Biogeochemical Budgets in a Mediterranean Catchment with High Rates of Atmospheric N Deposition – Importance of Scale and Temporal Asynchrony

In this study biogeochemical export in a set of catchments that vary from 6 ha to almost 1500 ha is investigated. Studying catchments across this large range of scales enables us to investigate the scale dependence and fundamental processes controlling catchment biogeochemical export that would not have been possible with a more limited data set. The Devil Canyon catchment, in the San Bernardino Mountains, California, has some of the highest atmospheric N deposition rates in the world (40–90 kg ha⁻¹year⁻¹ at the crest of the catchment). These high rates of deposition have translated into consistently high levels of NO⁻in 3 some streams of the San Bernardino Mountains. However, the streams of the Devil Canyon catchment have widely varying dissolved inorganic nitrogen (DIN) concentrations and export. These differences are also, to a more limited extent, present for dissolved organic carbon (DOC) but not in other dissolved species (Cl⁻, SO²⁻₄,Ca²⁺ and other weathering products). As catchment size increases DIN and DOC concentrations first increase until catchment area is ∼150 ha but then decrease as catchment scale increases beyond that size. The scale dependence of DIN export implies that catchments at different spatial scales are at different degrees of N saturation. The reason for this scale effect appears to be the dominance of flushing of DIN out of soil at small scales due to the temporal asynchrony between nutrient availability and biological N demand, the groundwater exfiltration of this flushed DIN at intermediate scales and the removal of this DIN from streamflow through in-stream processes and groundwater–surface water interaction at larger scales. While the particular scale effect observed here may not occur over the same range in catchment area in other ecosystems, it is likely that other ecosystems have similar scale dependant export for DIN and DOC.     

Phosphorus budgetary analysis of sediment–water interface in a short-term anoxic condition in shallow Lake Kasumigaura,Japan

To investigate the effective depth from the surface sediment, and phosphorus fractions related to phosphorus release under short-term anoxic conditions, varying lengths of sediment cores taken from Lake Kasumigaura, a large shallow polymictic lake in Japan, were incubated for a few weeks and then analyzed. Results showed few differences in total phosphorus (TP) amount per unit area in overlying waters irrespective of the core thickness, and sums of TP in both overlying water and 0- to 2-cm sediment layers were nearly equal before and after the experiment, indicating that phosphorus was released mainly from the 0- to 2-cm layer by dissolution. In contrast, phosphorus was decreased in pore water below a 2-cm depth, probably through sorption to sediment solids. The citrate-dithionite-bicarbonate total phosphorus (CBD-TP) and non-reactive phosphorus extracted by NaOH (NaOH-NRP) in sediment solids in the 0- to 2-cm layer decreased during the experiment. The decreases of CBD-TP were 10 times higher than those of NaOH-NRP, suggesting that the released phosphorus came mainly from the fraction bound to iron in Lake Kasumigaura.     

Environmental Impact of the Production of Mealworms as a Protein Source for Humans – A Life Cycle Assessment

The demand for animal protein is expected to rise by 70–80% between 2012 and 2050, while the current animal production sector already causes major environmental degradation. Edible insects are suggested as a more sustainable source of animal protein. However, few experimental data regarding environmental impact of insect production are available. Therefore, a lifecycle assessment for mealworm production was conducted, in which greenhouse gas production, energy use and land use were quantified and compared to conventional sources of animal protein. Production of one kg of edible protein from milk, chicken, pork or beef result in higher greenhouse gas emissions, require similar amounts of energy and require much more land. This study demonstrates that mealworms should be considered a more sustainable source of edible protein.     

``BACWAVE,' a Spatial–Temporal Model for Traveling Waves of Bacterial Populations in Response to a Moving Carbon Source in Soil

Abstract Previously, we discovered the phenomenon of wavelike spatial distributions of bacterial populations and total organic carbon (TOC) along wheat roots. We hypothesized that the principal mechanism underlying this phenomenon is a cycle of growth, death, autolysis, and regrowth of bacteria in response to a moving substrate source (root tip). The aims of this research were (i) to create a simulation model describing wavelike patterns of microbial populations in the rhizosphere, and (ii) to investigate by simulation the conditions leading to these patterns. After transformation of observed spatial data to presumed temporal data based on root growth rates, a simulation model was constructed with the Runge–Kutta integration method to simulate the dynamics of colony-forming bacterial biomass, with growth and death rates depending on substrate content so that the rate curves crossed over at a substrate concentration within the range of substrate availability in the model. This model was named ``BACWAVE,' standing for ``bacterial waves.' Cyclic dynamics of bacteria were generated by the model that were translated into traveling spatial waves along a moving nutrient source. Parameter values were estimated from calculated initial substrate concentrations and observed microbial distributions along wheat roots by an iterative optimization method. The kinetic parameter estimates fell in the range of values reported in the literature. Calculated microbial biomass values produced spatial fluctuations similar to those obtained for experimental biomass data derived from colony forming units. Concentrations of readily utilizable substrate calculated from biomass dynamics did not mimic measured concentrations of TOC, which consist not only of substrate but also various polymers and humic acids. In conclusion, a moving pulse of nutrients resulting in cycles of growth and death of microorganisms can indeed explain the observed phenomenon of moving microbial waves along roots. This is the first report of wavelike dynamics of microorganisms in soil along a root resulting from the interaction of a single organism group with its substrate. Received: 2 October 1999; Accepted: 9 March 2000; Online Publication: 28 August 2000     

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Background  

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.     

Oxidoreductases for the remediation of organic pollutants in water – a critical review

Water contamination by various recalcitrant organic aromatic compounds is an emerging environmental issue that is increasingly attracting the attention of environmental scientists. A great majority of these recalcitrant pollutants are industrial wastes, textile dyes, pharmaceuticals, hormones, and personal care products that are discharged into wastewater. Not surprisingly, various chemical, physical, and biological strategies have been proposed and developed to remove and/or degrade these pollutants from contaminated water bodies. Biological approaches, specifically using oxidoreductase enzymes (such as peroxidases and laccases) for pollutant degradation are a relatively new and a promising research area that has potential advantages over other methods due to their higher efficiency and the ease of handling. This review focuses on the application of different classes of oxidoreductase enzymes to degrade various classes of organic pollutants. In addition to classifying these enzymes based on structural differences, the major factors that can affect their remediation ability, such as the class of peroxidases employed, pH, molecular structure of the pollutant, temperature, and the presence of redox mediators are also examined and discussed. Interestingly, a literature survey combined with our unpublished data suggests that “peroxidases” are a very heterogeneous and diverse family of enzymes and have different pH profiles, temperature optima, thermal stabilities, requirements for redox mediators, and substrate specificities as well as varying detoxification abilities. Additionally, remediation of real-life polluted samples by oxidoreductases is also highlighted as well as a critical look at current challenges and future perspectives.     

Species introduction in restoration projects – Evaluation of different techniques for the establishment of semi-natural grasslands in Central and Northwestern Europe

During recent decades, many studies have shown that the successful restoration of species-rich grasslands is often seed-limited because of depleted seed banks and limited seed dispersal in modern fragmented landscapes. In Europe, commercial seed mixtures, which are widely used for restoration measures, mostly consist of species and varieties of non-local provenance. The regional biodiversity of a given landscape, however, can be preserved only when seeds or plants of local provenance are used in restoration projects. Furthermore, the transfer of suitable target species of local provenance can strongly enhance restoration success.We review and evaluate the success of currently used near-natural methods for the introduction of target plant species (e.g. seeding of site-specific seed mixtures, transfer of fresh seed-containing hay, vacuum harvesting, transfer of turves or seed-containing soil) on restoration sites, ranging from dry and mesic meadows to floodplain grasslands and fens. Own data combined with literature findings show species establishment rates during the initial phase as well as the persistence of target species during long-term vegetation development on restoration sites.In conclusion, our review indicates that seed limitation can be overcome successfully by most of the reviewed measures for species introduction. The establishment of species-rich grasslands is most successful when seeds, seed-containing plant material or soil are spread on bare soil of ex-arable fields after tilling or topsoil removal, or on raw soils, e.g. in mined areas. In species-poor grasslands without soil disturbance and on older ex-arable fields with dense weed vegetation, final transfer rates were the lowest. For future restoration projects, suitable measures have to be chosen carefully from case to case as they differ considerably in costs and logistic effort. Long-term prospects for restored grassland are especially good when management can be incorporated in agricultural systems.     

Determination of erythema-effective solar radiation in Japan and Germany with a spore monolayer film optimized for the detection of UVB and UVA – results of a field campaign

The available physical and biological broadband radiometers designed to determine erythema-effective radiation do not show any response or over/underestimate the biologically effective radiation to a high extent in the ultraviolet (UV)A spectral region. The data presented in this paper demonstrate that the biological system used in this study is the first one to make possible measurements of erythema-effective radiation in the sun in the UVA and UVB spectral region. These measurements were performed with a spore-film filter system as well as with spectroradiometers. It was demonstrated that this biotechnological method could be used to determine exact values expressed as minimal erythemal dose (MED). The spore-film system was tested in various field campaigns performed in Germany and in Japan. The seasonal daily variation of UV radiation in Germany determined in the period November 1995 to December 1996 using the spore-film filter system in sunny conditions tallied well with model calculations. The daily dose in Germany measured with the spore-film system close to the summer solstice, in sunny conditions (20.45 MED), was approximately 20 times higher than the lowest value measured close to the winter solstice (0.82 MED), a result which was in accordance with model calculations. The data determined with the spore-film filter system in Sapporo and Naha, Japan, fitted to the erythema-weighted data calculated from spectroradiometric measurements (Brewer), even at low solar radiation angles in a solar spectrum with less UVB but significant UVA. The spore-film dosimeter values were about 103 ± 8% of the integrated dose of the Brewer instrument. The standard deviation of the spore-film measurements obtained in Japan was 12.8%. The responsivity of the spore-film system towards longer wavelengths within the UVA spectrum was tested with the Okasaki Large Spectrograph with monochromatic radiation. At a wavelength of 365 nm – in a spectral region which is dominant in many tanning lamps and with minor importance for solar radiation in summer conditions – the tested spore-film system gave results that were close (112% compared to the calibration dose) to the calibration dose which was used for irradiation. Received: 27 January 1998 / Received last revision: 21 July 1998 / Accepted: 29 July 1998     

Evaluation of a Questionnaire-Based Method for the Estimation of Methylmercury Exposure of Recreational Anglers in the James Bay Territory (Québec,Canada)

The impoundment of reservoirs temporarily increases the methylation of mercury bound to flooded soils and vegetation and the transfer of methylmercury (MeHg) to fish. MeHg levels in various fish species of hydroelectric reservoirs located in the James Bay territory increased by factors of 3 to 7, then gradually declined toward initial concentrations 10 to 20 years after flooding, depending on reservoir characteristics. The potential risk of increased MeHg exposure for recreational anglers who consume fish from these reservoirs had not been assessed previously. A less invasive method than systematic measurement of Hg levels in hair was developed to determine MeHg exposure of recreational anglers. A fish consumption questionnaire-based approach was combined with a toxicokinetic model to estimate the corresponding hair MeHg concentrations. The results were compared with actual analytical determinations of hair Hg levels for the 94 recreational anglers recruited for the study. The values predicted by the model based on self-reporting consumption overestimated actual hair Hg levels by an average factor greater than 6. The mean hair level predicted for the most recent period (September-October) was 23.3?µg.g^?1 compared to 3.6 µg.g^?1 for the measured value. Although the questionnaire protocol may certainly be improved to increase the precision of estimations, direct hair Hg measurement remains the more effective means to assess Hg exposure.     

What Triggers a Diagnosis of HIV Infection in the Tokyo Metropolitan Area? Implications for Preventing the Spread of HIV Infection in Japan

Background

Japan has not succeeded in reducing the annual number of new HIV-infected patients, although the prevalence of HIV infection is low (0.02%).

Methods

A single-center observational study was conducted at the largest HIV clinic in Tokyo, which treats 15% of the total patients in Japan, to determine the reasons for having diagnostic tests in newly infected individuals. HIV-infected patients who visited our clinic for the first time between 2011 and 2014 were analyzed.

Results

The 598 study patients comprised one-third of the total reported number of new patients in Tokyo during the study period. 76% were Japanese MSM. The reasons for being tested which led to the diagnosis was voluntary testing in 32%, existing diseases in 53% (AIDS-defining diseases in 22%, sexually transmitted infections (STI) in 8%, diseases other than AIDS or STIs in 23%) and routine pre-surgery or on admission screening in 15%. 52% and 74% of the study patients and patients presented with AIDS, respectively, had never been tested. The median CD4 count in patients with history of previous testing (315/μL) was significantly higher than that of patients who had never been tested (203/μL, p<0.001).

Conclusions

Only 32% of the newly HIV diagnosed patients were diagnosed because of voluntary testing, and 53% were diagnosed due to presence of other diseases. These results remain unchanged from our previous report 10 years earlier (2000–2004) on newly diagnosed patients at the same clinic. HIV testing has not been widely used by newly diagnosed patients in the Tokyo metropolitan area.     

A study of the Werewilka Inlet of the saline Lake Wyara, Australia – a harbour of biodiversity for a sea of simplicity

Lake Wyara receives most of its water from Werewilka Creek, with the area between the two forming Werewilka Inlet which is highly variable in area, and salinity and has high habitat heterogeneity. Over 12 years, 84 species of macroinvertebrate were found in the inlet, but only 34 in the lake. Halobiont and halophilic species were the same in each, but there were many fewer salt-tolerant species in the lake and no freshwater species. The latter were excluded by salinity, but habitat homogeneity due to strong wave action in the lake seems to limit many salt-tolerant species to the inlet. Species richness in large saline lakes in inland Australia is limited by salinity, poor speciation opportunities engendered by their episodic nature, and habitat homogeneity.     

Phosphate Starvation-Inducible Gene ushA Encodes a 5′ Nucleotidase Required for Growth of Corynebacterium glutamicum on Media with Nucleotides as the Phosphorus Source

Phosphorus is an essential component of macromolecules, like DNA, and central metabolic intermediates, such as sugar phosphates, and bacteria possess enzymes and control mechanisms that provide an optimal supply of phosphorus from the environment. UDP-sugar hydrolases and 5′ nucleotidases may play roles in signal transduction, as they do in mammals, in nucleotide salvage, as demonstrated for UshA of Escherichia coli, or in phosphorus metabolism. The Corynebacterium glutamicum gene ushA was found to encode a secreted enzyme which is active as a 5′ nucleotidase and a UDP-sugar hydrolase. This enzyme was synthesized and secreted into the medium when C. glutamicum was starved for inorganic phosphate. UshA was required for growth of C. glutamicum on AMP and UDP-glucose as sole sources of phosphorus. Thus, in contrast to UshA from E. coli, C. glutamicum UshA is an important component of the phosphate starvation response of this species and is necessary to access nucleotides and related compounds as sources of phosphorus.     

Land-Applied Goat Manure as a Source of Human Q-Fever in the Netherlands, 2006–2010

Studies have shown a link between Q-fever positive farms (QFPFs) and community cases of human Q-fever. Our study is the first to investigate the potential role of contaminated land-applied manure in human Q-fever, based on a large set of nationwide notification and farm management data. Time between manure application and disease onset in geographically linked notified human cases coincided with the incubation period of Q-fever. Proximity of contaminated land parcels predicted human cases better than proximity of QFPFs (80% vs. 58%, 0–5 km in 2009). Incidence around QFPFs and contaminated land parcels decreased with distance, but not around non-contaminated land parcels. Incidence was higher around contaminated land parcels than non-contaminated land parcels (RR = [10],95%CI = [7], [1]–[14,2]). Our findings deliver evidence that, apart from QFPFs, land-applied contaminated manure may be another source of human Q-fever.     

Crystal Structure of BamB Bound to a Periplasmic Domain Fragment of BamA,the Central Component of the β-Barrel Assembly Machine

The β-barrel assembly machinery (BAM) mediates folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria. BAM is a five-protein complex consisting of the β-barrel OMP BamA and lipoproteins BamB, -C, -D, and -E. High resolution structures of all the individual BAM subunits and a BamD-BamC complex have been determined. However, the overall complex architecture remains elusive. BamA is the central component of BAM and consists of a membrane-embedded β-barrel and a periplasmic domain with five polypeptide translocation-associated (POTRA) motifs thought to interact with the accessory lipoproteins. Here we report the crystal structure of a fusion between BamB and a POTRA3–5 fragment of BamA. Extended loops 13 and 17 protruding from one end of the BamB β-propeller contact the face of the POTRA3 β-sheet in BamA. The interface is stabilized by several hydrophobic contacts, a network of hydrogen bonds, and a cation-π interaction between BamA Tyr-255 and BamB Arg-195. Disruption of BamA-BamB binding by BamA Y255A and probing of the interface by disulfide bond cross-linking validate the physiological relevance of the observed interface. Furthermore, the structure is consistent with previously published mutagenesis studies. The periplasmic five-POTRA domain of BamA is flexible in solution due to hinge motions in the POTRA2–3 linker. Modeling BamB in complex with full-length BamA shows BamB binding at the POTRA2–3 hinge, suggesting a role in modulation of BamA flexibility and the conformational changes associated with OMP folding and insertion.     

Development and validation of a serological potency test for the release of Leptospira vaccines – Requirements in the European Union

Both European Pharmacopoeia Monograph 01/2008:0447 “Canine Leptospirosis vaccine (inactivated)” and the more recent Monograph 01/2008:1939 “Bovine Leptospirosis vaccine (inactivated)” explicitly allow for a sero-response test to assess batch potency. Test setup and requirements for in vivo and in vitro validation are described. Furthermore, the two main strategies to assess batch potency and their specific demands are addressed.     

Is the Improvement of CF Patients,Hospitalized for Pulmonary Exacerbation,Correlated to a Decrease in Bacterial Load?

Background

Cystic Fibrosis (CF) patients are vulnerable to airway colonization with Pseudomonas aeruginosa. In case eradication fails after antibiotic treatment, patients become chronically colonized with P. aeruginosa, with recurrent pulmonary exacerbation, for which patients typically are hospitalized for 2 weeks and receive intravenous antibiotic treatment. Normally, improvement of the patients'' health is established.

Aim

Determination of the correspondence between patient improvement and changes of the P. aeruginosa and total bacterial load in the sputum.

Methods

Eighteen CF patients with exacerbation were included for a total of 27 hospitalization episodes. At day 1, 8 and 15, inflammation and lung function parameters were determined, together with the P. aeruginosa load in the sputum using culture, quantitative PCR (qPCR) and propidium monoazide qPCR.

Results

Patients improved during hospitalization (decrease in levels of C-reactive protein, white blood cell counts and erythrocyte sedimentation rate, increase of FEV₁), reaching normal values already after one week. Also the P. aeruginosa load and the total bacterial load decreased during the first week of antibiotic treatment (p<0.05), except for patients with a low lung function (FEV₁≤39.4%), for whom no significant decrease of P. aeruginosa was established. Comparison of culture-based and propidium monoazide qPCR-based quantification of P. aeruginosa showed that at the end of the treatment on average 62% of the P. aeruginosa cells are not cultivable, indicating that many cells are alive but dormant, or dead but still structurally intact.

Conclusion

Improvement of the clinical status is accompanied with a decrease of the P. aeruginosa load, whereby both occur mainly during the first week of antibiotic treatment. However, for patients with a low lung function, no decrease of the P. aeruginosa load is observed. Comparison of detection techniques shows that a large amount of noncultivable or dead bacteria are present in the samples.     

Creation and maintenance of habitat downstream from a weir for the greenside darter, Etheostoma blennioides – a rare fish in Canada

The biology, microhabitat use and migratory behaviour of the greenside darter, Etheostoma blennioides, was studied at the Mannheim Weir on the Grand River, Ontario during the summer of 1995 and 1996. Officially listed as vulnerable in Canada, greenside darters reached maturity at age 1 and lived up to 4 years. They were found in riffle habitats that consisted of cobble and loose boulders, with large mats of Cladophora. This type of unembedded substrate is uncommon in the Grand River watershed. However, local abundance of greenside darters immediately downstream from the Mannheim Weir was likely due to high water velocities from weir discharge, freshets and ice scour which help maintain unembedded riffle areas. Trap data indicated that greenside darters temporally partition this habitat with the stonecat, Noturus flavus. Other darter species were not commonly found in areas with greenside darters, whose depth selection and habitat choices were influenced by predators and morphology. Denil fishways at the Mannheim Weir rarely passed greenside darters due to prohibitively high water velocities and exclusion by larger fish. This revised version was published online in August 2006 with corrections to the Cover Date.