Dynamics of microbial community during bioremediation of phenanthrene and chromium(VI)-contaminated soil microcosms

The combined effect of phenanthrene and Cr(VI) on soil microbial activity, community composition and on the efficiency of bioremediation processes has been studied. Biometer flask systems and soil microcosm systems contaminated with 2,000 mg of phenanthrene per kg of dry soil and different Cr(VI) concentrations were investigated. Temperature, soil moisture and oxygen availability were controlled to support bioremediation. Cr(VI) inhibited the phenanthrene mineralization (CO₂ production) and cultivable PAH degrading bacteria at levels of 500–2,600 mg kg⁻¹. In the bioremediation experiments in soil microcosms the degradation of phenanthrene, the dehydrogenase activity and the increase in PAH degrading bacteria counts were retarded by the presence of Cr(VI) at all studied concentrations (25, 50 and 100 mg kg⁻¹). These negative effects did not show a correlation with Cr(VI) concentration. Whereas the presence of Cr(VI) had a negative effect on the phenanthrene elimination rate, co-contamination with phenanthrene reduced the residual Cr(VI) concentration in the water exchangeable Cr(VI) fraction (WEF) in comparison with the soil microcosm contaminated only with Cr(VI). Clear differences were found between the denaturing gradient gel electrophoresis (DGGE) patterns of each soil microcosm, showing that the presence of different Cr(VI) concentrations did modulate the community response to phenanthrene and caused perdurable changes in the structure of the microbial soil community.     

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO₂ production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5°C monthly maximum air temperature, +50 mm yr^-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q₁₀ of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.     

Effect of a Sinorhizobium meliloti Strain with a Modified putA Gene on the Rhizosphere Microbial Community of Alfalfa

The success of a rhizobial inoculant in the soil depends to a large extent on its capacity to compete against indigenous strains. M403, a Sinorhizobium meliloti strain with enhanced competitiveness for nodule occupancy, was recently constructed by introducing a plasmid containing an extra copy of a modified putA (proline dehydrogenase) gene. This strain and M401, a control strain carrying the same plasmid without the modified gene, were used as soil inoculants for alfalfa in a contained field release experiment at León, Spain. In this study, we determined the effects of these two strains on the indigenous microbial community. 16S rRNA genes were obtained from the rhizosphere of alfalfa inoculated with strain M403 or strain M401 or from noninoculated plants by amplification of DNA from soil with bacterial group-specific primers. These genes were analyzed and compared by restriction fragment length polymorphism and temperature gradient gel electrophoresis. The results allowed us to differentiate between alterations in the microbial community apparently caused by inoculation and by the rhizosphere effect and seasonal fluctuations induced by the alfalfa plants and by the environment. Only moderate inoculation-dependent effects could be detected, while the alfalfa plants appeared to have a much stronger influence on the microbial community.     

Relationships Between Microbial Community Structure and Soil Processes Under Elevated Atmospheric Carbon Dioxide

There is little current understanding of the relationship between soil microbial community composition and soil processes rates, nor of the effect climate change and elevated CO₂ will have on microbial communities and their functioning. Using the eastern cottonwood (Populus deltoides) plantation at the Biosphere 2 Laboratory, we studied the relationships between microbial community structure and process rates, and the effects of elevated atmospheric CO₂ on microbial biomass, activity, and community structure. Soils were sampled from three treatments (400, 800, and 1200 ppm CO₂), a variety of microbial biomass and activity parameters were measured, and the bacterial community was described by 16S rRNA libraries. Glucose substrate-induced respiration (SIR) was significantly higher in the 1200 ppm CO₂ treatment. There were also a variety of complex, nonlinear responses to elevated CO₂. There was no consistent effect of elevated CO₂ on bacterial diversity; however, there was extensive variation in microbial community structure within the plantation. The southern ends of the 800 and 1200 ppm CO₂ bays were dominated by β-Proteobacteria, and had higher fungal biomass, whereas the other areas contained more α-Proteobacteria and Acidobacteria. A number of soil process rates, including salicylate, glutamate, and glycine substrate-induced respiration and proteolysis, were significantly related to the relative abundance of the three most frequent bacterial taxa, and to fungal biomass. Overall, variation in microbial activity was better explained by microbial community composition than by CO₂ treatment. However, the altered diversity and activity in the southern bays of the two high CO₂ treatments could indicate an interaction between CO₂ and light.     

Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa

The success of a rhizobial inoculant in the soil depends to a large extent on its capacity to compete against indigenous strains. M403, a Sinorhizobium meliloti strain with enhanced competitiveness for nodule occupancy, was recently constructed by introducing a plasmid containing an extra copy of a modified putA (proline dehydrogenase) gene. This strain and M401, a control strain carrying the same plasmid without the modified gene, were used as soil inoculants for alfalfa in a contained field release experiment at León, Spain. In this study, we determined the effects of these two strains on the indigenous microbial community. 16S rRNA genes were obtained from the rhizosphere of alfalfa inoculated with strain M403 or strain M401 or from noninoculated plants by amplification of DNA from soil with bacterial group-specific primers. These genes were analyzed and compared by restriction fragment length polymorphism and temperature gradient gel electrophoresis. The results allowed us to differentiate between alterations in the microbial community apparently caused by inoculation and by the rhizosphere effect and seasonal fluctuations induced by the alfalfa plants and by the environment. Only moderate inoculation-dependent effects could be detected, while the alfalfa plants appeared to have a much stronger influence on the microbial community.     

Can commercial soil microbial treatments remediate plant–soil feedbacks to improve restoration seedling performance?

Seedling performance is often a limiting factor in ecological restoration. Changes in the soil microbial community generated by invasive plants contribute to seedling failure. A method to remediate invasive species‐induced changes to the soil microbial community that results in increased native species seedling performance and decreased invasive species seedling performance could have a large impact on the success of many restoration efforts. In a greenhouse experiment, we first examined the changes in the soil microbial community created by invasive compared to native grasses. Then, we investigated four microbial treatments (bacterial inoculant, fungal inoculant, fungicide, and bactericide/fungicide) to remediate microbial plant–soil feedbacks (PSFs) created by invasive species Bromus inermis and Poa pratensis and increase the performance of natives Andropogon gerardii, Elymus canadensis, Pascopyrum smithii, and Schizachyrium scoparium. We found that the PSF mitigation treatments had some context‐dependent utility for restoration. For example, all of the treatments decreased the performance of B. inermis and fungal inoculant decreased the performance of P. pratensis. However, no single treatment increased the performance of all natives. Fungicide increased the performance of A. gerardii and E. canadensis in soil previously occupied by B. inermis and the performance of S. scoparium in soil previously occupied by P. pratensis. If validated in the field, PSF mitigation treatments may have utility for restoration practitioners.     

低分子有机酸对土壤中菲降解及细菌群落结构的影响

多环芳烃是一类普遍存在于环境中的持久性有机污染物,其通过食物链进入生态系统,直接危害人类健康和整个生态系统的安全。为探讨低分子有机酸对土壤中菲降解及细菌群落结构的影响,通过室内培养的方式研究了在添加不同种类有机酸处理下第0—180天土壤中菲含量的变化状况,并采用高通量Illumina Miseq技术分析了土壤细菌群落种类和数量的变化特征。结果表明,低分子有机酸对于土壤中菲的降解有明显的促进作用,由一级动力学方程得出乙酸对菲降解的促进作用最明显。从细菌群落结构来看,土壤细菌的数量及其多样性或许不是导致土壤菲降解的主要因素,反而特定的菲降解菌的丰度对菲降解有重要影响。添加低分子有机酸减少了细菌OTU数及细菌菌群多样性,但增加了PAHs降解菌的丰度。随着时间推移细菌总OTU数呈现下降趋势,独有种类数均呈现出先增长后下降的趋势。检测到了6种典型的菲降解菌,分别为:Bacillus、鞘氨醇单胞菌属、Massilia、Azospirillum、Burkholderia-paraburkholderia、红球菌。研究结果可为多环芳烃污染土壤的植物修复提供基础数据和科学参考。     

Variation of Microbial Rhizosphere Communities in Response to Crop Species, Soil Origin, and Inoculation with Sinorhizobium meliloti L33

Abstract A greenhouse study with soil–plant microcosms was conducted in order to compare the effect of crop species, soil origin, and a bacterial inoculant on the establishment of microbial communities colonizing plant roots. Two crop species, alfalfa (Medicago sativa) and rye (Secale cereale), were grown separately in two soils collected from agricultural fields at different locations and with differing histories of leguminous crop rotation. A subset of microcosms was inoculated at 10⁶ cfu g^-1 soil with the luciferase marker gene-tagged Sinorhizobium meliloti strain L33, a symbiotic partner of M. sativa. Microbial consortia were collected from the rhizospheres of alfalfa after 10 weeks of incubation and from rye after 11 weeks. S. meliloti L33 populations were one to two orders of magnitude higher in the rhizospheres of alfalfa than of rye. In soil with previous alfalfa cultivation, 80% of the alfalfa nodules were colonized by indigenous bacteria, while in the other soil alfalfa was colonized almost exclusively (>90%) with S. meliloti L33. Three community-level targeting approaches were used to characterize the variation of the extracted microbial rhizosphere consortia: (1) Community level physiological profiles (CLPP), (2) fatty acid methyl ester analysis (FAME), and (3) diversity of PCR amplified 16S rRNA target sequences from directly extracted ribosomes, determined by temperature gradient gel electrophoresis (TGGE). All approaches identified the crop species as the major determinant of microbial community characteristics. Consistently, the influence of soil was of minor importance, while a modification of the alfalfa-associated microbial community structure after inoculation with S. meliloti L33 was only consistently observed by using TGGE. Received: 20 October 1999; Accepted: 15 January 2000; Online Publication: 18 July 2000     

Soil Amendment with <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> CHA0: Lasting Effects on Soil Biological Properties in Soils Low in Microbial Biomass and Activity

Pseudomonas fluorescens strains are used in agriculture as plant growth-promoting rhizobacteria (PGPR). Nontarget effects of released organisms should be analyzed prior to their large-scale use, and methods should be available to sensitively detect possible changes in the environments the organism is released to. According to ecological theory, microbial communities with a greater diversity should be less susceptible to disturbance by invading organisms. Based on this principle, we laid out a pot experiment with field-derived soils different in their microbial biomass and activity due to long-term management on similar parent geological material (loess). We investigated the survival of P. fluorescens CHA0 that carried a resistance toward rifampicine and the duration of potential changes of the soil microflora caused by the inoculation with the bacterium at the sowing date of spring wheat. Soil microbial biomass (C _mic, N _mic) basal soil respiration (BR), qCO₂, dehydrogenase activity (DHA), bacterial plate counts, mycorrhiza root colonization, and community level substrate utilization were analyzed after 18 and 60 days. At the initial stage, soils were clearly different with respect to most of the parameters measured, and a time-dependent effect between the first and the second set point were attributable to wheat growth and the influence of roots. The effect of the inoculum was small and merely transient, though significant long-term changes were found in soils with a relatively low level of microbial biomass. Community level substrate utilization as an indicator of changes in microbial community structure was mainly changed by the growth of wheat, while other experimental factors were negligible. The sensitivity of the applied methods to distinguish the experimental soils was in decreasing order N _mic, DHA, C _mic, and qCO₂. Besides the selective enumeration of P. fluorescens CHA0 rif⁺, which was only found in amended soils, methods to distinguish the inoculum effect were DHA, C _mic, and the ratio of C _mic to N _mic. The sampling time was most sensitively indicated by N _mic, DHA, C _mic, and qCO₂. Our data support the hypothesis—based on ecosystem theory—that a rich microflora is buffering changes due to invading species. In other words, a soil-derived bacterium was more effective in a relatively poor soil than in soils that are rich in microorganisms.     

Survival of a novel endophytic fungus Phomopsis liquidambari B3 in the indole-contaminated soil detected by real-time PCR and its effects on the indigenous microbial community

The recently isolated fungal strain Phomopsis liquidambari B3 can degrade high concentrations of indole, indicating its potential for the bioremediation of indole-contaminated soil. In this study, a specific real-time PCR was developed to detect the survival of P. liquidambari B3 in soil. Subsequently, degradation activity of strain B3 and its effects on indigenous microbial community were analyzed. Results showed the amount of P. liquidambari B3 genomic DNA increased to a maximum 5.67 log (pg g⁻¹ dry soil) 10 days after inoculation of 5.04 log (pg g⁻¹ dry soil), and then gradually decreased with time and after 40 days it was below the detection limit. By the end of the experiment (day 40), bioaugmented microsoms showed a 93.7% decrease in indole, while the values for biostimulated and control microcosms were much lower. Higher microbial biomass and enzyme activities were observed in bioaugmented soil. Denaturing gradient gel electrophoresis analysis showed bioaugmentation increased richness of resident microbial community. These results indicate that P. liquidambari B3 is effective for the remediation of indole-contaminated soil and also provides valuable information about the behavior of the inoculant population during bioremediation, which could be directly used in the risk assessment of inoculant population and optimization of bioremediation process.     

Effect of Metal Oxide Nanoparticles on Microbial Community Structure and Function in Two Different Soil Types

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe₃O₄) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe₃O₄ changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.     

Different Degrees of Plant Invasion Significantly Affect the Richness of the Soil Fungal Community

Several studies have shown that soil microorganisms play a key role in the success of plant invasion. Thus, ecologists have become increasingly interested in understanding the ecological effects of biological invasion on soil microbial communities given continuing increase in the effects of invasive plants on native ecosystems. This paper aims to provide a relatively complete depiction of the characteristics of soil microbial communities under different degrees of plant invasion. Rhizospheric soils of the notorious invasive plant Wedelia trilobata with different degrees of invasion (uninvaded, low-degree, and high-degree using its coverage in the invaded ecosystems) were collected from five discrete areas in Hainan Province, P. R. China. Soil physicochemical properties and community structure of soil microorganisms were assessed. Low degrees of W. trilobata invasion significantly increased soil pH values whereas high degrees of invasion did not significantly affected soil pH values. Moreover, the degree of W. trilobata invasion exerted significant effects on soil Ca concentration but did not significantly change other indices of soil physicochemical properties. Low and high degrees of W. trilobata invasion increased the richness of the soil fungal community but did not pose obvious effects on the soil bacterial community. W. trilobata invasion also exerted obvious effects on the community structure of soil microorganisms that take part in soil nitrogen cycling. These changes in soil physicochemical properties and community structure of soil microbial communities mediated by different degrees of W. trilobata invasion may present significant functions in further facilitating the invasion process.     

Soil microbiome responses to the short‐term effects of Amazonian deforestation

Slash‐and‐burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear‐cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism‐related functions. Co‐occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash‐and‐burning deforestation in the Amazon region.     

Elevated Atmospheric CO2 Alters Soil Microbial Communities Associated with Trembling Aspen (Populus tremuloides) Roots

Global atmospheric CO₂ levels are expected to double within the next 50 years. To assess the effects of increased atmospheric CO₂ on soil ecosystems, cloned trembling aspen (Populus tremuloides) seedlings were grown individually in 1 m³ open bottom root boxes under either elevated (720 ppm, ELEV) or ambient CO₂ (360 ppm, AMB). After 5 years, soil cores (40 cm depth) were collected from the root boxes and divided into 0–20 cm and 20–40 cm fractions. ELEV treatment resulted in significant decreases in both soil nitrate and total soil nitrogen in both the 0–20 cm and 20–40 cm soil fractions, with a 47% decrease in soil nitrate and a 50% decrease in total soil nitrogen occurring in the 0–20 cm fraction. ELEV treatment did not result in a significant change in the amount of soil microbial biomass. However, analysis of indicator phospholipid fatty acids (PLFA) indicated that ELEV treatment did result in significant increases in PLFA indicators for fungi and Gram-negative bacteria in the 0–20 cm fraction. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to analyze the composition of the soil bacterial communities (using primers targeting the 16SrRNA gene) and the soil fungal communities (using primers targeting the intergenic transcribed spacer region). T-RFLP analysis revealed shifts in both bacterial and fungal community structure, as well as increases in both bacterial and fungal species richness with ELEV treatment. These results indicated that increased atmospheric CO₂ had significant effects on both soil nutrient availability and the community composition of soil microbes associated with aspen roots.     

Pyrene and Phenanthrene Influence on Soil Microbial Populations

Two studies were conducted to evaluate microbial populations in polycyclic aromatic hydrocarbon-contaminated soil. Captina silt loam was freshly exposed to (1) 0 or 2000?mg pyrene/kg and sampled after 10- and 61-wk incubation and (2) 0 or 505?mg pyrene + 445?mg phenanthrene/kg and sampled after a 21-wk incubation. Microbial numbers were determined by plate-count techniques. Isolated bacteria, selected degraders, and wholesoil extracts were analyzed by fatty acid methyl ester analysis (FAME). In the pyrene experiment, pyrene did not affect total bacterial or fungal numbers, but pyrene degraders increased from undetectable levels to 7.09 log₁₀ degraders/g in the contaminated soil. The FAME analysis of bacterial isolates detected no pyrene effect, but wholesoil FAME indicated an increase in the contaminated soil of a fatty acid characteristic of protozoa and a major fatty acid detected in isolated degraders. In the pyrene + phenanthrene experiment, the contaminants had no impact on bacterial, fungal, or actinomycete numbers but increased degrader numbers. No effect of pyrene + phenanthrene was detected by isolate FAME, but whole-soil FAME indicated an effect similar to that in the pyrene experiment. The results indicate that pyrene, although not impacting microbial numbers, may have altered the soil microbial composition and that Captina silt loam can develop an effective degrader population under tested conditions.     

联合固氮菌叶面接种剂的优化及其在玉米叶际的定殖

【背景】联合固氮菌由于不具有宿主专一性,在土壤、叶际中广泛存在,对生态系统氮素供应有着重要贡献,它还可以通过分泌生长激素等间接作用促进植物生长,可作为重要的农业生产菌剂。土壤接种剂由于受土著微生物的竞争和土壤抑菌物质等的影响,接种效果不稳定,难以推广使用。相比于土壤环境,叶际生境相对简单且表面积巨大,进行叶际接种是固氮菌剂推广应用的一个新思路。【目的】优化联合固氮菌菌株W12接种添加剂,制备液体接种剂并研究其在玉米叶际的定殖效果。【方法】对菌株W12进行菌落PCR测序,构建系统发育树并确定分类地位。分别在培养液中添加不同浓度梯度的羧甲基纤维素(Carboxymethyl cellulose,CMC)和甘油(Glycerol,Gly),测量菌株W12生长曲线和固氮酶活性,优化添加剂浓度并制备液体接种剂,对接种剂的有效保存时间进行检测。将接种剂喷洒到玉米叶际,测量其对玉米产量和植株含氮量的影响,并通过低氮培养基进行回收计数。【结果】固氮菌菌株W12的16S r RNA基因序列与变栖克雷伯氏菌(Klebsiella variicola)的相似性高达99%,在培养液中添加CMC和甘油对菌株W12的生长无明显促进和抑制效果,但均提高了固氮酶活性。添加甘油制备的接种剂在盆栽和大田玉米叶面喷施后,在玉米生长末期叶际回收到的W12类似菌分别为4.3×105 CFU/g叶片和1.7×105 CFU/g叶片,显著高于未接种的处理;而且大田玉米籽粒、茎部和叶片的含氮量高于不接种的对照处理。经过90 d贮藏后,4°C保存的接种剂剩余活菌数均高于1.0×108 CFU/m L。【结论】羧甲基纤维素和甘油的添加不仅有利于固氮菌液体接种剂在叶片的附着,并能显著提高联合固氮菌菌株W12的固氮酶活性,低温冷藏可保证液体接种剂的有效活菌数;液体接种剂在玉米叶际喷施后,菌株W12能够成功定殖,并显著提高玉米植株和籽粒含氮量。研究结果为固氮菌叶面接种剂的制备和应用,以及实现农业氮肥减施保产的目标提供了借鉴意义。     

Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.     

Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community

The naphthalene-degrading activity of a Pseudomonas sp. strain isolated from a creosote-contaminated soil was shown to be encoded by the IncP9 plasmid pNF142 by transfer to Pseudomonas putida KT2442. The effects of the inoculant strain KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community were studied in microcosms with the following treatments: (I) soil, (II) soil with naphthalene, (III) soil with naphthalene and inoculated with KT2442 (pNF142). The inoculant became the dominant bacterial population in treatment (III) as evidenced by cultivation and denaturing gradient gel electrophoresis (DGGE) analysis. The bacterial DGGE profiles revealed drastically reduced complexity due to the numerical dominance of the inoculant. However, group-specific fingerprints (beta-proteobacteria, actinobacteria) that excluded KT2442 (pNF142) showed less severe changes in the bacterial community patterns. A major effect of naphthalene on the soil bacterial community was observed in treatment (II) after 21 days. Two dominant bands appeared whose sequences showed the highest similarity to those of Burkholderia sp. RP007 and Nocardia vinaceae based on 16S rRNA gene sequencing. These bands were less intense in treatment (III). The increased abundance of RP007-like populations due to naphthalene contamination was also confirmed by PCR amplification of the phnAc gene. The nahAc and nahH genes were detected in DNA and cDNA only in treatment III. Although the inoculant strain KT2442 (pNF142) showed good survival and expression of genes involved in naphthalene degradation, this study suggests that KT2442 (pNF142) suppressed the enrichment of indigenous naphthalene degraders.     

Vertical Distribution and Activity of Soil Microbial Population in a Sandy Desert Ecosystem

The vertical distribution of a microbial community on a temporal and spatial (vertical) scale under the Tamarix aphylla salt-resistant plant was studied. The uniqueness of this plant is in the creation of “islands of salinity” beneath the plant, due to salt excretion and leaf shedding at the plant base. Our working hypothesis was that the activity and biomass of the soil microbial population and the ratio between bacterial biomass and fungal biomass will decrease toward the driest season. Soil samples were collected beneath and between plants under the T. aphylla canopy down to the 0- to 50-cm depth at 10-cm intervals. The substrate-induced respiration method was used to estimate the total soil microbial biomass (MB), CO₂ evolution, metabolic quotient (qCO₂) index, and MB of both the fungal and bacterial communities. A significant difference was observed (p < 0.05) in MB and qCO₂ index between the different soil layers in the control samples, whereas there was no significant difference in the soil samples in the vicinity of the plant (p > 0.05) between the depths, due to the plant rhizosphere effect.     

The Impact of Biofumigation and Chemical Fumigation Methods on the Structure and Function of the Soil Microbial Community

Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.