pyrosequencing showed that more complex community structures were present in BIO than in OF treated soils. The dominant taxonomic phyla found in both samples were Proteobacteria, Firmicutes, Actinobacteria and Acidobacteria among bacteria and Ascomycota among fungi. Abundance of beneficial bacteria or fungi, such as Trichoderma, Hypoxylon, Tritirachium, Paenibacillus, Bacillus, Haliangium and Streptomyces, increased compared to the OF treatment, whereas the soil-borne pathogen, Fusarium, was markedly decreased. Overall, the results of this study demonstrate that the application of the BIO was a useful and effective approach to suppress Fusarium wilt and that the high-throughput 454 pyrosequencing was a suitable method for the characterization of microbial communities of rhizosphere soil of cucumber.     

Decomposition of carbon-14-labelled wheat straw in repeatedly fumigated and non-fumigated soils with different levels of heavy metal contamination

We analysed the decomposition of ¹⁴C-labelled straw at five different levels of heavy metal contamination (100-20,000 µg total Zn g^-1 soil) in non-fumigated and repeatedly fumigated soils. The soils were not spiked with Zn, but were taken from sites containing different heavy metal concentrations. Zn was only used as a reference and the effects observed are most likely due to this metal. Microbial biomass decreased with increasing heavy metal content of soils, paralleled generally by the decreasing amount of wheat straw ¹⁴C incorporated into the microbial biomass. In addition, the newly synthesised microbial biomass declined more rapidly as the incubation proceeded. In the repeatedly fumigated soils, microbial biomass ¹⁴C corresponded to roughly 50% of the maximum ¹⁴C incorporation of the non-fumigated soil. The relative decline during incubation was similar to that of the non-fumigated soil at the respective contamination level. These results reveal clearly that heavy metal effects on straw decomposition do not depend on the ratio of substrate C to microbial biomass C. In contrast to microbial biomass C, the mineralisation of the wheat straw was not seriously affected by heavy metal contamination. The same was true for all of the repeatedly fumigated treatments, where a much smaller microbial biomass mineralised nearly the same amount of straw as in the non-fumigated soils. However, repeated fumigation caused a strong reduction in the decomposition of soil organic matter. The ratio of CO₂-¹⁴C to microbial biomass ¹⁴C after 60 days was linearly related to the Zn concentration in both non-fumigated and repeatedly fumigated samples, clearly indicating that an additional energy cost is required by soil microorganisms with increasing heavy metal concentrations.     

根际促生菌Bacillus subtilisY-IVI在香草兰上的应用效果研究

【目的】香草兰为多年生热带经济作物,随着种植年限的增加,植株长势弱,土壤有益微生物减少,土壤微生物区系失衡,严重制约了香草兰产业的可持续发展。枯草芽孢杆菌作为一种根际促生菌,被广泛应用于促进作物生长,改善土壤微生物环境。本文将枯草芽孢杆菌Y-IVI接种在有机肥上,生产了生物有机肥,并就该生物有机肥对香草兰生长的影响进行了研究。【方法】采用温室盆栽试验,调查施用根际促生菌枯草芽孢杆菌(Bacillus subtilis)Y-IVI及其经固体发酵制得的微生物有机肥料(Y-IVI:3×108cfu/g)后,香草兰植株地上部及根系的生长状况,采用选择性培养基方法研究了Y-IVI在香草兰根际土壤中的定殖能力及对香草兰根茎腐病致病菌-尖孢镰刀菌数量的影响。【结果】施用Y-IVI及BIO 4个月后,香草兰根际土壤Y-IVI数量仍可达到106cfu/g土,二者无显著差异,在处理OF和对照中未检测到菌株Y-IVI。施用生物有机肥香草兰地上部干重和根系干重均显著高于对照,分别增加了63.1%和59.4%,与不接种Y-IVI的有机肥处理(OF)相比,地上部干重显著提高了43.2%,根系干重提高了18%,差异不显著;施用Y-IVI菌液的处理植株地上部干重和根系干重均高于对照,但无显著性差异;处理BIO根系直径、根系表面积和总体积与对照相比分别增加了41.9%、88.9%和80.4%,均显著高于对照,总根长与对照差异不显著;处理BIO根系表面积和总体积与有机肥处理OF相比分别显著增加了41.9%和30.8%,根系直径与OF相比增加了10.1%,差异不显著;处理Y-IVI根系直径与对照相比显著增加了25.5%,但根系表面积和总体积与对照差异不显著;与对照相比,施用BIO及Y-IVI的处理根际土壤尖孢镰刀菌数量分别明显降低了52.2%和41.8%,施用有机肥OF的处理降低了10%,差异不显著。【结论】Y-IVI可稳定定殖于香草兰根际土壤对其生长起有益作用,含促生菌Y-IVI的生物有机肥料比单独使用促生菌菌液可以更有效地减少根际土壤中尖孢镰刀菌数量,降低连作生物障碍。施用生物有机肥料比施用化肥和有机肥更有效地促进香草兰地上部及根系生长,因此,施用由根际促生菌枯草芽孢杆菌(Bacillus subtilis)Y-IVI制得的生物有机肥是解决香草兰连作生物障碍和提高收益的有效手段。     

Rhizosphere microbial communities and organic acids secreted by aluminum-tolerant and aluminum-sensitive soybean in acid soil

This study aimed to investigate the correlation between organic acids secreted by two soybeans genotypes, BX10 [aluminum (Al) tolerant] and BD2 (Al sensitive) and rhizosphere microbial communities in acid soil. The organic acids secreted by BX10 and BD2 were significantly different at each growth stage. Both fungi/bacteria and gram-negative bacteria/gram-positive bacteria ratio values were affected by the two soybean genotypes at different growth periods. Compared with BD2, phospholipid fatty acid of BX10 showed higher Shannon diversity at the seedling and flowering stages, but had lower Shannon diversity at the pod-setting stage. Redundancy analysis and canonical correspondence analysis revealed that the organic acids including tartaric acid, lactic acid, and citric acid significantly affected rhizosphere bacterial communities. Sequence analysis indicated that uncultured Acidobacterium, Chloroflexi, and actinomycete enriched in BD2, whereas some uncultured bacteria enriched in BX10. The two soybean genotypes exhibit distinct rhizosphere microbial communities; root organic acid exudates may affect composition of microbial communities of rhizosphere soil: tartaric acid may negatively affect rhizosphere bacteria at the seedling stage, lactic acid may positively affect rhizosphere actinomycetes at the flowering stage, and succinic acid may stimulate fungi at the pod-setting stage.     

Atmospheric CO2 enrichment and nutrient additions to planted soil increase mineralisation of soil organic matter, but do not alter microbial utilisation of plant- and soil C-sources

Plants link atmospheric and soil carbon pools through CO₂ fixation, carbon translocation, respiration and rhizodeposition. Within soil, microbial communities both mediate carbon-sequestration and return to the atmosphere through respiration. The balance of microbial use of plant-derived and soil organic matter (SOM) carbon sources and the influence of plant-derived inputs on microbial activity are key determinants of soil carbon-balance, but are difficult to quantify. In this study we applied continuous ¹³C-labelling to soil-grown Lolium perenne, imposing atmospheric CO₂ concentrations and nutrient additions as experimental treatments. The relative use of plant- and SOM-carbon by microbial communities was quantified by compound-specific ¹³C-analysis of phospholipid fatty acids (PLFAs). An isotopic mass-balance approach was applied to partition the substrate sources to soil respiration (i.e. plant- and SOM-derived), allowing direct quantification of SOM-mineralisation. Increased CO₂ concentration and nutrient amendment each increased plant growth and rhizodeposition, but did not greatly alter microbial substrate use in soil. However, the increased root growth and rhizosphere volume with elevated CO₂ and nutrient amendment resulted in increased rates of SOM-mineralisation per experimental unit. As rhizosphere microbial communities utilise both plant- and SOM C-sources, the results demonstrate that plant-induced priming of SOM-mineralisation can be driven by factors increasing plant growth. That the balance of microbial C-use was not affected on a specific basis may suggest that the treatments did not affect soil C-balance in this study.     

Funneliformis mosseae affects the root rot pathogen Fusarium oxysporum in soybeans

We analyzed the relationship between the dominant arbuscular mycorrhizal (AM) fungus Funneliformis mosseae and the dominant soybean root rot pathogen Fusarium oxysporum through the pot trials to help overcome obstacles to continuous cropping of soybean and to provide theoretical evidence that can be used to help prevent the reduced production induced by soybean root rot. Using qRT-PCR, we amplified the specific rDNA sequences of F. mosseae and F. oxysporum in soybean roots and rhizosphere soil and quantified the DNA contents of these fungi to determine the relationship between the dominant AM fungus F. mosseae and F. oxysporum. The DNA contents of F. oxysporum differed significantly depending on the presence of F. mosseae in both soybean roots and rhizosphere soil. Specifically, the DNA contents of F. oxysporum were reduced after inoculation with F. mosseae, suggesting that F. mosseae has a negative effect on the growth of F. oxysporum.     

Hydrocarbon degradation potential and activity of endophytic bacteria associated with prairie plants

Phytoremediation systems for organic compounds such as petroleum hydrocarbons rely on a synergistic relationship between plants and their root-associated microbial communities. To determine the probable role of endophytic bacterial communities in these systems, this study examined both rhizosphere and endophytic communities of five different plant species at a long-term phytoremediation field site. Hydrocarbon degradation potential and activity were assessed using MPN assays, PCR analysis of catabolic genes associated with hydrocarbon degradation, and mineralization assays with C-14 labeled hydrocarbons. Microbial community structure in each niche was assessed by DGGE analysis of 16S rRNA gene fragments and subsequent band sequencing. Both endophytic degrader populations and endophytic degrader activity showed substantial inter-species variation, largely independent of that shown by the respective rhizosphere populations. Endophytic hydrocarbon degradation was linked to dominant bacterial endophytes. Pseudomonas spp. dominated endophytic communities exhibited increased alkane hydrocarbon degradation potential and activity, while Brevundimonas and Pseudomonas rhodesiae dominated endophytic communities were associated with increased PAH degradation potential and activity. In one plant species, Lolium perenne, increased endophytic alkane hydrocarbon degradation was associated with increased rhizosphere alkane degradation and decreased rhizosphere PAH degradation. Our results show that diverse plant species growing in weathered-hydrocarbon contaminated soil maintain distinct, heterogeneously distributed endophytic microbial populations, which may impact upon the ability of plants to promote the degradation of specific types of hydrocarbons.