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Mangroves are complex, unique, and dynamic ecosystems that host organisms that have special physiological adaptations to fluctuations in salinity, temperature, and pH. Gastropods have an important role in the mangrove ecosystem for food cycles and webs by helping to provide nutrients and micro-habitats for microbes. Micro-fungi isolated from mangrove ecosystems are productive sources of enzymes and bioactive compounds such as antibacterial and antifungal. In this study a explored the enzymatic and anti-vibrio activity of fungi associated with the marine gastropod Cerithidea cingulata and Lottia scabra. collected in three mangrove forests in North Sulawesi, Indonesia. The fungi associated with the specimens were inoculated on malt extract agar (MEA) using the tapping method. Enzymatic and anti-vibrio assays were conducted applying the plug method. Positive effects of the fungal compounds on Vibrio were indicated by clear zones formed around the isolates. A total of 13 fungal species were isolated from C. cingulata (19MB-C5 and 19MBa-A4) and L. scabra (19MT-07 and 19MT-18). Most fungal isolates have moderate growth rate. The isolate with highest cellulolytic, proteolytic, and anti-vibriosis activity (Vibrio parahaemolyticus, V. harveyi, V. vulnificus, and V. alginolyticus), derived from C. cingulata 19MB-C5 was closely related to Aspergillus niger, as revealed by molecular analysis using the universal primers ITS1 and ITS4 (similarity value 99%). A. niger 19MB-C5-3 has potential as a bioremediation and anti-vibrio agent that can be applied in aquaculture.

BACKGROUND: A challenge of C2 pedicle screw placement is to avoid penetration into the C1-C2 facet joint, as this may alter normal biomechanics and accelerate joint degeneration. Our objective was to clarify how local anatomy and surgical technique may relate to C2 pedicle screw penetration into the C1-C2 facet joint. METHODS: C2 pedicle screws were inserted using a fluoroscopically assisted freehand technique. Independent fellowship-trained spine surgeons blindly reviewed intraoperative fluoroscopic and postoperative computed tomography (CT) images for evidence of facet joint penetration (FJP). C2 pedicle morphometry, the sagittal angle of the facet joint, axial and sagittal pedicle screw angles, and screw length were measured on the relevant CT images. RESULTS: A total of 34 patients fulfilled the study criteria, and a total of 68 C2 pedicle screws were placed. Eight screws (16%) penetrated the C1-C2 facet joint. The mean sagittal angle of the C1-C2 facet joint was significantly lower in the FJP group compared with the non-FJP group. The mean sagittal angle of the screws was significantly higher in the FJP group compared with the non-FJP group. The mean screw length was significantly greater for screws causing FJP compared with the non-FJP group. The mean axial screw angle was significantly lower in the FJP group compared with the non-FJP group. Pedicle width, length, height, and transverse angle were not significantly associated with FJP. Independent reviewers were able to identify FJP on intraoperative fluoroscopic imaging in 2 out of 8 cases. CONCLUSION: Lower sagittal angle of the facet joint, higher sagittal angle of the pedicle screw, and screw length >24 mm are associated with higher risk of C1-C2 FJP. When placing C2 pedicle screws under these conditions, caution should be taken to avoid FJP. CLINICAL RELEVANCE: Several anatomical and technical factors may increase the risk of C1-C2 FJP during placement of C2 pedicle screws using a fluoroscopically assisted freehand technique, underscoring the importance of preoperative planning and limiting screw length. LEVEL OF EVIDENCE: 3.

Pediatric acute hematogenous osteomyelitis (AHO) outcomes are highly dependent on the disease severity. Recently, the A-SCORE and C-SCORE, were proposed as predictors of an acute complicated course and chronic morbidity, respectively. The purpose of this study was to externally validate the A-SCORE and C-SCORE at a single institution.This IRB-approved retrospective chart review included AHO patients admitted at a tertiary referral hospital between October 1, 2015 and December 31, 2019. The inclusion criteria were ages 0 to 18 and clinical response to treatment. The exclusion criteria were immunocompromised status or penetrating inoculation.The A-SCORE demonstrated an area under the receiver operator curve (ROC area) of86% with regards to all acute complications. It also demonstrated sensitivities85% and specificities92% at the cut-off of 4 (Youden index) for all acute complications. The C-SCORE demonstrated an ROC area of 100% with regards to chronic osteomyelitis. It also demonstrated sensitivities70% and specificities93% for the chronic morbidity variables seen in our population at the cut-off of 3 (Youden index.).These novel composite clinical scores, in combination with clinical judgment, could help guide early care decisions. The A-SCORE and C-SCORE are useful risk stratification tools in the management of pediatric AHO and in predicting acute complicated courses or chronic sequelae of AHO, respectively. These scoring systems, if integrated into standardized pediatric AHO guidelines, can allow clinicians to stratify the AHO population and guide clinical decision making.Level III (prognostic study, retrospective chart review).

Although the diversity in orthopaedic residency programs has been studied, the diversity within academic orthopaedics has not.The board of specialty societies, five leading journals and the National Institutes of Health RePORTER tool, and three accreditation organizations were explored.The board of directors comprised 220 (72%) Caucasians, 36 (12%) Asians, 4 (1%) Hispanic/Latinos, 29 (9%) African Americans, and 18 (6%) Other individuals; 250 (81%) were men, and 57 (19%) were women. The editorial boards comprised 288 (77%) Caucasians, 62 (16%) Asians, 14 (4%) Hispanic/Latinos, 8 (2%) African Americans, and 4 (1%) Other individuals; 341 (91%) were men, and 35 (9%) were women. The National Institutes of Health grant recipients comprised 117 (64%) Caucasians, 58 (32%) Asians, 4 (2%) Hispanic/Latinos, and 3 (2%) African Americans; 128 (70%) were men, and 54 (30%) were women. On average, Caucasians, Asians, Hispanic/Latinos, and African Americans received $776,543, $439,600, $420,182, and $494,049, respectively. On average, men and women received $759,426 and $419,518, respectively. The accreditation boards comprised 45 (82%) Caucasians, 6 (11%) Asians, and 4 (7%) African Americans; 45 (82%) were men, and 10 (18%) were women.Academic orthopaedic surgery does not resemble the United States. Residency, fellowship committees, and professional organization boards need to become aware of these disparities.

Silver nanoparticles (AgNPs) have known anti-microbial properties and therefore have the potential to be used to control fungal plant pathogens. In this study we investigated the growth of a plant pathogenic fungus, Rhizoctonia solani (AG3-PT) in the presence of AgNPs. The effect of AgNPs at two different levels (20 and 50 mg L-1) on hyphal growth and sclerotium production and viability in R. solani was investigated. The results showed that at 20 mg AgNPs L-1 R. solani hyphal growth was reduced along with the production of sclerotia. The results indicate that AgNPs have the potential to control R. solani growth and subsequent development of plant disease symptoms.

Bacteria deploy rearrangement hotspot (Rhs) proteins as toxic effectors against both prokaryotic and eukaryotic target cells. Rhs proteins are characterized by YD-peptide repeats, which fold into a large β-cage structure that encapsulates the C-terminal toxin domain. Here, we show that Rhs effectors are essential for type VI secretion system (T6SS) activity in Enterobacter cloacae (ECL). ECL rhs(−) mutants do not kill Escherichia coli target bacteria and are defective for T6SS-dependent export of hemolysin-coregulated protein (Hcp). The RhsA and RhsB effectors of ECL both contain Pro−Ala−Ala−Arg (PAAR) repeat domains, which bind the β-spike of trimeric valine−glycine repeat protein G (VgrG) and are important for T6SS activity in other bacteria. Truncated RhsA that retains the PAAR domain is capable of forming higher-order, thermostable complexes with VgrG, yet these assemblies fail to restore secretion activity to ∆rhsA ∆rhsB mutants. Full T6SS-1 activity requires Rhs that contains N-terminal transmembrane helices, the PAAR domain, and an intact β-cage. Although ∆rhsA ∆rhsB mutants do not kill target bacteria, time-lapse microscopy reveals that they assemble and fire T6SS contractile sheaths at ∼6% of the frequency of rhs(+) cells. Therefore, Rhs proteins are not strictly required for T6SS assembly, although they greatly increase secretion efficiency. We propose that PAAR and the β-cage provide distinct structures that promote secretion. PAAR is clearly sufficient to stabilize trimeric VgrG, but efficient assembly of T6SS-1 also depends on an intact β-cage. Together, these domains enforce a quality control checkpoint to ensure that VgrG is loaded with toxic cargo before assembling the secretion apparatus.

© Copyright © 2020 Wohlgemuth, Gomes, Singleton, Rawson and Avery. We developed a top-down strategy to characterize an antimicrobial, oxidizing sanitizer, which has diverse proposed applications including surface-sanitization of fresh foods, and with benefits for water resilience. The strategy involved finding quenchers of antimicrobial activity then antimicrobial mode of action, by identifying key chemical reaction partners starting from complex matrices, narrowing down reactivity to specific organic molecules within cells. The sanitizer electrolyzed-water (EW) retained partial fungicidal activity against the food-spoilage fungus Aspergillus niger at high levels of added soils (30–750 mg mL–1), commonly associated with harvested produce. Soil with high organic load (98 mg g–1) gave stronger EW inactivation. Marked inactivation by a complex organics mix (YEPD medium) was linked to its protein-rich components. Addition of pure proteins or amino acids (≤1 mg mL–1) fully suppressed EW activity. Mechanism was interrogated further with the yeast model, corroborating marked suppression of EW action by the amino acid methionine. Pre-culture with methionine increased resistance to EW, sodium hypochlorite, or chlorine-free ozonated water. Overexpression of methionine sulfoxide reductases (which reduce oxidized methionine) protected against EW. Fluoroprobe-based analyses indicated that methionine and cysteine inactivate free chlorine species in EW. Intracellular methionine oxidation can disturb cellular FeS-clusters and we showed that EW treatment impairs FeS-enzyme activity. The study establishes the value of a top-down approach for multi-level characterization of sanitizer efficacy and action. The results reveal proteins and amino acids as key quenchers of EW activity and, among the amino acids, the importance of methionine oxidation and FeS-cluster damage for antimicrobial mode-of-action.

Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences., Graphical abstract Image 1

Shifts in the microbiome of the intertidal coral Coelastrea aspera (formally known as Goniastrea aspera) from Phuket, Thailand were noted over the course of a four day period of spring tides. During this time corals were naturally exposed to high temperatures, intense solar radiation, sub-aerial exposure and tidally-induced water fluxes. Analysis of the 16S microbiome highlighted that the corals harbored both ‘core and/or stable’ communities and those which appeared to be more ‘transient and/or sporadic’. Abundances of the transient or sporadic associates were likely to have been governed by tidally-induced variations in mucus thickness and water fluxes. The core or more stable members may have been key factors in determining coral health, although more research is needed to confirm the exact function they play in this regard. Similar to other studies, strong shifts in the bacterial community were observed, even over the short temporal scale examined here. However, we also show significant differences in the timing of these shifts between the two age-groups of corals studied. More rapid changes (within two days of sub-aerial exposure) occurred within the 4y old colonies, but a slightly delayed response was observed in the 10y old colonies, whereby the microbial associates only changed after 4 days. We hypothesize that these shifts are age related and could be influenced by the observed baseline differences in the microbiome of the 4 and 10 year old corals, bacteria-bacteria interactions, and/or host energetics.

A Delorme's procedure perineal surgical repair was performed in a wild adult male Sumatran orangutan (Pongo abelii) with a chronic persistent rectal prolapse that had been unsuccessfully treated by 6 previous surgeries. The rectal prolapse did not recur, and the orangutan was successfully released to the wild, 6 weeks later.

Listeria monocytogenes is sporadically detected on a range of ready to eat fresh produce lines, such as spinach and rocket, and is a threat to public health. However, little is known about the diversity of L. monocytogenes present on fresh produce and their potential pathogenicity. In this work, fifteen Listeria monocytogenes isolates from the UK fresh produce supply chain were characterised using whole genome sequencing (WGS). Additionally, isolates were characterised based on their ability to form biofilm. Whole genome sequencing data was used to determine the sequence type of isolates based on multi-locus sequence typing (MLST), construct a core single nucleotide polymorphism (SNP) phylogeny and determine the presence of virulence and resistance associated genes. MLST revealed 9 distinct sequence types (STs) spanning 2 lineages (I & II) with one isolate belonging to the ST6 subtype, strains from which have been recently implicated in two large, food-associated L. monocytogenes outbreaks in South Africa and across Europe. Although most of the 15 isolates were different, comparison of core genome SNPs showed 4 pairs of ‘indistinguishable’ strains (< 5 SNPs difference). Virulence profiling revealed that some isolates completely lacked the Listeria pathogenicity island-3 (LIPI-3) amongst other virulence factors. Investigation of the inlA gene showed that no strains in this study contained a premature stop codon (PMSC), an indicator of attenuated virulence. Assessment of biofilm production showed that isolates found in the fresh produce supply chain differ in their ability to form biofilm. This trait is considered important for L. monocytogenes to persist in environments associated with food production and processing. Overall the work indicates that a genetically diverse range of L. monocytogenes strains is present in the UK fresh produce supply chain and the virulence profiles found suggests that at least some of the strains are capable of causing human illness. Interestingly, the presence of some genetically indistinguishable isolates within the 15 isolates examined suggests that cross-contamination in the fresh produce environment does occur. These findings have useful implications in terms of food safety and for informing microbial surveillance programmes in the UK fresh produce supply chain.

Global food security remains one of the most important challenges that needs to be addressed to ensure the increasing demand for food of the fast growing human population is satisfied. Fruits and vegetables comprise an essential component of a healthy balanced diet as they are the major source of both macro- and micronutrients. They are particularly important for communities in developing countries whose nutrition often relies solely on a plant-based diet. Recent advances in agriculture and food processing technologies have facilitated production of fresh, nutritious and safe food for consumers. However, despite the development of sophisticated chemical and physical methods of food and equipment disinfection, fresh-cut produce and fruit juice industry still faces significant economic losses due to microbial spoilage. Furthermore, fresh produce remains an important source of pathogens that have been causing outbreaks of human illness worldwide. This chapter characterizes common spoilage and human pathogenic microorganisms associated with fresh-cut produce and fruit juice products, and discusses the methods and technology that have been developed and utilized over the years to combat them. Substantial attention is given to highlight advantages and disadvantages of using these methods to reduce microbial spoilage and their efficacy to eliminate human pathogenic microbes associated with consumption of fresh-cut produce and fruit juice products.

Fungi threaten the security of food supply to human populations on several fronts. They destroy up to 30 % of crop products through disease and spoilage processes, while mycotoxin-producing fungi and opportunistic pathogens endanger food safety. Control of these fungi is vital for improving food security, but current measures are inadequate and further challenges due to human-population growth and climate change are escalating. Investment and innovation in research on strategies to control fungal growth, harnessed through international, inter-disciplinary collaboration across socio-economic boundaries, provides one key to rising to this challenge.

Global food security remains one of the most important challenges that needs to be addressed to ensure the increasing demand for food of the fast growing human population is satisfied. Fruits and vegetables comprise an essential component of a healthy balanced diet as they are the major source of both macro- and micronutrients. They are particularly important for communities in developing countries whose nutrition often relies solely on a plant-based diet. Recent advances in agriculture and food processing technologies have facilitated production of fresh, nutritious and safe food for consumers. However, despite the development of sophisticated chemical and physical methods of food and equipment disinfection, fresh-cut produce and fruit juice industry still faces significant economic losses due to microbial spoilage. Furthermore, fresh produce remains an important source of pathogens that have been causing outbreaks of human illness worldwide. This chapter characterizes common spoilage and human pathogenic microorganisms associated with fresh-cut produce and fruit juice products, and discusses the methods and technology that have been developed and utilized over the years to combat them. Substantial attention is given to highlight advantages and disadvantages of using these methods to reduce microbial spoilage and their efficacy to eliminate human pathogenic microbes associated with consumption of fresh-cut produce and fruit juice products.

Fresh leafy produce, such as lettuce and coriander, are subject to post-harvest microbial contamination and decay. Because of increasing pesticide resistance and consumer pressures, alternative residue-free treatments, such as ozone, are being actively explored and encouraged to reduce microbial loads and curb spoilage of crops in storage/transit. However, several researchers have reported that a component of the bacterial population on leaf surfaces is resistant to ozone treatment. To investigate the potential reasons for this bacterial survival, confocal microscopy was used to visualise microbes on leaf surfaces before and after ozone treatment. Direct observation (live/dead cell staining) of cells after ozone exposure showed that some cells were still alive; this included cells in small colonies as well as individual cells. We hypothesised that cell (colony) age and prior stress (cold) contributes to, or is responsible for, the ozone resistance observed. Interestingly, cells derived from older agar-grown colonies (7–12-day-old) and cold stressed cells of a Pseudomonas sp. (isolated from coriander) showed higher ozone resistance than that of control cells (4-day-old colonies). These findings suggest that a range of factors are responsible for ozone resistance and further work to improve our understanding of the mechanisms of ozone resistance may lead to improved methods to reduce microbial spoilage of fresh produce.

Silver nanoparticles (AgNPs) are widely used in industry due to their anti-microbial properties. Despite of its beneficial, they may potentially affect the activity of beneficial soil microorganisms. Trichoderma harzianum was used in this to investigate the effect of AgNPs on beneficial soil fungi. Colony diameter and spore production of T. harzianum were observed in the presence of three levels of AgNPs (200, 600, 1000 mg L−1) in growth media. The results showed that the application of AgNPs at high levels reduced colony diameter and spore production of the tested fungi. The findings indicate that AgNPs have the potential to damage beneficial soil fungi.

Listeria monocytogenes is an intracellular human pathogen which enters the body through contaminated food stuffs and is known to contaminate fresh leafy produce such as spinach, lettuce and rocket. Routinely, fresh leafy produce is grown and processed on a large scale before reaching the consumer through various products such as sandwiches and prepared salads. From farm to fork, the fresh leafy produce supply chain (FLPSC) is complex and contains a diverse range of environments where L. monocytogenes is sporadically detected during routine sampling of produce and processing areas. This review describes sources of the bacteria in the FLPSC and outlines the physiological and molecular mechanisms behind its survival in the different environments associated with growing and processing fresh produce. Finally, current methods of source tracking the bacteria in the context of the food supply chain are discussed with emphasis on how these methods can provide additional, valuable information on the risk that L. monocytogenes isolates pose to the consumer.

The first International Peat Congress (IPC) held in the tropics – in Kuching (Malaysia) – brought together over 1000 international peatland scientists and industrial partners from across the world (“International Peat Congress with over 1000 participants!,” 2016). The congress covered all aspects of peatland ecosystems and their management, with a strong focus on the environmental, societal and economic challenges associated with contemporary large-scale agricultural conversion of tropical peat.

This work was financially supported by University of Zurich (UZH) Forschungskredit grants FK-10 (M.P.M.-G.), FK-15-103 (A. Nater), and FK-14-094 (T.B.S.), Swiss National Science Foundation grant 3100A-116848 (M.K.and C.P.v.S.), the Leakey Foundation (M.P.M.-G.), the A.H. Schultz Foundation (M.K. and M.P.M.-G.), UZH Research Priority Program “Evolution in Action” (M.K.), Arcus Foundation grant G-PGM-1411-1112 (E.M.), Australian National University (ANU) research fund (A. Nurcahyo), an ANU Vice Chancellor Travel Grant (A. Nurcahyo), Australia Awards Scholarship-DFAT (A. Nurcahyo), ERC Starting Grant 260372 (T.M.-B.), EMBOYIP 2013 (T.M.-B.), MINECOBFU2014-55090-P, BFU2015-7116-ERC, BFU2015-6215-ERCU01, and MH106874 (T.M.-B.), Fundacio Zoo Barcelona (T.M.-B.), Julius–Klaus Foundation (M.K.), MINECO/FEDERBFU2016-77961-P (J.B. and M.P.), Gates Cambridge Trust (T.D.), and the Department of Anthropology at the University of Zurich. Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. Postprint

Current non-invasive biomonitoring techniques to measure heavy metal exposure in free ranging birds using eggs, feathers and guano are problematic because essential metals copper (Cu) and zinc (Zn) deposited in eggs and feathers are under physiological control, feathers accumulate metals from surface contamination and guano may contain faecal metals of mixed bioavailability. This paper reports a new technique of measuring lead (Pb), Cu and Zn in avian urate spheres (AUS), the solid component of avian urine. These metal levels in AUS (theoretically representing the level of metal taken into the bloodstream, i.e. bioavailable to birds) were compared with levels in eggs (yolk and shell), feathers and whole guano from chickens (Gallus gallus domesticus) exposed to a heavy metal-contaminated soil (an allotment soil containing Pb 555 mg kg−1 dry mass (dm), Cu 273 mg kg−1 dm and Zn 827 mg kg−1 dm). The median metal levels (n = 2) in AUS from chickens exposed to this contaminated soil were Pb 208 μg g−1 uric acid, Cu 66 μg g−1 uric acid and Zn: 526 μg g−1 uric acid. Lead concentrations in egg yolk and shell samples (n = 3) were below the limit of detection (

In this study, three different soils with contrasting features, spiked with 300 mg benzo[a]pyrene (BaP)/kg dry soil, were incubated at 20 °C and 60% water holding capacity for 540 days. At different time points, BaP and DNA were extracted and quantified, and DNA adducts were quantified by 32P-postlabelling. After 540 days incubation, 69.3, 81.6 and 83.2% of initial BaP added remained in Cruden Bay, Boyndie and Insch soils, respectively. Meanwhile, a significantly different amount of DNA–BaP adducts were found in the three soils exposed to BaP over time. The work demonstrates the concept that DNA adducts can be detected on DNA extracted from soil. Results suggest the technique is not able to directly reflect bioavailability of BaP transformation products. However, this new method provides a potential way to detect mutagenic compounds in contaminated soil and to assess the outcomes of soil remediation.

Tomato fruit (Lycopersicon esculentum L.) were exposed to ozone concentrations between 0.005 (control) and 5.0 μmol mol-1 up to 13 days at 13 °C, prior to, or following, inoculation by Alternaria alternata or Colletotrichum coccodes (causes of black spot and anthracnose, respectively). Low-level atmospheric ozone-enrichment resulted in a modest, but statistically significant, reduction in fungal lesion development; higher concentrations of the gas resulting in greater effects. This finding implies concentration-specific impacts on fungal lesion development. A fluorescent lection assay revealed that the ozone-induced inhibition of visible lesion development was reflected in a similar reduction in fungal biomass below the fruit surface. Fungal spore production in vivo, was markedly reduced when fruit were stored in an ozone-enriched atmosphere. Higher concentrations/duration of exposure resulted in greater reduction in spore production, with considerable benefits resulting from exposure to low levels of ozone (i.e. below the 0.2 μmol mol-1 European threshold used for the protection of human health). In vitro, effects of ozone on spore germination depended on concentration and duration of exposure. Studies performed on fungi exposed to ozone on Potato Dextrose Agar at 13 °C and 95% relative humidity revealed no major effects on the growth of mycelia, implying the observed suppression of pathogen development was due in part to ozone-induced changes in fruit-pathogen interactions. © 2007 Elsevier B.V. All rights reserved.

Tomato fruit (Lycopersicon esculentum L. cv. Carousel) were exposed to ozone concentrations ranging between 0.005 (controls) and 1.0 μmol mol−1 at 13 °C and 95% RH. Quality-related attributes and organoleptic characteristics were examined during and following ozone treatment. Levels of soluble sugars (glucose, fructose) were maintained in ozone-treated fruit following transfer to ‘clean air’, and a transient increase in β-carotene, lutein and lycopene content was observed in ozone-treated fruit, though the effect was not sustained. Ozone-enrichment also maintained fruit firmness in comparison with fruit stored in ‘clean air’. Ozone-treatment did not affect fruit weight loss, antioxidant status, CO2/H2O exchange, ethylene production or organic acid, vitamin C (pulp and seed) and total phenolic content. Panel trials (employing choice tests, based on both appearance and sensory evaluation) revealed an overwhelming preference for fruit subject to low-level ozone-enrichment (0.15 μmol mol−1), with the effect persisting following packaging.

Tomatoes, strawberries, table grapes and plums were inoculated with Botrytis cinerea (grey mould), transferred to chilled storage (13 °C) and exposed to 'clean air' or low-level ozone-enrichment (0.1 μmol mol-1). Ozone-enrichment resulted in a substantial decline in spore production as well as visible lesion development in all treated fruit. Exposure-response studies performed specifically on tomato fruit (exposed to concentrations ranging between 0.005 and 5.0 μmol mol-1 ozone) revealed lesion development and spore production/viability to be markedly reduced in produce exposed to ozone prior to, or following, infection with B. cinerea; higher concentrations/duration of exposure yielding greater reductions in lesion development and spore production/viability. Impacts on Botrytis colonies grown on Potato Dextrose Agar (PDA) for 5-6 days at 13 °C and 95% relative humidity (RH) revealed less effects than studies on fruit inoculated with the pathogen in vivo. Taken as a whole, the results imply that ozone-induced suppression of pathogen development is due, to some extent, to impacts on fruit-pathogen interactions. This work suggests that ozone may constitute a desirable and effective residue-free alternative to traditional postharvest fungicide practices. Data presented illustrate that optimal ozone treatment regimes are likely to be commodity-specific and require detailed investigation before such practices can be contemplated commercially. © 2006 Elsevier B.V. All rights reserved.

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.

A study of soil polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F) concentrations was undertaken in the vicinity of a municipal solid waste incinerator (MSWI) in Newcastle upon Tyne as a result of concerns raised by local residents about potential contamination from fugitive and stack emissions. The study area was divided into four sectors (north-east (NE), south-east (SE), north-west (NW) and south-west (SW)) around the MSWI, and sampling sites were located up to a distance of 2.25 km. Based on air dispersion modelling, the sampling density was four times greater in the NE (downwind) sector compared to the SW (upwind) direction, and twice as great in the NW and SE sectors. PCDD/F concentrations found in soil samples ranged from 6 to 1911 ng I-TEQ/kg DW with a median of 32 ng I-TEQ/kg DW. There was no evidence of elevated concentrations downwind of the MSWI compared to other directions, nor of any trend in concentration at increasing distance from the MSWI. We concluded, therefore, that the MSWI fugitive and stack emissions were not a major source of PCDD/F contamination. Analysis of PCDD/F homologue profiles showed that samples exhibiting furan-dominated and OCDD-dominated profiles and a profile characteristic of the MSWI ash occurred in distinct clusters. Those samples showing the furan-dominated profile had the largest PCDD/F concentrations measured as I-TEQ, followed by samples with the incinerator profile, the deposition profile, and the OCDD-dominated profile. We identified some contamination hotspots located in the SW and SE sampling sectors (upwind of the MSWI), and potential sources for these hotspots were sought by using historic land use data from maps of the locality dating back to 1856. We concluded that the cluster of very high concentrations of PCDD/F in soils showing the furan homologue profile were most likely to have resulted from the disposal of graphite electrode sludges from brine electrolysis carried out at a chemical works between the 1890s and the 1930s.

Manganese is a common contaminant of mine water and other waste waters. Due to its high solubility over a wide pH range, it is notoriously difficult to remove from contaminated waters. Previous systems that effectively remove Mn from mine waters have involved oxidising the soluble Mn(II) species at an elevated pH using substrates such as limestone and dolomites. However it is currently unclear what effect the substrate type has upon abiotic Mn removal compared to biotic removal by in situ micro-organisms (biofilms). In order to investigate the relationship between substrate type, Mn precipitation and the biofilm community, net-alkaline Mn-contaminated mine water was treated in reactors containing one of the pure materials: dolomite, limestone, magnesite and quartzite. Mine water chemistry and Mn removal rates were monitored over a 3-month period in continuous-flow reactors. For all substrates except quartzite, Mn was removed from the mine water during this period, and Mn minerals precipitated in all cases. In addition, the plastic from which the reactor was made played a role in Mn removal. Manganese oxyhydroxides were formed in all the reactors; however, Mn carbonates (specifically kutnahorite) were only identified in the reactors containing quartzite and on the reactor plastic. Magnesium-rich calcites were identified in the dolomite and magnesite reactors, suggesting that the Mg from the substrate minerals may have inhibited Mn carbonate formation. Biofilm community development and composition on all the substrates was also monitored over the 3-month period using denaturing gradient gel electrophoresis (DGGE). The DGGE profiles in all reactors showed no change with time and no difference between substrate types, suggesting that any microbiological effects are independent of mineral substrate. The identification of Mn carbonates in these systems has important implications for the design of Mn treatment systems in that the provision of a carbonate-rich substrate may not be necessary for successful Mn precipitation.

Aims: To study the effect of co-contaminants (phenol) on the biodegradation of pyridine by freely suspended and calcium alginate immobilized bacteria. Methods and Results: Varying concentrations of phenol were added to free and calcium alginate immobilized Pseudomonas putida MK1 (KCTC 12283) to examine the effect of this pollutant on pyridine degradation. When the concentration of phenol reached 0·38 g l−1, pyridine degradation by freely suspended bacteria was inhibited. The increased inhibition with the higher phenol levels was apparent in increased lag times. Pyridine degradation was essentially completely inhibited at 0·5 g l−1 phenol. However, immobilized cells showed tolerance against 0·5 g l−1 phenol and pyridine degradation by immobilized cell could be achieved. Conclusions: This works shows that calcium alginate immobilization of microbial cells can effectively increase the tolerance of P. putida MK1 to phenol and results in increased degradation of pyridine. Significance and Impact of the Study: Treatment of wastewater stream can be negatively affected by the presence of co-pollutants. This work demonstrates the potential of calcium alginate immobilization of microbes to protect cells against compound toxicity resulting in an increase in pollutant degradation.

The potential of using ozone for the removal of phenanthrene from several different soils, both alone and in combination with biodegradation using a microbial inoculant (Pseudomonas alcaligenes PA-10), was examined. The greater the water content of the soil the less effective the ozone treatment, with air-dried soils showing the greatest removal of phenanthrene; while soils with higher levels of clay also reduced the effectiveness of the ozone treatments. However, at least a 50% reduction in phenanthrene levels was achieved in air-dried soil after an ozone treatment of 6 h at 20 ppm, with up to 85% removal of phenanthrene achieved in sandy soils. The biodegradation results indicate that P. alcaligenes PA-10 may be useful as an inoculant for the removal of PAHs from contaminated soils. Under the conditions used in our experiments, however, pre-ozonation did not enhance subsequent biodegradation of phenanthrene in the soils. Similar levels of phenanthrene removal occurred in both non-ozonated and ozonated Cruden Bay soil inoculated with P. alcaligenes PA-10. However, the biodegradation of phenanthrene in ozonated Boyndie soil was much slower. This may be due to the release of toxic products in this soil during ozonation.

Aims: The aim of the present study was to isolate and characterize a bacterium, strain EN3, capable of using diesel oil as a major carbon and energy source, and to analyse the enhancement of diesel oil degradation by this organism using synthetic mycolic acid (2-hexyl-3-hydroxyldecanoic acid). Method and Results: An actinomycete with the ability to degrade diesel oil was isolated from oil contaminated soil and characterized. The strain had phenotypic properties consistent with its classification in the genus Rhodococcus showing a 16S rRNA gene similarity of 99·7% with Rhodococcus baikonurensis DSM 44587T. The ability of the characterized strain to degrade diesel oil at various concentrations (1000, 5000, 10 000 and 20 000 mg l−1) was determined. The effect of synthetic mycolic acid on the biodegradation of diesel oil was investigated at the 20 000 mg l−1 concentration; the surfactant was added to the flask cultures at three different concentrations (10, 50 and 100 mg l−1) and degradation followed over 7 days. Enhanced degradation was found at all three concentrations of the surfactant. In addition, the enhancement of diesel oil degradation by other surfactants was observed. Conclusions: The synthetic mycolic acid has potential for the remediation of petroleum-contaminated sites from both an economic and applied perspective as it can stimulate biodegradation at low concentrations. Significance and Impact of the Study: This study showed that the synthesized mycolic acid can be used for potential applications in the bioremediation industries, for example, in oil spill clean-up, diesel fuel remediation and biostimulation.

Benzo[a]pyrene (BaP) is a significant environmental pollutant and rapid, accurate methods to quantify this compound in soil for both research and environmental investigation purposes are required. In this work, solvent extracts from five contrasting soils spiked with four different polycyclic aromatic hydrocarbons (PAHs) were rapidly analysed by using a synchronous fluorescence spectroscopy (SFS) method. The SFS method was validated using HPLC with ultraviolet detection. A good correlation for the quantification of BaP in soil extracts by the two methods was observed. The detection limit of the SFS method was 1.6 x 10(-9) g/ml in CTAB micellar medium (7.8 mmol/l). The work demonstrates that SFS has potential as a sensitive, accurate, rapid, simple and economic methodology and an efficient alternative to HPLC for fast confirmation and quantification of BaP in complex soil extracts.

Polycyclic aromatic hydrocarbons (PAHs) are a class of organic compounds that have accumulated in the natural environment mainly as a result of anthropogenic activities such as the combustion of fossil fuels. Interest has surrounded the occurrence and distribution of PAHs for many decadesdue to their potentially harmful effects to human health. This concern has promptedresearchers to address ways to detoxify/remove these organic compounds from the natural environment. Bioremediation is one approach that has been used to remediate contaminated land and waters, and promotes the natural attenuation of the contaminants using the in situ microbial community of the site. This review discusses the variety of fungi and bacteria that are capable of these transformations, describes the major aerobic and anaerobic breakdown pathways, and highlights some of the bioremediation technologies that are currently available.  2005 Society of Chemical Industry

DDT [1,1,1-trichloro-2,2-bis (p-chlorophenyl) ethane] is a major environmental pollutant and economical methods to remove DDT from the environment are required. In this work we used seaweed (dried and ground) to enhance DDT transformation in waterlogged soils. Initial daily rates of DDT biodegradation increased in the following order relating to the percentage by weight of added seaweed to soil 0.5 > 1 > 0 > 3 > 5 > 13 (w/w). The actual percentages of DDT biodegradation occurring within 6 weeks were 80, 64, 60, 50, 40 and 34 respectively. During soil incubation DDD [1,1,1-trichloro-2,2-bis (p-chlorophenyl) ethane] was the major metabolite found with small amounts of DDE [1,1,1-trichloro-2,2-bis (p-chlorophenyl) ethane] produced. The maximum amount of 4,4′-dichlorobenzophenone (DBP) (2.5%) produced was found in soil amended with 0.5% (w/w) seaweed, indicating that further degradation of DDD occurred. High levels of dissolved organic carbon (DOC), between 309 and 509 mg kg−1 soil, were present in soil amended with 3–13% (w/w) seaweed immediately after seaweed addition. It is possible that the high levels of DOC in soils amended with larger amounts of seaweed significantly retarded DDT biodegradation, possibly due to binding of DDT to DOC and subsequently decreasing the bioavailability of DDT to soil microbes. Copyright © 2004 Society of Chemical Industry

This study was conducted to assess whether the addition of exogenous nutrients and bioaugmentation by arsenic (As) methylating fungi could accelerate the rate of As volatilisation in cattle dip soils containing mixed As and DDT contamination. Increasing levels of manure application resulted in a greater loss of As from contaminated soils [30% (w/w) > 15% (w/w) > 5% (w/w) manure]. Loss of As was more pronounced at 75% of field capacity than at 35% of field capacity. The supplement of 30% (w/w) manure at 75% field capacity exerted the greatest reduction of As (8.3% loss of total As) in a contaminated dip soil containing 1390 mg As kg −1 and 194 mg DDT kg −1 over a 5-month incubation. The rates of As loss and microbial respiration (CO 2 production) were correlated with the levels of manure amendment ( P ≤0.05). Augmentation by As methylating fungi ( Penicillium sp. and Ulocladium sp.) was able to enhance arsine evolution rates in field contaminated soils and in freshly spiked soils. The amounts of arsine dissipated in augmented long-term contaminated soils and soils spiked with As alone were 3.7 and 8.3 orders of magnitude greater than uninoculated soils, respectively. DDT appears to inhibit the rates of microbial formation of arsine in the contaminated dip soils.

In order to design effective conservation measures for the orangutan, accurate information on their distribution and densities are needed. Nest counts along line transects allow for fairly accurate assessment of orangutan density. However, large sample sizes are needed to obtain accurate estimations of the decay rate of nests, preventing a rapid estimate. Moreover, due to the structure of tropical forests, nest numbers above and near the trail are underestimated. In this study, a rapid assessment method for the estimation of orangutan density is developed, allowing for the estimation of density with a single survey. Procedures are provided for estimating a correction factor which adjusts for underestimating nest numbers near the transect trail. Furthermore, we provide a shortcut to rapidly assess nest decay rate without the need for consecutive surveys. Finally, recommendations are made for determining orangutan density using two different techniques. These techniques incorporate correction factors and a shortcut to accurately assess orangutan density with only one or two visits to an area.

This work examined the effect of long-term arsenic (As) and DDT contamination on soil microbial properties at 11 cattle dip sites in northern New South Wales, Australia. Total As in the surface (0-10 cm) soils from these sites ranged from 34 to 2941 mg As kg(-1) soil and hexane-extractable DDT concentrations ranged between 2.9 and 7673 mg DDT kg(-1) soil. The concentrations of water and oxalate-extractable As were positively correlated with total As. Oxalate-extractable As was more strongly correlated (r(2)=0.87) with total As than water-extractable As (r(2)=0.34). A weak positive relationship was observed between the level of nutrient (organic carbon and nitrogen) and microbial biomass C (r(2)=0.61 and 0.45, respectively). There was a highly significant difference between the microbial properties of polluted and unpolluted sites (P0.001). In comparison to unpolluted soils, fungal counts, microbial biomass C, and respiration were dramatically reduced (P0.05) in polluted soils. However, the bacterial population between polluted and unpolluted soils were not different (P0.05). The results of this study suggested that (a) long-term contamination of soils adjacent to former cattle dipping sites by As and DDT adversely affected soil microbial properties with the fungal populations being the most sensitive and (b) there was little regeneration of microbiota despite 25 years of field ageing of the soils.

Soil metal contamination is an international problem and there is a recognised need for methods to detect the effects of such pollution. To this end, we investigated the use of soil protein extraction, quantification and expression as indicators of cadmium contamination of soil. A variety of methods to extract total soil protein were examined and the effects of cadmium and lime treatment on total soil protein, protein expression and microbial biomass were determined. A simple snap freeze protein extraction technique (using liquid nitrogen) was found to extract the most protein from soil samples compared to a bead beating method used commonly for DNA extraction from soil. Using the snap freeze method, cadmium (Cd) contamination was observed to significantly decrease total soil protein levels compared to an uncontaminated control soil (16 μg g−1 cf. 24 μg g−1) whilst liming significantly increased total soil protein in the control and contaminated treatments (35 and 22 μg g−1). These results were related to similar, but less pronounced, changes in microbial biomass in Cd contaminated and limed control soils. Limed Cd contaminated soils had similar amounts of total soil protein to unlimed control soils. The protein profiles (SDS-PAGE) of extracted soil protein from control and cadmium contaminated soils concentrated by both acetone precipitation and heating showed no obvious changes in protein expression between treatments. However, large amounts of presumably low molecular weight proteins (