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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.

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.

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.

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.

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

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.

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.

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.

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.

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 (

Geographic variation in some aspects of chimpanzee behavior has been interpreted as evidence for culture. Here we document similar geographic variation in orangutan behaviors. Moreover, as expected under a cultural interpretation, we find a correlation between geographic distance and cultural difference, a correlation between the abundance of opportunities for social learning and the size of the local cultural repertoire, and no effect of habitat on the content of culture. Hence, great-ape cultures exist, and may have done so for at least 14 million years.

Ammonia-oxidizer numbers decreased under conditions of moisture limitation in litter, fermentation and humus layers of forest soil in the field, but the extent of regrowth after rehydration varied between layers. Nitrosospira 16S rRNA genes were amplified from all layers, regardless of moisture content or soil pH which varied between 4.1 and 5.2. Nitrosomonas spp. were detected less often, but appeared to exhibit more rapid recovery than the Nitrosospira spp. when drought conditions were relieved by rainfall.

To unravel the mechanism by which low level atmospheric ozone-enrichment (0.05 μmol mol −1 ) increases the shelf-life of tomato fruit ( Lycopersicon esculentum Mill.) by suppressing the growth of pathogens ( Botrytis cinerea ), protein yield and composition were examined during and following exposure to the gas at 13 °C/95% RH. Ozone-enrichment caused marked changes in protein yield and composition in control tomato fruit and suppressed shifts in the proteome induced by wounding/fungal attack. Wound/fungal-inoculation with B. cinerea resulted in a 7% increase in protein yield, and the down-regulation of at least 32 proteins. A number of proteins affected under ozone and wound/fungal-inoculation treatments are involved in the control of cellular oxidative status. Proteins that may be enhanced under oxidative stress were induced during ozone exposure (e.g. thioredoxin peroxidase-TPX), but suppressed following transfer to ‘clean air’ (e.g. ascorbate peroxidase-APX1). Constitutively-expressed proteins tended to increase reversibly under ozone-treatment, however proteins involved in ripening such as an enzyme related to ethylene biosynthesis (1-aminocyclopropane-1-carboxylate oxidase-ACO) were markedly reduced in ozone-treated tomato fruit but increased in wound-inoculated fruit. Levels of proteins involved in carbohydrate metabolism, pentose phosphate pathway, terpenoid and flavonoid biosynthesis differentiated among the treatments. The presented dataset makes a central contribution to a comprehensive analysis of the manner in which tomato fruit react to ozone-enrichment and/or pathogen infection during storage/transit.

Three strains ofSaccharomyces cerevisiae and one strain of aCandida sp. obtained from different industrial sources were screened for uptake of silver and copper. Considerable differences in metal uptake capacities were found between the different strains ofS. cerevisiae and betweenS. cerevisiae and theCandida sp. used. Copper uptake capacities ranged from 0.05 mmol g−1 dry wt to 0.184 mmol g−1 dry wt while values of 0.034 mmol Ag g−1 dry wt and 0.193 mmol Ag g−1 dry wt biomass were observed. Use of ion-selective electrodes (ISEs) enabled the detection of copper complexing agents (possibly proteins and carbohydrates) released by yeasts into the surrounding medium. In contrast, these compounds had no silver complexation abilities. Langmuir and Scatchard transformations of metal adsorption isotherms suggested differences in the mechanisms involved in metal uptake by the various yeasts. The differences between strains ofS. cerevisiae were due possibly to differences in cell wal composition. Different methods of preparation of biomass (fresh, air, oven and freeze-dried) had little effect on metal uptake in comparison with fresh biomass. Storage of fresh waste biomass at 4°C for 20 days had no effect on metal biosorption capacities. It was also observed that individual batches of waste biomass produced from different fermentation runs had consistent metal uptake capacities. The implications of the above results on the use of waste yeast biomass for treatment of metal-containing effluents are discussed.

SummaryAnimal cultures are controversial [1, 2] because the method used to isolate culture in animals aims at excluding genetic and environmental influences rather than demonstrating social learning [3, 4]. Here, we analyzed these factors in parallel in captivity to determine their influences on tool use. We exposed Sumatran orangutan (Pongo abelii) orphans from tool-using and non-tool-using regions (western swamps and eastern Langkat, respectively) that differed in both genetic [5] and cultural [6] backgrounds to a raking task and a honey-dipping task [7, 8] to assess their understanding of stick use. Orangutans from both regions were equally successful in raking; however, swamp orangutans were more successful than Langkat orangutans in honey dipping, where previously acquired knowledge was required. A larger analysis suggested that the Alas River could constitute a geographical barrier to the spread of this cultural trait [9]. Finally, honey-dipping individuals were on average less than 4 years old, but this behavior is not observed in the wild before 6 years of age. Our results suggest first that genetic differences between wild Sumatran populations cannot explain their differences in stick use; however, their performances in honey dipping support a cultural differentiation in stick knowledge. Second, the results suggest that the honey-dippers were too young when arriving at the quarantine center to have possibly mastered the behavior in the wild individually [10], suggesting that they arrived with preestablished mental representations of stick use or, simply put, “cultural ideas.”

The aim of this study was to determine if ozone exposure could prevent spoilage in tomato fruit by fungal infection and to explore concomitant changes in expression of genes involved in signal transduction (ethylene, jasmonic acid and C 6 -aldehydes) and defence-related (chitinases, glucanases and defensin) pathways. Tomato fruit ( Lycopersicon esculentum Mill. cv. Mareta) were exposed to low-level ozone enrichment (0.05 μmol mol −1 ) for up to 6 days and then wounded and/or inoculated with Botrytis cinerea (grey mould) and transferred for one or two weeks’ post-fumigation exposure to ‘clean’ (i.e. Charcoal/Purafil ® -filtered) air in chilled storage (13 °C). Control fruit were maintained throughout in ‘clean’ air. Pre-exposure to ozone resulted in a marked reduction in lesion development when fruit were subsequently wounded and inoculated with a mycelial plug. Tomato fruit subjected to ozone-enrichment not only showed enhanced protection against fungal infection, but also retained firmness in comparison with fruit maintained in ‘clean’ air. Ozone treatment resulted in strong inhibition of expression of both signal transduction (1-aminocyclopropane-1-carboxylic acid oxidase, allene oxide synthase and hydroperoxide lyase), and defence-related (acidic chitinase, basic chitinase, acidic glucanase, basic glucanase, plant defensin) genes, and the pattern of change was consistent with suppression of fungal growth. Overall, ozone exposure would appear to enhance tomato resistance to B. cinerea infection and has potential commercial applications.

The Southeast Asian Sunda archipelago harbors a rich biodiversity with a substantial proportion of endemic species. The evolutionary history of these species has been drastically influenced by environmental forces, such as fluctuating sea levels, climatic changes, and severe volcanic activities. Orangutans (genus: Pongo), the only Asian great apes, are well suited to study the relative impact of these forces due to their well-documented behavioral ecology, strict habitat requirements, and exceptionally slow life history. We investigated the phylogeographic patterns and evolutionary history of orangutans in the light of the complex geological and climatic history of the Sunda archipelago. Our study is based on the most extensive genetic sampling to date, covering the entire range of extant orangutan populations. Using data from three mitochondrial DNA (mtDNA) genes from 112 wild orangutans, we show that Sumatran orangutans, Pongo abelii, are paraphyletic with respect to Bornean orangutans (P. pygmaeus), the only other currently recognized species within this genus. The deepest split in the mtDNA phylogeny of orangutans occurs across the Toba caldera in northern Sumatra and, not as expected, between both islands. Until the recent past, the Toba region has experienced extensive volcanic activity, which has shaped the current phylogeographic patterns. Like their Bornean counterparts, Sumatran orangutans exhibit a strong, yet previously undocumented structuring into four geographical clusters. However, with 3.50 Ma, the Sumatran haplotypes have a much older coalescence than their Bornean counterparts (178 kya). In sharp contrast to the mtDNA data, 18 Y-chromosomal polymorphisms show a much more recent coalescence within Sumatra compared with Borneo. Moreover, the deep geographic structure evident in mtDNA is not reflected in the male population history, strongly suggesting male-biased dispersal. We conclude that volcanic activities have played an important role in the evolutionary history of orangutans and potentially of many other forest-dwelling Sundaland species. Furthermore, we demonstrate that a strong sex bias in dispersal can lead to conflicting patterns in uniparentally inherited markers even at a genus-wide scale, highlighting the need for a combined usage of maternally and paternally inherited marker systems in phylogenetic studies.

Deforestation rates in Sumatra are amongst the highest in the tropics. Lowland forests, which support the highest densities of orangutans, are particularly vulnerable to clearance and fragmentation because they are highly accessible. Consequently, many orangutans will, in the future, live in strictly or partially isolated populations. Whilst orangutans have been extensively studied in primary forests, their response to living in human-dominated landscapes remains poorly known, despite it being essential for their future management. Here, we focus on an isolated group of critically endangered Sumatran orangutans (Pongo abelii) that co-exist with farmers in a mixed agroforest system consisting of degraded natural forest, smallholder (predominantly rubber) farms and oil palm plantations. Over 24 months we conducted the first ever spatial assessment of orangutan habitat use in the human-transformed landscape of Batang Serangan, North Sumatra. From 1,204 independent crop-raiding incidents recorded, orangutans showed strong foraging preference for mixed farmland/degraded forest habitat over oil palm patches. The core home range areas of the eight adult orangutans encompassed only 14% of the available study area. Monthly home range sizes averaged 423 ha (±139, SD) for males, and 131 ± 46 ha for females, and were positively influenced by wild and cultivated fruit presence, and by crop consumption. The average daily distance travelled was similar for both adult males (868 m ± 350, SD) and females (866 m ± 195), but increased when orangutans raided crops. These findings show that orangutans can survive, demographically, in certain types of degraded landscapes, foraging on a mixture of crops and wild fruits. However, the poor quality habitat offered to orangutans by oil palm plantations, in terms of low food availability and as a barrier to female movements, is cause for concern since this is the land use type that is most rapidly replacing the preferred forest habitat across both Sumatran and Bornean orangutan ranges.

Selenate reductase (SER) from Thauera selenatis is a periplasmic enzyme that has been classified as a type II molybdoenzyme. The enzyme comprises three subunits SerABC, where SerC is an unusual b-heme cytochrome. In the present work the spectropotentiometric characterization of the SerC component and the identification of redox partners to SER are reported. The mid-point redox potential of the b-heme was determined by optical titration (E(m) + 234 +/- 10 mV). A profile of periplasmic c-type cytochromes expressed in T. selenatis under selenate respiring conditions was undertaken. Two c-type cytochromes were purified ( approximately 24 and approximately 6 kDa), and the 24-kDa protein (cytc-Ts4) was shown to donate electrons to SerABC in vitro. Protein sequence of cytc-Ts4 was obtained by N-terminal sequencing and liquid chromatography-tandem mass spectrometry analysis, and based upon sequence similarities, was assigned as a member of cytochrome c(4) family. Redox potentiometry, combined with UV-visible spectroscopy, showed that cytc-Ts4 is a diheme cytochrome with a redox potential of +282 +/- 10 mV, and both hemes are predicted to have His-Met ligation. To identify the membrane-bound electron donors to cytc-Ts4, growth of T. selenatis in the presence of respiratory inhibitors was monitored. The specific quinol-cytochrome c oxidoreductase (QCR) inhibitors myxothiazol and antimycin A partially inhibited selenate respiration, demonstrating that some electron flux is via the QCR. Electron transfer via a QCR and a diheme cytochrome c(4) is a novel route for a member of the DMSO reductase family of molybdoenzymes.

In recognition of the fact that orang-utans (Pongo spp.) are severely threatened, a meeting of orang-utan experts and conservationists, representatives of national and regional governmental and non-governmental organizations, and other stakeholders, was convened in Jakarta, Indonesia, in January 2004. Prior to this meeting we surveyed all large areas for which orang-utan population status was unknown. Compilation of all survey data produced a comprehensive picture of orang-utan distribution on both Borneo and Sumatra. These results indicate that in 2004 there were c. 6,500 P. abelii remaining on Sumatra and at least 54,000 P. pygmaeus on Borneo. Extrapolating to 2008 on the basis of forest loss on both islands suggests the estimate for Borneo could be 10% too high but that for Sumatra is probably still relatively accurate because forest loss in orang-utan habitat has been low during the conflict in Aceh, where most P. abelii occur. When those population sizes are compared to known historical sizes it is clear that the Sumatran orang-utan is in rapid decline, and unless extraordinary efforts are made soon, it could become the first great ape species to go extinct. In contrast, our results indicate there are more and larger populations of Bornean orang-utans than previously known. Although these revised estimates for Borneo are encouraging, forest loss and associated loss of orang-utans are occurring at an alarming rate, and suggest that recent reductions of Bornean orang-utan populations have been far more severe than previously supposed. Nevertheless, although orang-utans on both islands are under threat, we highlight some reasons for cautious optimism for their long-term conservation.

Synchronous fluorescence spectroscopy (SFS) was directly applied to rapidly quantify selected polycyclic aromatic hydrocarbons (PAHs: benzo[a]pyrene and pyrene) in aqueous hydroxypropyl-beta-cyclodextrin (HPCD) soil extract solutions from a variety of aged contaminated soils containing four different PAHs. The method was optimized and validated. The results show that SFS can be used to analyse benzo[a]pyrene and pyrene in HPCD based soil extracts with high sensitivity and selectivity. The linear calibration ranges were 4.0 x 10(-6)-1.0 x 10(-3) mM for benzo[a]pyrene and 6.0 x 10(-6)- 1.2 x 10(-3) mM for pyrenein 10 mM HPCD aqueous solution alone. The detection limits according to the error propagation theory for benzo[a]pyrene and pyrene were 3.9 x 10(-6) and 5.4 x 10(-6) mM, respectively. A good agreement between SFS and HPLC was reached for both determinations of PAHs in HPCD alone and in soil HPCD extracts. Hence, SFS is a potential means to simplify the present non-exhaustive hydroxypropyl-beta-cyclodextrin (HPCD)-based extraction technique for the evaluation of PAH bioavailability in soil. (C) 2006 Elsevier Ltd. All rights reserved.}

We investigated the phospholipid fatty acid (PLFA) pattern and dehydrogenase activity (DHA) in soil samples from three sites (designated as low, medium, and high based on the level of chromium) in a long-term (25 years after last waste input) tannery waste-contaminated area rich in Cr. Soil samples, collected from different soil depths (0-100 cm), at each site were used in this study. In general, soil samples from all three contaminated sites had elevated pH, electrical conductivity, organic carbon (OC), total Cr, and hexavalent Cr [Cr(VI)]. The maximum total Cr concentration in surface soils (0-10 cm) at the highly contaminated site was 102 gkg(-1), with 4.6 mgkg(-1) present as the bioavailable water-soluble Cr. More than 50% of soluble Cr was in the form of Cr(VI) (2.7 mgkg(-1)). DHA (normalized to OC) was inhibited to a greater extent in soil samples from the highly contaminated site than in low- and medium-contaminated soil samples. PLFA analyses of surface soils indicated that there was a shift in PLFA patterns. PLFAs specific for bacteria (i15:0, a15:0, 15:0, i16:0, a17:0, and cy17:0) decreased significantly (P

Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance., BMC Genomics, 15, ISSN:1471-2164

DDT (1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane) and its principle metabolites, DDE (1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene) and DDD (1,1-dichloro-2,2-bis(p-chlorophenyl)ethane) are widespread environmental contaminants but little information is available concerning their effects on non-target microflora (especially microalgae and cyanobacteria) and their activities in long-term contaminated soils. For this reason a long-term DDT-contaminated soil was screened for DDT residues and toxicity to microorganisms (bacteria, fungi, algae), microbial biomass and dehydrogenase activity. Also, five pure cultures isolated from various sites (two unicellular green algae and three dinitrogen-fixing cyanobacteria) were tested for their ability to metabolise DDT. Viable counts of bacteria and algae declined with increasing DDT contamination while fungal counts, microbial biomass and dehydrogenase activity increased in medium-level contaminated soil (27 mg DDT residues kg(-1) soil). All the tested parameters were greatly inhibited in high-level contaminated soil (34 mg DDT residues kg(-1) soil). Species composition of algae and cyanobacteria was altered in contaminated soils and sensitive species were eliminated in the medium and high contaminated soils suggesting that these organisms could be useful as bioindicators of pollution. Microbial biomass and dehydrogenase activity may not serve as good bioindicators of pollution since these parameters were potentially influenced by the increase in fungal (probably DDT resistant) counts. All the tested algal species metabolised DDT to DDE and DDD; however, transformation to DDD was more significant in the case of dinitrogen-fixing cyanobacteria.