Concurrent corticosteroid and phenanthrene transformation by filamentous fungus Cunninghamella elegans

A filamentous fungus Cunninghamella elegans IM 1785/21Gp which displays ability of 17alpha,21-dihydroxy-4-pregnene-3,20-dione (cortexolone) 11-hydroxylation (yielding epihydrocortisone (eF) and hydrocortisone (F)) and polycyclic aromatic hydrocarbons (PAHs) degradation, was used as a microbial eucaryotic model to study the relationships between mammalian steroid hydroxylation and PAHs metabolization. The obtained results showed faster transformation of phenanthrene in Sabouraud medium supplemented with steroid substrate (cortexolone). Simultaneously phenanthrene stimulated epihydrocortisone production from cortexolone. In phenanthrene presence the ratio between cortexolone hydroxylation products (hydrocortisone and epihydrocortisone) was changed from 1:5.1-6.2 to 1:7.6-8.4 in the culture without phenanthrene. Cytochrome P-450 content significantly increased after the culture supplementation by the second substrate, phenanthrene or cortexolone, adequately. To confirm the involvement of cytochrome P-450 in phenanthrene metabolism, the inhibition studies were performed. The cytochrome P-450 inhibitors SKF 525-A (1.5mM) and 2-methyl-1,2-di-3-pyridyl-1-propanone (metyrapone) (2mM) inhibited phenanthrene transformation by 80 and 62%, respectively. 1-aminobenzotriazole (1mM) completely blocked phenanthrene metabolism. The obtained results suggest a presence of connections between steroid hydroxylases and enzymes involved in PAH degradation in C. elegans.     

The effect of co-substrate activation on indigenous and bioaugmented PCB dechlorinating bacterial communities in sediment microcosms

Microbial reductive dechlorination by members of the phylum Chloroflexi, including the genus Dehalococcoides, may play an important role in natural detoxification of highly chlorinated environmental pollutants, such as polychlorinated biphenyls (PCBs). Previously, we showed the increase of an indigenous bacterial population belonging to the Pinellas subgroup of Dehalococcoides spp. in Anacostia River sediment (Washington DC, USA) microcosms treated with halogenated co-substrates (“haloprimers”), tetrachlorobenzene (TeCB), or pentachloronitrobenzene (PCNB). The PCNB-amended microcosms exhibited enhanced dechlorination of weathered PCBs, while TeCB-amended microcosms did not. We therefore developed and used different phylogenetic approaches to discriminate the effect of the two different haloprimers. We also developed complementary approaches to monitor the effects of haloprimer treatments on 12 putative reductive dehalogenase (rdh) genes common to Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1. Our results indicate that 16S rRNA gene-based phylogenetic analyses have a limit in their ability to distinguish the effects of two haloprimer treatments and that two of rdh genes were present in high abundance when microcosms were amended with PCNB, but not TeCB. rdh gene-based phylogenetic analysis supports that these two rdh genes originated from the Pinellas subgroup of Dehalococcoides spp., which corresponds to the 16S rRNA gene-based phylogenetic analysis.     

Reductive dehalogenation of dichloroanilines by anaerobic microorganisms in fresh and dichlorophenol-acclimated pond sediment

We investigated the transformation of 2,4-dichloroaniline (2,4-DiCA) and 3,4-DiCA to monochloroanilines (CA) in anaerobic pond sediment. Dechlorination of 3,4-DiCA to 3-CA started after a lag period of 3 weeks and was complete after an additional 5 weeks. Although 2,4-DiCA disappeared over 8 weeks, the appearance of a CA product could not be detected. In contrast, anaerobic bacteria in pond sediment acclimated to dehalogenate 2,4-dichlorophenol (2,4-DiCP) or 3,4-DiCP rapidly dechlorinated 2,4-DiCA and 3,4-DiCA without any lag time. By comparison, anaerobic sediment bacteria acclimated to 3,4-DiCA rapidly degraded 3,4-DiCP without a lag. In all cases, the CA products were stable for the duration of the experiments. It is concluded that cross-acclimation occurred.     

Reductive dehalogenation of dichloroanilines by anaerobic microorganisms in fresh and dichlorophenol-acclimated pond sediment.

We investigated the transformation of 2,4-dichloroaniline (2,4-DiCA) and 3,4-DiCA to monochloroanilines (CA) in anaerobic pond sediment. Dechlorination of 3,4-DiCA to 3-CA started after a lag period of 3 weeks and was complete after an additional 5 weeks. Although 2,4-DiCA disappeared over 8 weeks, the appearance of a CA product could not be detected. In contrast, anaerobic bacteria in pond sediment acclimated to dehalogenate 2,4-dichlorophenol (2,4-DiCP) or 3,4-DiCP rapidly dechlorinated 2,4-DiCA and 3,4-DiCA without any lag time. By comparison, anaerobic sediment bacteria acclimated to 3,4-DiCA rapidly degraded 3,4-DiCP without a lag. In all cases, the CA products were stable for the duration of the experiments. It is concluded that cross-acclimation occurred.     

Microbial dechlorination of hexachlorobenzene in a sedimentation area of the Rhine River

In sedimentation areas of polluted rivers, microbial dechlorination of chlorinated aromatics may be of great environmental significance. This reaction may take place in the deeper, anaerobic sediment layers and involves replacement of a chlorine in the pollutant molecule by hydrogen. In this study, the microbial dechlorination of hexachlorobenzene in a sedimentation area of the Rhine River is evaluated by using Rhine water pollution data, concentrations in historical sediment samples and in recent sediment cores, and the results of anaerobic laboratory incubations with Lake Ketelmeer sediment. The various data support the conclusion that microbial dechlorination of hexachlorobenzene has occurred in the anaerobic sediment. Up to 80% of the hexachlorobenzene deposited in the early 1970s has been dechlorinated. The maximum half-life of hexachlorobenzene in the sediment is found to be 7 years.Two limitations of microbially mediated dechlorination in the natural environment have become clear. In the first place, a residual concentration of about 40 g/kg remains unaltered in the sediment or transformation rates of this fraction are at least extremely low. Secondly, the lower chlorinated benzenes that are produced from hexachlorobenzene appear to accumulate in the anaerobic sediment.     

Regiospecific dechlorination of pentachlorophenol by dichlorophenol-adapted microorganisms in freshwater, anaerobic sediment slurries.

The reductive dechlorination of pentachlorophenol (PCP) was investigated in anaerobic sediments that contained nonadapted or 2,4- or 3,4-dichlorophenol (DCP)-adapted microbial communities. Adaptation of sediment communities increased the rate of conversion of 2,4- or 3,4-DCP to monochlorophenols (CPs) and eliminated the lag phase before dechlorination was observed. Both 2,4- and 3,4-DCP-adapted sediment communities dechlorinated the six DCP isomers to CPs. The specificity of chlorine removal from the DCP isomers indicated a preference for ortho-chlorine removal by 2,4-DCP-adapted sediment communities and for para-chlorine removal by 3,4-DCP-adapted sediment communities. Sediment slurries containing nonadapted microbial communities either did not dechlorinate PCP or did so following a lag phase of at least 40 days. Sediment communities adapted to dechlorinate 2,4- or 3,4-DCP dechlorinated PCP without an initial lag phase. The 2,4-DCP-adapted communities initially removed the ortho-chlorine from PCP, whereas the 3,4-DCP-adapted communities initially removed the para-chlorine from PCP. A 1:1 mixture of the adapted sediment communities also dechlorinated PCP without a lag phase. Dechlorination by the mixture was regiospecific, following a para greater than ortho greater than meta order of chlorine removal. Intermediate products of degradation, 2,3,5,6-tetrachlorophenol, 2,3,5-trichlorophenol, 3,5-DCP, 3-CP, and phenol, were identified by a combination of cochromatography (high-pressure liquid chromatography) with standards and gas chromatography-mass spectrometry.     

Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing

The halogenated compound tetrachloroethene (perchloroethene, PCE) is a persistent contaminant of aquifers, soils and sediments. Although a number of microorganisms are known to reductively dechlorinate PCE by dehalorespiration, their diversity and community structure especially in pristine environments remain elusive. In this study, we report on the detection of a novel group of dehalorespiring bacteria that reductively dechlorinate PCE to cis -dichloroethene by RNA-based stable isotope probing. Pristine river sediment was incubated at 15°C with PCE at low aqueous concentration. Upon formation of dechlorination products, the microbial community was probed with ¹³C-labelled acetate as electron donor and carbon source. Terminal restriction fragment length polymorphism (T-RFLP) analysis of density-separated 16S rRNA revealed a predominantly ¹³C-labelled bacterial population only in the microcosm with PCE in high-density gradient fractions, whereas in the control without PCE Bacteria-specific rRNA was restricted to light gradient fractions. By cloning and sequence analysis of 16S rRNA, the predominant population was identified as a novel group of bacteria within the phylum Chloroflexi . These microorganisms, designated Lahn Cluster (LC), were only distantly related to cultivated dehalorespiring Dehalococcoides spp. (92–94% sequence identity). Minor clone groups detected ¹³C-labelled and thus, potentially involved in PCE dehalorespiration, were related to β-proteobacterial Dechloromonas spp., and δ- Proteobacteria ( Geobacteraceae , Desulfobacteraceae , Desulfobulbaceae ). In contrast, clones from an ethene-producing microcosm incubated at 20°C grouped with known Dehalococcoides spp. Our results show that stable isotope probing allows targeting dehalorespiring bacteria as functional guild, and to identify novel PCE-respiring populations previously not recognized.     

Bacterial communities in water and sediment shaped by paper mill pollution and indicated bacterial taxa in sediment in Daling River

Effluents from paper mills are highly toxic and are a major source of aquatic pollution. In this study, we collected water and sediment samples to examine the microbial communities using denaturing gradient gel electrophoresis and identified bacterial taxa greatly affected by paper mill pollution using next-generation sequencing data. Our results indicated that bacterial communities in downstream sediments were similar to those in paper mill discharge sites, indicating obvious effects of pollution, while bacterial communities in downstream water samples showed similar profiles to those in upstream sites, both being quite different from the bacterial communities in paper mill discharge sites. This was possibly because of the short contact period. In addition, bacterial communities in the estuary were quite different from those in other water and sediment samples, which was owing to the special habitat type. Considering the storage of paper mill pollutants in sediment and the significant effect on shifts in bacterial communities, we selected Clostridia and Epsilonproteobacteria at the class level and Fusibacter and Desulfobulbus at the genus level as bacterial indicators of paper mill pollution. To monitor the remediation of polluted aquatic environments, we propose Sphingobacteria, Alphaproteobacteria, Actinobacteria, Subdivision3, Planctomycetacia and Verrucomicrobiae at the class level and Bacillus, Steroidobacter, Nocardioides, Terrimonas, Pirellula and Methylibium at the genus level.     

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils

Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson’s correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.     

Prevalence and sequence comparison of Phyllodistomum folium from zebra mussel and from freshwater fish in the Ebro River

We utilised DNA analysis to detect the presence of the digenean Phyllodistomum folium in three cyprinid species, Scardinius erythrophthalmus, Cyprinus carpio and Rutilus rutilus. DNA sequencing of the region containing the genes ITS1-5.8S-ITS2 revealed 100% sequence identity between DNA from the sporocysts found in zebra mussels and DNA from adults located in the urinary system of 29 cyprinid fish. A second genetically different (variation=1.6%) sequence was observed in two samples from R. rutilus. In our opinion, the existence of a complex of species reported as P. folium is supported by recent genetic studies, including our own results. The overall prevalence of P. folium in mussels from the Ebro River was 4.67% in 2006, although during the summer months the rates frequently exceeded 10%.     

生物竞争抑制作用对渤海J油田微生物降解驱油聚合物功能的影响

【目的】揭示可降解驱油用聚合物的油藏内源微生物群落组成,分析生物竞争抑制作用(bio-competitive exclusion,BCX)对微生物聚合物降解功能的影响。【方法】通过室内培养实验,观察BCX对驱油用聚合物黏度的影响,随后借助高通量测序技术分析渤海J油田中与聚合物降解相关的微生物菌种,并探寻样本中丰度较高的聚合物降解功能基因─酰胺酶、加氧酶、硫化氢生成酶基因。之后,比对测序结果,采用实时荧光定量法验证上述功能基因在样本之间的含量差异,最后进一步注释携带上述功能基因的微生物群落组成。【结果】BCX可有效地延缓驱油聚合物黏度的损失。油田中与聚合物降解相关的微生物有Acetomicrobium、 Tepidiphilus、Thermoanaerobacter、Fervidobacterium、Ralstonia、Halomonas、Roseovarius、Deferribacteraceae和Comamonadaceae等9类菌种。高通量测序分析得到样本中BCX可显著下调丰度的聚合物降解功能基因共计有7种,其中酰胺酶基因ansB、加氧酶基因ssuD在样本之间的含量经定量验证,发现...     

南海Formosa冷泉区沉积物微生物多样性与分布规律研究

【目的】当前对全球冷泉生态系统微生物生态学研究显示，冷泉生态系统中主要微生物类群为参与甲烷代谢的微生物，它们的分布差异与所处冷泉区生物地球化学环境密切相关。但在冷泉区内也存在环境因子截然不同的生境，尚缺乏比较冷泉区内小尺度生境间微生物多样性和分布规律的研究。本研究旨在分析南海Formosa冷泉区内不同生境间微生物多样性差异，完善和理解不同环境因子对冷泉内微生物群落结构的影响。【方法】对采集自南海Formosa冷泉区不同生境(黑色菌席区、白色菌席区和碳酸盐岩区)沉积物样本中古菌和细菌16S rRNA基因进行测序，结合环境因子，比较微生物多样性差异，分析环境因子对微生物分布的影响。【结果】发现在Formosa冷泉内的不同生境中，甲烷厌氧氧化古菌(anaerobic methanotrophic archaea,ANME)是主要古菌类群，占古菌总体相对丰度超过70%；在菌席区ANME-1b和ANME-2a/b是主要ANME亚群，碳酸盐岩区则是ANME-1b。硫酸盐还原菌(sulfate-reducing bacteria,SRB)和硫氧化菌(sulfur-oxidizing bacteria...     

Exposure to Metals through the Consumption of Fish and Seafood by the Population Living Near the Ebro River in Catalonia,Spain: Health Risks

The health risks due to metal exposure from consuming various fish and seafood species were assessed for the Catalan population living near the Ebro River (Spain). The concentrations of arsenic, cadmium, chromium, copper, mercury, manganese, nickel, and lead were determined in samples of mussel, clam, hake, sole, cuttlefish, sardine, and anchovy randomly acquired in various localities of the zone under evaluation. In general terms, metal concentrations were similar or lower than the levels recently reported in the literature. The current dietary intake of metals is analogous to that recently estimated for the non-exposed population of Catalonia. Metal exposure through fish and seafood consumption would only mean a slight increase of noncarcinogenic and carcinogenic risk for arsenic, whereas the remaining elements showed risk values below the corresponding threshold levels.     

海洋沉积物微生物介导有机碳转化研究进展

海洋沉积物是地球上最大的有机碳库,其中生存的微生物总量大、分布范围广、类群多样、代谢方式复杂,并共同构成海洋沉积物微生物组。海洋沉积物微生物组介导的有机碳降解与矿化过程不但能为沉积物中的生命活动提供物质和能量,也能参与调控碳循环过程,并在长时间尺度上对地球气候系统产生重大影响。沉积物中的有机碳在复杂多样的微生物代谢活动下被逐步降解,其最终的矿化过程与不同的电子受体消耗相偶合,并形成对应的地球化学分区。研究海洋沉积物微生物及其介导的有机碳转化过程对我们深入认识沉积物中的元素循环过程,并进一步评估其对整个地球系统的影响具有重要科学意义。本文对海洋沉积物微生物组的体量、包含的微生物多样性、代谢活性以及在不同地球化学分区中主要的微生物类群和代谢机制进行综述,最后基于研究现状展望了海洋沉积物微生物组的未来研究方向。     

Relative role of eukaryotic and prokaryotic microorganisms in phenanthrene transformation in coastal sediments

THE RELATIVE ROLE OF EUKARYOTIC VERSUS PROKARYOTIC MICROORGANISMS IN PHENANTHRENE TRANSFORMATION WAS MEASURED IN SLURRIES OF COASTAL SEDIMENT BY TWO DIFFERENT APPROACHES: detection of marker metabolites and use of selective inhibitors on phenanthrene biotransformation. Phenanthrene biotransformation was measured by polar metabolite formation and CO(2) evolution from [9-C]phenanthrene. Radiolabeled metabolites were tentatively identified by high-performance liquid chromatography (HPLC) separation combined with UV/visible spectral analysis of HPLC peaks and comparison to authentic standards. Both yeasts and bacteria transformed phenanthrene in slurries of coastal sediment. Two products of phenanthrene oxidation by fungi, phenanthrene trans-3,4-dihydrodiol and 3-phenanthrol, were produced in yeast-inoculated sterile sediment. However, only products of phenanthrene oxidation typical of bacterial transformation, 1-hydroxy-2-naphthoic acid and phenanthrene cis-3,4-dihydrodiol, were isolated from slurries of coastal sediment with natural microbial populations. Phenanthrene trans-dihydrodiols or other products of fungal oxidation of phenanthrene were not detected in the slurry containing a natural microbial population. A predominant role for bacterial transformation of phenanthrene was also suggested from selective inhibitor experiments. Addition of streptomycin to slurries, at a concentration which suppressed bacterial viable counts and rates of [methyl-H]thymidine uptake, completely inhibited phenanthrene transformation. Treatment with colchicine, at a concentration which suppressed yeast viable counts, depressed phenanthrene transformation by 40%, and this was likely due to nontarget inhibition of bacterial activity. The relative contribution of eukaryotic microorganisms to phenanthrene transformation in inoculated sterile sediment was estimated to be less than 3% of the total activity. We conclude that the predominant degraders of phenanthrene in muddy coastal sediments are bacteria and not eukaryotic microorganisms.