Use of microbial enrichments for the study of the anaerobic degradation of cholesterol

To demonstrate the potential of model microbial assemblages in studies of the biogeochemistry of complex organic molecules, anaerobic microbial populations capable of degrading cholesterol (cholest-5-en-3β-ol) have been enriched from marine sediment sources. The bacterial enrichments actively mineralized the C-4 nucleus of the cholesterol ring system to carbon dioxide when nitrate was present as the terminal electron acceptor. Nitrite was found as an intermediate in the reduction of nitrate, indicating the presence of denitrifying bacteria in the enrichments. When sulfate was supplied as the sole electron acceptor, active dissimilation of cholesterol was not observed. In enrichments containing 5 mM nitrate, 95–98% of the added cholesterol was recovered as carbon dioxide (2–5%), transformation products (20–30%), or as the unmodified sterol (70–80%). Cholesterol transformation products thus far identified include 5α- and 5β-cholestan-3β-ol, cholest-4-en-3-one, 5α-androstan-3, 17-dione and androst-4-en-3, 17 dione.     

Stable Sulfur Isotopic Evidence for Historical Changes of Sulfur Cycling in Estuarine Sediments from Northern Florida

Data on abundance and isotopic composition of porewater and sedimentary sulfur species are reported for relatively uncontaminated and highly contaminated fine-grained anoxic sediments of St. Andrew Bay, Florida. A strong contrast in amount and composition of sedimentary organic matter at the two sites allows a comparative study of the historical effects of increased organic loading on sulfur cycling and sulfur isotopic fractionation. In the contaminated sediments, an increase in organic loading caused increased sedimentary carbon/sulfur ratios and resulted in higher rates of bacterial sulfate reduction, but a lower efficiency of sulfide oxidation. These differences are well reflected in the isotopic composition of dissolved sulfate, sulfide, and sedimentary pyrite. Concentration and isotopic profiles of dissolved sulfate, organic carbon, and total sulfur suggest that the anaerobic decomposition of organic matter is most active in the upper 8cm but proceeds at very slow rates below this depth. The rapid formation of more than 90% of pyrite in the uppermost 2 cm which corresponds to about 3 years of sediment deposition allows the use of pyrite isotopic composition for tracing changing diagenetic conditions. Sediment profiles of the sulfur isotopic composition of pyrite reflect present-day higher rates of bacterial sulfate reduction and lower rates of sulfide oxidation, and record a profound change in the diagenetic cycling of sulfur in the contaminated sediments coincident with urban and industrial development of the St. Andrew Bay area.     

The transition of a freshwater karst aquifer to an anoxic marine system

Jewfish Sink is located in the shallow seagrass flats of the Gulf of Mexico in west central Florida. Jewfish Sink was a submarine spring until the drought of 1961–1962 when it ceased flowing. Today, the sink is an anaerobic marine basin and provides the opportunity to study the implications of saltwater intrusion in coastal karstic areas. The biogeochemistry of Jewfish Sink was studied from summer 2001 through spring 2004. A distinct feature of the sink is the uniform cold temperature (16–17°C) of the deeper anoxic water that does not match groundwater found nearshore or onshore (22–24°C). There are four zones within the sink: oxic zone, transition zone, upper anoxic zone, and anoxic bottom water. The anoxic bottom water does not mix with water from above but may be linked to deep Gulf shelf water through ancient aquifer conduits. The other three zones vary seasonally in oxygen, salinity, and temperature because of limited mixing in the winter due to cooding and sinking of surface water. The walls of the anoxic zones have characteristic microbial mats that are found in other sulfidic karstic features in the area. Bacterial activity appears to be carbon, limited in the anoxic zones where sulfate reduction appears to be the major metabolic process. The reduction of sulfate to sulfide appears to be driven by irregular influexes of organic matter including macroalgae, horseshoe crabs, and stingrays that become entrapped within the sink. Bacterial activity in the oxic zones appears to be phosphate limited. Although the system is partially isolated from the overlying marine ecosystem, organic input from above drives the bacterial anaerobic ecosystem, resulting in a sulfide pump. In this model, sulfide percolates up through the karst and removes oxygen from the overlying sediment, which has likely caused changes in the shallow benthic ecosystem. Jewfish Sink appears to be part of an extensive anoxic subterranean estuary that extends under parts of at least three coastal counties in Florida and serve as a model for the effects of rising sea levels or aquifer mining.     

Coupled physicochemical and bacterial reduction mechanisms for passive remediation of sulfate- and metal-rich acid mine drainage

Treatment of acid mine drainage (AMD) highly rich in sulfate and multiple metal elements has been investigated in a continuous flow column experiment using organic and inorganic reactive media. Treatment substrates that composed of spent mushroom compost (SMC), limestone, activated sludge and woodchips were incorporated into bacterial sulfate reduction (BSR) treatment for AMD. SMC greatly assisted the removals of sulfate and metals and acted as essential carbon source for sulfate-reducing bacteria (SRB). Alkalinity produced by dissolution of limestone and metabolism of SRB has provided acidity neutralization capacity for AMD where pH was maintained at neutral state, thus aiding the removal of sulfate. Fe, Pb, Cu, Zn and Al were effectively removed (87–100%); however, Mn was not successfully removed despite initial Mn reduction during early phase due to interference with Fe. The first half of the treatment was an essential phase for removal of most metals where contaminants were primarily removed by the BSR in addition to carbonate dissolution function. The importance of BSR in the presence of organic materials was also supported by metal fraction analysis that primary metal accumulation occurs mainly through metal adsorption onto the organic matter, e.g., as sulfides and onto Fe/Mn oxides surfaces.     

陆架边缘海沉积物有机碳矿化及其对海洋碳循环的影响

边缘海沉积物是海洋重要的碳储库,其内部的碳循环主要是由有机质矿化分解过程来驱动的。有机碳进入边缘海沉积物后,矿化分解为溶解无机碳(DIC)进入沉积物孔隙水并扩散到上层水柱,参与海洋系统碳循环;同时还有部分DIC与钙镁等离子结合形成自生碳酸盐,保存于沉积物碳库。从生物地球化学角度探讨有机质埋藏机制和效率,在此基础上重点综述沉积物硫酸盐还原、产甲烷和甲烷厌氧氧化过程的耦合机制,以及有机质矿化对自生碳酸盐形成的影响等方面的研究进展,以期加深对陆架边缘海沉积物在全球碳循环收支平衡中的作用及其气候环境效应的认识。     

Sedimentary Organic Carbon Mineralization and Its Contribution to the Marine Carbon Cycle in the Marginal Seas

Continental margin sediments are important ocean carbon repository, and the internal carbon cycle is mainly driven by the mineralization processes of sedimentary organic matter. Most organic carbon is transformed to Dissolved Inorganic Carbon (DIC) by mineralization processes after being delivered to continental margin sediments, and DIC from pore water diffuses into the upper water column and participates in the ocean carbon cycle. At the same time, some DIC combines ions such as Ca²⁺ and Mg²⁺ and precipitates as authigenic carbonate minerals so that carbon is stored in the deposits. Based on the biogeochemical study of the mechanism and efficiency of organic matter burial, we discussed the interaction among sulfate reduction, methanogenesis and anaerobic oxidation of methane, and the effect of organic mineralization on the formation of authigenic carbonate. By reviewing the above-mentioned aspects, we can obtain a better understanding of the role of continental margin sediments in the global carbon cycling budgets as well as its climate and environmental effects.     

Accumulation Conditions of Organic Matter during the Deposition of Black Shales of the Buxin Formation (Early Paleogene) in the Sanshui Basin, South China

Analyses of organic carbon, nitrogen, sulfur and iron have been performed in order to understand sources and preservation of organic matter in black shale of the Buxin Formation (Early Paleogene) from the Sanshui Basin. The C/N ratios show that the organic matter is characterized by a mixture of terrestrial and phytoplanktonic contributions. The relative importance of different sources depend on climate conditions and most of organic matter is of terrestrial origin. The relationships between C, S and Fe indicate that the brackish environment with alternation of anoxia and low-O2 developed in the bottom waters during the deposition of these organic-rich sediments as a result of a mixed setting of thermal stratification and salinity stratification, the latter being the consequence of intermittent sea water incursion. Bacterial sulfate reduction is the most effective early diagenesis affecting the preservation of organic matter. The intensity of sulfate reduction is related to the relative proportion of met     

Mathematical modeling of biologically mediated redox processes of iron and arsenic release in groundwater

A one dimensional reactive transport model was developed in order to illustrate the biogeochemical behavior of arsenic and iron reduction and release to groundwater that accounts for the reaction coupling the major redox elements under reducing environment. Mass transport equation and the method of characteristics were used considering fundamental geochemical processes to simulate transport processes of different pollutants in mobile phase. The kinetic sub-model describes the heterotrophic metabolisms of several microorganisms. To model a complete redox sequence (aerobic or denitrifiers, Fe(III)-reduction, respiration bacteria of iron and arsenic compounds, and As(V) reduction) four functional bacterial groups (X ₁, X ₂, X ₃, and X ₄) were defined. Microbial growth was assumed to follow Monod type kinetics. The exchange between the different phases (mobile, bio, and matrix) was also considered in this approach. Results from a soil column experiment were used to verify the simulation results of the model. The model depicts the utilization of oxygen, nitrate, iron oxide and arsenic as electron acceptors for oxidation of organic carbon (OC) in a column. The OC as electron donor is one of the most important factors that affect the iron and arsenic reduction bacterial activity.     

Molecular and cultivation-dependent analysis of metal-reducing bacteria implicated in arsenic mobilisation in south-east asian aquifers

The reduction of sorbed As(V) to the potentially more mobile As(III) by As-respiring anaerobic bacteria has been implicated in the mobilisation of the toxic metalloid in aquifer sediments in SE Asia. However, there is currently only a limited amount of information on the identity of the organisms that can respire As(V) in these sediment systems. Here experiments are described that have targeted As(V)-respiring bacteria using cultivation-independent molecular techniques, and also more traditional microbiological approaches that have used growth media highly selective for organisms that can grow using arsenate as the sole electron acceptor supplied for anaerobic growth. The molecular techniques used have initially targeted DNA from microcosms displaying maximal rates of arsenate reduction, both with and without added electron donor. More recent studies from the authors’ laboratory have used stable isotope probing techniques, targeting DNA from the active microbial fraction in microcosms labelled with [¹³C]acetate supplied as an electron donor for arsenate reduction. Phylogenetic analyses using a highly conserved genetic marker (the 16S rRNA gene) have suggested the involvement of Sulfurospirillum and Geobacter species in arsenate-respiration, and this has been supported further by complimentary experiments using more traditional microbiological techniques. Additional research required to clarify the role of these organisms in the mobilisation of As in situ are discussed.     

三水盆地古近系(土布)心组黑色页岩中黄铁矿的形成及其控制因素

黄铁矿是富有机质沉积的特征矿物。根据TOC/S、TOC/DOP、S/Fe关系以及S TOC Fe多重线性回归分析结果对三水盆地古近系〖HT5”,6”〗土〖KG-*3〗布〖HT5”SS〗心组红岗段黑色页岩中沉积黄铁矿的形成及其控制因素进行了分析。土布心组红岗段黑色页岩的黄铁矿有成岩黄铁矿和同生黄铁矿两种成因组分。红岗段下部（亚段A）有机碳含量普遍较低,底部水体以弱氧化条件为主,硫酸盐还原作用发生于沉积物/水界面以下,黄铁矿为成岩成因,其形成主要受有机质的限制。红岗段中上部（亚段B和C）的沉积条件变化频繁,其有机碳含量变化幅度大。富有机质（TOC>4%）岩层形成于缺氧的底部水体条件下。水体中可含H2S,碎屑铁矿物在埋藏之前即与之在水体中反应形成同生黄铁矿。这一过程不受有机质的限制,而是受活性铁与H2S接触时间的限制。同时,由于大量淡水输入导致硫酸盐浓度的降低,从而对硫化物形成有一定的限制作用。对于低有机质（TOC<4%）样品,黄铁矿由同生和成岩组分组成。其中以成岩黄铁矿为主,其形成过程主要受有机质限制,而同生黄铁矿受铁矿物与H2S接触时间的限制。     

地表灌溉对沉积含水层中碘迁移释放过程的影响

灌溉等人为活动会造成外源物质的输入,如硝酸盐、有机质等,从而引起浅层地下水环境发生周期性波动。为研究农业灌溉对沉积含水层中碘迁移富集过程的影响,选取代表性富碘沉积物,通过室内实验模拟了灌溉活动外源物质输入条件下,盆地地下水系统中碘迁移释放的（生物）地球化学过程。实验结果表明：厌氧条件下,外源有机质输入可促使微生物利用有机质作为电子供体,还原固相铁矿物相,进而造成搭载于铁氧化物/氢氧化物表面的碘释放,以碘离子形式在地下水中富集;而在NO₃^-输入情况下,微生物会优先利用NO₃^-为电子受体,至硝酸盐被全部消耗后,Fe（Ⅲ）可进一步被还原为Fe（Ⅱ）。研究结果表明,人为活动造成浅表环境外源物质的输入可直接影响浅层地下水中碘的迁移释放过程。伊利石黏土矿物吸附的铁氧化物矿物相可能为浅层环境中碘的主要搭载介质,微生物作用下,铁氧化物/氢氧化物的还原溶解是高碘地下水形成的主控因素。     

硫酸盐对磁赤铁矿—磁铁矿厌氧转化过程的影响

磁赤铁矿可以在厌氧微生物作用下固相转化为磁铁矿,这种转化过程具有重要的矿物学及环境磁学意义。文章通过开展硫酸盐还原菌（SRB） —磁赤铁矿交互作用实验,重点探讨了SRB 活性对磁赤铁矿—磁铁矿固相转化速率的影响。在31 d 培养期内,SO₄^2-+SRB+磁赤铁矿体系中SRB 的生长导致16.7%的SO₄^2-转化为酸可挥发性硫（AVS）,部分还原释放的Fe（II） 与AVS 反应生成单硫化物、双硫化物和多硫化物,同时铁氧化物因溶解作用粒径减小;在无SO₄^2-的SRB+磁赤铁矿体系中, SRB 还原产生的Fe （II） 主要存在于铁氧化物中,没有次生沉淀产生。X 射线衍射和穆斯堡尔谱分析结果表明在SRB 作用下纳米磁赤铁矿逐渐向磁铁矿转化,加入SO₄^2-时转化速率加快,与矿物接触的SRB 菌体的数量及其向磁赤铁矿传递电子的能力均得到了增强。在天然或人工厌氧条件下,SO₄^2-是制约磁赤铁矿向磁铁矿转化的重要因素。     

A revised isotope fractionation model for dissimilatory sulfate reduction in sulfate reducing bacteria

Sulfur isotope fractionation during dissimilatory sulfate reduction has been conceptually described by the widely accepted Rees model as related to the stepwise reduction of sulfate to sulfide within the cells of bacteria. The magnitude of isotope fractionation is determined by the interplay between different reduction steps in a chain of reactions. Here we present a revision of Rees’ model for bacterial sulfate reduction that includes revised fractionation factors for the sulfite-sulfide step and incorporates new forward and reverse steps in the reduction of sulfite to sulfide, as well as exchange of sulfide between the cell and ambient water. With this model we show that in contrast to the Rees model, isotope fractionations well in excess of −46‰ are possible. Therefore, some of the large sulfur isotope fractionations observed in nature can be explained without the need of alternate pathways involving the oxidative sulfur cycle. We use this model to predict that large fractionations should occur under hypersulfidic conditions and where electron acceptor concentrations are limiting.     

Temperature induced decoupling of enzymatic hydrolysis and carbon remineralization in long-term incubations of Arctic and temperate sediments

Extracellular enzymatic hydrolysis of high-molecular weight organic matter is the initial step in sedimentary organic carbon degradation and is often regarded as the rate-limiting step. Temperature effects on enzyme activities may therefore exert an indirect control on carbon mineralization. We explored the temperature sensitivity of enzymatic hydrolysis and its connection to subsequent steps in anoxic organic carbon degradation in long-term incubations of sediments from the Arctic and the North Sea. These sediments were incubated under anaerobic conditions for 24 months at temperatures of 0, 10, and 20 °C. The short-term temperature response of the active microbial community was tested in temperature gradient block incubations. The temperature optimum of extracellular enzymatic hydrolysis, as measured with a polysaccharide (chondroitin sulfate), differed between Arctic and temperate habitats by about 8-13 °C in fresh sediments and in sediments incubated for 24 months. In both Arctic and temperate sediments, the temperature response of chondroitin sulfate hydrolysis was initially similar to that of sulfate reduction. After 24 months, however, hydrolysis outpaced sulfate reduction rates, as demonstrated by increased concentrations of dissolved organic carbon (DOC) and total dissolved carbohydrates. This effect was stronger at higher incubation temperatures, particularly in the Arctic sediments. In all experiments, concentrations of volatile fatty acids (VFA) were low, indicating tight coupling between VFA production and consumption. Together, these data indicate that long-term incubation at elevated temperatures led to increased decoupling of hydrolytic DOC production relative to fermentation. Temperature increases in marine sedimentary environments may thus significantly affect the downstream carbon mineralization and lead to the increased formation of refractory DOC.     

Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps

The anaerobic oxidation of methane in aquatic environments is a globally significant sink for a potent greenhouse gas. Significant gaps remain in our understanding of the anaerobic oxidation of methane because data describing the distribution and abundance of putative anaerobic methanotrophs in relation to rates and patterns of anaerobic oxidation of methane activity are rare. An integrated biogeochemical, molecular ecological and organic geochemical approach was used to elucidate interactions between the anaerobic oxidation of methane, methanogenesis, and sulfate reduction in sediments from two cold seep habitats (one brine site, the other a gas hydrate site) along the continental slope in the Northern Gulf of Mexico. The results indicate decoupling of sulfate reduction from anaerobic oxidation of methane and the contemporaneous occurrence of methane production and consumption at both sites. Phylogenetic and organic geochemical evidence indicate that microbial groups previously suggested to be involved in anaerobic oxidation of methane coupled to sulfate reduction were present and active. The distribution and isotopic composition of lipid biomarkers correlated with microbial distributions, although concrete assignment of microbial function based on biomarker profiles was complicated given the observed overlap of competing microbial processes. Contemporaneous activity of anaerobic oxidation of methane and bicarbonate-based methanogenesis, the distribution of methane-oxidizing microorganisms, and lipid biomarker data suggest that the same microorganisms may be involved in both processes.     

Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study

The stratified water column of the Black Sea is partitioned into oxic, suboxic, and euxinic zones, each characterized by different biogeochemical processes and by distinct microbial communities. In 2003, we collected particulate matter by large volume in situ filtration at the highest resolution to date for lipid biomarker analysis and bacterioplankton for enumeration of major prokaryotic groups. Abundances of several prokaryotic groups were estimated using CARD-FISH probes specific for Bacteria, Archaea (Crenarchaeota and Euryarchaeota), epsilonproteobacteria (mainly sulfide oxidizers) and sulfate reducing bacteria. We also measured a wide range of bacterial and archaeal lipid biomarkers. Depth distributions of diagnostic biomarkers are matched with zonation of microbial processes, including aerobic bacterial oxidation of methane, oxidation of ammonium by bacteria and archaea, metal reduction, and sulfide oxidation at the chemocline, and bacterial sulfate reduction and anaerobic oxidation of methane by archaea in the anoxic zone. Cell densities for archaea and sulfate reducing bacteria are estimated based on water column biomarker concentrations and compared with CARD-FISH results.     

贵州红枫湖沉积物有机质的酶及微生物降解

文章通过DNA、α-葡萄糖苷酶和硫酸盐还原菌等的变化,研究了贵州红枫湖沉积物中有机质的酶及微生物降解.有机质在微生物及其分泌的胞外酶的作用下被降解,在沉积物深度11cm以下被降解到相对较低的含量.DNA的分布表明表层9cm的沉积物深度内微生物的活动较为强烈,是微生物降解有机质的主要位置.α-葡萄糖苷酶在悬浮层含量最高,达0.75μmol/min*g干沉积物,提示有机质中的淀粉和糖原等物质在悬浮层降解较为激烈,被大量分解;随着沉积物深度的增加α-葡萄糖苷酶活性减弱,在有机质降解明显开始变缓的11cm沉积物中,α-葡萄糖苷酶活性已降低到0.17μmol/ming干沉积物.分子生物学的研究表明红枫湖沉积物表层7cm是硫酸盐还原菌的主要分布位置,结合有机质和SO_2-4含量的研究结果,提示红枫湖沉积物中SO_2-4不可能成为有机质氧化的主要电子受体,硫酸盐还原的限制因素也不是有机质供应.     

Bacterial calcification as a possible trigger for francolite precipitation under sulfidic conditions

Francolite (carbonate-fluor-apatite) is known to form in sediments where intense organic-matter decay occurs, but under oxic-to-suboxic conditions, because the alkalinity rise accompanying bacterial sulfate reduction (anoxic conditions) increases francolite solubility, hence preventing its supersaturation and precipitation. However, lagoonal, organic matter-rich, cryptalgal carbonates of Jurassic age located in the French Jura Mountains contain francolite that formed during early diagenesis, under anoxic-sulfidic and highly alkaline conditions. To explain this paradoxical situation, we propose the following “chain of reactions”: the presence of abundant biomass in the sediment would supply the “raw material” to the reactional system, i.e., the initial P budget, released through organic decay. The development of cryptalgal, bacterial mats at the sediment–water interface would have limited exchanges between the water column and the pore space, hampering pore water renewal and favoring the early onset of sulfate-reducing reactions. The onset of sulfate reduction would increase pore water alkalinity, potentially preventing francolite precipitation. In addition, the presence of sulfide ions would induce organic matter sulfurization, resulting in a relative pH rise. Alkalinity and pH rises would trigger the development of conditions leading to carbonate supersaturation, inducing bacterial-structure calcification. The sudden fall in alkalinity induced by early calcification would allow francolite precipitation, despite sulfidic conditions.     

海洋天然气水合物系统硫同位素研究进展

在海洋天然气水合物的地质系统中,甲烷的渗漏作用形成了独特的地球化学微环境。渗漏的甲烷在硫酸根-甲烷氧化还原界面与硫酸根之间发生厌氧氧化反应,同时硫酸盐发生还原反应,形成具有特殊同位素组成的自生碳酸盐、硫化物（AVS、黄铁矿等）和硫酸盐（重晶石、石膏）等。反应过程中硫酸盐还原菌的作用使得产物中硫的同位素发生了强烈分馏,具体表现为低δ34S值的硫化物矿物和高δ³⁴S值的硫酸盐矿物的形成。沉积物中这种独特的硫同位素特征与海洋天然气水合物系统中独特地球化学微环境有关,是硫酸盐还原反应过程中细菌控制的硫酸盐分馏和厌氧细菌对硫的歧化反应（disproportionation）的共同作用结果。     

Bioclogging in porous media under continuous-flow condition

Bioclogging extensively exists in porous media, such as permeable reactive barrier, constructed wetland, reverse osmosis, and biofilter systems. Microorganisms overproduce and affect the efficiency of sewage treatment. In this paper, variations in biochemical and hydraulic parameters during the clogging process were obtained using various column experiments. The hydraulic conductivity first decreased sharply to 18.32 % of the original value at the 12th day and decreased to 2.71 % at the end of the experiment, a reduction of more than an order of magnitude. The hydrodynamic dispersion had the highest increase at 7.13 times the initial value and ultimately decreased to 29 %. The porosity decreased to 47.24 % of the initial value, and the total bacterial count in the inlet of the column increased from 3.4 × 10⁶ to 8.8 × 10⁸ cells/mL. Based on the biochemical and hydraulic parameter variation, the clogging process can be divided into four stages: (1) severe clogging occurs, and aerobic microorganisms reproduce rapidly in the inlet; (2) clogging exists in the entire column, and hydrodynamic dispersion increases sharply as aerobic and anaerobic microorganisms reproduce; (3) anaerobic microorganisms reproduce rapidly and produce more gas, and hydrodynamic dispersion decreases quickly; (4) aerobic and anaerobic microorganisms multiply continuously, and hydrodynamic dispersion, hydraulic conductivity, and porosity decrease steadily. Bioclogging then transforms into a steady stage.