Iron Cycling Potentials of Arsenic Contaminated Groundwater in Bangladesh as Revealed by Enrichment Cultivation

The activities of iron-oxidizing and reducing microorganisms impact the fate of arsenic in groundwater. Phylogenetic information cannot exclusively be used to infer the potential for iron oxidation or reduction in aquifers. Therefore, we complemented a previous cultivation-independent microbial community survey covering 22 arsenic contaminated drinking water wells in Bangladesh, with the characterization of enrichments of microaerophilic iron oxidizers and anaerobic iron reducers, conducted on the same water samples. All investigated samples revealed a potential for microbial iron oxidation and reduction. Microbial communities were phylogenetically diverse within and between enrichments as was also observed in the previous cultivation-independent analysis of the water samples from which these enrichments were derived. Enrichment uncovered a larger diversity in iron-cycling microorganisms than previously indicated. The iron-reducing enrichments revealed the presence of several 16S ribosomal RNA (16S rRNA) gene sequences most closely related to Acetobacterium, Clostridium, Bacillus, Rhizobiales, Desulfovibrio, Bacteroides, and Spirochaetes, in addition to well-known dissimilatory iron-reducing Geobacter and Geothrix species. Although a large diversity of Geobacteraceae was observed, they comprised only a small part of the iron-reducing consortia. Iron-oxidizing gradient tube enrichments were dominated by Comamonadaceae and Rhodocyclaceae instead of Gallionellaceae. Forty-five percent of these enrichments also revealed the presence of the gene encoding arsenite oxidase, which converts arsenite to less toxic and less mobile arsenate. Their potential for ferric (oxyhydr)oxides precipitation and arsenic immobilization makes these iron-oxidizing enrichments of interest for rational bioaugmentation of arsenite contaminated groundwater.     

Microbial methylation of metalloids: arsenic, antimony, and bismuth.

A significant 19th century public health problem was that the inhabitants of many houses containing wallpaper decorated with green arsenical pigments experienced illness and death. The problem was caused by certain fungi that grew in the presence of inorganic arsenic to form a toxic, garlic-odored gas. The garlic odor was actually put to use in a very delicate microbiological test for arsenic. In 1933, the gas was shown to be trimethylarsine. It was not until 1971 that arsenic methylation by bacteria was demonstrated. Further research in biomethylation has been facilitated by the development of delicate techniques for the determination of arsenic species. As described in this review, many microorganisms (bacteria, fungi, and yeasts) and animals are now known to biomethylate arsenic, forming both volatile (e.g., methylarsines) and nonvolatile (e.g., methylarsonic acid and dimethylarsinic acid) compounds. The enzymatic mechanisms for this biomethylation are discussed. The microbial conversion of sodium arsenate to trimethylarsine proceeds by alternate reduction and methylation steps, with S-adenosylmethionine as the usual methyl donor. Thiols have important roles in the reductions. In anaerobic bacteria, methylcobalamin may be the donor. The other metalloid elements of the periodic table group 15, antimony and bismuth, also undergo biomethylation to some extent. Trimethylstibine formation by microorganisms is now well established, but this process apparently does not occur in animals. Formation of trimethylbismuth by microorganisms has been reported in a few cases. Microbial methylation plays important roles in the biogeochemical cycling of these metalloid elements and possibly in their detoxification. The wheel has come full circle, and public health considerations are again important.     

Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth

A significant 19th century public health problem was that the inhabitants of many houses containing wallpaper decorated with green arsenical pigments experienced illness and death. The problem was caused by certain fungi that grew in the presence of inorganic arsenic to form a toxic, garlic-odored gas. The garlic odor was actually put to use in a very delicate microbiological test for arsenic. In 1933, the gas was shown to be trimethylarsine. It was not until 1971 that arsenic methylation by bacteria was demonstrated. Further research in biomethylation has been facilitated by the development of delicate techniques for the determination of arsenic species. As described in this review, many microorganisms (bacteria, fungi, and yeasts) and animals are now known to biomethylate arsenic, forming both volatile (e.g., methylarsines) and nonvolatile (e.g., methylarsonic acid and dimethylarsinic acid) compounds. The enzymatic mechanisms for this biomethylation are discussed. The microbial conversion of sodium arsenate to trimethylarsine proceeds by alternate reduction and methylation steps, with S-adenosylmethionine as the usual methyl donor. Thiols have important roles in the reductions. In anaerobic bacteria, methylcobalamin may be the donor. The other metalloid elements of the periodic table group 15, antimony and bismuth, also undergo biomethylation to some extent. Trimethylstibine formation by microorganisms is now well established, but this process apparently does not occur in animals. Formation of trimethylbismuth by microorganisms has been reported in a few cases. Microbial methylation plays important roles in the biogeochemical cycling of these metalloid elements and possibly in their detoxification. The wheel has come full circle, and public health considerations are again important.     

Selenate reduction by bacteria from a selenium-rich environment.

Samples collected from Kesterson Reservoir were screened for bacterial presence and selenate reduction capability. Selenate concentrations of 100 mg/liter were not toxic to indigenous bacteria. Of the 44 samples collected, 20 possessed microbial populations capable of reducing selenate. Reduction was observed in 4% of the water samples, 92% of the sediment samples, and 100% of the soil samples. Microbial reduction of 100 mg of selenate per liter was complete within 1 week of incubation. Up to 75 mg of selenate per liter was reduced beyond selenite to an insoluble red precipitate. Data collected indicate that indigenous bacteria have a significant role in the biogeochemical cycling of selenium.     

Selenate reduction by bacteria from a selenium-rich environment

Samples collected from Kesterson Reservoir were screened for bacterial presence and selenate reduction capability. Selenate concentrations of 100 mg/liter were not toxic to indigenous bacteria. Of the 44 samples collected, 20 possessed microbial populations capable of reducing selenate. Reduction was observed in 4% of the water samples, 92% of the sediment samples, and 100% of the soil samples. Microbial reduction of 100 mg of selenate per liter was complete within 1 week of incubation. Up to 75 mg of selenate per liter was reduced beyond selenite to an insoluble red precipitate. Data collected indicate that indigenous bacteria have a significant role in the biogeochemical cycling of selenium.     

“吃”砒霜的细菌--解析微生物的砷代谢

研究发现一些微生物可以利用剧毒的类金属砷(As)为自身生长获取能量甚至用砷代替磷维持生长。本文综合分析了近期的研究进展,从以下6方面解析微生物多重的砷代谢产能机制:(1)化能无机自养As(Ⅲ)氧化供能;(2)有机异养型As(Ⅲ)氧化供能;(3)呼吸性As(Ⅴ)还原供能;(4)As(Ⅲ)氧化偶联的光合作用;(5)As(Ⅲ)氧化、As(Ⅴ)、还原As(Ⅲ)氧化偶联的光合作用之间的关联;(6)As(Ⅴ)代替磷维持细菌生长。阐明微生物利用砷的机理在生命起源、生命多样性、进化、地球化学循环及污染治理等方面都具有重要价值。     

稳定性同位素核酸探针技术DNA-SIP 原理与应用

稳定性同位素核酸探针技术DNA-SIP(Stable isotope probing),是将复杂环境中微生物物种组成及其生理功能耦合分析的有力工具.微生物的体积在μm尺度,因此,自然环境中微生物群落在μm尺度下生理过程的发生、发展,其新陈代谢物质在环境中累积与消减的动力学变化规律,形成了微生物生理生态过程,决定了不同尺度下生态系统物质和能量的良性循环.利用稳定性同位素示踪复杂环境中微生物基因组DNA,实现了单一微生物生理过程研究向微生物群落生理生态研究的转变,能在更高更复杂的整体水平上定向发掘重要微生物资源,推动微生物生理生态学和生物技术开发应用.本文重点探讨了DNA-SIP的技术原理、主要技术瓶颈及对策,初步展望了DNA-SIP为基础的环境微生物基因组学发展趋势.     

Microbial Precipitation of Arsenic Sulfides in Andean Salt Flats

An abiotic origin has traditionally been assumed for the arsenic minerals realgar and orpiment associated with thermal springs. Microbial precipitation of arsenic, however, has been studied in pure cultures and the isotopic composition of arsenic sulfides associated with some borate deposits suggests a biotic origin for those minerals. The aim of the present study is to demonstrate the role of bacterial arsenic precipitation in the biogeochemical cycle of arsenic in such borate deposits. For this purpose both enrichment and pure cultures were obtained from the natural arsenic minerals and the composition and isotopic signatures of the arsenic sulfide minerals precipitated by the cultures and those associated with boron deposits from an Andean salt flat in northern Chile were compared. Based on the microbiological and chemical evidence gathered, it is concluded that bacteria contributed to the formation of the arsenic minerals. This interpretation is based on the consistent association of a variety of features that strongly indicate microbial involvement in the precipitation process. These include: (1) enrichment and isolation of cultures with arsenic precipitation capacity from arsenic mineral samples, (2) high numbers of arsenic-precipitating bacteria in the Andean minerals and brines, (3) chemical and mineralogical properties of precipitates experimentally formed under biotic and abiotic conditions, (4) similarities in stoichiometry between natural and laboratory obtained minerals, and (5) the consistent depletion in δ³⁴S values for natural versus laboratory obtained sulfides. Thus, microbial precipitation of arsenic sulfides is a geochemically relevant metabolism.     

Characterization of bacterial diversity associated with microbial mats,gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava,Salar de Atacama,Chile

In this paper, we report the presence of sedimentary microbial ecosystems in wetlands of the Salar de Atacama. These laminated systems, which bind, trap and precipitate mineral include: microbial mats at Laguna Tebenquiche and Laguna La Brava, gypsum domes at Tebenquiche and carbonate microbialites at La Brava. Microbial diversity and key biogeochemical characteristics of both lakes (La Brava and Tebenquiche) and their various microbial ecosystems (non-lithifying mats, flat and domal microbialites) were determined. The composition and abundance of minerals ranged from trapped and bound halite in organic-rich non-lithifying mats to aragonite-dominated lithified flat microbialites and gypsum in lithified domal structures. Pyrosequencing of the V4 region of the 16s rDNA gene showed that Proteobacteria comprised a major phylum in all of the microbial ecosystems studied, with a marked lower abundance in the non-lithifying mats. A higher proportion of Bacteroidetes was present in Tebenquiche sediments compared to La Brava samples. The concentration of pigments, particularly that of Chlorophyll a, was higher in the Tebenquiche than in La Brava. Pigments typically associated with anoxygenic phototrophic bacteria were present in lower amounts. Organic-rich, non-lithifying microbial mats frequently formed snake-like, bulbous structures due to gas accumulation underneath the mat. We hypothesize that the lithified microbialites might have developed from these snake-like microbial mats following mineral precipitation in the surface layer, producing domes with endoevaporitic communities in Tebenquiche and carbonate platforms in La Brava. Whereas the potential role of microbes in carbonate platforms is well established, the contribution of endoevaporitic microbes to formation of gypsum domes needs further investigation.     

Geomicrobial Processes and Biodiversity in the Deep Terrestrial Subsurface

The concept of a deep microbial biosphere has advanced over the past several decades from a hypothesis viewed with considerable skepticism to being widely accepted. Phylogenetically diverse prokaryotes have been cultured from or detected via characterization of directly-extracted nucleic acids from a wide range of deep terrestrial environments. Recent advances have linked the metabolic potential of these microorganisms, determined directly or inferred from phylogeny, to biogeochemical reactions determined via geochemical measurements and modeling. Buried organic matter or kerogen is an important source of energy for sustaining anaerobic heterotrophic microbial communities in deep sediments and sedimentary rock although rates of respiration are among the slowest rates measured on the planet. In contrast, Subsurface Lithoautotrophic Microbial Ecosystems based on H ₂ as the primary energy source appear to dominate in many crystalline rock environments. These photosynthesis-independent ecosystems remain an enigma due to the difficulty in accessing and characterizing appropriate samples. Deep mines and dedicated rock laboratories, however, may offer unprecedented opportunities for investigating subsurface microbial communities and their interactions with the geosphere.     

木质素在海洋中的生物转化及其对海洋碳循环的影响

微型生物参与的海洋碳汇是海洋重要的储碳途径,可调节全球气候变化。木质素是地球上第二大光合而成的碳库,其在海洋中的生物地球化学过程与海洋碳循环密切相关。异养微生物所主导的代谢活动是木质素生物转化的主要途径。近年来,迅速发展的高通量测序技术与传统微生物技术相结合,在探索自然生境中木质素代谢菌群,发现木质素代谢新物种,挖掘相关功能基因等方面已取得一系列成果。然而绝大多数的研究主要集中于陆地生态系统,对于海洋生态系统的研究仍较少。陆源有机碳在海洋中的转化过程仍是一个"谜",故解析海洋木质素碳转化是海洋碳循环研究的重要任务。本文综述了参与海洋木质素转化的功能微生物、木质素代谢机理以及微生物碳代谢活动与海洋碳汇过程的内在联系,为今后的研究提供参考。     

Cloning of a Serratia marcescens Gene Encoding Chitinase

The availability of dead microbial biomass in a marine beach sand to degradation and mineralization was examined. Microbial sand populations were labeled with [¹⁴C]glutamic acid, [³H]adenine, or [³H]thymidine and killed with chloroform. Live sand or seawater (or both) was added to the sterile labeled sand, and biochemical components of the populations were monitored for 10 days. Labeled RNA was degraded more quickly than labeled DNA, but both nucleic acids were degraded to approximately the same extent (60 to 70%). ³H₂O was a major acid-soluble breakdown product. RNA (and possibly DNA) breakdown products were reincorporated into DNA (and possibly RNA) during the incubation period. In addition to metabolite salvage, 32% of the total macromolecular ¹⁴C was respired in the 10-day period regardless of whether sand or seawater was used as the inoculum. Respiration was essentially complete in 3 days, whereas nucleic acid degradation continued throughout the 10-day incubation. The results indicate that dead microbial biomass is a labile component of the sediment ecosystem.     

微生物基因数据库在氮循环功能基因注释中的应用

氮循环是微生物和化学过程介导的生物地球化学循环。利用基因测序技术研究环境中参与氮循环的微生物群落、微生物及功能基因,是环境基因组学和微生物生态学的重要研究热点。近年来,各种类型的数据库被开发并应用到功能分析中。本文结合时下最新研究成果,聚焦由微生物引起的同化硝酸盐还原作用、异化硝酸盐还原作用、反硝化作用、固氮作用、硝化作用(包括完全氨氧化作用)和厌氧氨氧化作用等6种无机氮循环途径的功能基因,对比了National Center for Biotechnology Information (NCBI)、Integrated Microbial Genomes (IMG)、Universal Protein (UniProt)、Kyoto Encyclopedia of Genes and Genomes (KEGG)、Protein Families (Pfam)、Functional Gene (FunGene)、Clusters of Orthologous Groups (COG)和NCycDB等数据库的设计理念和功能特点,并结合环境介质、表征基因、分析方法和比对方法等影响因素,分析了以上数据库在氮循环功能基因注释中的选择及应用方式,展望了未来氮循环基因数据库的发展方向,以期为研究人员了解氮循环基因家族和选择合适的数据分析平台提供参考。     

陆地和淡水生态系统新型微生物氮循环研究进展

氮生物地球化学循环是地球物质循环的重要枢纽,是决定陆地生态系统生产力水平、水资源安全、温室气体生成排放的关键过程。氮循环是由微生物介导的一系列复杂过程,不同形态、价态氮化合物的转化分别由相应的功能微生物驱动完成。随着厌氧氨氧化、完全氨氧化等新型氮转化过程的相继报道和发现更新了人们对氮循环的认识。本文综述了陆地和淡水生态系统中厌氧氨氧化(anammox)、硝酸盐异化还原为铵(DNRA)、完全氨氧化(comammox)等新型氮循环过程的发生机制、热区分布及环境效应,并总结了这三种氮循环的相互关系。     

Microbial responses to environmental arsenic

Microorganisms have evolved dynamic mechanisms for facing the toxicity of arsenic in the environment. In this sense, arsenic speciation and mobility is also affected by the microbial metabolism that participates in the biogeochemical cycle of the element. The ars operon constitutes the most ubiquitous and important scheme of arsenic tolerance in bacteria. This system mediates the extrusion of arsenite out of the cells. There are also other microbial activities that alter the chemical characteristics of arsenic: some strains are able to oxidize arsenite or reduce arsenate as part of their respiratory processes. These type of microorganisms require membrane associated proteins that transfer electrons from or to arsenic (AoxAB and ArrAB, respectively). Other enzymatic transformations, such as methylation-demethylation reactions, exchange inorganic arsenic into organic forms contributing to its complex environmental turnover. This short review highlights recent studies in ecology, biochemistry and molecular biology of these processes in bacteria, and also provides some examples of genetic engineering for enhanced arsenic accumulation based on phytochelatins or metallothionein-like proteins.     

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia,China

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12–267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO₄^2-, SO₄^2-/total sulfur ratio, and Fe²⁺ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.     

Use of activated carbon as a support medium for H<Subscript>2</Subscript>S biofiltration and effect of bacterial immobilization on available pore surface

The use of support media for the immobilization of microorganisms is widely known to provide a surface for microbial growth and a shelter that protects the microorganisms from inhibitory compounds. In this study, activated carbon is used as a support medium for the immobilization of microorganisms enriched from municipal sewage activated sludge to remove gas-phase hydrogen sulfide (H₂S), a major odorous component of waste gas from sewage treatment plants. A series of designed experiments is used to examine the effect on bacteria-immobilized activated carbon (termed biocarbon) due to physical adsorption, chemical reaction, and microbial degradation in the overall removal of H₂S. H₂S breakthrough tests are conducted with various samples, including microbe-immobilized carbon and Teflon discs, salts-medium-washed carbon, and ultra-pure water-washed carbon. The results show a higher removal capacity for the microbe-immobilized activated carbon compared with the activated carbon control in a batch biofilter column. The increase in removal capacity is attributed to the role played by the immobilized microorganisms in metabolizing adsorbed sulfur and sulfur compounds on the biocarbon, hence releasing the adsorption sites for further H₂S uptake. The advantage for activated carbon serving as the support medium is to adsorb a high initial concentration of substrate and progressively release this for microbial degradation, hence acting as a buffer for the microorganisms. Results obtained from surface area and pore size distribution analyses of the biocarbon show a correlation between the available surface area and pore volume with the extent of microbial immobilization and H₂S uptake. The depletion of surface area and pore volume is seen as one of the factors which cause the onset of column breakthrough. Microbial growth retardation is due to the accumulation of metabolic products (i.e., sulfuric acid); and a lack of water and nutrient salts in the batch biofilter are other possible causes of column breakthrough.     

Effect of the fuel system icing inhibitor diethylene glycol monomethyl ether on the biodegradation of jet fuel in soil

Microbial degradation of jet fuel leads to the accumulation of sludge in fuel distribution systems and storage tanks. To prevent this phenomenon, the biocidal anti-icing inhibitor diethylene glycol monomethyl ether (DiEGME) is routinely added to the fuel. The fate of DiEGME in soil and its consequent effect on the biodegradation of jet fuel by indigenous soil microflora have not been investigated. The aim of this work was to study the kinetics of biodegradation of jet fuel in dark rendzina soil, as affected by the presence of DiEGME. Our data show that the degradability in soil of jet fuel amended with DiEGME was tenfold higher than that of non-amended fuel. Consequently, there was an increase in the jet-fuel-utilizing soil microbial populations during the 100 days of incubation of soil samples amended with jet fuel containing DiEGME. Gas chromatograms of distilled fractions of jet fuel extracted from the soil demonstrated that most of the light fractions' extracts could not be detected at the end of the 100-day incubation. The relative concentration of aromatic compounds in the soil contaminated with DiEGME-amended jet fuel increased during incubation, demonstrating the lower biodegradation rate of these components compared with other fuel components. DiEGME was partially degraded by the general microbial population of the soil. Maximal DiEGME degradation was obtained with specific jet-fuel-utilizing microbial strains – Pseudomonas aeruginosa and Cladosporium resinae – that were added to a carbon-free mineral medium. The degradation rate of DiEGME by specific strains or by soil mixed populations bore an inverse relationship to the DiEGME concentration. The finding that DiEGME can be degraded by indigenous soil microorganisms may have facilitated its utilization also by jet-fuel-degrading microorganisms.     

Persistence of Halophylic Methanogens and Oil-Degrading Bacteria in an Offshore Oil-Producing Facility

Microbial communities in a high saline, Tetrakis-Hydroxymethyl Phosphonium Sulfate (THPS) and nitrate-treated Nigerian oil-producing facilities were investigated. Methanogens in produced water samples preferred methanol, while those in pig-run samples (oily wastes from pipelines) preferred H₂/CO₂, as substrates to produce methane and stimulate metal corrosion. The results coincide with the dominance of methylotrophic and hydrogenotrophic methanogens in the respective samples. The same microbial populations were also THPS and high salinity tolerant. The nitrate reducers and hydrocarbon degraders were also dominant in the reservoir. A more inclusive and effective mitigation strategy is therefore required to effectively tackle biocide resistant methanogens in biocide treated oilfield.     

青稞根腐病对根际土壤微生物及酶活性的影响

选取甘肃省卓尼县青稞种植区为研究地点,调查青稞根腐病的发病情况,并分别采集其健康植株和发病株根际的土壤,对比分析其土壤微生物生物量(碳、氮、磷)、微生物数量(细菌、真菌、放线菌)以及过氧化氢酶、蔗糖酶、脲酶、碱性磷酸酶、纤维素酶5种酶活性。结果发现,研究区10个采样点均有青稞根腐病的发生,发病率在5%—20%之间,不同地点发病率不同。根腐病的发生,会显著影响青稞根际微生物生物量,导致微生物生物量碳、氮、磷的含量发生变化,其中微生物生物量氮和磷含量整体降低,且不同采样点微生物量不同。土壤微生物数量总体呈现细菌放线菌真菌的趋势,但不同微生物对根腐病发病的响应不同,细菌和放线菌数量因根腐病的发生而减少,真菌的数量则增多;不同采样点土壤微生物数量不相同,细菌和真菌呈现区域性特征,放线菌的数量不呈现地域性。根腐病的发生还造成土壤酶活性的改变,其中蔗糖酶、脲酶、磷酸酶的含量因根腐病的发生而降低,而纤维素酶则升高,过氧化氢酶的变化没有规律。总而言之,根腐病的发生会使青稞根际土壤微生物组成发生改变,碳、氮、磷等物质代谢受到抑制,而能量代谢发生紊乱。因此,研究和防治青稞根腐病就必须重视土壤微生物及土壤酶的作用。