Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system

Widespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean-up strategy. However, few bioremediation studies have investigated the behaviour of the indigenous PAH-degrading community after long-term exposure to a PAH. In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene ( approximately 1.2 mg l-1) for a 6-month period to examine the temporal response of the indigenous phenanthrene-degrading community. Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders. Phenanthrene-degrading isolates were grouped by colony morphology. For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level. Twenty-five phenanthrene-degrading isolates, potentially representing 19 genera, were obtained from this analysis. Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus. Results indicate that the dominant phenanthrene-degrading population changed over the course of this 6-month experiment. Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment. Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples. This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable.     

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。     

Factors affecting the microbial degradation of phenanthrene in soil

Summary Because phenanthrene was mineralized more slowly in soils than in liquid media, a study was conducted to determine the environmental factors that may account for the slow biodegradation in soil. Mineralization was enhanced by additions of phosphate but not potassium, and it was reduced by additions of nitrate. Aeration or amending the soil with glucose affected the rate of mineralization, although not markedly. Phenanthrene was sorbed to soil constituents, the extent of sorption being directly related to the percentage of organic matter in the soil. Soluble phenanthrene was not detected after addition of the compound to a muck soil. The rate of mineralization was slow in the organic soil and higher in mineral soils with lower percentages of organic matter. We suggest that sorption by soil organic matter slows the biodegradation of polycyclic aromatic hydrocarbons that are otherwise readily metabolized. Offprint requests to: M. Alexander     

Relationship between bacterial diversity and function under biotic control: the soil pesticide degraders as a case study

In soil, the way biotic parameters impact the relationship between bacterial diversity and function is still unknown. To understand these interactions better, we used RNA-based stable-isotope probing to study the diversity of active atrazine-degrading bacteria in relation to atrazine degradation and to explore the impact of earthworm-soil engineering with respect to this relationship. Bulk soil, burrow linings and earthworm casts were incubated with ¹³C-atrazine. The pollutant degradation was quantified by liquid chromatography–mass spectrometry for 8 days, whereas active atrazine degraders were identified at 2 and 8 days by sequencing the 16S ribosomal RNA in the ¹³C-RNA fractions from the three soil microsites. An original diversity of atrazine degraders was found. Earthworm soil engineering greatly modified the taxonomic composition of atrazine degraders with dominance of α-, β- and γ-proteobacteria in burrow linings and of Actinobacteria in casts. Earthworm soil bioturbation increased the γ-diversity of atrazine degraders over the soil microsites generated. Atrazine degradation was enhanced in burrow linings in which primary atrazine degraders, closely related to Pelomonas aquatica, were detected only 2 days after atrazine addition. Atrazine degradation efficiency was not linearly related to the species richness of degraders but likely relied on keystone species. By enhancing soil heterogeneity, earthworms sustained high phylogenetic bacterial diversity and exerted a biotic control on the bacterial diversity–function relationships. Our findings call for future investigations to assess the ecological significance of biotic controls on the relationships between diversity and function on ecosystem properties and services (for example, soil detoxification) at larger scales.     

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty‐five 1 m² plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.     

蚯蚓对细菌降解土壤中菲的作用

通过30d室内培养试验,分别研究了接种蚯蚓(E)、细菌(B)以及同时接种细菌和蚯蚓(BE)对土壤中菲降解的影响.结果表明: 在土壤中菲的初始污染浓度为50 mg*kg-1的条件下,各处理间菲的降解率差异显著,其降解率的大小顺序依次为:BE》B》E》CK(对照); 在150 mg*kg-1菲的初始污染浓度下,BE处理中菲的降解率高达98.86%,显著高于CK和E处理.B处理中细菌的双加氧酶活性在3种菲初始污染浓度下没有显著差异,而BE处理中双加氧酶的活性随着土壤中菲的初始污染浓度的升高而增加.在相同菲污染浓度下BE处理中蚯蚓体内的菲含量明显高于E处理.表明蚯蚓能够通过生物富集作用降低土壤中菲的浓度,而蚯蚓与细菌的相互作用能够进一步促进土壤中菲的降解.     

Coevolution with phages does not influence the evolution of bacterial mutation rates in soil

Coevolution with phages drive the evolution of high bacterial mutation rates in vitro, but the relevance of this finding to natural populations is unclear. Here, we investigated how coevolution affects mutation rate evolution in soil, in the presence and absence of the rest of the natural microbial community. Although mutation rate on average increased threefold, neither coevolving phages nor the rest of natural community significantly affected mutation rates. Our results suggest that features of the soil over and above directly interacting organisms constrain the evolution of strong mutators, helping to explain their relatively low frequency compared with some laboratory and clinical settings.     

Metabolic diversity in bacterial degradation of aromatic compounds

Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.     

Current plant diversity but not its soil legacy influences exotic plant invasion

植物多样性而非其土壤遗留效应影响外来植物入侵 植物多样性可以影响外来植物入侵,然而植物多样性的土壤遗留效应是否能够影响外来植物入侵目前仍不清楚。植物多样性能够改变土壤微生物群落和土壤理化性质,这种遗留效应可能会对该土壤中外来植物的生长产生影响。因此,我们假设植物多样性的土壤遗留效应会影响外来植物的入侵。为了检验该假说,我们开展了一个两阶段的植物-土壤反馈实验。在土壤驯化阶段,我们将12个植物物种(4种禾草植物、3种豆科植物和5种杂类草植物)分别单独种植,或者随机选择8个物种(包含3个功能型)混合种植在土壤中。在反馈阶段,我们将入侵植物三叶鬼针草(Bidens pilosa)分别与本地禾草荩草(Arthraxon hispidus)、本地杂类草翅果菊(Pterocypsela indica)或者同时与荩草和翅果菊种植在被驯化过的土壤中。研 究结果显示,三叶鬼针草相对于其本地竞争植物的生长取决于驯化植物和竞争植物物种的功能型。驯化植物的多样性对三叶鬼针草与其本地竞争植物之间的生长差异没有显著影响。然而,随着本地竞争植物物种多样性的增加,三叶鬼针草相对于其本地竞争植物的生长显著降低。这些结果表明,当前的植物多样性可以通过增加入侵植物和本地植物之间的生长不平衡性来减少外来植物的入侵。但是,植物多样性的土壤遗留效应对外来植物入侵的影响可能很小。     

Effect of copper on the degradation of phenanthrene by soil micro-organisms

AIMS: The effect of copper on the degradation by soil micro-organisms of phenanthrene, a polycyclic aromatic hydrocarbon, was investigated. METHODS AND RESULTS: Inert nylon filters were incubated in the soil for 28 days at 25 degrees C. Each filter was inoculated with a soil suspension, phenanthrene (400 ppm), copper (0, 70, 700 or 7000 ppm) and nitrogen/phosphorus sources. The filters were assessed for phenanthrene degradation, microbial respiration and colonization. Phenanthrene degradation proceeded even at toxic copper levels (700/7000 ppm), indicating the presence of phenanthrene-degrading, copper-resistant and/or -tolerant microbes. However, copper at these high levels reduced microbial activity (CO2 evolution). CONCLUSION: High levels of copper caused an incomplete mineralization of phenanthrene and possible accumulation of its metabolites. SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of heavy metals in soils could seriously affect the bioremediation of PAH-polluted environments.     

The degradation of the herbicide bromoxynil and its impact on bacterial diversity in a top soil

Aims: To study how repeated applications of an herbicide bromoxynil to a soil, mimicking the regime used in the field, affected the degradation of the compound and whether such affects were reflected by changes in the indigenous bacterial community present. Methods and Results: Bromoxynil degradation was monitored in soil microcosms using HPLC. Its impact on the bacterial community was determined using denaturing gradient gel electrophoresis (DGGE) and quantitative PCR of five bacterial taxa (Pseudomonads, Actinobacteria, α‐Proteobacteria, Acidobacteria and nitrifying bacteria). Three applications of 10 mg kg^?1 of bromoxynil at 28‐day intervals resulted in rapid degradation, the time for removal of 50% of the compound decreasing from 6·4 days on the first application to 4·9 days by the third. Bacterial population profiles showed significant similarity throughout the experiment. With the addition of 50 mg kg^?1 bromoxynil to soil, the degradation was preceded by a lag phase and the time for 50% of the compound to be degraded increased from 7 days to 28 days by the third application. The bacterial population showed significant differences 7 days after the final application of bromoxynil that correlated with an inhibition of degradation during the same period. Conclusions: These analyses highlighted that the addition of bromoxynil gave rise to significant shifts in the community diversity and its structure as measured by four abundant taxa, when compared with the control microcosm. These changes persisted even after bromoxynil had been degraded. Significance and Impact of the Study: Here we show that bromoxynil can exert an inhibitory effect on the bacterial population that results in decreased rates of degradation and increased persistence of the compound. In addition, we demonstrate that molecular approaches can identify statistically significant changes in microbial communities that occur in conjunction with changes in the rate of degradation of the compound in the soil.     

Light availability affects stream biofilm bacterial community composition and function,but not diversity

Changes in riparian vegetation or water turbidity and browning in streams alter the local light regime with potential implications for stream biofilms and ecosystem functioning. We experimented with biofilms in microcosms grown under a gradient of light intensities (range: 5–152 μmole photons s^?1 m^?2) and combined 454‐pyrosequencing and enzymatic activity assays to evaluate the effects of light on biofilm structure and function. We observed a shift in bacterial community composition along the light gradient, whereas there was no apparent change in alpha diversity. Multifunctionality, based on extracellular enzymes, was highest under high light conditions and decoupled from bacterial diversity. Phenol oxidase activity, involved in the degradation of polyphenolic compounds, was twice as high on average under the lowest compared with the highest light condition. This suggests a shift in reliance of microbial heterotrophs on biofilm phototroph‐derived organic matter under high light availability to more complex organic matter under low light. Furthermore, extracellular enzyme activities correlated with nutrient cycling and community respiration, supporting the link between biofilm structure–function and biogeochemical fluxes in streams. Our findings demonstrate that changes in light availability are likely to have significant impacts on biofilm structure and function, potentially affecting stream ecosystem processes.     

Hydrocarbon degradation in relation to cell-surface hydrophobicity among bacterial hydrocarbon degraders from petroleum-contaminated Kuwait desert environment

Forty six bacterial isolates able to grow on crude oil were isolated from various hydrocarbon-contaminated sites in Kuwait. The extent of crude oil degradation varied over a wide range (1–87%) among the isolates. Isolates were predominantly Gram-positive bacteria (79% of total isolates) belonging to the genera Bacillus (93%) and Paenibacillus (7%). Among the few Gram-negative isolates were from the genera Acinetobacter, Alcaligenes, Klebsiella, Burkholderia, Pseudomonas, and Williamsia. Analyses of their cell-surface hydrophobicity (CSH) by various methods equally showed a wide variation among the isolates. About 74% of isolates that degraded significant amounts of crude oil (>40% degradation) possessed high level of CSH, while 58% of all the isolates exhibited high levels of CSH. Statistical analyses showed significantly high correlation between the ability to degrade crude oil and CSH. The ability of the isolates to bind to polystyrene and salt-aggregation test as measures of CSH were more strongly correlated with hydrocarbon-degrading ability than adherence to hydrocarbons.     

土壤中多环芳烃的微生物降解及土壤细菌种群多样性

利用室内模拟方法,研究中、低浓度多环芳烃(PAHs)污染土壤的微生物修复效果,阐明土壤微生物（接种和土著）与PAHs降解的关系.结果表明:投加PAHs高效降解菌可以促进土壤中PAHs的降解,2周内效果显著;典型PAHs降解的难易程度依据为：菲<蒽<芘<苯并(a)芘和屈;细菌种群丰度和多样性均与PAHs降解呈负相关关系,同一处理细菌种群结构随时间变化不大.对于中、低浓度PAHs原位污染土壤,增强土著菌的活性是提高土壤PAHs降解率的有效途径之一.     

Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by Mycobacterium spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene pdo1. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no pdo1 genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.     

Fertilization alters the abundance but not the diversity of soil fauna: A meta-analysis

Aim

Soil fauna, a functionally important group of soil organisms, are greatly affected by fertilization. However, it is still debated whether and how fertilization affects the soil faunal community. Here, we aimed to synthesize the global patterns of soil fauna communities in response to fertilization in terrestrial ecosystems.

Location

Global.

Time period

1997–2021.

Major taxa studied

Soil fauna.

Methods

We examined the effects of fertilization on the abundance, number of groups and Shannon diversity of soil fauna by synthesizing 1218 observations based on 39 published studies. We also explored the associations between fertilization-induced changes in the soil faunal community and changes in soil and microbial properties.

Results

Fertilization increased the abundance of soil fauna by 56.3%, without significantly affecting the number of groups and the Shannon index. The type of fertilizer affected the responses of soil faunal abundance, and the effects of fertilizer type were altered by climate zones, ecosystem types and soil depths. Both organic and organic–mineral fertilizer treatments significantly increased the abundance of soil fauna in most climate zones, ecosystem types and soil depths, whereas mineral fertilizer treatment had no such effect. Additionally, we found inconsistent responses of soil fauna to fertilization among different taxonomic groups, not only at the order level but also at the class level, providing evidence for the idiosyncratic nature of the effects of fertilization on soil fauna. Furthermore, our regression analysis showed that changes in food resources, including soil nutrients and microbes, were crucial controls for the response of soil faunal abundance to fertilization.

Main conclusions

Fertilization generally increased soil faunal abundance at the global scale by affecting food resources, and the effects of fertilization were dependent on the specific soil fauna and type of fertilizer. We suggest the use of organic or organic–mineral fertilizers, rather than mineral fertilizers, to increase the benefits on specific soil fauna.     

The role of salicylate and biosurfactant in inducing phenanthrene degradation in batch soil slurries

The majority of polycyclic aromatic hydrocarbons (PAHs) sorb strongly to soil organic matter posing a complex barrier to biodegradation. Biosurfactants can increase soil-sorbed PAHs desorption, solubilisation, and dissolution into the aqueous phase, which increases the bioavailability of PAHs for microbial metabolism. In this study, biosurfactants, carbon sources, and metabolic pathway inducers were tested as stimulators of microorganism degradation. Phenanthrene served as a model PAH and Pseudomonas putida ATCC 17484 was used as the phenanthrene degrading microorganism for the liquid solutions and soil used in this investigation. Bench-scale trials demonstrated that the addition of rhamnolipid biosurfactant increases the apparent aqueous solubility of phenanthrene, and overall degradation by at least 20% when combined with salicylate or glucose in liquid solution, when compared to solutions that contained salicylate or glucose with no biosurfactant. However, salicylate addition, with no biosurfactant addition, increased the total degradation of phenanthrene 30% more than liquid systems with only biosurfactant addition. In soil slurries, small amounts of biosurfactant (0.25 g/L) showed a significant increase in total removal when only biosurfactant was added. In soil slurries containing salicylate, the effects of biosurfactant additions were negligible as there was greater than 90% removal, regardless of the biosurfactant concentration. The results of experiments performed in this study provide further evidence that an in situ enhancement strategy for phenanthrene degradation could focus on providing additional carbon substrates to induce metabolic pathway catabolic enzyme production, if degradation pathway intermediates are known.