Bacterial Input Research Articles

Effects of watershed land use on sources and nutritional value of particulate organic matter in temperate headwater streams

Suspended particulate organic matter (POM) in headwater streams is an important source of food and energy to stream food webs. In order to determine the effects of watershed land use on the sources and characteristics of POM, we compared the lipid composition of POM (fatty acid, aliphatic alcohol and sterol) from streams influenced by different types of watershed land use. Eight first-order streams discharging to the York River Estuary (Virginia, USA) were sampled during baseflow conditions bi-monthly from February to November 2009, including streams draining forest-dominated, pasture-dominated, cropland-dominated, and urban land-dominated watersheds. Allochthonous vs. autochthonous lipids showed that POM in most of these streams was dominated by allochthonous sources (59.5 ± 14.2 vs. 39.6 ± 14.5 % for aliphatic alcohols and 52.9 ± 11.5 vs. 34.1 ± 10.3 % for sterols). The relative abundance of allochthonous vs. autochthonous lipid inputs to POM varied as a function of land use type. POM in streams draining forest-dominated watersheds contained a higher proportion of allochthonous lipids and a lower proportion of autochthonous lipids than the streams influenced by human land use. The contribution of bacterial fatty acids differed significantly among sampling times (P = 0.003), but not among land use types (P = 0.547). Stepwise linear regression model selected nitrate and temperature as the best predictors of variation in bacterial inputs to POM. Proxies used to assess the nutritional value of POM potentially available to stream consumers included C:N ratios, and the concentrations of total long-chain polyunsaturated fatty acids, eicosapentaenoic acid, arachidonic acid, and cholesterol. None of these nutritional proxies differed among sampling months (P ≥ 0.171), but the proxies showed that the nutritional value of POM in forest streams was lower than in urban streams. Collectively, these findings suggest that human land use in upstream watersheds alters the source composition and nutritional value of stream POM, which not only impacts food quality for stream biota, but also potentially changes the characteristics of OM reaching downstream ecosystems.

Characterization and sources of extractable organic matter from sediment cores of an urban lake (Tasik Perdana), Kuala Lumpur, Malaysia

The extractable organic matter of sediment samples from six sampling sites in Lake Perdana, Kuala Lumpur, was analyzed to characterize the source inputs. The analysis of aliphatic homologous series indicated that terrestrial higher plant waxes can be assigned as the major sources of the identified aliphatic components in the lake sediments. The presence of an unresolved complex mixture of branched and cyclic compounds and a series of hopanes ranging from C27 to C35 reflected the contamination by petroleum residues from urban vehicular emissions brought in by runoff and fallout. The steroids present included stenols and stanols and showed an input of organic matter from higher plants. The detected pentacyclic triterpenoids comprised oleanane, ursane, lupane and friedelane skeletons including unsaturated oxygenated, mono-, di- and triaromatic counterparts. They are recognized as biomarkers for angiosperms. The presence of des-A-triterpenoids and their aromatized derivatives as the major diagenetic products of triterpenoids reflected the degradation of natural organic matter in the sediments occurring under mainly anoxic conditions. In addition, the presence of tetrahymanol and ββ-bishomohopan-32-ol indicated a minor algal/plankton and bacterial input to the sediments.

Diversity of Bacterial Communities in the Snowcover at Tianshan Number 1 Glacier and its Relation to Climate and Environment

The bacterial distribution, and its relationship with climate and environment factors were investigated in the snowcover at Tianshan Number 1 Glacier. The results showed that psychrotrophs were the preponderant bacteria in pit samples, though they were not the dominant species in the new fallen snow. The quantity and diversity of the cultivable bacteria decreased with the passage of time, indicating that the bacterial community acclimatized to low temperature by changing its structure. During this time, the peak number of the cultivable bacteria was associated with dirt layers, indicating that the bacterial input came with dust. Concurrently, the quantity and diversity of the cultivable bacteria showed a trend of variation similar to that shown by the δ18O values and the soluble ion concentrations, indicating that the bacterial distribution was related to both temperature and the amount of dust transported onto the glacier. Phylogentic analyses of 16S rRNA indicated that all the isolates fell into six categories: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, high G+C gram-positive bacteria, and low G+C gram-positive bacteria. In the snow pit, the abundance of the CFB group bacteria (mainly of the genus Flavobacterium) decreased from 55.5% to 1.49% with age, and fluctuated similar to the ion concentrations and the δ18O value. Meanwhile the α-Proteobacteria (mainly of the genus Brevundimonas) increased from 0.9% to 88.1%, indicating that Brevundimonas was the dominant psychrotroph in the study area, whose abundance varied inversely compared to the above-mentioned chemical properties. All the results suggest that bacterial abundance and diversity vary with climate and the physical chemical microenvironment. The pattern of bacterial distribution could be a biological index for the record of climate and environment change in the Tianshan Number 1 Glacier.

Relationship between lipid distribution and geochemical environment within Champagne Pool, Waiotapu, New Zealand

The lipid biomarkers associated with various geothermal facies within Champagne Pool were investigated and compared with previous microbiological characterisation. Biomarker analysis revealed two distinct microbial communities spanning the margin of Champagne Pool: the first in the subaqueous domal stromatolites, subaqueous orange precipitate and spicular microstromatolites at the air–water interface, and the second in an acidic sinter from the overhanging ledge. Lipid biomarkers were detected in all facies and are consistent with previous microbiological analysis, suggesting that encapsulated biomarkers do record microbial community structure. Results suggest a microbial community principally comprising Aquificales, Thermodesulfobacteriales, Sulfolobus and Thermofilum populations in all facies. In the acidic sinter, additional bacterial ( Actinomycetales and Planctomycetales), archaeal ( Thermoplasmatales) and algal ( Cyanidium caldarium) inputs were observed, the predominance of algal biomarkers suggesting that these organisms are major contributors to the microbial community in this facies. It is evident that local geochemistry plays a fundamental role in defining community composition and, consequently, microbial lipids entrained in Champagne Pool sinters, with metabolic activity of the microbial community reflecting the physicochemical conditions in each microenvironment.

Bacterial hopanoids as tracers of organic carbon sources and processing across the western Arctic continental shelf

Tracing the inputs of bacterial organic carbon to marine systems has been constrained by the lack of distinguishing geochemical tracers and limited contribution in sediments compared to other sources of organic matter. Bacteriohopanepolyols (BHPs) provide a direct means to identify bacterial inputs which also reflect potential bacterial groups and their activities in aquatic systems. We applied recent analytical approaches to identify and quantify bacterial derived carbon contributions to surface sediments from the western Arctic Ocean using BHPs. The abundance and distribution of BHPs resemble trends of water column primary production and suggest active heterotrophic recycling of in situ production with some component of long term preservation. BHPs proposed as terrestrial derived signatures (i.e. adenosylhopanes) were also abundant in western Arctic sediments and reflect offshore trends of other terrigenous lipid signatures with a fraction representing their degradative products. Analysis of BHPs in organic rich peat and surface sediments from two Arctic rivers showed the highest inputs of adenosylhopanes, implying active bacterial recycling of recalcitrant terrigenous material. BHPs observed in western Arctic surface sediments reveal significant contributions of bacteria associated with organic carbon from multiple sources.

Trophic ecology of the sea urchin Spatangus purpureus elucidated from gonad fatty acids composition analysis

Irregular sea urchins such as the spatangoid Spatangus purpureus are important bioturbators that contribute to natural biogenic disturbance and the functioning of biogeochemical cycles in soft sediments. In the coastal waters of the Balearic Islands S. purpureus occurs in soft red algal beds, and can reach high densities. The diet of S. purpureus is unknown and it is particularly difficult to analyze the stomach contents of this group; therefore, we analyzed the fatty acid (FA) composition of the gonads and potential food resources in order to assess the trophic relationships of this species. The FA profiles of the gonads of S. purpureus agree well with the FA composition of the potential trophic resources (algae and sediment) and reveals changes between localities with different available resources. Three polyunsaturated FAs mainly contributes in the composition in the S. purpureus gonads: eicosapentaenoic acid (C20:5 n-3) and arachidonic acid (C20:4 n-6), both abundant in the macroalgal material, and palmitoleic acid (C16:1 n-7), which is characteristic of sediment samples. Trophic markers of bacterial input and carnivorous feeding were significantly more abundant in sea urchins caught on bottoms with less vegetation. The current study demonstrates that the FA content of S. purpureus gonads is a useful marker of diet, as differences in the profiles reflected the variations in detritus composition. The results of this study show that this species has omnivorous feeding behavior; however, viewed in conjunction with available abundance data the results suggest that phytodetritus found within algal beds is an important carbon source for this species.

Key Residues in Mycobacterium tuberculosis Protein Kinase G Play a Role in Regulating Kinase Activity and Survival in the Host

Protein kinase G (PknG) in Mycobacterium tuberculosis has been shown to modulate phagosome-lysosome fusion. The protein has three distinct domains, an N-terminal Trx domain, a kinase domain, and a C-terminal TPR domain. The present study extensively analyzes the roles of these domains in regulating PknG kinase activity and function. We find that the kinase domain of PknG by itself is inactive, signifying the importance of the flanking domains. Although the deletion of the Trx domain severely impacts the activity of the protein, the C-terminal region also contributes significantly in regulating the activity of the kinase. Apart from this, PknG kinase activity is dependent on the presence of threonine 309 in the p + 1 loop of the activation segment. Mutating the conserved cysteine residues in the Trx motifs makes PknG refractory to changes in the redox environment. In vitro experiments identify threonine 63 as the major phosphorylation site of the protein. Importantly, we find that this is the only site in the protein that is phosphorylated in vivo. Macrophage infection studies reveal that the first 73 residues, the Trx motifs, and the threonine 63 residue are independently essential for modulating PknG-mediated survival of mycobacteria in its host. We have extended these studies to investigate the role of PknG and PknG mutants in the pathogenesis of mycobacteria in mice. Our results reinforce the findings from the macrophage infection experiments, and for the first time demonstrate that the expression of PknG in non-pathogenic mycobacteria allows the continued existence of these bacteria in host tissues.

Abundance and diversity of snow bacteria in two glaciers at the Tibetan Plateau

Snow bacterial abundance and diversity at the Guoqu Glacier and the East Rongbuk Glacier located in the central and southern Tibetan Plateau were investigated using a 16S rRNA gene clone library and flow cytometry approach. Bacterial abundance was observed to show seasonal variation, with different patterns, at the two glaciers. High bacterial abundance occurs during the monsoon season at the East Rongbuk Glacier and during the non-monsoon season at the Guoqu Glacier. Seasonal variation in abundance is caused by the snow bacterial growth at the East Rongbuk Glacier, but by bacterial input from the dust at the Guoqu Glacier. Under the influence of various atmospheric circulations and temperature, bacterial diversity varies seasonally at different degrees. Seasonal variation in bacterial diversity is more distinct at the Guoqu Glacier than at the East Rongbuk Glacier. Bacterial diversity at the two glaciers exhibits different responses to various environmental conditions. More bacteria at the Guoqu Glacier are connected with those from a soil environment, while more bacteria affiliated with a marine environment occur at the East Rongbuk Glacier.

Tracking petroleum systems in the Perth Basin by integrating microscopic, molecular and isotopic information on petroleum fluid inclusions

The composition of petroleum trapped in fluid inclusions (FI) provides insights into petroleum systems active in the geological past. In this study of the Perth Basin we have analysed oil-bearing FIs in siliciclastics from the top of the Early Permian Carynginia Formation in the Cliff Head oil field and in the Leander Reef-1 well. Quantitative fluorescence spectroscopic and organic geochemical techniques were used to detect and characterise the hydrocarbon fluid types in inclusions, resulting in better definition of the nature and extent of the basin's petroleum systems. The FI oil from Cliff Head-3 (1285–90 m) and production oil from Cliff Head-6 (1488 m) are geochemically similar. Inversion of their source indicators points to a marine source rock such as found in the basal Hovea Member of the Early Triassic base Kockatea Shale. This is shown by the presence of an anomalously high abundance of C33 alkylcyclohexane (C33 ACH) and relatively low pristane to phytane ratios of ≤1.4 in both the FI and production oils. These oils also contain high relative abundances of extended tricyclic terpanes (NC28) and npropylcholestanes, pointing to strong algal and/or bacterial organic matter inputs to their effective source rocks, and supporting a marine depositional environment for the latter. Oil inclusions from Cliff Head-3 are contemporaneous with a phase of quartz overgrowth cement, and fluoresce in the yellow region of the visible spectrum. Production oil from the Cliff Head field fluoresces in thewhite-yellow region of the visible spectrum, consistent with oils of 30–36°-API gravity. The shift to whiter fluorescence may be due to the slightly higher thermal maturity of the production oil.

Molecular Evidence for Bacterial Mediation of Calcite Formation in Cold High-Altitude Caves

Three samples of moonmilk from high-altitude caves in northeast Italy were analysed for their lipid biomarker content, providing the first organic geochemical investigation into the relationship between cave bacterial communities and calcitic speleothems. The results demonstrate a positive association between the moonmilk deposits analysed and bacterial input, which we propose relates to bio-mediation of calcite nucleation processes. Comparison of the analysed moonmilk and a stalagmite from a geographically and climatically related cave suggest that this association is at least partially driven by the characteristics of the soil and overlying vegetation, thus demonstrating the potential use of moonmilk in palaeoenvironmental research.

Composition and sources of extractable organic matter from a sediment core in Lake Kivu, East African rift valley

Abstract Lake Kivu is a gas-charged East African rift lake with currently anoxic bottom water. The extractable compounds and residual organic matter of a short sediment core have δ13C values typical of lacustrine microbial detritus. The total extracts consist primarily of polar compounds such as n-alkanoic acids, hydroxyalkanoic acids, triterpenoids, steroids and monosaccharides, with minor amounts of n-alkanes and n-alkanols. These tracer compounds and δ13C values indicate that the organic matter in the surficial and deeper sedimentary record was dominated by bacterial sources. The sapropelic sediment between these horizons contains organic matter from primarily algal with lesser bacterial input. Terrestrial organic markers are minor in all samples. The major fractions of the compounds in the total extracts were oxidized in the upper water column prior to transit through the anoxic bottom water to sedimentary deposition. The sapropelic horizon may reflect lake water turnover with ventilation or hydrothermal activity and consequently increased algal blooms.

FOOD SOURCES OF THREE BIVALVES LIVING IN TWO HABITATS OF JIAOZHOU BAY (QINGDAO, CHINA): INDICATED BY LIPID BIOMARKERS AND STABLE ISOTOPE ANALYSIS

Food sources of three filter-feeding bivalves from two habitats (intertidal oyster Crassostrea gigas, mussel Mytilus galloprovincialis, and subtidal cultured scallop Chlamys farreri) of Jiaozhou Bay (Qingdao, China) were determined by fatty acid and stable isotope analysis. Cultured scallop was characterized by significant diatom markers such as 16:1/16:0 close to 1 and high ratio of 20:5(n − 3)/22:6(n − 3), hence we assume that the scallop mainly feeds on diatoms. Fatty acid biomarkers specific to bacteria and terrestrial materials were also found in considerable amounts in scallop tissue, which suggested that there were substantial bacterial and terrestrial input into the food of the species. Intertidal oyster and mussel, however, exhibited significant flagellate marker, 22:6(n − 3), and lower level of diatom markers, which indicated that flagellates are also part of intertidal bivalves’ planktonic food sources; meanwhile, high level of Chlorophyta fatty acid marker, Σ18:2(n − 6) 18:3(n − 3), suggested that Ulva pertusa (Chlorophyta) seaweed bed supplied important food sources to intertidal bivalves. Additionally, result of stable isotope analysis showed that phytoplankton contributed 86.2 to 89.0% to intertidal bivalves’ carbon budget; macroalga U. pertusa origin source had a contribution of 8.7% to 11.0%, which indicated its role as an important supplemental food source to intertidal bivalves. From this study, it is concluded that the dietary difference of three bivalves probably relates to the different potential food sources in the scallop farm and intertidal zone in Jiaozhou Bay.

Investigation of the solvent extracts of humic organic matter (HOM) isolated from the Ravenna Lagoon to study environmental pollution and microbial communities

Solvent extracts of HOM isolated from highly polluted sediments from the Ravenna Lagoon were studied. Diagnostic indicators included polycyclic aromatic hydrocarbons (PAHs) and nonylphenols as hazardous organic pollutants to characterize anthropogenic pollution, as well as fatty acids (FA, analysed as methyl esters, FAME) to characterize microbial communities responsible for natural attenuation processes. The distribution of PAHs including cyclopentafused surrogates pointed to a significant pyrogenic origin, characteristic for methane combustion. The PAH distribution was characterized by high concentrations of highly carcinogenic analytes with molecular weights of 276 Da (benzo[ ghi]perylene prevailing) and 300 Da (coronene prevailing). The PAH pattern as obtained by solvent extraction was very different from that obtained from pyrolysis/thermochemolysis of the HOM polymeric matrix. The FA pattern indicated strong bacterial input, with a significant contribution from methanotrophic bacteria as revealed by monounsaturated members with n:1 ω8 and n:1 ω5 double bonds in the alkyl chain. Terrestrial inputs as revealed by FAME analysis beyond C 20 with pronounced even-over-odd discrimination were of minor significance. This was confirmed by the pattern of nC 24– nC 30 alcohols in strong even-over-odd prevalence occurring in relatively low concentrations. The hopane hydrocarbon distribution reflected a distinctive impact from industrial processes utilizing heavy fractions of petroleum as feedstock. Hopanols along with the 17β( H),21β( H)-bishomohopanoic acid pointed to hopane producers, including methanotrophic and sulfate-reducing bacteria. Nonylphenols, which could not be detected in the pyrograms of solvent-extracted HOM matrix, had a total concentration of about 70 μg g −1 referred to the HOM in the solvent extract. In addition to common phytosterols including β-sitosterol, coprostanol could be detected in the solvent extracts pointing to human fecal matter contamination. Concentration of resin acids turned out to be very low, thus no harmful environmental effects are to be expected from these compounds.

Growth variability and feeding of scallop Patinopecten yessoensis on different bottom sediments: Evidence from fatty acid analysis

Growth and feeding of the Japanese scallop, Patinopecten (= Mizuhopecten) yessoensis, from two populations inhabiting neighboring sites with similar water temperature, salinity, and hydrodynamic regimes but with different bottom sediment types were investigated. Fatty acid biomarkers were used to investigate the diets of scallops and to evaluate the food availability at the sites with different bottom sediments. Fatty acid composition of digestive gland and soft tissues of scallops from two populations were examined and compared to those of plankton, particular organic matter of near-bottom water and bottom sediments as its potential food sources. The high level of 20:5( n − 3) coupled with the high ratio of 16:1( n − 7) to 16:0 in the digestive gland of scallop indicated an important contribution of diatoms to scallop nutrition. The relatively high proportions of 18:2( n − 6), 20:4( n − 6), and 22:6( n − 3) suggested that heterotrophic flagellates, ciliates, and invertebrate larvae were also an important source of nutrition for the scallop. Trace amounts of branched and odd fatty acids were indicative of an insignificant contribution of detritus to scallop diet. Lipid and fatty acid compositions of scallops from two sites were characterized by pronounced differences pointing to the different food availability in near-bottom water at the muddy and sandy sites. Higher food availability at the muddy site resulted in an increase in the total lipid content in scallop's digestive gland due to increased proportion of triacylglycerols. Increased contents of diatom biomarkers indicated that scallops inhabiting muddy bottom were more reliant on diatom food sources. Scallops from the sandy site showed higher proportions of biomarkers derived from flagellates, ciliates, and invertebrate larvae, compared to scallops from the muddy site. This is consistent with the distribution of the fatty acids in near-bottom water POM at the study sites. In spite of the high microbial biomass in muddy bottom sediments and elevated proportion of bacterial fatty acids in near-bottom water POM, bacterial input in scallop diet increased slightly. Thus, the distribution of marker fatty acids in scallops collected at the two sites indicated spatial variability primarily due to the composition and abundance of near-bottom POM, suggesting that scallop feeding is dependent on food availability. Comparison of linear and weight parameters of scallops showed that, in spite of the best food potential at the muddy site, scallops grew significantly slower at the muddy site than at the sandy site. Thus, food potential was not the only factor regulating growth of scallops inhabiting different bottom sediments. It was found, that oxygen concentration in near-bottom water and bottom sediment resuspension depended on the grain-size composition of the sediments. Most probably, low oxygen concentration in the near-bottom water and high resuspension of inorganic fine-grained particles enriched with inedible dead organic matter are the main reasons of the reduction in growth of scallop inhabiting the muddy site.

Oil Families and Their Potential Sources in the Southern Gulf of Suez, Egypt

Four oil families are identified in the southern Gulf of Suez, through high-resolution geochemical studies including gas chromatography, gas chromatography–mass spectrometry, and carbon isotope analyses. Biological features characterize oils in family 1a, suggesting tertiary carbonate source rocks for these oils, rich in type II organic matter and deposited under anoxic depositional environment. Family 1b oil shows minor variations in the source of organic matter and the depositional environment, as it was derived from carbonate source rock with more algal and bacterial contribution and minor input of terrestrial organic sources, deposited under less saline condition compared to family 1a oil. Family 2 oil, although genetically related to family 1a oil, has some distinctive features, such as diasterane to sterane and pristane to phytane ratios, which suggest clay-rich source rocks and a more oxic depositional environment. Also, the lack of oleanane indicates pre-tertiary source rocks for this oil. In contrast, family 3 oil is of mixed sources (marine and non-marine), generated from low sulfur and clay-rich source rock of tertiary and/or younger age. Family 4 oil seems to be mixed from family 1b and family 3 oils, sourced mainly from carbonate source rocks rich in clay minerals with algal and bacterial contributions. Family 4 oil is highly mature, family 1b oil lies within equilibrium values (peak oil generation stage), while the other families are more or less near equilibrium.

C3/C4 variations in salt-marsh sediments: An application of compound specific isotopic analysis of lipid biomarkers to late Holocene paleoenvironmental research

In salt-marshes, bulk carbon isotope values reflect organic matter contributions not only from salt-marsh plants, but also from algal and bacterial inputs, as well as allochthonous terrestrial organic matter. In the present study, compound specific isotope analysis was applied to a core and modern plant samples collected from a Machiasport, Maine salt-marsh. We sampled 10 plant species common to the marsh including Spartina alterniflora, Spartina patens, Juncus gerardi, Solidago sempervirens, Salicornia europa, Potentilla anserina, Atriplex patula, Plantago maritima, Suaeda maritima and Limonium nashii. Isolation of two n-alkanes (C 27 and C 29) present in marsh plant samples allowed for the reconstruction of past plant communities present in the cored deposits. For the C 27 and C 29 homologues there is a 3–10‰ separation in carbon isotopic composition between C3 and C4 species. Carbon isotopic values down core show a transition from a C4 dominated plant community to a C3 dominated community, attributable to the migration of lower marsh zones onto brackish/freshwater marsh zones during a late Holocene relative sea-level rise. The two homologues used have the potential to provide paleoenvironmental information in future core work, where the sea-level variable will be controlled.

Application of Light Hydrocarbon (C7+) and Biomarker Analyses in Characterizing Oil from Wells in the North and North Central Sinai, Egypt

Seven representative oil show samples from wells in the north and north central Sinai have been characterized by means of a variety of organic geochemical techniques (C7 hydrocarbon and biomarker analyses), to illustrate origin, differences, and similarity among oils. These oils were obtained from Cretaceous and Jurassic reservoirs. The C7 oil correlation star diagram (OCSD) suggests closely related oils, derived mainly from similar source rocks, while the C7 oil transformation star diagram (OTSD) and C7 light hydrocarbon analyses indicate a minor degree of transformation of some oils, as Misri-1, Halal-1, and Nakhl-1 oils were subjected to evaporative fractionation. Moreover, the studied oils show no sign of water washing and biodegradation. Molecular characteristics suggest pre-Tertiary shales and carbonate source rocks, deposited under a saline oxic environment, rich in terrigeneous organic sources with significant bacterial and algal input. Since the studied oils are of mixed marine and terrestrial origin, C7 signature of these oils is not representative of their origin and should be supported by other geochemical evidence (e.g., biomarkers) to predict their origin.

Investigation of bacterial hopanoid inputs to soils from Western Canada

Hopanoids have been widely used as characteristic biomarkers to study inputs of bacterial biomass to sediments because they are preserved in the geologic record. A limited number of studies have been performed on hopanoid biomarkers in soils. The present study examined the distribution and potential preservation of hopanoids in soils that are developed under different climatic conditions and varying vegetative inputs. Solvent extraction and sequential chemical degradation methods were employed to extract both “free” and “bound” hopanoids, from three grassland soils, a grassland–forest transition soil, and a forest soil from Western Canada. Identification and quantification of hopanoids in the soil samples were carried out by gas chromatography–mass spectrometry. Methylbishomohopanol, bishomohopanol and bishomohopanoic acid were detected in all solvent extracts. The base hydrolysis and ruthenium tetroxide extracts contained only bishomohopanoic acid at a concentration range of 0.8–8.8 μg/gC and 2.2–28.3 μg/gC, respectively. The acid hydrolysis procedure did not release detectable amounts of hopanoids. The solvent extraction yielded the greatest amounts of “free” hopanoids in two of the grassland soils (Dark Brown and Black Chernozems) and in the forest soil (Gray Luvisol). In contrast, the chemical degradation methods resulted in higher amounts of “bound” hopanoids in the third grassland soil (Brown Chernozem) and the transition soil (Dark Gray Chernozem), indicating that more hopanoids exist in the “bound” form in these soils. Overall, the forest and the transition soils contained more hopanoids than the grassland soils. This is hypothesized to be due to the greater degradation of hopanoids in the grassland soils and or sorption to clay minerals, as compared to the forest and transition soils.

Modelling the fate of faecal indicators in a coastal basin

The paper describes a modelling study of near-shore coastal waters, undertaken to assess the impact of various bacterial input loads on the receiving waters in a coastal basin in the UK. Total and faecal coliforms, used as the indicators for bathing water quality under the European Union (EU) Bathing Water Directive, were numerically modelled using a 2D depth integrated hydro-environmental model. Details are given of the governing equations and solution methods used in the numerical model, together with a discussion of the recent development in faecal bacterial indicator modelling. Details are also given of a field data collection exercise, which involved initially collecting existing information on effluent input loads and followed by an intensive field survey. Using the water quality model, the mortality rate of the pathogen bacteria was investigated. Three methods were used to represent the relationship between the decay rate and the level of solar radiation including: a constant decay rate, day- and night-time decay rates and a solar radiation related time varying decay rate. Relatively close agreement between model predicted and measured total and faecal coliform concentration distributions were obtained for different day- and night-time decay rates and time varying decay rates. No significant differences were found in the optimum decay rates for total and faecal coliform levels. Finally, the impact of the individual inputs on the bathing water quality of the basin was also statistically and numerically investigated. Results showed that the River Irvine was the most significant input during high river flows, and that under these conditions the bathing waters were likely to fail to comply with the European Union Bathing Water Directive. For base river flow conditions the Meadowhead effluent input was found to be critical for both total and faecal coliform level predictions.

Chemical and carbon isotopic evolution of hydrocarbons during prograde metamorphism from 100°C to 550°C: Case study in the Liassic black shale formation of Central Swiss Alps

Hydrocarbon distributions and stable isotope ratios of carbonates (δ 13C car, δ 18O car), kerogen (δ 13C ker), extractable organic matter (δ 13C EOM) and individual hydrocarbons of Liassic black shale samples from a prograde metamorphic sequence in the Swiss Alps were used to identify the major organic reactions with increasing metamorphic grade. The studied samples range from the diagenetic zone (<100°C) to amphibolite facies (∼550°C). The samples within the diagenetic zones (<100 and 150°C) are characterized by the dominance of C <20 n-alkanes, suggesting an origin related with marine and/or bacterial inputs. The metamorphic samples (200 to 550°C) have distributions significantly dominated by C 12 and C 13 n-alkanes, C 14, C 16 and C 18 n-alkylcyclopentanes and to a lesser extend C 15, C 17 and C 21 n-alkylcyclohexanes. The progressive 13C-enrichment (up to 3.9‰) with metamorphism of the C >17 n-alkanes suggests the occurrence of cracking reactions of high molecular weight compounds. The isotopically heavier (up to 5.6 ‰) C <17 n-alkanes in metamorphic samples are likely originated by thermal degradation of long-chain homologous with preferential release of isotopically light C 1 and C 2 radicals. The dominance of specific even C-number n-alkylcyclopentanes suggests an origin related to direct cyclization mechanism (without decarboxylation step) of algal or bacterial fatty acids occurring in reducing aqueous metamorphic fluid conditions. The regular increase of the concentrations of n-alkylcycloalkanes vs. C >13 n-alkanes with metamorphism suggests progressive thermal release of kerogen-linked fatty acid precursors and degradation of n-alkanes. Changes of the steroid and terpenoid distributions are clearly related to increasing metamorphic temperatures. The absence of 18α(H)-22,29,30-trisnorneohopane (Ts), the occurrence of 17β(H)-trisnorhopane, 17β(H), 21α(H)-hopanes in the C 29 to C 31 range and 5α(H),14α(H),17α(H)-20R C 27, C 29 steranes in the low diagenetic samples (<100°C) are characteristic of immature bitumens. The higher thermal stress within the upper diagenetic zone (150°C) is marked by the presence of Ts, the disappearance of 17β(H)-trisnorhopane and thermodynamic equilibrium of the 22S/(22S + 22R) homohopane ratios. The increase of the ααα-sterane 20S/(20S + 20R) and 20R ββ/(ββ + αα) ratios (from 0.0 to 0.55 and from 0.0 to 0.40, respectively) in the upper diagenetic zone indicates the occurrence of isomerization reactions already at <150°C. However, the isomerization at C-20 (R → S) reaches thermodynamic equilibrium values already at the upper diagenesis (∼150°C) whereas the epimerisation at C-14 and C-17 (αα → ββ) arrives to constant values in the lower anchizone (∼200°C). The ratios Ts vs. 17α(H)-22,29,30-trisnorneohopane [(Ts/(Ts + Tm)] and 18α(H)-30-norneohopane (C 29Ts) vs. 17α(H),21β(H)-30-norhopane [C 29Ts/(C 29Ts + C 29)] increase until the medium anchizone (200 to 250°C) from 0.0 to 0.96 and from 0.0 to 0.44, respectively. An opposite trend towards lower values is observed in the higher metamorphic samples. The occurrence of specific hydrocarbons (e.g., n-alkylcyclopentanes, cadalene, hydrogenated aromatic compounds) in metamorphic samples points to kerogen degradation reactions most probably occurring in the presence of water and under reducing conditions. The changes of hydrocarbon distributions and carbon isotopic compositions of n-alkanes related to metamorphism suggest that the organic geochemistry may help to evaluate the lowest grades of prograde metamorphism.