Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil

Using cultivation-independent methods the ciliate communities of a clay-rich soil with a 90-year record of pollution by polycyclic aromatic hydrocarbons (PAH) (4.5 g kg−1 PAH) were compared with that of a nonpolluted soil collected in its vicinity and with similar properties. A ciliate-specific set of 18S rRNA gene targeting primers was designed and used to amplify DNA extracted from both soils (surface and 20 cm depth). Four clone libraries were generated with PCR products that covered an 18S rRNA gene fragment of up to 670 bp. Comparative sequence analysis of representative clones proved that the primer set was highly specific for ciliates. Calculation of similarity indices based on operational taxonomic units after amplified ribosomal DNA restriction analysis of the clones showed that the community from the nonpolluted surface soil was highly dissimilar to the other communities. The presence of several taxa, namely sequences affiliated to the orders Phyllopharyngia, Haptoria, Nassophorea, Peniculida and Scuticociliatia in samples from nonpolluted soil, points to the existence of various trophic functional groups. In contrast, the 18S rRNA gene diversity was much lower in the clone libraries from the polluted soil. More than 90% of these sequences belonged to the class Colpodea, a well-known clade of mainly bacterivorous and r-selected species, thus potentially also indicating a lower functional diversit

Microbial community response to petroleum hydrocarbon contamination in the unsaturated zone at the experimental field site Værløse, Denmark

This study investigates the influence of petroleum hydrocarbons on a microbial community in the vadose zone under field conditions. An artificial hydrocarbon mixture consisting of volatile and semi-volatile compounds similar to jet-fuel was emplaced in a previously uncontaminated vadose zone in nutrient-poor glacial melt water sand. The experiment included monitoring of microbial parameters and CO2 concentrations in soil gas over 3 months in and outside the hydrocarbon vapor plume that formed around the buried petroleum. Microbial and chemical analyses of soil and vadose zone samples were performed on samples from cores drilled to 3.3 m depth on three dates and three lateral distances from the buried petroleum mass. Significantly elevated CO2 concentrations were observed after contamination. Total cell numbers as determined by fluorescence microscopy were strongly correlated with soil organic carbon and nitrogen content but varied little with contamination. Redundancy analysis (RDA) allowed direct analysis of effects of selected environmental variables or the artificial contamination on microbiological parameters. Variation in biomass and CO2 production was explained by soil parameters, to 46%, and by the duration of contamination, to 39.8%. The microbial community structure was assessed by community level physiological profiles (CLPP) analysis using BiologTM Eco-Plates. In the CLPP data only 35.9% of the variation could be linked to soil parameters and contamination, however, the samples with greatest exposure to hydrocarbons grouped together on RDA plots. It is concluded that, at this nutrient-poor site, the microbial community was dominated by natural heterogeneity and that the influence of petroleum hydrocarbon vapors was wea

Impacts of heavy metal contamination and phytoremediation on a microbial community during a twelve-month microcosm experiment

The effects of heavy metals and phytoextraction practices on a soil microbial community were studied during 12 months using a hyperaccumulating plant (Thlaspi caerulescens) grown in an artificially contaminated soil. The 16S ribosomal RNA genes of the Bacteria and the β-Proteobacteria and the amoA gene (encoding the α-subunit of ammonia monooxygenase) were PCR-amplified and analysed by denaturing gradient gel electrophoresis (DGGE). Principal component analysis (PCA) of the DGGE data revealed that: (i) the heavy metals had the most drastic effects on the bacterial groups targeted, (ii) the plant induced changes which could be observed in the amoA and in the Bacteria 16S rRNA gene patterns, (iii) the changes observed during 12 months in the DGGE-patterns of the planted contaminated soil did not indicate recovery of the initial bacterial community present in the non-contaminated soil. The potential function of the microbial community was assessed recording community level physiological profiles (CLPP) and analysing them by PCA. The lower capability of the bacterial community to degrade the substrates provided in the BIOLOG plates, in particular the amino acids, amides and amines, as well as a delay in the average well colour development (AWCD) differentiated the bacterial community of the contaminated samples from that of the non-contaminated ones. However, the plant had a positive effect on substrate utilization as shown by the greater number of substrates used in all planted samples compared to unplanted ones. Finally, the measurement of the potential ammonia oxidation indicated that ammonia oxidising bacteria were completely inhibited in the contaminated soil. The stimulation of ammonia oxidation by the plant observed in the non-contaminated samples was surpassed by the inhibitory effect of the heavy metals in the contaminated soil. This study emphasises the combined use of culture-independent techniques with conventional methods to investigate the ecology of bacteria in their natural habitat

Sorption Phenomena at Environmental Solid Surfaces

Sorption phenomena from the aqueous and from the gaseous phase to solid surfaces play an important role for the fate of inorganic and organic compounds and of bacteria in the environment. Case studies illustrating the role of different sorption mechanisms for various classes of compounds and for bacteria are presented. They show that sorption at solid surfaces ranges from weak unspecific interactions to very specific and strong complexation. Strong surface complexation in particular affects the surface reactivity. Studies of model systems provide a conceptual framework to understand and predict the behavior of substances and of bacteria in complex environmental systems, such as aquifers and sediments

Impacts of heavy metal contamination and phytoremediation on a microbial community during a twelve-month microcosm experiment

The effects of heavy metals and phytoextraction practices on a soil microbial Community were studied during 12 months using a hyperaccumulating plant (Thlaspi caerulcseens) grown in an artificially contaminated soil. The 16S ribosomal RNA genes of the Bacteria and the beta-Proteobacteria and the amoA gene (encoding the a-subunit of ammonia monooxygenase) were PCR-amplified and analysed by denaturing gradient gel electrophoresis (DGGE). Principal component analysis (PCA) of the DGGE data revealed that: (i) the heavy metals had the most drastic effects on the bacterial groups targeted, (ii) the plant induced changes which could be observed in the amoA and in the Bacteria 16S rRNA gene patterns, (iii) the changes observed during 12 months in the DGGE-patterns of the planted contaminated soil did not indicate recovery of the initial bacterial community present in the non-contaminated soil. The potential function of the microbial community was assessed recording community level physiological profiles (CLPP) and analysing them by PCA. The lower capability of the bacterial community to degrade the substrates provided in the BIOLOG plates, in particular the amino acids, amides and amines, as well as a delay in the average well colour development (AWCD) differentiated the bacterial community of the contaminated samples from that of the non-contaminated ones. However, the plant had a positive effect on substrate utilization as shown by the greater number of substrates used in all planted samples compared to implanted ones. Finally, the measurement of the potential ammonia oxidation indicated that ammonia oxidising bacteria were completely inhibited in the contaminated soil. The stimulation of ammonia oxidation by the plant observed in the non-contaminated samples was surpassed by the inhibitory effect of the heavy metals in the contaminated soil. This study emphasises the combined use of culture-independent techniques with conventional methods to investigate the ecology of bacteria in their natural habitats. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved

Isolation and characterization of <i>Magnetospirillum</i> sp strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model

Previously, Planted Fixed-Bed Reactors (PFRs) have been used to investigate microbial toluene removal in the rhizosphere of constructed wetlands. Aerobic toluene degradation was predominant in these model systems although bulk redox conditions were hypoxic to anoxic. However, culture-independent approaches indicated also that microbes capable of anaerobic toluene degradation were abundant. Therefore, we aimed at isolating anaerobic-toluene degraders from one of these PFRs. From the obtained colonies which consisted of spirilli-shaped bacteria, a strain designated 15-1 was selected for further investigations. Analysis of its 16S rRNA gene revealed greatest similarity (99%) with toluene-degrading Magnetospirillum sp. TS-6. Isolate 15-1 grew with up to 0.5 mM of toluene under nitrate-reducing conditions. Cells reacted to higher concentrations of toluene by an increase in the degree of saturation of their membrane fatty acids. Strain 15-1 contained key genes for the anaerobic degradation of toluene via benzylsuccinate and subsequently the benzoyl-CoA pathway, namely bssA, encoding for the alpha subunit of benzylsuccinate synthase, bcrC for subunit C of benzoyl-CoA reductase and bamA for 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Finally, most members of a clone library of bssA generated from the PFR had highest similarity to bssA from strain 15-1. Our study provides insights about the physiological capacities of a strain of Magnetospirillum isolated from a planted system where active rhizoremediation of toluene is taking place

AgNPs Change Microbial Community Structures of Wastewater

Due to their strong antimicrobial activity, silver nanoparticles (AgNPs) are massively produced, applied, consumed and, as a negative consequence, released into wastewater treatment plants. Most AgNPs are assumed to be bound by sludge, and thus bear potential risk for microbial performance and stability. In this lab-scale study, flow cytometry as a high-throughput method and 16S rRNA gene amplicon Illumina MiSeq sequencing were used to track microbial community structure changes when being exposed to AgNPs. Both methods allowed deeper investigation of the toxic impact of chemicals on microbial communities than classical EC50 determination. In addition, ecological metrics were used to quantify microbial community variations depending on AgNP types (10 and 30 nm) and concentrations. Only low changes in α- and intra-community β-diversity values were found both in successive negative and positive control batches and batches that were run with AgNPs below the EC50 value. Instead, AgNPs at EC50 concentrations caused upcoming of certain and disappearance of formerly dominant subcommunities. Flavobacteriia were among those that almost disappeared, while phylotypes affiliated with Gammaproteobacteria (3.6-fold) and Bacilli (8.4-fold) increased in cell abundance in comparison to the negative control. Thus, silver amounts at the EC50 value affected community structure suggesting a potential negative impact on functions in wastewater treatment systems

Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities

Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens

Exploitation of northern peatlands and biodiversity maintenance: a conflict between economy and ecology.

Peatlands are ecosystems of exceptional conservation value because of their beauty, biodiversity, importance in global geochemical cycles, and the paleoenvironmental records they preserve. Commercial extraction and drainage for forestry or agriculture have caused the destruction of many peatlands, especially in or close to urban areas of the northern temperate zone. Are these commercial and environmental interests irreconcilable? A close analysis suggests that limited peat extraction may actually increase biodiversity in some cases, and may be sustainable over the long term. As we learn more about how peatlands spontaneously regenerate following disturbance, and what conditions govern the re-establishment of a diverse community and the ability to sequester carbon, we increase our chances of being able to restore damaged peatlands. Preserving the chronological records hidden in the peat profile, the natural heritage value of peatlands, and the bulk of sequestered carbon, however, will remain incompatible with any form of exploitation