Dissolved organic carbon in rainwater: Glassware decontamination and sample preservation and volatile organic carbon

The efficiency of different methods for the decontamination of glassware used for the analysis of dissolved organic carbon (DOC) was tested using reported procedures as well as new ones proposed in this work. A Fenton solution bath (1.0 mmol L-1 Fe2+ and 100 mmol L-1 H2O2) for 1 h or for 30 min employing UV irradiation showed to combine simplicity, low cost and high efficiency. Using the optimized cleaning procedure, the DOC for stored UV-irradiated ultrapure water reached concentrations below the limit of detection (0.19 mu mol C L-1). Filtered (0.7 mu m) rain samples maintained the DOC integrity for at least 7 days when stored at 4 degrees C. The volatile organic carbon (VOC) fraction in the rain samples collected at two sites in São Paulo state (Brazil) ranged from 0% to 56% of their total DOC content. Although these high-VOC concentrations may be derived from the large use of ethanol fuel in Brazil, our results showed that when using the high-temperature catalytic oxidation technique, it is essential to measure DOC rather than non-purgeble organic carbon to estimate organic carbon, since rainwater composition can be quite variable, both geographically and temporally. (C) 2007 Elsevier Ltd. All rights reserved.

Handbook for sampling and sample preservation of water and wastewater.

Mode of access: Internet.

Preservation methods alter stable isotope values in gelatinous zooplankton: implications for interpreting trophic ecology

Jellyfish are increasingly topical within studies of marine food webs. Stable isotope analysis represents a valuable technique to unravel the complex trophic role of these long-overlooked species. In other taxa, sample preservation has been shown to alter the isotopic values of species under consideration, potentially leading to misinterpretation of trophic ecology. To identify potential preservation effects in jellyfish, we collected Aurelia aurita from Strangford Lough (54(o)22'44.73aEuro(3)N, 5(o)32'53.44aEuro(3)W) during May 2009 and processed them using three different methods prior to isotopic analysis (unpreserved, frozen and preserved in ethanol). A distinct preservation effect was found on delta N-15 values: furthermore, preservation also influenced the positive allometric relationship between individual size and delta N-15 values. Conversely, delta C-13 values remained consistent between the three preservation methods, conflicting with previous findings for other invertebrate, fish and mammalian species. These findings have implications for incorporation of jellyfish into marine food webs and remote sampling regimes where preservation of samples is unavoidable.

Critical review on the stability of illicit drugs in sewers and wastewater samples

Wastewater-based epidemiology (WBE) applies advanced analytical methods to quantify drug residues in wastewater with the aim to estimate illicit drug use at the population level. Transformation processes during transport in sewers (chemical and biological reactors) and storage of wastewater samples before analysis are expected to change concentrations of different drugs to varying degrees. Ignoring transformation for drugs with low to medium stability will lead to an unknown degree of systematic under- or overestimation of drug use, which should be avoided. This review aims to summarize the current knowledge related to the stability of commonly investigated drugs and, furthermore, suggest a more effective approach to future experiments. From over 100 WBE studies, around 50 mentioned the importance of stability and 24 included tests in wastewater. Most focused on in-sample stability (i.e., sample preparation, preservation and storage) and some extrapolated to in-sewer stability (i.e., during transport in real sewers). While consistent results were reported for rather stable compounds (e.g., MDMA and methamphetamine), a varying range of stability under different or similar conditions was observed for other compounds (e.g., cocaine, amphetamine and morphine). Wastewater composition can vary considerably over time, and different conditions prevail in different sewer systems. In summary, this indicates that more systematic studies are needed to: i) cover the range of possible conditions in sewers and ii) compare results more objectively. To facilitate the latter, we propose a set of parameters that should be reported for in-sewer stability experiments. Finally, a best practice of sample collection, preservation, and preparation before analysis is suggested in order to minimize transformation during these steps.

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Low voltage and variable-pressure scanning electron microscopy of fractured composites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Strontium isotope ratios of pore waters and planktonic foraminifera from DSDP holes

A detailed record of the strontium-87 to strontium-86 ratio in seawater during the last 100 million years was determined by measuring this ratio in 137 well-preserved and well-dated fossil foraminifera samples. Sample preservation was evaluated from scanning electron microscopy studies, measured strontium-calcium ratios, and pore water strontium isotope ratios. The evolution of the strontium isotopic ratio in seawater offers a means to evaluate long-term changes in the global strontium isotope mass balance. Results show that the marine strontium isotope composition can be used for correlating and dating well-preserved authigenic marine sediments throughout much of the Cenozoic to a precision of +/- 1 million years. The strontium-87 to strontium-86 ratio in seawater increased sharply across the Cretaceous/Tertiary boundary, but this feature is not readily explained as strontium input from a bolide impact on land.

Radiolarian biostratigraphy in the central Indian Ocean

Identifiable radiolarians of stratigraphic importance were recovered at eight of the sites drilled on Leg 115. The assemblages range in age from Holocene to middle Eocene (Dictyoprora mongolfieri Zone, about 48 Ma). Faunal preservation is particularly good in two stratigraphic intervals: the Holocene through upper Miocene (0-9 Ma), and the lowermost Oligocene to middle Eocene (35-48 Ma). Fluctuating rates of silica accumulation at these drill sites during the Cenozoic reflect changing tectonic and paleoceanographic conditions. In particular, the gradual closure of the Indonesian and Tethyan seaways and the northward migration of the Indian subcontinent severely restricted zonal circulation and silica accumulation in tropical latitudes during the late Oligocene through middle Miocene. By the late Miocene the Indian subcontinent had moved sufficiently north of the equator to allow trans-Indian zonal circulation patterns to become reestablished, and biosiliceous sedimentation resumed. The composition of the radiolarian assemblages in the tropical Indian Ocean is closely comparable with that of the 'stratotype' sequences in the equatorial Pacific. However, there are some notable exceptions in Indian Ocean assemblages: (1) the scarcity of the genera Pterocanium and Spongaster in the Neogene; (2) the absence of the stratigraphically important Podocyrtis lineage, P. diamesa -> P. phyxis -> P. ampla, in the middle Eocene; and (3) the scarcity of taxa of the genus Dorcadospyris, with the exception of D. ateuchus. The succession of radiolarian events was tabulated for those stratigraphic intervals where the assemblages were well preserved. We identified 55 events in the middle Eocene to earliest Oligocene, and 31 events in the late Miocene to Holocene. The succession of events is closely comparable with that of the tropical Pacific. However, there are exceptions that appear to be real, rather than artifacts of sample preservation, mixing, and core disturbance.

Gas hydrate structures and C1-C5 hydrocarbons at individual sites in the Gulf of Mexico

Gas hydrate samples from various locations in the Gulf of Mexico (GOM) differ considerably in their microstructure. Distinct microstructure characteristics coincide with discrete crystallographic structures, gas compositions and calculated thermodynamic stabilities. The crystallographic structures were established by X-ray diffraction, using both conventional X-ray sources and high-energy synchrotron radiation. The microstructures were examined by cryo-stage Field-Emission Scanning Electron Microscopy (FE-SEM). Good sample preservation was warranted by the low ice fractions shown from quantitative phase analyses. Gas hydrate structure II samples from the Green Canyon in the northern GOM had methane concentrations of 70-80% and up to 30% of C2-C5 of measured hydrocarbons. Hydrocarbons in the crystallographic structure I hydrate from the Chapopote asphalt volcano in the southern GOM was comprised of more than 98% methane. Fairly different microstructures were identified for those different hydrates: Pores measuring 200-400 nm in diameter were present in structure I gas hydrate samples; no such pores but dense crystal surfaces instead were discovered in structure II gas hydrate. The stability of the hydrate samples is discussed regarding gas composition, crystallographic structure and microstructure. Electron microscopic observations showed evidence of gas hydrate and liquid oil co-occurrence on a micrometer scale. That demonstrates that oil has direct contact to gas hydrates when it diffuses through a hydrate matrix.

Sampling tissue for DNA analysis of trees: Trunk cambium as an alternative to canopy leaves

The number of studies of tropical tree species that use molecular tools is increasing, most of which collect leaf tissue for genomic DNA extraction. In tropical trees the canopy is not only frequently inaccessible, but also, once reached, the leaf tissue is often heavily defended against herbivory by high concentrations of anti-predation compounds, which may inhibit downstream applications, particularly PCR. Cambium tissue, accessed directly from the tree trunk at ground level, offers a readily accessible resource that is less hampered by the presence of defensive chemicals than leaf tissue. Here we describe a simple method for obtaining tissue from the cambial zone for DNA extraction and test the applicability of the method in a range of tropical tree species. The method was used successfully to extract DNA from 11 species in nine families. A subset of the DNA extracts was tested in more detail and proved to be highly suitable for AFLP analysis.

A convenient sample preparation protocol for scanning electron microscope examination of xylem-occluding bacterial biofilm on cut flowers and foliage

Microbes and their exopolysaccharides (EPS) can block xylem vessels, thereby increasing the hydraulic resistance and decreasing the vase life of cut flowers and foliage. Scanning electron microscopy (SEM) provides a powerful tool for investigation of bacteria-induced xylem occlusion. However, conventional preparation protocols for SEM involving chemicals can cause loss of hydrated EPS material, and thereby damage the bacterial biofilms during dehydration. A modified chemical fixation protocol involving pre-fixation with 75 mM lysine plus 2.5% glutaraldehyde followed by the normal fixation in 3% glutaraldehyde was, therefore, tested for improved preservation of bacterial biofilm at the stem-ends of cut Acacia holosericea foliage stems. Stem-end segments with different stages of bacterial growth were obtained from stems stood into water. The lysine-based protocol was compared with four other processing protocols of critical point drying (CPD) without fixation (control), freeze-drying (FD), conventional chemical fixation followed by drying with hexamethyldisilazane (HMDS), and conventional chemical fixation with CPD. The non-fixed control. FD and the glutaraldehyde fixation with HMDS drying gave poor preservation of hydrated material, including bacterial EPS. Conventional glutaraldehyde fixation followed by CPD was superior to these three methods in terms of better preserving the EPS. However, this fourth method gave condensation of biofilms during dehydration. In contrast, the modified lysine-based protocol resulted in superior preservation of EPS and biofilm structure. Thus, this fifth method was the most appropriate for examination of bacterial stem-end blockage in cut ornamentals. (C) 2012 Elsevier B.V. All rights reserved.

Formation and preservation of pedogenic carbonates in South India, links with paleo-monsoon and pedological conditions: Clues from Sr isotopes, U-Th series and REEs

The influence of the pedogenic and climatic contexts on the formation and preservation of pedogenic carbonates in a climosequence in the Western Ghats (Karnataka Plateau, South West India) has been studied. Along the climosequence, the current mean annual rainfall (MAR) varies within a 80 km transect from 6000 mm at the edge of the Plateau to 500 mm inland. Pedogenic carbonates occur in the MAR range of 500-1200 mm. In the semi-arid zone (MAR: 500-900 mm), carbonates occur (i) as rhick hardpan calcretes on pediment slopes and (ii) as nodular horizons in polygenic black soils (i.e. vertisols). In the sub-humid zone (MAR: 900-1500 mm), pedogenic carbonates are disseminated in the black soil matrices either as loose, irregular and friable nodules of millimetric size or as indurated botryoidal nodules of centimetric to pluricentimetric size. They also occur at the top layers of the saprolite either as disseminated pluricentimetric indurated nodules or carbonate-cemented lumps of centimetric to decimetric size. Chemical and isotopic (Sr-87/Sr-86) compositions of the carbonate fraction were determined after leaching with 0.25 N HCl. The corresponding residual fractions containing both primary minerals and authigenic clays were digested separately and analyzed. The trend defined by the Sr-87/Sr-86 signatures of both labile carbonate fractions and corresponding residual fractions indicates that a part of the labile carbonate fraction is genetically linked to the local soil composition. Considering the residual fraction of each sample as the most likely lithogenic source of Ca in carbonates, it is estimated that from 24% to 82% (55% on average) of Ca is derived from local bedrock weathering, leading to a consumption of an equivalent proportion of atmospheric CO2. These values indicate that climatic conditions were humid enough to allow silicate weathering: MAR at the time of carbonate formation likely ranged from 400 to 700 mm, which is 2- to 3-fold less than the current MAR at these locations. The Sr, U and Mg contents and the (U-234/U-238) activity ratio in the labile carbonate fraction help to understand the conditions of carbonate formation. The relatively high concentrations of Sr, U and Mg in black soil carbonates may indicate fast growth and accumulation compared to carbonates in saprolite, possibly due to a better confinement of the pore waters which is supported by their high (U-234/U-238) signatures, and/or to higher content of dissolved carbonates in the pore waters. The occurrence of Ce, Mn and Fe oxides in the cracks of carbonate reflects the existence of relatively humid periods after carbonate formation. The carbonate ages determined by the U-Th method range from 1.33 +/- 0.84 kyr to 7.5 +/- 2.7 kyr and to a cluster of five ages around 20 kyr, i.e. the Last Glacial Maximum period. The young occurrences are only located in the black soils, which therefore constitute sensitive environments for trapping and retaining atmospheric CO2 even on short time scales. The maximum age of carbonates depends on their location in the climatic gradient: from about 20 kyr for centimetric nodules at Mule Hole (MAR = 1100 mm/yr) to 200 kyr for the calcrete at Gundlupet (MAR = 700 mm/yr, Durand et al., 2007). The intensity of rainfall during wet periods would indeed control the lifetime of pedogenic carbonates and thus the duration of inorganic carbon storage in soils. (C) 2010 Elsevier Ltd. All rights reserved.

Length correction for larval and early-juvenile Atlantic menhaden (Brevoortia tyrannus) after preservation in alcohol

Body length measurement is an important part of growth, condition, and mortality analyses of larval and juvenile fish. If the measurements are not accurate (i.e., do not reflect real fish length), results of subsequent analyses may be affected considerably (McGurk, 1985; Fey, 1999; Porter et al., 2001). The primary cause of error in fish length measurement is shrinkage related to collection and preservation (Theilacker, 1980; Hay, 1981; Butler, 1992; Fey, 1999). The magnitude of shrinkage depends on many factors, namely the duration and speed of the collection tow, abundance of other planktonic organisms in the sample (Theilacker, 1980; Hay, 1981; Jennings, 1991), the type and strength of the preservative (Hay, 1982), and the species of fish (Jennings, 1991; Fey, 1999). Further, fish size affects shrinkage (Fowler and Smith, 1983; Fey, 1999, 2001), indicating that live length should be modeled as a function of preserved length (Pepin et al., 1998; Fey, 1999).

Improved handling and preservation of freshwater giant prawn, Macrobrachium rosenbergii for producing safe and wholesome products

Studies were undertaken to evaluate the quality changes in freshwater giant prawn, Macrobrachium rosenbergii during various storage conditions of handling and preservation and producing safe and quality products. The samples kept in ice immediately after catch with head-on and head-less condition were found to be acceptable for 6 days and 7 days, respectively. Delaying of icing considerably shortened the shelf-life. The pH value increased from 6.36 to 8.0 after 10 days in ice. The initial average TVB-N value of sample increased from below 10 mg/100 g to 25 mg/100 g with the lapse of storage period. The Ca++ ATPase activity in presence of 0.1M KCl slightly decreased at the end of 10 days of ice storage. Immediately after harvest, initial aerobic plate count (APC) was 2.88x10^6 CFU/g which gradually increased to 1.12x10^8 CFU/g after 6 days in ice storage and showed early signs of spoilage. Initial bacterial genera in the prawn iced at 0 hours were comprised of Coryneform (22.21 %), Bacillus (7.40%), Micrococcus (11.11 %), Achromobacter (48.14%), Flavobacterium/Cytophaga (7.40%), Pseudomonas (3.70%) and Aeromonas (3.70%). During ice storage Coryneforms and Bacillus were always dominating along with less prominent ones - Micrococcus, Achromobacter and Flavobacterium. Studies were conducted on the stability of myofibrillar protein of M. rosenbergii under different storage and pH conditions. The influence of a wide range of pH on the remaining Ca++ ATPase activity of M. rosenbergii muscle myofibrils after storage at -20°C for 2 days, at 0°C for 2 days and at 35°C for 30 minutes demonstrated that ATPase activities were lower in acidic and alkaline pH regions and the activity remained relatively high. Mg++ ATPase activities both in presence and absence of Ca++ remained high at neutral pH compared to those of acidic and alkaline region. The solubility of myofibrillar protein decreased gradually both in acidic and alkaline pH regions. The study also examined the bacteriological quality of freshly harvested M. rosenbergii, pond sediment and pond water from four commercial freshwater prawn farms at Fulpur and Tarakanda upazilas in the district of Mymensingh. The study included aerobic plate count (APC), total coliform count, detection, isolation and identification of suspected public health hazard bacteria and their seasonal variation, salt tolerance test, antibiotic sensitivity test of the isolates and washing effect of chlorinated water on the bacterial load in the prawn samples. APC in sediment soil and water of the farm and gill and hepatopancreas of freshly harvested prawns varied considerably among the farms and between summer and winter season. The range of coliform count in water, gill and hepatopancreas ranged between 6 - 2.8x10^2 CFU/ml, 1.2x10^2 - 3.32x10^2 CFU/g and 1.43x10^2 - 3.89 x10^3 CFU/g, respectively. No coliform was detected in pond sediment sample. Suspected health hazard bacteria isolated and identified from pond sediment, water, gill and hepatopancreas included Streptococcus, Bacillus, Escherichia coli, Klebsialla, Salmonella, Staphylococcus, Pseudomonas and Aeromonas. Bacillus, Salmonella and Staphyloccus [sic], and were found to be highly salt tolerant and capable of growing at 10% NaCl. The antibiotic discs with different concentration of antibiotics were used for the sensitivity test. The organisms were found to be most sensitive against Tetracyclin and Gentamycin.