Fe(III)的微生物异化还原*

异化Fe(III)还原微生物是厌氧环境中广泛存在的一类主要微生物类群,它们的共同特片是可以利用Fe(III)作为末端电子受体而获能。异化Fe(III)还原微生物具有强大的代谢功能;可还原许多有毒重金属包括一些放射性核素,还可降解利用许多有机污染物,在污酒女环境的生物修复中具有重要的应用价值。本文对异化Fe(III)还原微生物的分布、分类、代谢功能多样性以及异化Fe(III)还原的意义做了评述,旨在加强相关领域的研究人同对此的了解和重视,通过学科和交叉和合作加快我国在这一领域的研究。     

Fe(Ⅲ)的微生物异化还原

异化Fe（Ⅲ）还原微生物是厌氧环境中广泛存在的一类主要微生物类群,它们的共同特征是可以利用Fe（Ⅲ）作为末端电子受体而获能。异化Fe（Ⅲ）还原微生物具有强大的代谢功能,可还原许多有毒重金属包括一些放射性核素,还可降解利用许多有机污染物,在污染环境的生物修复中具有重要的应用价值。本文对异化Fe（Ⅲ）还原微生物的分布、分类,代谢功能多样性以及异化Fe（Ⅲ）还原的意义做了评述,旨在加强相关领域的研究人员对此的了解和重视,通过学科的交叉和合作加快我国在这一领域的研究。     

异化Fe(Ⅲ)还原微生物研究进展

铁是地壳中含量第四丰富的元素,微生物介导的异化铁还原是自然界中Fe(Ⅲ)还原的主要途径。介绍了Fe(Ⅲ)还原菌的分类及多样性,总结了Fe(Ⅲ)还原菌还原铁氧化物机制及其产能代谢机制,概述了Fe(Ⅲ)还原菌的生态环境意义,并对未来Fe(Ⅲ)还原菌的分子生态学研究方向提出了探索性的建议。     

土壤Fe(Ⅲ)异化还原机理及影响因素研究进展

微生物的异化Fe(Ⅲ)还原指以Fe(Ⅲ)为末端电子受体在厌氧条件下氧化有机物的产能过程,在生物地球化学循环中起着重要的作用,异化还原的产物为Fe(Ⅱ)。目前对Fe(Ⅲ)微生物还原的物理、生物化学特性的认识还十分有限。本文系统介绍了异化Fe(Ⅲ)还原的机理及影响因素,包括还原不溶性Fe(Ⅲ)氧化物的机制及与Fe(Ⅲ)还原相关的分子生物学的研究进展。分析了目前研究中存在的问题,并从分子生物学及生物地球化学角度对异化Fe(Ⅲ)还原研究方向进行了评述与展望。旨在加强相关领域研究人员对该科学问题的了解和重视,通过学科交叉和合作加快我国在这一领域的研究。     

水稻土中铁还原菌多样性

微生物介导的异化Fe(III) 还原是非硫厌氧环境中Fe(III) 还原生成Fe(II) 的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性（T-RFLP）技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明：无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌（Geobacter）和梭菌（Clostridiales）是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌（Rhodocyclaceae）;因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.     

水稻土中铁还原菌多样性

微生物介导的异化Fe(III) 还原是非硫厌氧环境中Fe(III) 还原生成Fe(II) 的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性（T-RFLP）技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明：无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌（Geobacter）和梭菌（Clostridiales）是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌（Rhodocyclaceae）;因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.     

异化Fe(Ⅲ)还原酶促反应及调控机制的研究进展

异化Fe(Ⅲ)还原菌不是分类学上的概念,它具有系统发育及环境来源多样性的特点。与其他大多数的电子受体不同,在近中性pH值条件下,Fe(Ⅲ)的溶解度很低,通常以不溶性的Fe(Ⅲ)氧化物的形式存在。目前,对微生物如何获得和还原不溶性Fe(Ⅲ)的机理仍缺乏系统的了解。以希瓦氏菌和地杆菌为例,本文综述了3种异化Fe(Ⅲ)还原的酶促反应机制及其分子调控机理：异化Fe(Ⅲ)还原菌与Fe(Ⅲ)氧化物直接接触机制、电子穿梭体的作用机制、铁载体作用机制,多种膜蛋白特别是多血红素的细胞色素蛋白参与微生物的异化Fe(Ⅲ)还原过程,并形成复杂的调控网络。此外,本文也对异化Fe(Ⅲ)还原酶促反应及其分子调控机理将来的研究方向进行了展望,以期对这一重要的生化过程有更为全面的认识。     

铁还原菌降解石油烃的研究进展

铁还原菌是指能够利用细胞外Fe(III)作为末端电子受体,通过氧化有机物将Fe(III)还原为Fe(II)微生物的总称。铁还原作用广泛存在于土壤、河流、海洋、地表含水层以及高温高压的地下深部油藏。在厌氧或兼性厌氧条件下,Fe(III)还原耦合有机物的降解,对铁、碳元素的生物地球化学循环具有重要意义。本文介绍了铁还原菌的多样性和铁还原作用机理,综述了铁还原菌在石油烃降解方面的研究进展。此外,还总结了铁还原菌在生物修复中的潜在作用,并对未来的研究方向进行了展望。     

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.     

异化金属还原菌的研究进展*

微生物利用金属氧化物作呼吸作用的最终电子受体是一种新的代谢途径。该过程微生物利用有机底物异化还原金属氧化物进行生长代谢。异化金属还原菌对于研究探索古生物呼吸形式、界定生命的上限温度等生命科学问题具有重要研究价值,同时在生物整治、微生物燃料电池等方面具有广阔的应用前景。对异化金属还原菌进行了综述,并对这类菌的研究应用给予评述和展望。     

Comparison of Humic Substance- and Fe(III)-Reducing Microbial Communities in Anoxic Aquifers

Humic substances can mediate electron transfer between microorganisms and Fe(III) minerals. Because it is unknown which microorganisms reduce humics in anoxic aquifers, we analyzed the diversity and physiological flexibility of Fe(III)-, humics-, and AQDS-reducers, which were present at up to 10⁶ cells g^?1. No significant differences in 16S rRNA gene based diversity were found between enrichment cultures reducing ferrihydrite, humics or AQDS. Even after repeated transfers many of the enrichments retained the ability to switch to other electron acceptors. This suggests that humics- and Fe(III)-reducing microorganisms in anoxic aquifers are rather versatile and able to reduce different extracellular electron acceptors.     

Direct Fe(III) Reduction from Synthetic Ferrihydrite by Haloalkaliphilic Lithotrophic Sulfidogens

Ability to reduce insoluble Fe(III) compounds has not been shown for alkaliphilic lithotrophic sulfate and sulfur reducers. Detection of this metabolic process in sulfidogenic prokaryotes could significantly expand the present knowledge on physicochemical range of their growth and physiological activity, which is now limited by low negative ambient redox potential. Capacity for direct reduction of Fe(III) from chemically synthesized ferrihydrite was tested for eight species of hydrogenotrophic haloalkaliphilic sulfidogens grown with formate or H2 as electron donors in the absence of sulfur compounds in the medium. Out of eight tested species, six reduced iron with formate and five, with hydrogen as the electron donor. Iron reduction correlated with stimulation of growth on formate or hydrogen only in two sulfidogenic species. Analysis of available genomes of five tested species revealed that only Dethiobacter alkaliphilus and Desulfuribacillus alkaliarsenatis possess the gene sets of multiheme cytochromes c required for typical dissimilatory iron reduction. The presence of these genes in two strains with high iron-reducing activity indicates the capacity of some haloalkaliphilic sulfidogenic bacteria for carrying out direct dissimilatory reduction of insoluble Fe(III) forms in the absence of sulfur-containing electron acceptors, i.e., without using sulfide as a soluble mediator of iron reduction. In other studied microorganisms, the ability to reduce iron is probably caused by nonspecific metabolic activity and is not directly linked to energy generation for growth, although the rates of Fe(III) reduction determined in our experiments make it possible to suggest significant role of sulfidogenic microorganisms (normally reducing sulfur and sulfate) in the iron cycle in haloalkaline ecosystems upon decreased content of sulfur compounds.     

Review: microbial mechanisms of accessing insoluble Fe(III) as an energy source

Of all the terminal electron acceptors, Fe(III) is the most naturally abundant in many subsurface environments. Fe(III)-reducing microorganisms are phylogenetically diverse and have been isolated from a variety of sources. Unlike most electron acceptors, Fe(III) has a very low solubility and is usually present as insoluble oxides at neutral pH. The mechanisms by which microorganisms access and reduce insoluble Fe(III) are poorly understood. Initially, it was considered that microorganisms could only reduce insoluble Fe(III) through direct contact with the oxide. However, recent studies indicate that extracellular electron shuttling or Fe(III)-chelating compounds may alleviate the need for cell–oxide contact. These include microbially secreted compounds or exogenous electron shuttling agents, mainly from humic substances. Electron shuttling via humic substances is likely a significant process for Fe(III) reduction in subsurface environments. This paper reviews the various mechanisms by which Fe(III) reduction may be occurring in pure culture and in soils and sediments.     

OmcB,a c-type polyheme cytochrome,involved in Fe(III) reduction in Geobacter sulfurreducens

Microorganisms in the family Geobacteraceae are the predominant Fe(III)-reducing microorganisms in a variety of subsurface environments in which Fe(III) reduction is an important process, but little is known about the mechanisms for electron transport to Fe(III) in these organisms. The Geobacter sulfurreducens genome was found to contain a 10-kb chromosomal duplication consisting of two tandem three-gene clusters. The last genes of the two clusters, designated omcB and omcC, encode putative outer membrane polyheme c-type cytochromes which are 79% identical. The role of the omcB and omcC genes in Fe(III) reduction in G. sulfurreducens was investigated. OmcB and OmcC were both expressed during growth with acetate as the electron donor and either fumarate or Fe(III) as the electron acceptor. OmcB was ca. twofold more abundant under both conditions. Disrupting omcB or omcC by gene replacement had no impact on growth with fumarate. However, the OmcB-deficient mutant was greatly impaired in its ability to reduce Fe(III) both in cell suspensions and under growth conditions. In contrast, the ability of the OmcC-deficient mutant to reduce Fe(III) was similar to that of the wild type. When omcB was reintroduced into the OmcB-deficient mutant, the capacity for Fe(III) reduction was restored in proportion to the level of OmcB production. These results indicate that OmcB, but not OmcC, has a major role in electron transport to Fe(III) and suggest that electron transport to the outer membrane is an important feature in Fe(III) reduction in this organism.     

Dissimilatory Fe(III) and Mn(IV) reduction.

The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater. This process, which may have been the first globally significant mechanism for the oxidation of organic matter to carbon dioxide, plays an important role in the oxidation of natural and contaminant organic compounds in a variety of environments and contributes to other phenomena of widespread significance such as the release of metals and nutrients into water supplies, the magnetization of sediments, and the corrosion of metal. Until recently, much of the Fe(III) and Mn(IV) reduction in sedimentary environments was considered to be the result of nonenzymatic processes. However, microorganisms which can effectively couple the oxidation of organic compounds to the reduction of Fe(III) or Mn(IV) have recently been discovered. With Fe(III) or Mn(IV) as the sole electron acceptor, these organisms can completely oxidize fatty acids, hydrogen, or a variety of monoaromatic compounds. This metabolism provides energy to support growth. Sugars and amino acids can be completely oxidized by the cooperative activity of fermentative microorganisms and hydrogen- and fatty-acid-oxidizing Fe(III) and Mn(IV) reducers. This provides a microbial mechanism for the oxidation of the complex assemblage of sedimentary organic matter in Fe(III)- or Mn(IV)-reducing environments. The available evidence indicates that this enzymatic reduction of Fe(III) or Mn(IV) accounts for most of the oxidation of organic matter coupled to reduction of Fe(III) and Mn(IV) in sedimentary environments. Little is known about the diversity and ecology of the microorganisms responsible for Fe(III) and Mn(IV) reduction, and only preliminary studies have been conducted on the physiology and biochemistry of this process.     

Fe(III) Reducing Microorganisms from Iron Ore Caves Demonstrate Fermentative Fe(III) Reduction and Promote Cave Formation

The banded iron formations (BIF) of Brazil are composed of silica and Fe(III) oxide lamina, and are largely covered by a rock cap of BIF fragments in a goethite matrix (canga). Despite both BIF and canga being highly resistant to erosion and poorly soluble, >3,000 iron ore caves (IOCs) have formed at their interface. Fe(III) reducing microorganisms (FeRM) can reduce the Fe(III) oxides present in the BIF and canga, which could account for the observed speleogenesis. Here, we show that IOCs contain a variety of microbial taxa with member species capable of dissimilatory Fe(III) reduction, including the Chloroflexi, Acidobacteria and the Alpha- Beta- and Gammaproteobacteria; however, Fe(III) reducing enrichment cultures from IOCs indicate the predominance of Firmicutes and Enterobacteriaceae, despite varying the carbon/electron donor, Fe(III) type, and pH. We used model-based inference to evaluate multiple candidate hypotheses that accounted for the variation in medium chemistry and culture composition. Model selection indicated that none of the tested variables account for the dominance of the Firmicutes in these cultures. The addition of H₂ to the headspace of the enrichment cultures enhanced Fe(III) reduction, while addition of N₂ resulted in diminished Fe(III) reduction, indicating that these Enterobacteriaceae and Firmicutes were reducing Fe(III) during fermentative growth. These results suggest that fermentative reduction of Fe(III) may play a larger role in iron-rich environments than expected. Our findings also demonstrate that FeRM are present within the IOCs, and that their reductive dissolution of Fe(III) oxides, combined with mass transport of solubilized Fe(II) by groundwater, could contribute to IOC formation.     

Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 microm by 1.0 to 1.2 microm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100 degrees C with an optimum of 85 to 90 degrees C. To our knowledge this is the highest temperature optimum of any organism in the BACTERIA: Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the Bacteria. The name Geothermobacterium ferrireducens gen. nov., sp. nov., is proposed (ATCC BAA-426).     

Importance of clay size minerals for Fe(III) respiration in a petroleum-contaminated aquifer

The availability of Fe(III)‐bearing minerals for dissimilatory Fe(III) reduction was evaluated in sediments from a petroleum‐contaminated sandy aquifer near Bemidji, Minnesota (USA). First, the sediments from a contaminated area of the aquifer, in which Fe(III) reduction was the predominant terminal electron accepting process, were compared with sediments from a nearby, uncontaminated site. Data from 0.5 m HCl extraction of different size fractions of the sediments revealed that the clay size fraction contributed a significant portion of the ‘bio‐available’ Fe(III) in the background sediment and was the most depleted in ‘bio‐available’ Fe(III) in the iron‐reducing sediment. Analytical transmission electron microscopy (TEM) revealed the disappearance of thermodynamically unstable Fe(III) and Mn(IV) hydroxides (ferrihydrite and Fe vernadite), as well as a decrease in the abundance of goethite and lepidocrocite in the clay size fraction from the contaminated sediment. TEM observations and X‐ray diffraction examination did not provide strong evidence of Fe(III)‐reduction‐related changes within another potential source of ‘bio‐available’ Fe(III) in the clay size fraction – ferruginous phyllosilicates. However, further testing in the laboratory with sediments from the methanogenic portion of the aquifer that were depleted in microbially reducible Fe(III) revealed the potential for microbial reduction of Fe(III) associated with phyllosilicates. Addition of a clay size fraction from the uncontaminated sediment, as well as Fe(III)‐coated kaolin and ferruginous nontronite SWa‐1, as sources of poorly crystalline Fe(III) hydroxides and structural iron of phyllosilicates respectively, lowered steady‐state hydrogen concentrations consistent with a stimulation of Fe(III) reduction in laboratory incubations of methanogenic sediments. There was no change in hydrogen concentration when non‐ferruginous clays or no minerals were added. This demonstrated that Fe(III)‐bearing clay size minerals were essential for microbial Fe(III) reduction and suggested that both potential sources of ‘bio‐available’ Fe(III) in the clay size fraction, poorly crystalline Fe(III) hydroxides and structural Fe(III) of phyllosilicates, were important sources of electron acceptor for indigenous iron‐reducing microorganisms in this aquifer.     

Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus

Aromatic compounds are an important component of the organic matter in some of the anaerobic environments that hyperthermophilic microorganisms inhabit, but the potential for hyperthermophilic microorganisms to metabolize aromatic compounds has not been described previously. In this study, aromatic metabolism was investigated in the hyperthermophile Ferroglobus placidus . F. placidus grew at 85°C in anaerobic medium with a variety of aromatic compounds as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. Aromatic compounds supporting growth included benzoate, phenol, 4-hydroxybenzoate, benzaldehyde, p -hydroxybenzaldehyde and t -cinnamic acid (3-phenyl-2-propenoic acid). These aromatic compounds did not support growth when nitrate was provided as the electron acceptor, even though nitrate supports the growth of this organism with Fe(II) or H₂ as the electron donor. The stoichiometry of benzoate and phenol uptake and Fe(III) reduction indicated that F. placidus completely oxidized these aromatic compounds to carbon dioxide, with Fe(III) serving as the sole electron acceptor. This is the first example of an Archaea that can anaerobically oxidize an aromatic compound. These results also demonstrate for the first time that hyperthermophilic microorganisms can anaerobically oxidize aromatic compounds and suggest that hyperthermophiles may metabolize aromatic compounds in hot environments such as the deep hot subsurface and in marine and terrestrial hydrothermal zones in which Fe(III) is available as an electron acceptor.