Investigation of Microbes in the Rhizosphere of Selected Trees for the Rhizoremediation of Hydrocarbon-Contaminated Soils

Hydrocarbon-degrading microorganisms (HDMs), associated with the rhizosphere of Conocarpus lancifolius and Ficus infectoria trees grown in bioremediated soil, were isolated under controlled laboratory conditions. The selected trees were used to phytoremediate oil-contaminated soil for three successive growing seasons. At the end of the phytoremediation experiment, 85.7% of measurable total petroleum hydrocarbon was degraded in the rhizosphere soil associated with Conocarpus lancifolius compared to 78.6% in the rhizosphere of Ficus infectoria. The detectable concentrations of some polyaromatic hydrocarbons were less than 0.02 ppm. The HDM isolation process was conducted at 35°C under aerobic conditions. The isolated HDMs were identified using 16S rRNA gene sequencing and fatty acid methyl ester analysis. Differences in the genera of the isolated HDMs and their assessed efficiency in degrading a mixture of hydrocarbon compounds between the two trees were noted.     

Investigation of Microbes in the Rhizosphere of Selected Grasses for Rhizoremediation of Hydrocarbon-Contaminated Soils

Hydrocarbon-degrading microorganisms (HDM) associated with the rhizosphere of Paspalum vaginatum and Zoysia tenuifolia grown in bioremediated soil were isolated under controlled laboratory conditions. The isolation process was conducted at 30°C and 45°C to isolate mesophilic and thermotolerant microorganisms, respectively, under aerobic conditions. The isolated HDMs were identified using 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Although differences in the genera of the isolated HDMs occurred between the two grasses, Arthrobacter spp and Bacillus spp were isolated from the rhizosphere of both plants. The efficiency of the isolated microorganisms in degrading a mixture of hydrocarbon compounds (HC) was also assessed. Among the bacterial isolates, Pseudomonas boreopolis was found to be the most effective HC degrader, while the only fungal isolate, Fusarium solani, demonstrated higher degradation rates than most of the bacterial isolates. A mixture of all the microbial isolates demonstrated a high degradation percent of HC. The isolated microorganisms thus appear to work synergistically to degrade efficiently all the tested organic compounds.     

Enhanced Hydrocarbons Degradation in the Rhizosphere of Mangrove Plants by a Halophilic Bacillus Subtilis Subtilis Strain

Sulaibikhat Embayment is a severely contaminated coastline in the State of Kuwait. The contaminating pollutants include hydrocarbons, heavy metals, and suspended particles. The objective of this study is to assess the ability of mangroves planted in the Sulaibikhat Embayment to enhance hydrocarbons degradation by the activities of rhizospheric hydrocarbon degrading bacteria (HDB). Accordingly, samples were collected from the rhizosphere of selected mangrove plants and from sediments in the same location but away from mangrove marshes. The samples were analyzed chemically and microbiologically before being enriched with a mixture of hydrocarbon compounds (HC) to isolate HDB.

A number of halophilic HDB were isolated from mangroves rhizosphere and the surrounding sediments such as Pseudomonas balearica, Microbacterium barkeri and Gordonia soli. On the other hand, Bacillus velezensis and Bacillus subtilis subtilis were both isolated only from mangroves rhizosphere. Among the isolated HDB, Bacillus subtilis subtilis was distinguished with its high degradation rates of the tested HC including poly aromatic hydrocarbons. According to our knowledge, this is the first Bacillus subtilis HC-degrading strain that was isolated from Kuwait Bay and from mangroves rhizosphere.     

Effects of Crude and Bioremediated Thermal Power Plant Effluents in Brassica Juncea

Crude phenol and cyanides are the major components of the effluents discharged by industries involved in the manufacture of many synthetic inorganic and organic compounds, pharmaceuticals, electroplating units, and thermal power plants.

In this study, an effort was made to use effluents as manure. The effect of various amendments (10, 40, 70, and 100%) of bioremediated and crude effluents was checked on plants of Brassica juncea. Roots, shoot lengths, and the mean dry weights were maximum in the plants irrigated with 10% treated and 10% crude effluent as compared to the control plants. Total plant phenolics increased with an increase in the amendment of the effluents in the plants irrigated with bioremediated as well as crude effluents. Applications of lower amendments of treated and untreated effluents in Brassica juncea improved the chlorophyll levels in the experimental plants and the values obtained were similar to the control plants. Effect of bioremediated and crude effluents on antioxidant enzymes of Brassica juncea showed a differential effect. The activity of antioxidant enzymes peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) was observed to increase with an increase in the effluent concentration.

Here we demonstrate that the industrial effluents, when bioremediated of their harmful components, can also serve as a nourishment for plants, which can further help in the rehabilitation of wastelands.     

Exhaled breath profiling by electronic nose enabled discrimination of allergic rhinitis and extrinsic asthma

Aim: To assess whether an e-nose could discriminate between subjects affected by allergic rhinitis with and without concomitant extrinsic asthma, as well as from healthy controls, in terms of exhaled VOC-profile.

Methods: Fourteen patients with Extrinsic Asthma and Allergic Rhinitis (AAR), 14 patients with Allergic Rhinitis without asthma (AR) and 14 healthy controls (HC) participated in a cross-sectional study. Exhaled breath was collected by a standardized method and sampled by an e-nose (Cyranose 320). Raw data were reduced by Principal component analysis and analyzed by canonical discriminant analysis. Cross-validation accuracy (CVA) and Receiver Operating Characteristic(ROC)-curves were calculated. External validation in newly recruited patients (7 AAR, 7?AR and 7 HC) was tested using the previous training model.

Results: Breathprints of patients with AR clustered from those with AAR (CVA?=?85.7%), as well as HC (CVA?=?82.1%). Breathprints from AAR were also separated from those of HC (CVA?=?75.0%). External validation confirmed the above findings.

Conclusions: An e-nose can discriminate exhaled breath from subjects with allergic rhinitis with and without extrinsic asthma, which represent two different diseases with partly overlapping features. This supports the view of using breath profiling to diagnose asthma also in patients with allergic rhinitis.     

Diverse scaling relationships of tree height and diameter in five tree species

Background: Allometric scaling relationships are important in ecology and forestry. The metabolic scaling theory (MST) predicts a universal invariant scaling relationship for tree growth, relating height and diameter to each other.

Aims: Data on five tree species (Pinus taeda L., Pinus virginiana Mill., Liquidambar styraciflua L., Liriodendron tulipifera L., and Pinus palustris Mill.) were used to test the predictions from MST on the scaling of height–diameter and also diameter growth.

Methods: Data on tree height and diameter for five tree species from both natural forests and plantations were collected to study two types of scaling relationships: tree height–diameter and stem diameter growth. A reduced major axis of regression analysis model type II was used to determine scaling exponents from each species under different environmental conditions.

Results: No universal invariant scaling exponent was found in height–diameter and diameter growth for the five species. The scaling varied across natural forests, plantations and scales (e.g., time and number of measured trees). However, in some situations the scaling exponents failed to show significant difference with the predicted values (e.g., 2/3 or 1).

Conclusions: Diverse scaling exponents were observed for the five tree species with the scaling relationships varying with environmental settings.     

Habitat use and tree selection of a declining Afro-Palaearctic migrant at sub-Saharan staging and wintering sites

Capsule: Wood Warblers Phylloscopus sibilatrix showed significant selection for tree species and woodland characteristics at staging and wintering sites in sub-Saharan Africa.

Aims: To investigate home range size, habitat and tree species selection of Wood Warblers at a staging site in Burkina Faso (Koubri) and a wintering site in Ghana (Pepease).

Methods: Comparing habitat recorded at locations of radio-tagged birds and at control points, we investigated whether there was habitat and tree species selection. We also compared home range size of individual birds between the two sites.

Results: Home range size did not differ between the two sites. There was significant selection for tree species at both Koubri and Pepease: Anogeissus leiocarpus and Albizia zygia, respectively. At Koubri, there was significant avoidance of the most common tree species (Azadirachta indica, Mangifera indica (both non-native), Vitellaria paradoxa and Acacia spp.). In addition, there was a preference for taller trees and greater tree density at both sites. However, the probability of a point being used declined with increasing number of taller (>14?m) trees.

Conclusion: Fine-scale selection of woodland habitats suggests that Wood Warblers are likely to suffer the consequences of ongoing land-use change in their West African wintering grounds.     

Bioremediation of Diesel Fuel Contaminated Soil: Comparison of Individual Compounds to Complex Mixtures

Bioremediation is a cost effective means of remediating soils contaminated with petroleum hydrocarbons. Various factors affect the efficiency of the process, including environmental conditions, microbial population present and composition of the hydrocarbon spill. To evaluate the impact of mixture composition on individual compound and overall degradation, biodegradation experiments were conducted in sealed, 1-liter bioreactor/respirometer vessels containing soil spiked with hydrocarbon compounds in isolation and in mixtures. The influence of bacteria and fungi on the degradation process was also monitored. The degradation behavior of the various compounds was monitored using the fraction of contaminant remaining and first-order degradation coefficients based on hydrocarbon loss.

The results showed that the degradation trend of a compound changed when present in a simple mixture or when degraded in isolation. The presence of the compounds as either an aliphatic or aromatic mixture did not change the degradation trend. The presence of a mixture also affected the amount of degradation with some compounds degrading to a greater extent when in isolation. Overall, the majority of degradation occurred in the first 10 d, suggesting that the first-order model may not be an appropriate model for degradation periods longer than 10 d when nutrient limited. It was also found that fungal metabolism is important for the degradation of hydrocarbons, particularly for branched species such as pristane as the decay rate increased one order of magnitude when bacteria were inhibited.     

A territory scale analysis of habitat preferences of the declining Ortolan Bunting Emberiza hortulana

Capsule Ortolan Bunting occurrence is associated with bare ground, Lucerne, shrub cover and hedgerows/tree rows.

Aims To assess the habitat features selected by Ortolan Buntings at the territory level in semi-open landscapes, in the northern Apennines of Italy.

Methods We mapped territories in ten different plots and built a habitat selection model comparing 52 occupied cells with 52 unoccupied ones (cell size: 1?ha). We built multivariate adaptive regression splines models based on ground-measured variables.

Results The model revealed an association with intermediate Lucerne cover (50% of the cell), high shrub cover, bare ground (≥5%) and hedgerows/tree rows (≥25?m/ha). The most important driver of occurrence was bare ground (optimum at 5–20%).

Conclusion The maintenance of the mosaic and low-intensity farmed landscape, the promotion of Lucerne and the conservation/restoration of hedgerows/tree rows, may be promoted through the Rural Development Programme. The conservation of bare soil, grassland and shrubs at optimum amount at fine-scale could be the object of an agri-environment scheme targeted specifically at the Ortolan Bunting.     

Heparanase is a predictive marker for high thrombus burden in patients with ST-segment elevation myocardial infarction

Objective: Heparanase (HPA) is an endo-β-D-glucuronidase capable of degrading heparin sulphate (HS) and heparin side chains. HPA plays a role in tumour growth, angiogenesis, cell invasion and in activation of the coagulation system. We aimed to investigate the relationship between HPA and thrombus burden (TB) in patients with ST-Segment Elevation Myocardial Infarction (STEMI).

Methods: This prospective study enrolled 187 patients with STEMI who were treated with primary percutaneous coronary intervention (pPCI). Blood samples were taken to determine serum HPA levels prior to coronary angiography and heparin administration. Serum HPA analysis was performed with a commercially available Human Elisa kit.

Results: Patients were divided into two groups: high TB (n:58) and low TB (n:129) group. Serum HPA levels were significantly higher in patients with high TB than low TB [250.1 (188.5–338.1) vs. 173.6 (134.3–219.8) pg/mL] (p?<?0.001). Serum HPA levels were higher in patients with no-reflow phenomenon compared with others [(409.3 (375.6–512.5) pg/mL vs. 186.2 (144.2–247.4) pg/mL, p?<?0.001]. In multiple logistic regression analysis HPA was a predictor of high TB.

Conclusion: Elevated HPA level in patients with STEMI is related to high TB. Furthermore, increased HPA level may be associated with thrombotic complications such as no-reflow phenomenon in patients with STEMI.     

Effects of dominant tree species on insectivorous birds breeding in Mediterranean oak woodlands

Capsule Differences in Cork Oak Quercus suber and Holm Oak Quercus rotundifolia dominance had little influence on bird communities though bark-gleaners showed a foraging preference for Cork Oak.

Aims Examine the use of Cork and Holm Oak trees by insectivorous birds in Mediterranean oak woodlands.

Methods Point-counts were used to compare species abundance among Cork Oak-dominated, Holm Oak-dominated and mixed woodlands. Focal foraging observations were used to evaluate the use of Cork and Holm Oaks in the three habitats and to relate tree characteristics with the foraging time of foliage- and bark-gleaners.

Results Bird densities in the three habitats were not different for most foliage- and bark-gleaners. Tree preference index values and foraging time per tree showed no significant differences between tree species and foraging guilds, however bark-gleaners had positive index values for Cork Oak in the three habitats. The foraging time of foliage- and bark-gleaners on both tree species showed a positive relationship with characteristics associated with arthropod abundance.

Conclusion Cork and Holm Oak trees are equally preferred by foliage-gleaners but bark-gleaners moderately preferred Cork Oak. Characteristics regarding morphology, phenology and physiological condition of trees can be used to predict habitat quality for insectivorous forest birds in Mediterranean oak woodlands.     

Seasonal dynamics of avian guilds inside and outside core protected areas in an Andean Biosphere Reserve of southern Chile

Capsule: Many protected forests at high elevations show higher endemic biodiversity than unprotected habitats at low elevations. In seasonal ecosystems, however, harsh environmental conditions during winter may force individuals to move from protected forests to unprotected degraded forests in lowlands.

Aims: To examine how forest types and seasons affect avian diversity and habitat-use guilds in protected and unprotected forests.

Methods: Habitat and seasonal avian surveys were conducted to test forest type and seasonal differences on avian species richness, relative abundances and relative abundance of habitat-use guilds.

Results: Twenty-three avian species (～40% endemics) were recorded. Highland old growth forests showed the highest richness (4.1–4.9 species/point count). The lowest richness was recorded in mid-elevation secondary forests (3.1 species/point count). The highest relative abundances for habitat-specialist understorey users and large tree users were recorded in highland old growth forests. However, the abundance of large tree users was higher in secondary forests at low elevations during colder seasons.

Conclusions: Some species and guilds may move to lower elevations outside protected areas during winter. Increasing degradation of unprotected areas will likely affect the suitability of ‘winter habitat’ for specialist guilds, and thus the ecological processes and source/sink dynamics occurring across boundaries of protected and unprotected areas.     

Use of materials in nest construction by Pied Flycatchers Ficedula hypoleuca reflects localized habitat and geographical location

Capsule: Pied Flycatchers Ficedula hypoleuca use different materials to construct their nests according to local availability and geographical location.

Aims: This study tested the hypotheses that Pied Flycatcher nests were constructed from the leaves of different tree species in proportion to their occurrence within the breeding territories and that nest composition varied between geographical locations.

Methods: In Lancashire, Pied Flycatcher nests were collected from nestboxes built in locations dominated by different tree species and were deconstructed to determine which materials were used.

Results: The leaves found in nests generally reflected their availability within the locality of the territories rather than showing evidence of selective use of some leaf species. However, the use of moss was dominated by the use of one species in all but two nests. Nests from Lancashire were significantly different in composition when compared with published data for nests from north Wales and central Spain.

Conclusion: Pied Flycatchers exhibit plasticity in nest construction behaviour because they were opportunistic in their choice of most leaves as nesting materials, although they may be selective in their choice of moss.     

Supercritical Fluid Extraction of a Light PAH Contaminated Sand

This work was aimed at evaluating the feasibility of a remediation treatment performed by means of a supercritical carbon dioxide extraction on a sandy soil recently contaminated by light polycyclic aromatic hydrocarbons.

The soil utilized in this study was artificially contaminated by naphthalene and anthracene. The artificial contamination process was intended to simulate a recent accidental spillage of hydrocarbon fuels.

Several extractions, aimed at singling out the operating parameters (pressure, temperature, supercritical fluid mass flow rate) that are able to obtain the residual required concentration (50 mg/kg dry soil) in the shortest time, were carried out on a on-purpose made system.

The best extraction conditions were 120 bar and 40°C for a naphthalene contaminated soil and 200 bar and 80–100°C for an anthracene contaminated soil.

The results obtained in the experimental tests made it possible to build an analytical model able to correlate, for the given soil, the extraction length to the operating parameters such as supercritical fluid density, temperature and mass flow rate.

In order to evaluate the economic feasibility of the process, a unit treatment cost was evaluated for the case of an extraction carried out in a 10 m³ reactor in the presence of the best extraction conditions that were previously determined. The extraction unit cost was therefore equal to 35 000–65 000 €/t for a soil with a starting contaminant concentration equal to 1000 mg/kg of dry soil.     

Environment is more relevant than spatial structure as a driver of regional variation in tropical tree community richness and composition

Background: Understanding how factors related to environment and geographical distance explain community variation allows insights about how ecological niche and neutral processes control tropical community assembly.

Aims: Quantify how variation in regional tree community richness and composition in a humid tropical forest across a mountain chain are related to niche and putative neutral processes.

Methods: We used a variation partitioning routine based on Redundancy Analysis to model tropical tree community richness and composition within three distinct elevation belts, as a function of environment and spatial structure, using data from 32 studies in the Serra do Mar Range, south-eastern Brazil.

Results: Environmental effects were greater than spatial structure effects to explain community variation in the three elevation belts. There was a trend of decreasing spatial structure effects while environmental effects remained constant from lower to higher elevations. Patterns were congruent for species richness and composition.

Conclusions: We suggest that on tropical mountains, niche-related processes are equally relevant for tropical forest community assembly at all elevations, while neutral processes become weaker towards higher elevations. Determining if this trend is a consequence of the greater heterogeneity of environmental conditions associated with higher elevations in tropical mountainous terrain remains an important area of research.     

Bioremediation of oil‐contaminated soil in Kuwait. I. landfarming to remediate oil‐contaminated soil

During the Gulf Crisis, the State of Kuwait was subjected to hazards caused by the oil well fires. The discharged oil formed over 300 oil lakes, covering land areas in excess of 49 km². In addition, deposits from aerial fallout covered massive areas of Kuwait's desert soil. It has been widely recognized that the heavily oil‐contaminated soil must be remediated in order to avoid total damage to the land, water ecosystems, and/or the eventual release of hazardous particulate compositions to the atmosphere. A large number of diverse technological options were being considered for the remediation of contaminated soil. Bioremediation techniques involving enhanced landfarming was selected and evaluated at pilot scale

The experiments were initiated in November 1992 at the Burgan oil field in which 16 landfarming plots of 120 m² each were constructed. The study continued for 18 months, during which time petroleum hydrocarbon concentration, polycyclic aromatic hydrocarbon (PAH), and heavy metals were monitored regularly. The result obtained showed that landfarming treatment resulted in more than 80% reduction of oil contamination within 15 months. The treatment also resulted in a substantial reduction of the PAHs concentrations.     

From evergreen to deciduous tropical forests: how energy–water balance,temperature, and space influence the tree species composition in a high diversity region

Background: Understanding floristic and geographic patterns in one of the most biodiverse regions in the world – the Atlantic forest of eastern Bahia, Brazil – can identify the drivers of diversity in tropical forests and provide useful information for biological conservation.

Aims: To understand the role of both climate and geographical location on variation in tree species composition in a region characterised by an abrupt transition from wet forests to semi-arid thorn-woodlands. To test whether a regional classification of forests according to elevation belts and leaf flush pattern is consistent with floristic composition.

Methods: We submitted 14,094 tree species occurrence records and 31 geo-climatic variables prepared for 57 sites in eastern Bahia, Brazil, to multivariate and regression analyses and variance partitioning.

Results: Climate and space were both significantly (P ≤ 0.05) contributing to explaining floristic variations. Actual evapotranspiration, duration of water deficit, and minimum temperature of coldest month were the main predictors. Floristic differences were significant except when comparing evergreen lower plains and upper plains forests.

Conclusions: Although distance among sites may play an important role, species composition is chiefly influenced by environmental gradients. This highlights environmental heterogeneity as a key factor in the planning of biodiversity conservation in tropical forests.     

Importance of soil-water relations in assessing the endpoint of bioremediated soils

This study was conducted to investigate water movement in hydrocarbon contaminated soils. Three soils were studied, a hydrocarbon contaminated soil, the same soil after 3 years of bioremediation, and a control soil from the same site. There was a critical soil water content around 18% (bioremediated soil) and 20% (contaminated soil), above which the sorptivity of the contaminated soil was near that of the control soil. For soils with water contents below this value, there was a strong divergence in sorptivity between contaminated and control or bioremediated soils. Results suggest that water availability in contaminated soils will be highly dependent on soil water properties as water potential approaches the permanent wilting point (-1.5 MPa matrix potential).Infiltration of water into air dry (2% m.c. w/w) hydrocarbon contaminated soils was up to three orders of magnitude slower than for the control soil. For air dried soils, the infiltration rate of the contaminated and bioremediated soils was constant with time. This was in contrast to the control soil where infiltration rate was a function of the reciprocal of the square root of time.     

Epiphytes in human settlements in rural Panama

Background: An ever-increasing proportion of tropical ecosystems are affected by on-going land-use changes, stressing the importance of understanding how organisms cope with biotic and abiotic challenges outside their natural habitat. An important group in the tropics are vascular epiphytes, whose response to human disturbance is poorly understood.

Aims: Creating a baseline data set of epiphyte diversity in human settlements and assessing differences with assemblages of less disturbed habitats.

Methods: We surveyed the vascular epiphyte assemblages in 25 settlements of south-west Panama along a rainfall gradient. We tested how epiphyte assemblages were affected by human disturbance and climate by comparing our data to that of pastures and forest.

Results: Almost half (238 of 499) of all studied trees hosted at least one epiphyte. Altogether, 10,700 epiphytes of 56 species were found. Rainfall strongly affected both composition and diversity of epiphyte assemblages, whereas geographic proximity did not. In settlements, the species pool was considerably smaller than in pastures and undisturbed forest; however, settlements’ diversity was only significantly lower compared to pastures.

Conclusions: Epiphyte assemblages in settlements had a diminished species pool but diversity per tree was comparable to less disturbed habitats. Unsurprisingly, rainfall seems to be the main determinant of epiphyte diversity in rural settlements.     

Validation of a protein panel for the noninvasive detection of recurrent non-muscle invasive bladder cancer

Context: About 50–70% of patients with non-muscle invasive bladder cancer (NMIBC) experience relapse of disease.

Objective: To establish a panel of protein biomarkers incorporated in a multiplexed microarray (BCa chip) and a classifier for diagnosing recurrent NMIBC.

Materials and methods: Urine samples from 45 patients were tested. Diagnostic performance was evaluated by receiver operating characteristic (ROC) analysis.

Results: A multi biomarker panel (ECadh, IL8, MMP9, EN2, VEGF, past recurrences, BCG therapies and stage at diagnosis) was identified yielding an area under the curve of 0.96.

Discussion and conclusion: This biomarker panel represents a potential diagnostic tool for noninvasive diagnosis of recurrent NMIBC.