Microbiological characterizations of contaminant biodegradation in fractured sedimentary rock have primarily focused on the biomass suspended in groundwater samples and disregarded the biomass attached to fractures and in matrix pores. In fractured sedimentary rock, diffusion causes nearly all contaminant mass to reside in porous, low-permeability matrix. Microorganisms capable of contaminant degradation can grow in the matrix pores if the pores and pore throats are sufficiently large. In this study, the presence of dechlorinating microorganisms in rock matrices was investigated at a site where a fractured, flat-lying, sandstone–dolostone sequence has been contaminated with a mixture of chlorinated and aromatic hydrocarbons for over 40 years. The profile of organic contaminants as well as the distribution and characterization of the microbial community spatial variability was obtained through depth-discrete, high-frequency sampling along a 98-m continuous rock core. Dechlorinating microorganisms, such as Dehalococcoides and Dehalobacter, were detected in the rock matrices away from fracture surfaces, indicating that biodegradation within the rock matrix blocks should be considered as an important component of the system when evaluating the potential for natural attenuation or remediation at similar sedimentary rock sites.

Understanding the mechanisms of Cu pollution-induced community tolerance (PICT) in soil requires the characterization of Cu-resistant microorganisms at a community level using modern molecular tools. A primer pair (copAF2010 (5′-TGCAC CTGAC VGGSC AYAT-3′)/copAR2333 (5′-GVACT TCRCG GAACA TRCC-3′)) tentatively targeting Pseudomonas-like Cu-resistant microorganisms was designed in this study. The specification of the primers was tested through conventional polymerase chain reaction (PCR) and the construction of a Pseudomonas-like copA gene fragment library, and then the primers were used to quantify the Cu-resistant microorganisms using quantitative PCR technique. A significant increase of Cu-resistant microorganisms targeted by the primers was observed in a paddy soil from Jiaxing, China which has been exposed to one-year Cu contamination. The results provided direct evidence for Cu PICT in the soil, and the quantification method developed in this study has the potential to be used as a molecular assay for soil Cu pollution.

Lake Karla, Greece, was dried up in 1962 and its refilling started in 2009. We examined the Cyanobacteria and unicellular eukaryotes found during two fish kill incidents, in March and April 2010, in order to detect possible causative agents. Both microscopic and molecular (16S/18S rRNA gene diversity) identification were applied. Potentially toxic Cyanobacteria included representatives of the Planktothrix and Anabaena groups. Known toxic eukaryotes or parasites related to fish kill events were Prymnesium parvum and Pfiesteria cf. piscicida, the latter being reported in an inland lake for the second time. Other potentially harmful microorganisms, for fish and other aquatic life, included representatives of Fungi, Mesomycetozoa, Alveolata, and Heterokontophyta (stramenopiles). In addition, Euglenophyta, Chlorophyta, and diatoms were represented by species indicative of hypertrophic conditions. The pioneers of L. Karla’s plankton during the first months of its water refilling process included species that could cause the two observed fish kill events.

A greenhouse pot experiment was carried out to investigate the effects of different P‐fertilizer application forms (triple superphosphate [TSP], compost + TSP, TSP‐enriched compost) on the growth of ryegrass and the soil microbial biomass. The fertilizers were applied at equivalent doses for all nutrients to a neutral Luvisol in comparison with an acidic Ferralsol. Fertilizer application led to significantly increased contents of microbial biomass C, N, and P. Furthermore, yields of shoot C and root C, and concentrations of P, Ca, Mg, K, Fe, and Mn in shoots and roots were significantly increased. These increases always followed the order TSP < compost + TSP < TSP‐enriched compost. Sole TSP application led only to maximum concentrations of N and S. In the Ferralsol, TSP had only minimal positive effect on the P concentration of the grass shoots. The positive effect of TSP‐enriched compost, i.e., incubating TSP together with compost for 24 h, did not differ between the neutral Luvisol and the acidic Ferralsol, i.e., the effect is independent of the soil type. Consequently, soluble inorganic P fertilizer should generally be mixed into an organic fertilizer before application to soil.

Due to global warming, large volumes of methane may get released from marine sediments by melting gas hydrates, enhancing ocean acidification, bottom water hypoxia and global warming. In anoxic marine sediments, microbial induced anaerobic oxidation of methane provides a long- term sink for methane via the formation of methane derived authigenic carbonates (MDAC). In the view of destabilizing gas hydrates it is mandatory to understand, how fast AOM communities can adapt to an onset of methane flux. So far, the response of AOM consortia has been studied in theoretical models only. In laboratory experiments it was shown that AOM organisms showed extremely slow growth rates (doubling time: 4-7 months). In 1990 an oil rig caused a blow-out in the northern North Sea and formed a 20 m deep crater at the seafloor. More than 20 years later, the blow-out still releases significant amounts of methane. The site provides a unique natural laboratory to study the adaption of AOM communities in a newly formed methane-seep. A sediment core was recovered from in-side the blow-out crater, a reference core 50 m away from the crater. Both cores were sliced into three horizons (0-6, 6-12 and 12-18 cm bsf). Methane dependent sulphate reduction, which is equivalent to AOM activity, was determined by measuring total alkalinity and sulphide over 47 days in samples from the blow-out sediments incubated at 4, 13, 20, 37 and 60 °C. These long-term measurements revealed high potential rates of methanedependent sulfate reduction in all horizons (1.5 - 3.5 μmol SO42- cm-3 sediment d-1). Potential AOM rates determined by radiotracer measurements in short-term incubations (24 h, 13 °C) showed similar patterns but slightly lower rates (0.6 - 2.4 μmol CH4 cm-3 sediment d-1). The temperature optimum of AOM was between 13 and 20 °C indicating the presence of psychrophilic to mesophilic microorganisms, adapted to the relatively constant in-situ temperature (7 °C). No AOM activity was detected in incubations at 37 and 60 °C, indicating sensitivity of the AOM organisms against higher temperatures. Highest AOM activity was found in the deepest horizon. Both, long and short-term measurements of potential AOM rates show, the vast majority of sulphate reduction in the core was coupled to AOM. Neither an increase of total alkalinity nor of sulphide concentrations was detected in the sediments from the reference core incubated at 13 °C for 21 days. Samples from sediments of the blow-out crater were analyzed for their mineral composition using X-ray powder diffraction (XRD). Three out of six samples were composed of brucite (Mg(OH)2), mainly. Overall, different polymorphs of calcium carbonate such as aragonite, calcite, magnesium calcite and vaterite were the dominant minerals. Aragonite and magnesian calcite have been related to AOM. However, no indications for MDAC formation were found by stable isotope analyzes. Typically, MDAC show distinct stable isotope values (δ13C <-20 and δ18O > 0), if formed und er present day conditions in the marine environment. Some samples show negative δ13C values (-7.3 to -17.6 ‰) indicating that carbonates were, at least partly, derived from AOM. Corresponding δ18O values (between -12 and -3), clearly argue against a recent MDAC formation. All other samples showed positive δ13C which argue against microbial induced carbonate formation. Unspecific cell staining using DAPI revealed cell aggregates, which are typical for AOM consortia, in high numbers in all horizons {2.5*1012 aggregates m-2). Total cell counts were one order of magnitude higher in the blow-out core (23 - 68*108 cells ml-1), compared to the reference core (3.9-7.3*108 cells mL-1). Methane turnover and AOM aggregate density were similar to very active cold seep environments. Pore water profiles measured in a replicate core, show sufficient sulphate supply throughout the sandy and porous sediments. Therefore, it is likely that the extreme broad AOM zone exceeded the sampling depth of 18 cm. This study demonstrates that the AOM community at the North Sea blow-out is extremely active; suggesting that adaptation to strongly increasing methane fluxes might take less than 20 years. The question, whether or not, the AOM community has established within the last 20 years, cannot be answered finally. To gain certainness, it is necessary to analyze the sediment layers at reference sites 20 m bsf. lt needs to be analyzed whether or not AOM activity is there as weil.

Microorganisms are well known for their positive, as well as negative, effects on health, which mean that there is a great need for methods of discovery, identification and determination of microorganisms. In the past decade, capillary electrophoresis (CE) began to be an interesting tool for analysis of microorganisms, interestingly sometimes with similar dimensions for the separation capillary and the microorganisms. This review focuses on the use of CE in the analysis of microorganisms. First, it looks at the origin of microbial surface charge and then describes key points in the analysis of microbes by capillary zone electrophoresis [first approaches using poly(ethylene oxide), covalent modification of the inner capillary wall, reversed electroosmotic flow, advances in detection, and on-line preconcentration] and capillary isoelectric focusing.

Detecting microorganisms on textiles is useful for many purposes, for example to determine the bioburden before laundering, assess the reduction in bacterial counts in connection with various laundry processes, or trace transfer routes in infection control investigations. Therefore a validated, reproducible and rational method is needed. For sampling microorganisms on textile surfaces the most commonly used method is the contact plate method using RODAC plates, first described by Hall and Hartnett followed by the swab sampling technique. Both methods can only capture microorganisms on the surface of the textiles while microorganisms that have penetrated into the deeper structure of the material will not be detected. In our research the contact plate method and the swabbing technique were compared with two wash-off methods. For the first wash-off method the destructive elution method was used, where microorganisms were eluted from the fabrics by shaking the fabrics for a certain time in an elution medium. For the fourth sampling method a nondestructive method that included a compact test device called Morapex® was used, which is based on forced desorption by pressing the microorganisms through the fabric without destroying the fabric. In our research, two types of microorganisms were included (Klebsiella pneumoniae and Staphylococcus aureus) that cause common nosocomial infections. The aim of this study was to compare the efficiency of the four sampling methods for detecting microorganisms on textiles and to determine the lowest concentration, which can still be detected. The percentage of microorganisms that were detected by both elution methods was substantially higher than by sampling of fabrics with the contact plate method or swabbing. It can be concluded that a nondestructive method using a modified Morapex® device can be applied for quick determination of the hygienic condition of textiles.

This study investigated the hydrocarbonoclastic microbial community present on weathered crude oil and their ability to degrade weathered oil in seawater obtained from the Gulf St. Vincent (SA, Australia). Examination of the native seawater communities capable of utilizing hydrocarbon as the sole carbon source identified a maximum recovery of just 6.6 × 10¹ CFU/ml, with these values dramatically increased in the weathered oil, reaching 4.1 × 10⁴ CFU/ml. The weathered oil (dominated by greater than C∧30 fractions; 750,000 ± 150,000 mg/l) was subject to an 8 week laboratory-based degradation microcosm study. By day 56, the natural inoculums degraded the soluble hydrocarbons (initial concentrations 3,400 ± 700 mg/l and 1,700 ± 340 mg/l for the control and seawater, respectively) to below detectable levels, and biodegradation of the residual oil reached 62% (254,000 ± 40,000 mg/l) and 66% (285,000 ± 45,000 mg/l) in the control and seawater sources, respectively. In addition, the residual oil gas chromatogram profiles changed with the presence of short and intermediate hydrocarbon chains. 16S rDNA DGGE sequence analysis revealed species affiliated with the genera Roseobacter, Alteromonas, Yeosuana aromativorans, and Pseudomonas, renowned oil-degrading organisms previously thought to be associated with the environment where the oil contaminated rather than also being present in the contaminating oil. This study highlights the importance of microbiological techniques for isolation and characterisation, coupled with molecular techniques for identification, in understanding the role and function of native oil communities.

The mobilisation of diesel-degrading microorganisms in soils of three different textures (sandy, clay and silty) using electrokinetic techniques was studied. The mobilisation tests were performed using a laboratory-scale electrokinetic cell in which a synthetic soil column was inserted between the cathode and anode compartments. Microorganisms were located at the anode compartment at the beginning of each assay. A constant cell voltage was applied, and samples were taken from the cathode and anode compartments. Microbial transport through the soil strongly depended on soil particle size. Small particle sizes (silty and clay soil) travelled at low velocities (microbial transport rates of approximately 0.06 and 0.17 cm/min, respectively), while large particle sizes (sandy soil) led to high numbers of microorganisms passing through the soil column. In sandy soil, an increase in the voltage gradient did not increase the quantity of mobilised microorganisms (approximately 10⁷ CFU/mL for every voltage gradient applied). For clay and silty soils, a higher voltage gradient led to a higher quantity of microorganisms mobilised to the cathodic compartment and a lower delay time for detecting the presence of microorganisms in the same compartment.