有机卤呼吸微生物菌群营养交互的作用机制

有机卤呼吸细菌(organohalide-respiringbacteria,OHRB)是污染场地土壤与地下水中厌氧降解及生物修复有机卤代污染物的主力军。微生物种群间的资源竞争、生长抑制、代谢交叉喂养(crossfeeding,即营养的动态交换,包括碳源、氮源、氨基酸、维生素、核苷酸、电子供体、电子受体和其他生长因子等)、水平基因转移及其他交互作用机制是群落结构稳定平衡的基础,有利于促进有机卤代污染物消减效率的最大化。本文围绕OHRB种群及与其他微生物种群间的互作机制(如交叉喂养机制、竞争机制及抑制机制等)进行了概述,并对未来互作机制的研究进行了探讨与展望,旨在为有机卤代物污染场地生物修复效率的提高提供科学理论和技术参考依据。     

地下水脱卤过程中的微生物种间代谢互作：提高原位氯代烯烃厌氧脱氯效能的有效途径

有机卤呼吸细菌(organohalide-respiring bacteria, OHRB)在氯代烯烃污染地下水的原位生物修复中扮演着关键性的角色,提高其丰度及活性对氯代烯烃的完全去除具有重要意义。在实际环境中,有机卤呼吸细菌往往与多种微生物共存,微生物种间代谢互作现象十分普遍,有机污染物的完全无害化往往需要通过微生物菌群的协同代谢作用来实现。因此,本文围绕微生物种间代谢互作进行综述,对目前获得的脱氯微生物菌种资源及脱氯机理进行了回顾,重点阐述了专性OHRB、非专性OHRB和非OHRB的种间代谢互作行为及机制,并提出以种间代谢互作为指导进行合成微生物群落的构建来有效提高氯代烯烃厌氧生物降解效率,为实现环境氯代烯烃类有机污染物的快速、彻底无害化提供理论指导。     

1,2,3-三氯丙烷降解机制与污染场地修复技术研究进展

1,2,3-三氯丙烷(1,2,3-trichloropropane,1,2,3-TCP)是一种人工合成的脂肪族氯代烃,在工、农业生产中得到广泛应用。1,2,3-TCP作为环氧氯丙烷工业生产的中间产物,可作为前体物质用于生产土壤熏蒸剂、有机溶剂等。因其环境持久性、迁移性和生态毒性,国内外机构逐渐开始关注该有机氯污染物的环境归趋、生态健康风险和环境管控。当前,1,2,3-TCP污染物的降解与场地修复仍然是研究热点,但是对于1,2,3-TCP降解转化机制尚缺乏深入研究与总结。鉴于此,文中在讨论1,2,3-TCP的来源、环境污染、生态效应及物理化学降解方法与技术等的基础上,进一步综述了1,2,3-TCP的微生物降解与修复机制(如好氧共代谢降解、厌氧降解等);重点讨论了地下水等厌氧环境中1,2,3-TCP的厌氧微生物降解转化途径与机制,并从热力学角度论证了厌氧条件下1,2,3-TCP作为电子受体被有机卤呼吸微生物利用并降解的可行性;最后,对1,2,3-TCP污染场地原位生物修复进行了总结并对未来研究发展方向进行了展望。     

石油污染生态系统中细菌群落结构及其代谢机制研究进展

石油化工产品的不合理处置与泄漏导致石油及其衍生物大量释放到环境中,由此造成的环境污染问题日益严重,石油污染已成为全球性公害之一。微生物修复技术凭借其成本低、环境友好等优势,广泛应用于石油污染的治理。大量研究表明功能微生物群落在石油污染生态系统的修复体系中发挥了重要的作用。其中,细菌是最主要、最活跃的石油降解微生物。然而,在原位/异位生物修复过程中,存在功能菌群在污染体系中难维持、易失调及石油烃降解途径不明晰等问题。因此,本文总结了石油污染自然生态系统和微宇宙实验体系中的细菌群落结构、石油烃代谢机制及相关功能基因,并对微生物法处理石油污染的未来研究方向提出展望,为石油污染场地生物修复方案的制定提供理论参考。     

腐殖质呼吸作用及其生态学意义

腐殖质呼吸是厌氧环境中普遍存在的一种微生物呼吸代谢模式.自1996年发现以来,日益成为生态学与环境科学领域的研究热点.在厌氧条件下,一些微生物能以腐殖质作为唯一电子受体,氧化环境中的有机质或者甲苯等环境有毒物质,产生CO2,参与碳循环;同时,腐殖质呼吸作用产生的还原态腐殖质可以还原环境中的一些氧化态物质,如Fe(III)、Mn(IV)、Cr(VI)、U(VI) 、硝基芳香化合物和多卤代污染物.因此,腐殖质呼吸能够影响环境中C、N、Fe、Mn以及一些痕量金属元素的生物地球化学循环,并且能够促进重金属以及有机污染物的脱毒,在水体自净、污染土壤原位修复、污水处理等方面具有积极作用.     

微生物厌氧呼吸与有机污染水体沉积物修复

水体沉积物有机污染是当前全球关注的重要环境问题。微生物具有呼吸和代谢多样性,能以多种污染物作为厌氧呼吸的电子供体或受体,与周围环境中的生物和非生物因素组成代谢网络耦合有机污染物降解转化,是有机污染水体沉积物修复的重要驱动者。本文重点综述了微生物厌氧呼吸、电子传递网络及其对有机污染水体沉积物的修复机制研究进展,并对有机污染水体沉积物微生物修复理论和技术研究的问题和挑战进行了探讨。     

脱卤单胞菌属在厌氧降解有机氯化物及污染场地修复应用中的研究进展

脱卤单胞菌 Dehalogenimonas 是绿弯菌门 (Chloroflexi) 脱卤球菌纲 (Dehalococcoidia) 的一个属。脱卤单胞菌属目前包含 Dehalogenimonas lykanthroporepellens、Dehalogenimonas alkenigignens 和 Dehalogenimonas formicexedens 这 3 个已正式命名的物种,其成员均为严格厌氧的专性有机卤呼吸细菌,利用氢气和甲酸作为电子供体,以氯代烷烃 (例如 1,2,3-三氯丙烷、1,2-二氯丙烷和 1,2-二氯乙烷) 作为电子受体,通过介导还原性脱氯反应获得能量进行生长。我国污染场地地下水中氯代烷烃等有机氯污染较为突出,脱卤单胞菌的产能方式使其在污染场地原位修复中具有重要的应用价值。新近发现的 WBC-2 菌株和"Candidatus Dehalogenimonas etheniformans" GP 菌株可以脱氯降解某些氯代烯烃,其中 GP 菌株能够将一氯乙烯完全脱氯至乙烯,拓展了有限的一氯乙烯脱氯菌种资源,丰富了脱卤单胞菌的生态学功能。文中围绕脱卤单胞菌属的生理生化特性、生态功能及基因组信息进行综述,旨在为污染场地有机氯污染物的清理及工程实施提供理论指导。     

有机污染土壤和地下水生物修复研究热点和趋势——基于Web of Science数据库的文献计量学分析

生物修复作为经济有效、绿色可持续的修复技术,在有机污染土壤和地下水修复上具有广阔的应用前景。基于WebofScience核心数据库,通过文献计量可视化应用软件VOSviewer和CiteSpace,分析了1990–2020年有机污染土壤和地下水生物修复领域的研究热点及趋势。结果表明,有机污染土壤和地下水生物修复领域的论文发表数量呈增长趋势,发文总量最多的国家是美国和中国,但是2012年后中国年发文量快速增加,并位居第一。该领域的相关研究主要发表在Chemosphere、Environmental ScienceTechnology、Science of the Total Environment等top期刊上。全球研究机构中中国科学院发文量最多,但是来自美国加州大学的总被引频次和h-index最高。发文量最多的是来自英国兰卡斯特大学的学者Semple教授,我国发文量最多的是来自中国科学院南京土壤研究所的骆永明研究员。下一步研究重点和热点:针对复合污染土壤和地下水,研发新型耦合强化生物修复技术,采用先进的分子生物学方法探索功能微生物及其功能基因,阐明生物降解机理,明确原位污染土壤和地下水的靶向性调控机制。     

有机污染环境的植物修复研究进展

分析了近年来国内外的文献资料,对有机污染物污染环境的植物修复研究进展作了综述。植物能通过根系从环境中吸收和积累PCBs、PAHs等有机污染物,并将吸收的TNT、TCE及有机农药降解为高极性产物、水和CO2;另一方面植物根际可促进有机污染物的根际生物吸收与,使植物对有机污染环境的修复效果更明显。文中探讨了有机污染环境的植物修复技术的优势、问题与未来的研究。     

细菌分解代谢转座子研究

近年来 ,随着人工合成化学物质大量进入环境 ,现已在环境中发现了新的适应性的细菌对有机污染物的代谢机制。许多分解代谢基因与插入元件或转座子相连 ,因此 ,分解代谢基因可以在细菌间快速传播。这种快速传播有利于新的降解途径的产生。因此 ,这种代谢全能性可以被开发并在生物修复污染环境中起到关键作用     

Bioremediation of diesel-contaminated soils: Evaluation of potential in situ techniques by study of bacterial degradation

The development of a simple laboratory methodology allows theimplementation of in situbioremediation of polluted soils with diesel fuel. In thisinvestigation microbiological and chemical analyses and a suitable bioreactor design, were veryuseful for suggesting the best ways to improve biodegradation extents in a diesel-enrichedsoil. Biostimulation with inorganic nitrogen and phosphorus produced the best resultsin a simple bioreactor, with biodegradation extents higher than 90% after 45 days. Also,the addition of activated sludge from a domestic wastewater plant increased the degradationrate to a great extent. In both cases, microbiological studies showed the presence ofAcinetobacter sp. degrading most of thehydrocarbons. Simultaneously, a diesel fuel release(approximately 400,000 l) was studied. Samples taken in polluted soil and water revealed thatbacteria from the genus Acinetobacterwere predominant. In plate studies, Acinetobacter coloniesproduced a whitish substance with the characteristics of a biosurfactant. Remarkably, thepresence of this product was evident at the field site, both in the riverbanks and in the physicalrecovery plant. The study of the similarities between laboratory results and the diesel spillsite strongly suggested that natural conditions at the field site allowed the implementationof in situ bioremediation after physical removal of LNAPL (light nonaqueous-phase liquids).     

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation.     

Protocol for determining bioavailability and biokinetics of organic pollutants in dispersed, compacted and intact soil systems to enhance in situ bioremediation

The development of effective in situ and on-site bioremediation technologies can facilitate the cleanup of chemically-contaminated soil sites. Knowledge of biodegradation kinetics and the bioavailability of organic pollutants can facilitate decisions on the efficacy of in situ and on-site bioremediation of contaminated soils and determine the attainable treatment end-points. Two kinds of compounds have been studied: (1) phenol and alkyl phenols, which represent hydrophilic compounds, exhibiting high water solubility and moderate to low soil partitioning; and (2) polycyclic aromatic hydrocarbons which are hydrophobic compounds with low water solubility and exhibit significant partitioning in soil organic carbon. Representative data are given for phenol and naphthalene. The results provide support for a systematic multi-level protocol using soil slurry, wafer and porous tube or column reactors to determine the biokinetic parameters for toxic organic pollutants. Insights into bioremediation rates of soil contaminants in compact soil systems can be attained using the protocol. Received 04 December 1995/ Accepted in revised form 31 January 1997     

Application of Pneumatic Fracturing to Enhance In Situ Bioremediation

A field pilot demonstration integrating pneumatic fracturing and in situ bioremediation was carried out in a gasoline-contaminated, low permeability soil formation. A pneumatic fracturing system was used to enhance subsurface air flow and transport rates, as well as to deliver soil amendments directly to the indigenous microbial populations. An in situ bioremediation zone was established and operated for a period of 50 weeks, which included periodic subsurface injections of phosphate, nitrate, and ammonium salts. Off-gas data indicated the formation of a series of aerobic, denitrifying, and methanogenic microbial degradation zones. Based on soil samples recovered from the site, 79% of soil-phase benzene, toluene, and xylenes (BTX) was removed by the integrated technology. From mass balance calculations, accounting for all physical losses, it was estimated that 85% of the total mass of BTX removed (based on mean concentration levels) was attributable to biodegradation.     

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.     

Potential for bioremediation of fuel‐contaminated soil in Antarctica

A preliminary investigation was conducted to identify the presence of bacteria in fuel‐contaminated Antarctic soil that could potentially be used to bioremediate the contaminated soil at McMurdo Station and other sites in Antarctica. The ability of soil microorganisms to metabolize fuels under the extreme climatic and oligotrophic conditions of Antarctica was of concern. Bacteria were isolated from fuel‐contaminated soil on site at McMurdo Station. Bacteria from noncontaminated soil near the station were also studied for comparison. The Antarctic soil microorganisms exhibited the ability to endure cold and oligotrophic environments. Experiments also showed that bacteria from the fuel spill site were active in their contaminated environment and that acclimation to xenobiotic compounds was necessary. Application of bioremediation in the extreme environmental conditions found at McMurdo Station, Antarctica, were also considered. The possibility of altering environmental factors necessary to adequately support in situ bioremediation in this extreme climate is discussed.     

Effects of nutrient dosing on subsurface methanotrophic populations and trichloroethylene degradation

In in situ bioremediation demonstration at the Savannah River Site in Aiken, South Carolina, trichloroethylene-degrading microorganisms were stimulated by delivering nutrients to the TCE-contaminated subsurface via horizontal injection wells. Microbial and chemical monitoring of groundwater from 12 vertical wells was used to examine the effects of methane and nutrient (nitrogen and phosphorus) dosing on the methanotrophic populations and on the potential of the subsurface microbial communities to degrade TCE. Densities of methanotrophs increased 3–5 orders of magnitude during the methane- and nutrient-injection phases; this increase coincided with the higher methane levels observed in the monitoring wells. TCE degradation capacity, although not directly tied to methane concentration, responded to the methane injection, and responded more dramatically to the multiple-nutrient injection. These results support the crucial role of methane, nitrogen, and phosphorus as amended nutrients in TCE bioremediation. The enhancing effects of nutrient dosing on microbial abundance and degradative potentials, coupled with increased chloride concentrations, provided multiple lines of evidence substantiating the effectiveness of this integrated in situ bioremediation process. Received 13 November 1995/ Accepted in revised form 12 September 1996     

Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample‐specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)‐reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.