Impact of the nematophagous fungus Pochonia chlamydosporia on nematode and microbial populations

The microbial and nematode populations associated with two plants (tomato and cabbage) inoculated with the nematophagous fungus, Pochonia chlamydosporia var. chlamydosporia or root knot nematode (Meloidogyne incognita), or both, were compared with those in unplanted controls. The dominant factor affecting culturable microbial populations was found to be the presence or absence of tomato plants. Generally microbial colony counts were lowest in unplanted soil, small increases were associated with cabbage and significantly greater numbers with tomato plants. Differences in microbial diversity (estimated from community profiles of carbon substrate utlisation, using Biolog) were observed between planted and unplanted soils, however, there were few differences between soils with either of the two plants. The presence of P. chlamydosporia was associated with a reduction in the numbers of plant parasitic nematodes (51%-78%) including the migratory ectoparasites, whereas free-living nematodes, culturable bacteria and bacterial populations assessed by Biolog were unaffected by the application of fungus.     

Herbicides induce change in metabolic and genetic diversity of bacterial community from a cold oligotrophic lake

Pristine cold oligotrophic lakes show unique physical and chemical characteristics with permanent fluctuation in temperature and carbon source availability. Incorporation of organic toxic matters to these ecosystems could alter the bacterial community composition. Our goal was to assess the effects of simazine (Sz) and 2,4 dichlorophenoxyacetic acid (2,4-D) upon the metabolic and genetic diversity of the bacterial community in sediment samples from a pristine cold oligotrophic lake. Sediment samples were collected in winter and summer season, and microcosms were prepared using a ration 1:10 (sediments:water). The microcosms were supplemented with 0.1 mM 2,4-D or 0.5 mM Sz and incubated for 20 days at 10 °C. Metabolic diversity was evaluated by using the Biolog Ecoplate? system and genetic diversity by 16S rDNA amplification followed by denaturing gradient gel electrophoresis analysis. Total bacterial counts and live/dead ratio were determined by epifluorescence microscopy. The control microcosms showed no significant differences (P > 0.05) in both metabolic and genetic diversity between summer and winter samples. On the other hand, the addition of 2,4-D or Sz to microcosms induces statistical significant differences (P < 0.05) in metabolic and genetic diversity showing the prevalence of Actinobacteria group which are usually not detected in the sediments of these non-contaminated lacustrine systems. The obtained results suggest that contaminations of cold pristine lakes with organic toxic compounds of anthropic origin alter their homeostasis by inhibiting specific susceptible bacterial groups. The concomitant increase of usually low representative bacterial groups modifies the bacterial composition commonly found in this pristine lake.     

Effects of gravel-sand mulching on soil bacterial community and metabolic capability in the semi-arid Loess Plateau,China

Gravel and sand mulching is an indigenous technology used for the crop yield for at least 300 years in the loess area of northwest China; however, little is known about the changes of soil bacterial community and metabolic capability under the mulching. In this study, we investigated the soil microbial community structure and metabolic functional diversity during mulching using Illumina MiSeq sequencing and Biolog ECO method. Totally, 9417 OTUs were classified at 97% similarity level for soil samples after 0 (control), 4, 7, and 10 years of mulching. Dendrogram result indicated that mulching affected the soil bacterial community; and the higher richness and diversity of bacterial community were detected in mulching samples. The average abundance of soil bacteria (such as Proteobacteria, Actinobacteria, Firmicutes and Nitrospirae) in mulching samples was higher than samples without mulching. Besides, some microbial communities (such as Rhodobacteraceae, Phenylobacterium, Pseudonocardia, Nonomuraea and Aeromicrobium) were only present in the mulched soil samples. However, the lower metabolic capability was observed in mulching samples based on Biolog method, which the main reason for the opposite result might be that the soil objects detected by the two methods are different. In conclusion, these results demonstrated that gravel and sand mulching affected the structure and metabolic capability of bacterial community and was one reason for crop yield.     

Effect of Crude Oil and Chemical Additives on Metabolic Activity of Mixed Microbial Populations in Fresh Marsh Soils

Abstract Hydrocarbons increase abundance of hydrocarbon-degrading microorganisms, but also decrease microbial diversity. This could disrupt ecosystem dynamics by altering soil organic matter mineralization and resultant nutrient remineralization rates. Crude oil, which is known to contain toxins and reduce microbial diversity, was hypothesized to reduce gross metabolic activity of mixed microbial populations in wetland soils. Soil respiration and Eh were compared, for 6 months, among microcosms containing marsh soils that differed in soil organic matter (Panicum hemitomon Shult. or Sagittaria lancifolia L. dominated marshes), crude oil (Arabian crude, Louisiana crude, or no oil), and additives (a cleaner, a dispersant, fertilizer, or no additive). No treatment slowed activity; instead, Louisiana plus fertilizer and all Arabian treatments temporarily accelerated activity. Additional C respired from oiled microcosms exceeded C added as crude oil by 1.4 to 3.5 times. Thus, much additional C originated from soil organic matter rather than crude oil. Crude oils temporarily lowered soil Eh, which is consistent with accelerated metabolism and demand for electron acceptors. The lack of inhibition observed at the community level does not necessarily indicate an absence of toxicity. Instead, tolerant species with metabolic versatility probably maintained activity. Stimulation probably resulted from removal of micronutrient limitation, rather than removal of grazing pressure or macronutrient limitation. Regardless, accelerated soil organic matter mineralization surely accelerated nutrient remineralization. This might explain some reports of crude oil stimulating plant growth. These results are not inconsistent with theoretical and experimental conclusions regarding effects of biodiversity on ecosystem stability and productivity, nor are they inconsistent with conclusions that crude oils contain components that are toxic to microbes, vegetation, and fauna. However, these data do indicate that crude oils also contain components that temporarily stimulate metabolic activity of surviving microbes. Received: 27 April 1998; Accepted: 15 July 1998     

金沙土遗址土壤细菌群落结构和推测的代谢特征

【背景】金沙土遗址被认为是3 200年前商周时期大型祭祀场所,具有重要的古文化和历史意义,目前金沙土遗址在物理、化学、生物等因素的影响下已出现不同程度的劣化,物理、化学因素的影响已有报道,而生物因素尚鲜有关注。【目的】研究金沙土遗址中微生物群落结构组成,解析微生物菌群活性及代谢特征,为金沙土遗址的科学保护提供依据。【方法】根据遗址目前的保存状况,从金沙土遗址采集具有代表性的土壤样品,所采区域样品的劣化程度依次为J4J3J2J1,应用Biolog平板法与PCR-DGGE技术对各样品中的微生物群落结构组成和代谢功能多样性进行研究。【结果】Biolog结果显示,随着金沙土遗址的劣化,各土壤样品中的微生物功能多样性存在较大差异,各样品的微生物群落代谢活性依次为:J2J3J4J1,表明随着土壤的劣化,微生物的代谢活性表现出增大的趋势。主成分分析结果反映出4个样品中的微生物碳代谢方式具有显著的变化,样品J2中的细菌群落对底物碳源利用种类最多,且偏好的碳源类型与其它样品存在明显的不同。PCR-DGGE图谱显示,金沙土遗址不同土壤样品中的细菌多样性和种群组成存在明显差异,在DNA和RNA水平上,各样品的微生物组成多样性依次为:J2J4J3J1。主成分分析结果显示,除了样品J1,劣化样品的细菌群落结构和活性细菌群落结构具有较高的一致性,表明随着金沙土遗址的劣化,土壤中微生物多样性呈现出上升趋势。DGGE图谱主要条带的测序结果表明,样品中主要的细菌类群归属于放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)、变形菌门(Proteobacteria)和异常球菌-栖热菌门(Deinococcus-Thermus),分属于7个属,在DNA和RNA水平上均能检测到红色杆菌属(Rubrobacter)和短波单胞菌属(Brevundimonas)。【结论】首次对金沙土遗址的细菌群落结构组成和功能进行分析,结果表明随着金沙土遗址劣化程度的增加,土壤微生物类群及功能多样性都随之增大,其中仅在劣化土壤样品中检出或者具有高表达活性的红色杆菌属、Tellurimicrobium、短状杆菌属细菌可能参与了土壤劣化过程,这为今后土遗址的科学保护提供了理论依据。     

Impact of Carbon and Flooding on the Metabolic Diversity of Microbial Communities in Soils

The assumption that carbon and soil water content are major determinants of microbial community structure and function is rarely questioned because of substantial evidence of the impacts of these variables on specific populations and functions. The significance of carbon and water for metabolic diversity at the microbial community level was tested on the field scale in agricultural plots varying in carbon inputs and in whether they were flooded. Surface soils in which rice straw was incorporated or burned and which were flooded or unflooded were sampled at monthly intervals three times during the flooded winter period (January to March) and again 1 month postdraining. Biomass carbon and nitrogen were not affected by treatments, active bacterial counts showed slight increases, and respiration rates were increased by carbon inputs and flooding. Biolog microplates were inoculated with soil extracts to quantify the metabolic diversity of the soil microbial community. Canonical correspondence analysis and the Monte Carlo permutation testing showed that differences in substrate utilization patterns were significantly related (P < 0.001) to carbon and flooding treatments. Biolog substrates whose metabolism was altered by the treatments were consistent across dates and tended to be positively related (utilization enhancement) to carbon inputs and negatively related to winter flooding. The importance of carbon as an environmental variable increased over time after straw treatment, whereas the importance of water became evident after flooding and decreased after drainage. The effect of long-term rice straw incorporation on substrate utilization patterns at another field site was consistent with these results despite the dissimilarities of the two soils.     

生物肥与甲壳素和恶霉灵配施对香蕉枯萎病的防治效果

通过盆栽试验研究了生物肥与甲壳素和恶霉灵配施防治香蕉枯萎病效果,试验结果表明,生物肥与恶霉灵配施(H+F)处理香蕉枯萎病病情指数最高,生物肥与甲壳素配施(C+F)处理病情指数最低。单独生物肥处理防病效果为32.8%,生物肥与甲壳素配施处理为42.5%,而生物肥与恶霉灵配施加重了香蕉枯萎病病情。Biolog Eco微平板研究发现,AWCD(平均每孔颜色变化率)和Shannon等4个多样性指数变化趋势与防病效果相反:防病效果好的处理,土壤细菌功能多样性指数反而低,经检测发现病原真菌(Fusarium oxysporum f. sp. cubense)可利用Biolog Eco微平板上碳源底物并发生颜色变化,干扰测定结果。T-RFLP分析土壤细菌DNA多样性,对照(灭菌生物肥)土壤中TRFs末端限制性片段最少,生物肥与甲壳素配施处理最多。与网上数据库比较,生物肥与甲壳素配施增加了土壤中芽胞杆菌种类,与恶霉灵配施降低了芽胞杆菌种类。分析发现,T-RFLP和Biolog的主成份分析载荷图具有较高一致性。因此,生物肥与生物农药甲壳素配施,从生态角度控制土传病害,优势互补,提高了土壤细菌多样性,改善了土壤细菌群落结构,有利于提高防病效果。     

Maintenance of soil functioning following erosion of microbial diversity

The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.     

Biomass Carbon Measurements and Substrate Utilization Patterns of Microbial Populations from Soils Amended with Cadmium, Copper, or Zinc

Samples of a sandy loam soil taken from a long-term liming experiment in southeast England were amended with solutions of metal sulfate salts. Soils with a range of pHs were amended to contain Cu, Cd, or Zn at concentrations around the maximum permissible values for these metals in agricultural land receiving sewage sludge. After a 3-year equilibration period, the microbial biomass was determined by the fumigation-extraction technique. These results were compared with data from substrate utilization patterns of microbial populations extracted by using a weak salt solution. There was no reduction in microbial biomass due to pH or metal treatment in any of the soils except the Cu treatment. Principal-component analysis of the respiration patterns in Biolog plates demonstrated effects of both pH and metal treatment on the extracted microbial population which were independent of gross biomass size. pH and soil amendments with Cu and Zn were found to reduce the metabolic potential of the extracted soil microbial population.     

Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance

Analysing the consequences of the decrease in biodiversity for ecosystem functioning and stability has been a major concern in ecology. However, the impact of decline in soil microbial diversity on ecosystem sustainability remains largely unknown. This has been assessed for decomposition, which is insured by a large proportion of the soil microbial community, but not for more specialized and less diverse microbial groups. We determined the impact of a decrease in soil microbial diversity on the stability (i.e. resistance and resilience following disturbance) of two more specialized bacterial functional groups: denitrifiers and nitrite oxidizers. Soil microbial diversity was reduced using serial dilutions of a suspension obtained from a non-sterile soil that led to loss of species with low cell abundance, inoculation of microcosms of the same sterile soil with these serial dilutions, and subsequent incubation to enable establishment of similar cell abundances between treatments. The structure, cell abundance and activity of denitrifying and nitrite-oxidizing communities were characterized after incubation. Increasing dilution led to a progressive decrease in community diversity as assessed by the number of denaturating gradient gel electrophoresis (DGGE) bands, while community functioning was not impaired when cell abundance recovered after incubation. The microcosms were then subjected to a model disturbance: heating to 42 degrees C for 24 h. Abundance, structure and activity of each community were measured 3 h after completion of the disturbance to assess resistance, and after incubation of microcosms for 1 month to assess resilience. Resistance and resilience to the disturbance differed between the two communities, nitrite oxidizers being more affected. However, reducing the diversity of the two microbial functional groups did not impair either their resistance or their resilience following the disturbance. These results demonstrate the low sensitivity of the resistance and resilience of both microbial groups to diversity decline provided that cell abundance is similar between treatments.     

Effect of an introduced inoculum on soil microbial diversity

Abstract A laboratory study was carried out to evaluate the impact of the introduction of genetically modified microorganisms into soil, in terms of effect on the diversity of the indigenous microflora, and at the process level. The impact on microbial phenotypic diversity, and on soil denitrification of an inoculum of a lux -modified denitrifier, Pseudomonas fluorescens , was examined using two different soil types in re-packed soil microcosms. The effect on diversity was found to depend on the soil pore size class into which the modified inoculum was introduced. The introduction of lux -modified cells into the 15–30 μm pore neck size class caused a short-term reduction in the overall microbial diversity. There was no significant change in the diversity of the indigenous microbial community, however, when cells were introduced into the 40–60 μm pore class. Partial chloroform fumigation proved useful in differentiating cell populations with respect to pore location. No change in diversity was observed when dead cells (either heat killed or glutaraldehyde fixed) were introduced into either pore size class. At the process level, the effect on soil denitrification of introduction of lux -modified P. fluorescens was not significantly different from introduction of the equivalent inoculum of the parental wild-type, although denitrification was found to be dependent upon both soil structure and pore size location of the introduced inoculum.     

The effects of pesticides on the diversity of culturable soil bacteria

The numbers of culturable soil bacteria in plots that had received either no pesticides or the full combination (aldicarb, chlorfenvinphos, benomyl, glyphosate, plus chlorotoluron or triadimefon) over a 20 year period were compared. Differences were very small although there were consistently higher numbers on the treated plot, possibly reflecting the greater crop yields which had been reported previously. There was no significant difference in numbers of bacterial colonies with homology to a nif gene probe in soils from the two plots. Genetic fingerprinting of Pseudomonas fluorescens isolates from the plots, using ERIC-PCR, showed that the dominant strains in the two populations were not the same although there was no obvious difference in the degree of diversity. Substrate utilization by microbial populations from the two plots was compared using Biolog plates. The population from the pesticide-treated plot showed a higher rate of substrate utilization which could reflect a slightly higher inoculum of heterotrophic bacteria, but could also indicate greater metabolic diversity in the population.     

土壤样品长期保存对微生物群落代谢活性和功能类群的影响

【目的】评估土壤长期保存(4个月)对土壤微生物群落代谢活性的影响。【方法】采用Biolog? EcoPlateTM生态板研究4 °C风干保存和?20 °C低温冻存的农田土壤和森林土壤中微生物群落的碳源利用模式。【结果】与新鲜土壤样品相比,长期保存的土壤样品的微生物群落对碳源的利用能力大大降低,其多样性、均匀度和Simpson指数均降低;风干保存和低温冻存两者对土壤微生物的碳源利用的影响没有显著差异;除风干保存的土壤样品中利用多聚物类的微生物类群的代谢活性外,两种保存方法显著降低微生物群落的代谢活性,降低幅度为54.5%–99.8%。【结论】长期保存土壤可能会导致对微生物群落信息的低估,土壤微生物代谢活性研究的最佳样品为新鲜 土壤。     

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly

The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.     

Effect of introducing genetically engineered microorganisms on soil microbial community diversity

Abstract Introducing the genetically engineered microorganism Pseudomonas cepacia AC1100 into soil microcosms resulted in elevated taxonomic diversity determined by phenotypic analyses of culturable isolates and genetic diversity determined by analysis of the heterogeneity of total microbial community DNA reannealing kinetics. The greatest impact occurred when P. cepacia AC1100 was introduced along with the herbicide 2,4,5-T, which P. cepacia AC1100 can degrade. The data suggests that both changes in the balance of populations and genetic recombination contributed to the increased diversity.     

Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities

Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.     

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential.     

Biolog和PCR-DGGE技术解析施肥对德惠黑土细菌群落结构和功能的影响

试验采用Biolog和PCR-DGGE技术研究了不同施肥处理对吉林省德惠市黑土细菌群落结构和功能的影响.Biolog试验结果表明,单施有机肥处理的土壤细菌群落对底物碳源利用种类最多,代谢功能多样性最高;而施用化肥处理降低了土壤细菌群落代谢功能.DGGE图谱表明,不同施肥处理的土壤细菌16S rDNA多数条带分布相同,说明这些细菌类群在黑土中较稳定,在本试验中未受到施肥的影响,但也有一些特殊条带出现或缺失,施用化肥处理降低了土壤细菌群落结构组成多样性.对Biolog和DGGE试验结果的主成分分析显示,未施肥和单施有机肥处理的土壤细菌群落结构和功能相似,表明单施有机肥处理主要是增加了土壤微生物的总量,而对黑土细菌群落结构组成影响是次要的;单施化肥和半量有机肥 化肥处理的土壤细菌群落代谢功能多样性相似,但其结构组成产生了分离.研究表明化肥处理主要是影响到土壤中快速生长和富营养的细菌类群,施用化肥降低了这些细菌类群的代谢活性.     

Reduction of perchlorate and nitrate by microbial communities in vadose soil

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.