Relationship between structures of substituted indolic compounds and their degradation by marine anaerobic microorganisms

Degradation of selected indolic compounds including indole, 1-methylindole, 2-methylindole, and 3-methylindole was assessed under methanogenic and sulfate-reducing conditions using the serum-bottle anaerobic technique and marine sediment from Victoria Harbour, Hong Kong as an inoculum. Our results showed that indole degradation was achieved in 28 days by a methanogenic consortium and 35 days by a sulfate-reducing consortium. During degradation under both conditions, two intermediates were isolated, purified and identified as oxindole and isatin (indole-2,3-dione) suggesting that both methanogenic and sulfate-reducing bacteria use an identical degradation pathway. Degradation processes followed two steps of oxidation accomplished by hydroxylation and then dehydrogenation at 2- and then 3-position sequentially prior to the cleavage of the pyrrole ring between 2- and 3-positions. However, none of 1-methylindole or 2-methylindole was degraded under any conditions. 3-Methylindole (3-methyl-1H-indole, skatole) was transformed under methanogenic conditions and mineralized only under sulfate-reducing conditions. It is clear that methyl substitution on 1- or 2-position inhibits the initial attack by hydroxylation enzymes making them more persistent in the environment and posing longer toxic impact.     

Structure of microbial communities and hydrocarbon-dependent sulfate reduction in the anoxic layer of a polluted microbial mat

The bacterial communities in the anoxic layer of a heavily polluted microbial mat and their growth on hydrocarbons under sulfate-reducing conditions were investigated. Microbial communities were dominated by members of Alphaproteobacteria (27% of the total rRNA), Planctomycetes (21.1%) and sulfate-reducing bacteria (SRB: 17.5%). 16S rRNA cloning revealed sequences beloning to the same bacterial groups with SRB affiliated to the genera Desulfobulbus, Desulfocapsa, Desulfomicrobium, Desulfobacterium and Desulfosarcina/Desulfococcus. The derived enrichment cultures on crude oil, hexadecane and toluene were dominated by SRB. While most SRB sequences of the toluene and hexadecane cultures were related to the sequence of Desulfotignum toluolica, the crude oil enrichment showed a more diverse bacterial community with sequences from the genera Desulfotignum, Desulfobacter, Desulfatibacillus, Desulfosalina, and Desulfococcus. We conclude that the anoxic layer of the studied mats contains a diverse community of anaerobic bacteria, dominated by SRB, some of which are able to grow on hydrocarbons.     

Evidence of methylmercury production and modification of the microbial community structure in estuary sediments contaminated with wastewater treatment plant effluents

The Seine’s estuary (France) waters are the receptacle of effluents originating from wastewater treatment plants (WWTP). In this estuary, mudflats are deposition zones for sediments and their associated contaminants, and play an essential role in the mercury (Hg) biogeochemical cycle mainly due to indigenous microorganisms. Microcosms were used to assess the impact of WWTP-effluents on mercury methylation by monitoring Hg species (total dissolved Hg in porewater, methylmercury and total mercury) and on microbial communities in sediments. After effluent amendment, methylmercury (MeHg) concentrations increased in relation with the total Hg and organic matter content of the WWTP-effluents. A correlation was observed between MeHg and acid-volatile-sulfides concentrations. Quantification of sulfate-reducing microorganisms involved in Hg methylation showed no increase of their abundance but their activity was probably enhanced by the organic matter supplied with the effluents. WWTP-effluent spiking modified the bacterial community fingerprint, mainly influenced by Hg contamination and the organic matter amendment.     

The Microbial Metabolic Characteristics in the Course of Sulfate-Reduction

Acid-producing phase reactor of two-phase anaerobic treatment process has remarkable advantages treating sulfate-laden wastewater. In order to investigate SRB population‘s capability of utilizing substrate and the microbial acidification type formed during the course of sulfate reduction, continuous-flow and batch tests were conducted in a continuous stirred tank bio-film reactor supplied with sodium sulfate as electron acceptor. The experimental results demonstrated that the acidification type formed b...     

Imaging the heterogeneity of mineral surface reactivity using Ag(I) and synchrotron X-ray microscopy

Microscopic-scale imaging of reduced zones on the surfaces of minerals can be achieved by reaction with dilute Ag(I) solutions and subsequent analysis using synchrotron X-ray microscopy (XRM) above the Ag K-edge (25.5 keV). The principal reductant is Fe(II), but other reductants such as sulfide may contribute. Reduced zones may exist instrinsically, as in the structure of biotite and augite, or may be generated by reaction with chemical agents such as dithionite or treatment with sulfate-reducing bacteria (SRB). We demonstrate the method on flakes of specular hematite and biotite, as well as on thin sections of different rocks (arfvedsonitic granite, oolitic hematite, diabase, and quartz conglomerate) treated with SRB, and discuss possible artifacts that can occur. To our knowledge, this is the only microscopic technique that can image Fe(II) zones on the surface of an Fe-bearing mineral with monolayer sensitivity.     

青藏高原湖泊沉积物硫酸盐还原菌种群分布

采用聚合酶链式反应(PCR,Polymerase Chain Reaction)、变性梯度凝胶电泳(DGGE,Denaturing Gra-dient Gel Electrophoresis)与实时荧光定量聚合酶链式反应(Q-PCR,Quantitative PCR)相结合的综合分析技术,研究了青藏高原洱海、青海湖、尕海1、尕海2、小柴旦湖沉积物硫酸盐还原菌多样性及丰度。研究结果显示,5个盐湖沉积物中dsrB(编码亚硫酸还原酶β亚基,为硫酸盐还原菌所共有)基因的丰度为每克沉积物1.71×108～1.55×109拷贝,与盐度无明显相关性;所获得的dsrB基因序列分属于3个科:Desulfobacter-aceae,Desulfobulbaceae和Peptococcaceae。其中,Desulfobacteraceae科是主要类群。硫酸盐还原菌多样性(DGGE结果)与盐度呈现出负相关性。故在所研究的盐湖中,盐度可能不是影响硫酸盐还原菌种群分布的唯一因素,可能还受其它未知环境因素的影响,有待于进一步研究。     

海洋环境中甲烷厌氧氧化机理及环境效应

作为全球碳循环的重要环节之一,甲烷厌氧氧化作用（Anaerobic Oxidation of Methane,AOM）不仅是微生物生态学领域最具科学魅力、充满学术争议的问题之一,也是调节地质历史时期地球环境和气候变化的重要因素之一。近年来,针对包括海洋在内的各种环境中的AOM展开了大量的研究,然而迄今为止,对该反应的运作机制仍缺乏足够了解,其中包括该作用对海洋环境和气候系统在过去、现在和未来的影响机理和程度问题,这说明对于甲烷最重要汇的了解还存在着盲区。以现代海洋地质环境中的AOM为研究对象,综述了其产生机理、反应底物、电子受体、以及涉及到其中的微生物等方面的最新研究成果,探讨了该作用对于地球环境、气候的影响意义及地质学启示,并尝试展望了需要进一步研究的几点方向,希望藉此能引起广大研究者的兴趣与重视。     

Analyses of the vertical and temporal distribution of sulfate-reducing bacteria in Lake Aha (China)

In April and September of 2005, two sediment cores were collected from Lake Aha, which is polluted by the acid mine drainage of the mining industries. Sulfate-reducing bacteria (SRB) groups and their quantity were analyzed by using PCR and FISH (fluorescence in situ hybridization), respectively. The results showed that four SRB groups (Desulfotomaculum, Desulfobulbus, Desulfococcus–Desulfonema–Desulfosarcina and Desulfovibrio–Desulfomicrobium) were detected in September, while only three SRB groups (Desulfotomaculum, Desulfobulbus and Desulfococcus–Desulfonema–Desulfosarcina) were detected in April. Desulfovibrio–Desulfomicrobium was not detected and was expected to exist inactively, in April. Meanwhile, the distribution of every SRB group was wider in September than in April. The results indicated that different SRB groups had different vertical and temporal distribution. The vertical and temporal distribution of SRB was mainly in the upper sediments, and the number of SRB groups and quantity were larger in September than in April. It suggested that the environmental conditions of sediments in September were more suitable for SRB. An erratum to this article can be found at     

Rates of microbial hydrogen oxidation and sulfate reduction in Opalinus Clay rock

Hydrogen gas (H₂) may be produced by the anoxic corrosion of steel components in underground structures, such as geological repositories for radioactive waste. In such environments, hydrogen was shown to serve as an electron donor for autotrophic bacteria. High gas overpressures are to be avoided in radioactive waste repositories and, thus, microbial consumption of H₂ is generally viewed as beneficial. However, to fully consider this biological process in models of repository evolution over time, it is crucial to determine the in situ rates of microbial hydrogen oxidation and sulfate reduction. These rates were estimated through two distinct in situ experiments, using several measurement and calculation methods. Volumetric consumption rates were calculated to be between 1.13 and 1.93 μmol cm⁻³ day⁻¹ for H₂, and 0.14 and 0.20 μmol cm⁻³ day⁻¹ for sulfate. Based on the stoichiometry of the reaction, there is an excess of H₂ consumed, suggesting that it serves as an electron donor to reduce electron acceptors other than sulfate, and/or that some H₂ is lost via diffusion. These rate estimates are critical to evaluate whether biological H₂ consumption can negate H₂ production in repositories, and to determine whether sulfate reduction can consume sulfate faster than it is replenished by diffusion, which could lead to methanogenic conditions.     

Geochemical insights into contribution of petroleum hydrocarbons to the formation of hydrates in the Taixinan Basin,the South China Sea

Methane hydrate in the South China Sea(SCS)has extensively been considered to be biogenic on the basis of itsδ13C and δD values.Although previous efforts have greatly been made,the contribution of thermogenic oil/gas has still been underestimated.In this study,biomarkers and porewater geochemical parameters in hydrate-free and hydrate-bearing sediments in the Taixinan Basin,the SCS have been measured for evaluating the contribu-tion of petroleum hydrocarbons to the formation of hydrate deposits via a comparative study of their source inputs of organic matters,environmental conditions,and microbial activities.The results reveal the occurrence of C14-C16 branched saturated fatty acids(bSFAs)with relatively high concentrations from sulfate-reducing bacteria(SRBs)in hydrate-bearing sediments in comparison with hydrate-free sediments,which is in accord with the positive δ13C values of dissolved inorganic carbon(DIC),increasing methane concentrations,decreasing alka-linity,and concentration fluctuation of ions(Cl-,Br,SO2-,Ca2+,and Mg2+).These data indicate the relatively active microbial activities in hydrate-bearing sediments and coincident variations of environmental conditions.Carbon isotope compositions of bSFAs(-34.0％o to-21.2％o),n-alkanes(-34.5％o to-29.3％o),and methane(-70.7％o to-69.9％o)jointly demonstrate that SRBs might thrive on a different type of organic carbon rather than methane.Combining with numerous gas/oil reservoirs and hydrocarbon migration channels in the SCS,the occurrence of unresolved complex mixtures(UCMs),odd-even predominance(OEP)values(about 1.0),and biomarker patterns suggest that petroleum hydrocarbons from deep oil/gas reservoirs are the most probable carbon source.Our new results provide significant evidence that the deep oil/gas reservoirs may make a contribution to the formation of methane hydrate deposits in the SCS.