Field-scale isotopic labeling of phospholipid fatty acids from acetate-degrading sulfate-reducing bacteria

Application of Nanodiamonds in Modelled Bioremediation of Phenol Pollution in River Sediments

The pollution of aquatic ecosystems is a big problem that has its impact on river sediments. In recent decades, an effective solution to this problem has been the application of bioremediation technologies. Nanoremediation is an innovative part of these technologies. We still know little about the efficiency of nanoparticles, especially nanodiamonds, in modelled conditions. The aim of the present study is to investigate the effect of nanodiamonds on the key parameters of modelled bioremediation of river sediments that are polluted with phenol, as well their effect on the structures and functions of microbial communities. An important indicative mechanism that was used is the application of fluorescent in situ hybridization for sediment microbial communities. The results of this study revealed the positive role of nanodiamonds that is associated with their intoxication with high concentrations of phenol. Readaptation was also found, in which the xenobiotic biodegradation potential evolved by increasing the relative proportions of non-culturable bacteria, namely Acinetobacter (at the 144th hour) and Pseudomonas (at the 214th hour). The results can help to find an effective solution to the question of how information from such precise molecular methods and the application of nanodiamonds can be translated into the accessible language of management and bioremediation technologies.

Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability

Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.

In-situ sonication for enhanced recovery of aquifer microbial communities

Sampling methods for characterization of microbial communities in aquifers should target both suspended and attached microorganisms (biofilms). We investigated the effectiveness and reproducibility of low-frequency (200 Hz) sonication pulses on improving extraction efficiency and quality of microorganisms from a petroleum-contaminated aquifer in Studen (Switzerland). Sonication pulses at different power levels (0.65, 0.9, and 1.1 kW) were applied to three different groundwater monitoring wells. Groundwater samples extracted after each pulse were compared with background groundwater samples for cell and adenosine tri-phosphate concentration. Turbidity values were obtained to assess the release of sediment fines and associated microorganisms. The bacterial community in extracted groundwater samples was analyzed by terminal-restriction-fragment-length polymorphism and compared with communities obtained from background groundwater samples and from sediment cores. Sonication enhanced the extraction efficiency up to 13-fold, with most of the biomass being associated with the sediment fines extracted with groundwater. Consecutive pulses at constant power were decreasingly effective, while pulses with higher power yielded the best results both in terms of extraction efficiency and quality. Our results indicate that low-frequency sonication may be a viable and cost-effective tool to improve the extraction of microorganisms from aquifers, taking advantage of existing groundwater monitoring wells.

Microbial syntrophy: interaction for the common good

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.

Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples

Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II.

Monitoring of microbial hydrocarbon remediation in the soil

Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review.

Bioremediation of petroleum hydrocarbons in anoxic marine sediments: consequences on the speciation of heavy metals

We investigated the effects of biostimulation and bioagumentation strategies applied to harbor sediments displaying reducing conditions and high concentrations of petroleum hydrocarbons and heavy metals. We compared the microbial efficiency of hydrocarbon removal from sediments maintained for 60 days in anoxic conditions and inoculated with acetate, sulfate-reducing bacterial strains and acetate and sulfate-reducing bacteria. All treatments determined a significant increase in the microbial growth and significant decreases of hydrocarbon contents and of redox potential values. The addition of sulfate-reducing bacterial strains to the sediment was the most efficient treatment for the hydrocarbon removal. In all experiments, significant changes of the heavy metals' phase repartition were observed. The results reported here suggest that the biodegradation of petroleum hydrocarbons in anoxic marine sediments may be enhanced by stimulating microbial anaerobic metabolism, but care should be applied to monitor the potential changes in the mobility and bioavailability of heavy metals induced by bio-treatments.

Biodegradation in contaminated aquifers: incorporating microbial/molecular methods

In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.

The use of molecular techniques to characterize the microbial communities in contaminated soil and water

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

Effect of water-table fluctuation on dissolution and biodegradation of a multi-component, light nonaqueous-phase liquid

Light nonaqueous-phase liquids (LNAPLs) such as gasoline and diesel fuel are among the most common causes of soil and groundwater contamination. Dissolution and subsequent advective transport of LNAPL components can negatively impact water supplies, while biodegradation is thought to be an important sink for this class of contaminants. We present a laboratory investigation of the effect of a water-table fluctuation on dissolution and biodegradation of a multi-component LNAPL (85% hexadecane, 5% toluene, 5% ethylbenzene, and 5% 2-methylnapthalene on a molar basis) in a pair of similar model aquifers (80 cm x 50 cm x 3 cm), one of which was subjected to a water-table fluctuation. Water-table fluctuation resulted in LNAPL and air entrapment below the water table, an increase in the vertical extent of the LNAPL source zone (by factor 6.7), and an increase in the volume of water passing through the source zone (by factor ~18). Effluent concentrations of dissolved LNAPL components were substantially higher and those of dissolved nitrate lower in the model aquifer where a fluctuation had been induced. Thus, water-table fluctuation led to enhanced biodegradation activity (28.3 mmol of nitrate consumed compared to 16.3 mmol in the model without fluctuation) as well as enhanced dissolution of LNAPL components. Despite the increased biodegradation, fluctuation led to increased elution of dissolved LNAPL components from the system (by factors 10-20). Hence, water-table fluctuations in LNAPL-contaminated aquifers might be expected to result in increased exposure of downgradient receptors to LNAPL components. Accordingly, water-table fluctuations in contaminated aquifers are probably undesirable unless the LNAPL is of minimal solubility or the dissolved-phase plume is not expected to reach a receptor due to distance or the presence of some form of containment.

Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity

Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient 13C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of 13CH4 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in non-amended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and some cross-feeding of 13C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of 13CH4, resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of 13C into active methanotrophs while avoiding the cross-feeding of 13C.

2,4-Dichlorophenoxyacetic acid (2,4-D) biodegradation in river sediments of Northeast-Scotland and its effect on the microbial communities (PLFA and DGGE)

A bench-scale study was conducted to investigate 2,4-D biodegradation rates at different concentrations (10, 100 and 1000 microg per gram of dry weight) in distinct sediments samples collected on the River Ythan, Northeast-Scotland. Mineralisation of 14C 2,4-D occurred mostly within 30 days for all tested concentrations with a degradation rate ranging from 5 to 750 microg d(-1). Biodegradation rates were affected by the biological and biochemical characteristics of the indigenous microbial community in the studied sediments rather than factors such as compound bioavailability and/or toxicity. PLFA-profiling provided evidences of the effect of 2,4-D amendments on the microbial communities and DGGE-profiling showed changes in the genetic potential of the microbial populations which might affect metabolic characteristics of the sediment. PLFAs biomarkers suggested that the pathway of alpha-ketoglutarate-dependent dioxygenase was the main route of 2,4-D biodegradation. This pathway is commonly found in microorganisms of the beta-subdivision of proteobacteria.

A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries

Marine sediment slurries enriched for anaerobic, sulfate-reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable-isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C-labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 microM) were used over a 7-day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C-glucose slurry but this changed with time, suggesting the presence of an active glucose-utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose-utilizers was unclear as 13C-enriched PLFA were common (16:0, 16:1, 18:1omega7, highest incorporation) and there was little difference between 12C- and 13C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C-incorporation (approximately 10 times) into PLFA compared with 13C-acetate or 13C-pyruvate. 13C-PLFA in the 13C-acetate and 13C-pyruvate slurries were similar to each other and to those that developed in the 13C-glucose slurry after 4 days. These were more diagnostic, with branched odd-chain fatty acids (i15:0, a15:0 and 15:1omega6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate-reducing bacteria (SRB) and sequences related to these SRB were in the 13C-acetate-DNA dsrA gene library. The 13C-acetate-DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate-utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In contrast, analysis of DGGE bands from 13C-DNA demonstrated that the candidate division JS1 and Firmicutes were actively assimilating 13C-acetate. Denaturing gradient gel electrophoresis also confirmed the presence of JS1 in the 13C-DNA from the 13C-glucose slurry. These results demonstrate that JS1, originally found in deep subsurface sediments, is more widely distributed in marine sediments and provides the first indication of its metabolism; incorporation of acetate and glucose (or glucose metabolites) under anaerobic, sulfate-reducing conditions. Here we demonstrate that PLFA- and DNA-SIP can be used together in a sedimentary system, with low concentrations of 13C-substrate and overlapping incubation times (up to 7 days) to provide complementary, although not identical, information on carbon flow and the identity of active members of an anaerobic prokaryotic community.

The Challenge of Micropollutants in Aquatic Systems

The increasing worldwide contamination of freshwater systems with thousands of industrial and natural chemical compounds is one of the key environmental problems facing humanity. Although most of these compounds are present at low concentrations, many of them raise considerable toxicological concerns, particularly when present as components of complex mixtures. Here we review three scientific challenges in addressing water-quality problems caused by such micropollutants. First, tools to assess the impact of these pollutants on aquatic life and human health must be further developed and refined. Second, cost-effective and appropriate remediation and water-treatment technologies must be explored and implemented. Third, usage and disposal strategies, coupled with the search for environmentally more benign products and processes, should aim to minimize introduction of critical pollutants into the aquatic environment.

13C-Labelling of lipids to investigate microbial communities in the environment

The introduction of (13)C-labelled substrates to soils, sediments or cultures followed by (13)C analysis of phospholipid fatty acids (PLFAs) provides quantitative and chemotaxonomic information for the groups of microorganisms utilizing a given substrate. Gas chromatography-combustion-isotope ratio mass spectrometry has provided the high precision necessary to measure small isotopic changes (differences in the relative abundances of (13)C to (12)C expressed as delta(13)C values) for nanogram amounts of individual compounds, such as microbial PLFAs. This methodology constitutes a powerful new culture-independent method for investigating microbial communities in the environment. The information obtained is highly complementary to that obtained from gene-probe-based methods, and considerable possibilities exist to extend this methodology to include other biochemical components of microorganisms.

Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer

Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate. Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4',6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.