A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that beta-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus(+) ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram(+) bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus(+) fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded beta-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.

Gene transfer to plants by diverse species of bacteria

Agrobacterium is widely considered to be the only bacterial genus capable of transferring genes to plants. When suitably modified, Agrobacterium has become the most effective vector for gene transfer in plant biotechnology1. However, the complexity of the patent landscape2 has created both real and perceived obstacles to the effective use of this technology for agricultural improvements by many public and private organizations worldwide. Here we show that several species of bacteria outside the Agrobacterium genus can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria were made competent for gene transfer by acquisition of both a disarmed Ti plasmid and a suitable binary vector. This alternative to Agrobacterium-mediated technology for crop improvement, in addition to affording a versatile ‘open source’ platform for plant biotechnology, may lead to new uses of natural bacteria– plant interactions to achieve plant transformation.

Rationalizing the SER spectra of bacteria

The SER spectra of riboflavin and FAD are identical and are resonance enhanced at 514 or 532 nm. Signals from FAD/ riboflavin dominated SER spectra whenever these compounds were present with proteins or bacteria. SER spectra of very different bacteria such as Pseudomonas. aeruginosa, Bacillu. subtilis and Geobacillus. stearothermophilus were dominated by signals from FAD, even when these bacteria were added to a preformed colloid. The SERS signal of FAD is greatly reduced at 785 nm, and SER spectra of bacteria excited at 785 nm are quite different than those collected at 514 or 532 nm. This supports the assignment of the peaks in the 514 nm SER spectra of bacteria to FAD rather to amino acids or N-acetylglucosamine. The SER spectra of certain mixes of adenine and FAD showed similar changes to those of bacteria when the excitation was changed from 514/532 nm to 785 nm. The ratio of colloid: bacteria was of critical important for obtaining good SER spectra, and the addition of sodium sulfate was also beneficial. Removal of EPS from bacteria before analysis facilitated interaction with the silver surface, and may be a useful step to include in identification protocols.

Observation of the suppression of water uptake by marine particles

A 4 week intensive measurement campaign was conducted in March–April 2007 at Agnes Water, a remote coastal site on the east coast of Australia. A Volatility-Hygroscopicity-Tandem Differential Mobility Analyser (VH-TDMA) was used to investigate changes in the hygroscopic properties of ambient particles as volatile components were progressively evaporated. Nine out of 18 VH-TDMA volatility scans detected internally mixed multi-component particles in the nucleation and Aitken modes in clean marine air. Evaporation of a volatile, organic-like component in the VH-TDMA caused significant increases in particle hygroscopicity. In 3 scans the increase in hygroscopicity was so large it was explained by an increase in the absolute volume of water uptake by the particle residuals, and not merely an increase in their relative hygroscopicity. This indicates the presence of organic components that were suppressing the hygroscopic growth of mixed particles on the timescale of humidification in the VH-TDMA (6.5 secs). This observation was supported by ZSR calculations for one scan, which showed that the measured growth factors of mixed particles were up to 18% below those predicted assuming independent water uptake of the individual particle components. The observed suppression of water uptake could be due to a reduced rate of hygroscopic growth caused by the presence of organic films or organic-inorganic interactions in solution droplets that had a negative effect on hygroscopicity.

Agglutinins from marine macroalgae of the southeastern United States

Protein extracts from 22 species of marine macroalgae from Florida and North Carolina were compared for their abilities to agglutinate sheep and rabbit erythrocytes. Protein extracts from 21 algal species agglutinated rabbit erythrocytes compared to 19 for sheep erythrocytes. However, agglutination by brown algal extracts was variable. The agglutination produced by protein extracts from Dictyota dichotoma could be blocked by addition of polyvinylpyrrolidone. Protein extracts from North Carolina macroalgae were also tested against five bacterial species. Three of these agglutinated bacterial cells. Ulva curvata and Bryopsis plumosa agglutinated all five species. Protein extracts from five species of Florida algae were tested for their effects on mitogenesis in mouse splenocytes and human lymphocytes. Gracilaria tikvahiae HBOI Strain G-5, Ulva rigida and Gracilaria verrucosa HBOI Strain G-16S stimulated mitogenesis in mouse splenocytes, while Gracilaria tikvahiae HBOI Strain G-16stimulated mitogenesis in human lymphocytes.

Investigation of the effect of organics on the water uptake of marine aerosols

Water uptake refers to the ability of atmospheric particles to take up water vapour from the surrounding atmosphere. This is an important property that affects particle size and phase and therefore influences many characteristics of aerosols relevant to air quality and climate. However, the water uptake properties of many important atmospheric aerosol systems, including those related to the oceans, are still not fully understood. Therefore, the primary aim of this PhD research program was to investigate the water uptake properties of marine aerosols. In particular, the effect of organics on marine aerosol water uptake was investigated. Field campaigns were conducted at remote coastal sites on the east coast of Australia (Agnes Water; March-April 2007) and west coast of Ireland (Mace Head; June 2007), and laboratory measurements were performed on bubble-generated sea spray aerosols. A combined Volatility-Hygroscopicity-Tandem Differential Mobility Analyser (VH-TDMA) was employed in all experiments. This system probes the changes in the hygroscopic properties of nanoparticles as volatile organic components are progressively evaporated. It also allows particle composition to be inferred from combined volatility-hygroscopicity measurements. Frequent new particle formation and growth events were observed during the Agnes Water campaign. The VH-TDMA was used to investigate freshly nucleated particles (17-22.5 nm) and it was found that the condensation of sulphate and/or organic vapours was responsible for driving particle growth during the events. Aitken mode particles (~40 nm) were also measured with the VH-TDMA. In 3 out of 18 VH-TDMA scans evaporation of a volatile, organic component caused a very large increase in hygroscopicity that could only be explained by an increase in the absolute water uptake of the particle residuals, and not merely an increase in their relative hygroscopicity. This indicated the presence of organic components that were suppressing the hygroscopic growth of mixed particles on the timescale of humidification in the VH-TDMA (6.5 secs). It was suggested that the suppression of water uptake was caused by either a reduced rate of hygroscopic growth due to the presence of organic films, or organic-inorganic interactions in solution droplets that had a negative effect on hygroscopicity. Mixed organic-inorganic particles were rarely observed by the VH-TDMA during the summer campaign conducted at Mace Head. The majority of particles below 100 nm in clean, marine air appeared to be sulphates neutralised to varying degrees by ammonia. On one unique day, 26 June 2007, particularly large concentrations of sulphate aerosol were observed and identified as volcanic emissions from Iceland. The degree of neutralisation of the sulphate aerosol by ammonia was calculated by the VH-TDMA and found to compare well with the same quantity measured by an aerosol mass spectrometer. This was an important verification of the VH-TMDA‘s ability to identify ammoniated sulphate aerosols based on the simultaneous measurement of aerosol volatility and hygroscopicity. A series of measurements were also conducted on sea spray aerosols generated from Moreton Bay seawater samples in a laboratory-based bubble chamber. Accumulation mode sea spray particles (38-173 nm) were found to contain only a minor organic fraction (< 10%) that had little effect on particle hygroscopicity. These results are important because previous studies have observed that accumulation mode sea spray particles are predominantly organic (~80% organic mass fraction). The work presented here suggests that this is not always the case, and that there may be currently unknown factors that are controlling the transfer of organics to the aerosol phase during the bubble bursting process. Taken together, the results of this research program have significantly improved our understanding of organic-containing marine aerosols and the way they interact with water vapour in the atmosphere.

Autonomous aerial navigation and tracking of marine animals

In this paper, we describe the development of an independent and on-board visual servoing system which allows a computationally impoverished aerial vehicle to autonomously identify and track a moving surface target. Our image segmentation and target identification algorithms were developed with the specific task of monitoring whales at sea but could be adapted for other targets. Observing whales is important for many marine biology tasks and is currently performed manually from the shore or from boats. We also present hardware experiments which demonstrate the capabilities of our algorithms for object identification and tracking that enable a flying vehicle to track a moving target.

Vacuum cleaner emissions as a source of indoor exposure to airborne particles and bacteria

Vacuuming can be a source of indoor exposure to biological and non-biological aerosols, although there is little data that describes the magnitude of emissions from the vacuum cleaner itself. We therefore sought to quantify emission rates of particles and bacteria from a large group of vacuum cleaners and investigate their potential determinants, including temperature, dust bags, exhaust filters, price and age. Emissions of particles between 0.009 and 20 µm and bacteria were measured from 21 vacuums. Ultrafine (<100 nm) particle emission rates ranged from 4.0 × 10^6 to 1.1 × 10^11 particles min-1. Emission of 0.54 to 20 µm particles ranged from 4.0 × 10^4 to 1.2 × 10^9 particles min-1. PM2.5 emissions were between 2.4 × 10-1 and 5.4 × 10^3 µg min-1. Bacteria emissions ranged from 0 to 7.4 × 10^5 bacteria min-1 and were poorly correlated with dust bag bacteria content and particle emissions. Large variability in emission of all parameters was observed across the 21 vacuums we assessed, which was largely not attributable to the range of determinant factors we assessed. Vacuum cleaner emissions contribute to indoor exposure to non-biological and biological aerosols when vacuuming, and this may vary markedly depending on the vacuum used.

A comparative study of the number and mass of fine particles emitted with diesel fuel and marine gas oil (MGO)

The current investigation reports on diesel particulate matter emissions, with special interest in fine particles from the combustion of two base fuels. The base fuels selected were diesel fuel and marine gas oil (MGO). The experiments were conducted with a four-stroke, six-cylinder, direct injection diesel engine. The results showed that the fine particle number emissions measured by both SMPS and ELPI were higher with MGO compared to diesel fuel. It was observed that the fine particle number emissions with the two base fuels were quantitatively different but qualitatively similar. The gravimetric (mass basis) measurement also showed higher total particulate matter (TPM) emissions with the MGO. The smoke emissions, which were part of TPM, were also higher for the MGO. No significant changes in the mass flow rate of fuel and the brake-specific fuel consumption (BSFC) were observed between the two base fuels.