Sampling Depth (sampling + depth)

Distribution by Scientific Domains


Selected Abstracts


Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh

ENVIRONMENTAL MICROBIOLOGY, Issue 11 2008
Hendrikus J. Laanbroek
Summary Like many functional groups or guilds of microorganisms, the group of ammonia-oxidizing bacteria (AOB) consists of a number of physiologically different species or lineages. These physiological differences suggest niche differentiation among these bacteria depending on the environmental conditions. Species of AOB might be adapted to different zones in the flooding gradient of a tidal marsh. This issue has been studied by sampling sediments from different sites and depths within a tidal freshwater marsh along the river Scheldt near the village of Appels in Belgium. Samples were taken in February, April, July and October 1998. Communities of AOB in the sediment were analysed on the basis of the 16S rRNA gene by application of polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE). In addition, moisture content and concentrations of ammonium and nitrate were determined as well as the potential ammonia-oxidizing activities. Six different DGGE bands belonging to the ,-subclass of the Proteobacteria were observed across the marsh. The community composition of AOB was determined by the elevation in the flooding gradient as well as by the sampling depth. The presence of plants was less important for the community composition of AOB. DGGE bands affiliated with the Nitrosospira lineage were mostly found in the upper part of the marsh and in the deeper layers of the sediment. Two of the three DGGE bands related to the Nitrosomonas oligotropha lineage were more broadly distributed over the marsh, but were predominantly found in the upper layers of the sediment. Members of the environmental Nitrosomonas lineage 5 were predominantly detected in the deeper layers in the lower parts of the marsh. Potential driving factors for niche differentiation are discussed. [source]


Variable carbon recovery of Walkley-Black analysis and implications for national soil organic carbon accounting

EUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2007
S. Lettens
Summary There is considerable interest in the computation of national and regional soil carbon stocks, largely as the result of the provisions of the Kyoto Protocol. Such stocks are often calculated and compared without proper reference to the uncertainties induced by different analytical methodologies. We illustrate the nature and magnitude of these uncertainties with the present soil organic carbon (SOC) study in Belgium. The SOC recovery of the Walkley-Black method was investigated based on a database of 475 samples of silt loam and sandy soils, which cover different soil depths and vegetation types in northern Belgium. The organic carbon content of the soil samples was measured by the original Walkley-Black method and by a total organic carbon analyser. The recovery was computed as the ratio of these two results per soil sample. Land use, texture and soil sampling depth had a significant influence on the recovery as well as their three-way interaction term (land use × texture × sampling depth). The impact of a land use, texture and sampling depth dependent Walkley-Black correction on the year 2000 SOC inventory of Belgium was determined by regression analysis. Based on new correction factors, the national SOC stocks increased by 22% for the whole country, ranging from 18% for cropland to 31% for mixed forest relative to the standard corrected SOC inventory. The new recovery values influenced therefore not only C stocks in the year 2000, but also the expected SOC change following land use change. Adequate correction of Walkley-Black measurements is therefore crucial for the absolute and comparative SOC assessments that are required for Kyoto reporting and must be computed to take into account the regional status of soil and land use. ,Universal' corrections are probably an unrealistic expectation. [source]


Sampling and analyzing metals in soils for archaeological prospection: A critique

GEOARCHAEOLOGY: AN INTERNATIONAL JOURNAL, Issue 8 2004
Rob Haslam
This paper presents a critique of current methods of sampling and analyzing soils for metals in archaeological prospection. Commonly used methodologies in soil science are shown to be suitable for archaeological investigations, with a concomitant improvement in their resolution. Understanding the soil-fraction location, concentration range, and spatial distribution of autochthonous (native) soil metals is shown to be a vital precursor to archaeological-site investigations, as this is the background upon which anthropogenic deposition takes place. Nested sampling is suggested as the most cost-effective method of investigating the spatial variability in the autochthonous metal concentrations. The use of the appropriate soil horizon (or sampling depth) and point sampling are critical in the preparation of a sampling regime. Simultaneous extraction is proposed as the most efficient method of identifying the location and eventual fate of autochthonous and anthropogenic metals, respectively. © 2004 Wiley Periodicals, Inc. [source]


Macro- and Micro-Purge Soil-Gas Sampling Methods for the Collection of Contaminant Vapors

GROUND WATER MONITORING & REMEDIATION, Issue 1 2009
Brian A. Schumacher
Purging influence on soil-gas concentrations for volatile organic compounds (VOCs), as affected by sampling tube inner diameter and sampling depth (i.e., system volume) for temporary probes in fine-grained soils, was evaluated at three different field sites. A macro-purge sampling system consisted of a standard, hollow, 3.2-cm outer diameter (OD) drive probe with a retractable sampling point attached to an appropriate length of 0.48-cm inner diameter (ID) Teflon® tubing. The macro-purge sampling system had a purge system volume of 24.5 mL at a 1-m depth. In contrast, the micro-purge sampling systems were slightly different between the field sites and consisted of a 1.27-cm OD drive rod with a 0.10-cm ID stainless steel tube or a 3.2-cm OD drive rod with a 0.0254-cm inner diameter stainless steel tubing resulting in purge system volumes of 1.2 and 7.05 mL at 1-m depths, respectively. At each site and location within the site, with a few exceptions, the same contaminants were identified in the same relative order of abundances indicating the sampling of the same general soil atmosphere. However, marked differences in VOC concentrations were identified between the sampling systems, with micro-purge samples having up to 27 times greater concentrations than their corresponding macro-purge samples. The higher concentrations are the result of a minimal disturbance of the ambient soil atmosphere during purging. The minimal soil-gas atmospheric disturbance of the micro-purge sampling system allowed for the collection of a sample that is more representative of the soil atmosphere surrounding the sampling point. That is, a sample that does not contain an atmosphere that has migrated from distance through the geologic material or from the surface in response to the vacuum induced during purging soil-gas concentrations. It is thus recommended that when soil-gas sampling is conducted using temporary probes in fine-grained soils, the sampling system use the smallest practical ID soil-gas tubing and minimize purge volume to obtain the soil-gas sample with minimal risk of leakage so that proper decisions, based on more representative soil-gas concentrations, about the site can be made. [source]


Comparison of Transcranial Color-Coded Sonography and Magnetic Resonance Angiography in Acute Ischemic Stroke

JOURNAL OF NEUROIMAGING, Issue 4 2001
Li-Ming Lien MD
ABSTRACT Background and Purpose. This study was designed to assess the accuracy of transcranial color-coded sonography (TCCS) as compared to magnetic resonance angiography (MRA) for detecting intracranial arterial stenosis in patients with acute cerebral ischemia. Methods. The authors prospectively identified 120 consecutive patients admitted with acute ischemic stroke and performed both TCCS and MRA with a mean interval of 1 day. TCCS data (sampling depth, peak systolic and end diastolic angle-corrected velocity, mean angle-corrected velocity, and pulsatility index) for middle cerebral arteries (MCAs) were compared to MRA data and classified into 4 grades: normal (grade 1): normal caliber and signal; mild stenosis (grade 2): irregular lumen with reduced signal; severe stenosis (grade 3): absent signal in the stenotic segment (flow gap) and reconstituted distal signal; and possible occlusion (grade 4): absent signal. The cutoffs were chosen to maximize diagnostic accuracy. Results. Interobserver agreement for MRA grading resulted in a weighted-kappa value of 0.776. The rate of poor temporal window was 37% (89/240). Doppler signals were obtained in 135 vessels, and the angle-corrected velocities (peak systolic, end diastolic, mean) were significantly different (P= .001, P= .006, P < .001) among the MRA grades: grade 1 (100, 47, 68 cm/s), grade 2 (171, 72, 110 cm/s), grade 3 (226, 79, 134 cm/s), grade 4 (61, 26, 39 cm/s). Additionally, an angle-corrected MCA peak systolic velocity ,120 cm/s correlates with intracranial stenosis on MRA (grade 2 or worse) with high specificity (90.5%; 95% confidence interval = 78.5%,96.8%) and positive predictive value (93.9%) but relatively low sensitivity (66.7%; 95% confidence interval = 61.2%,69.5%) and negative predictive value (55.1%). Conclusion. Elevated MCA velocities on TCCS correlate with intracranial stenosis detected on MRA. An angle-corrected peak systolic velocity ,120 cm/s is highly specific for detecting intracranial stenosis as defined by significant MRA abnormality. [source]


Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

ENVIRONMENTAL MICROBIOLOGY, Issue 8 2008
Anna Edlund
Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source]


Variability in the origin of carbon substrates for bacterial communities in mangrove sediments

FEMS MICROBIOLOGY ECOLOGY, Issue 2 2004
Steven Bouillon
Abstract Organic carbon in mangrove sediments originates from both local sources (mangroves, microphytobenthos) and tidal inputs (e.g. phytoplankton, seagrass-derived material). The relative inputs of these sources may vary strongly, both within and between different mangrove sites. We combined elemental (TOC/TN) and bulk ,13C analysis on sediment cores from various mangrove sites with ,13C data of bacteria-specific phospholipid fatty acids (PLFA) in order to identify the dominant carbon substrates used by in situ bacterial communities. ,13C values of each of these markers showed a range of 10% or more across the different sites and sampling depths, but generally followed the ,13C trend observed in bulk organic carbon. Several sediment cores show a strong vertical gradient in PLFA ,13C, suggesting a selectivity for algal-derived carbon in the surface layers. Our data demonstrate that the origin of bacterial carbon substrates varies widely across different mangrove sites, and imply that data on mineralization of organic matter cannot be directly incorporated in ecosystem carbon budgets without an estimation of the contribution of various sources. [source]


Effects of short- and long-term water-level drawdown on the populations and activity of aerobic decomposers in a boreal peatland

GLOBAL CHANGE BIOLOGY, Issue 2 2007
KRISTA JAATINEN
Abstract We analysed the response of microbial communities, characterized by phospholipid fatty acids (PLFAs), to changing hydrological conditions at sites with different nutrient levels in a southern boreal peatland. Although PLFAs of Gram-negative bacteria were characteristic of the peatland complex, microbial communities differed among sites (ombrotrophic bog, oligotrophic fen, mesotrophic fen) and sampling depths (0,5, 5,10, 10,20, 20,30 cm). The microbial communities in each site changed significantly following water-level drawdown. The patterns of change varied among sites and sampling depths. The relative proportion of Gram-negative bacteria decreased in the upper 10 cm but increased in deeper layers of the fen sites. Fungi benefited from water-level drawdown in the upper 5 cm of the mesotrophic fen, but suffered in the drier surfaces of the ombrotrophic bog, especially in the 5,10 cm layer. In contrast, actinobacteria suffered from water-level drawdown in the mesotrophic fen, but benefited in the drier surfaces of the ombrotrophic bog. Basal respiration rate correlated positively with pH and fungal PLFA, and negatively with depth. We suggest that the changes in microbial community structure after persistent water-level drawdown follow not only the hydrological conditions but also the patterns of vegetation change. Our results imply that changes in structure and activity of the microbial community in response to climate change will be strongly dependent on the type of peatland. [source]


Assessment of the ecological status of north-eastern Adriatic coastal waters (Istria, Croatia) using macroalgal assemblages for the European Union Water Framework Directive

AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 1 2009
Ljiljana Ive
Abstract 1.Based on the inclusion of macroalgae in the European Union Water Framework Directive as quality elements for the evaluation of the ecological status of coastal waters, the suitability of one (Ecological Evaluation Index, EEI) of several previously proposed evaluation methods in the particular ecological conditions of the northern Adriatic Sea was tested. 2.The EEI was assessed for 10 locations (polluted and putatively pristine) scattered along 60,km of the western Istrian coast. The sampling was performed seasonally at 1 and 3,m depth by destructive (determination of species cover and biomass) and non-destructive (determination of species coverage using digital photography) methods. 3.When assessed at 1,m depth the spatial scale weighted EEI for the west Istrian coast was 8.1, corresponding to an ecological status class (ESC) value of high. However, data for 3,m depth gave a spatial EEI of 6.72 which corresponds to an ESC value of good. Regressions of the ratio of ecological state group I (ESG I, i.e. thick leathery, calcareous and crustose species) over total algal abundance with the pollution gradient (obtained using principal components analysis (PCA) ordination of environmental variables) were significant at 3,m but not at 1,m depth. This was due to the high abundance of ESG I macroalgae Corallina elongata and Cystoseira compressa at 1,m depth at polluted stations. Similar regressions were obtained using cover, biomass and coverage. 4.It is concluded that the EEI method may be suitable for the classification of coastal waters in the northern Adriatic only in certain cases. A better assessment of ecological status using this method would require more realistic estimations based on the inclusion of data from several sampling depths. As all three abundance measures (cover, biomass, coverage) gave similar results, coverage (using digital photography) is suggested as being a preferred measure owing to the rapidity of sampling at several depths and less time-consuming laboratory work. Copyright © 2008 John Wiley & Sons, Ltd. [source]