Key publications
Lappin-Scott H, Burton S, Stoodley P (2014). Revealing a world of biofilms — the pioneering research of Bill Costerton. Nature Reviews Microbiology, 12(11), 781-787.
Smith AM, Sharma D, Lappin-Scott H, Burton S, Huber DH (2013). Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Applied Microbiology and Biotechnology, 98(5), 2321-2334.
Lappin-Scott HM, Burton SK (2011). Biofilms. 26th Brazilian Congress of Microbiology.
Lappin-Scott HM, Burton SK, Burton SK (2011). Biofilms working together, interactions and proteomics. 6th International Conference on Genomics.
Frenzel M, Scarlett A, Rowland SJ, Galloway TS, Burton SK, Lappin-Scott HM, Booth AM (2010). Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons.
Sci Total Environ,
408(19), 4093-4101.
Abstract:
Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons.
Environmentally persistent aromatic hydrocarbons known as unresolved complex mixtures (UCMs) derived from crude oil can be accumulated by, and elicit toxicological responses in, marine organisms (e.g. mussels, Mytilus edulis). Comprehensive two-dimensional gas chromatography time-of-flight mass-spectrometry (GCxGC-ToF-MS) previously revealed that these UCMs included highly branched alkylated aromatic hydrocarbons. Here, the effects of biodegradation on the toxicity and chemical composition of an aromatic UCM hydrocarbon fraction isolated from Tia Juana Pesado (TJP) crude oil were examined. 48h exposure of mussels to the aromatic hydrocarbon fraction (F2) resulted in tissue concentrations of 900microgg(-1) (dry wt.) and approximately 45% decrease in clearance rate. Over 90% of the hydrocarbon burden corresponded to an UCM. Following a 5day recovery period, GCxGC-ToF-MS analysis of the tissues indicated depuration of most accumulated hydrocarbons and clearance rates returned to those observed in controls. To assess the potential of biodegradation to reduce UCM toxicity, TJP F2 was exposed to bacteria isolated from Whitley Bay, UK, for 46days. Mussels exposed to the undegraded TJP F2 from the abiotic control exhibited a reduction in clearance rate comparable with values for the pure crude oil TJP F2. Clearance rates of mussels exposed to biodegraded TJP F2 were statistically similar to seawater controls, suggesting biodegradation had reduced the TJP F2 toxicity. GCxGC-ToF-MS analysis revealed the same compound groups in the tissue of mussels exposed to pure TJP F2, undegraded TJP F2 and biodegraded TJP F2 samples; however >300 fewer compounds were observed in the biodegraded (954 compounds) compared to the undegraded TJP F2 (1261). The compound distributions were markedly different, possibly accounting for the decrease in toxicity. Extraction and analysis of pelleted bacterial cell material revealed that a significant proportion of the TJP F2 had adsorbed onto the cells. Thus extreme care must be taken in interpreting biodegradation data from recalcitrant UCM hydrocarbons.
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Publications by year
2014
Lappin-Scott H, Burton S, Stoodley P (2014). Revealing a world of biofilms — the pioneering research of Bill Costerton. Nature Reviews Microbiology, 12(11), 781-787.
2013
Smith AM, Sharma D, Lappin-Scott H, Burton S, Huber DH (2013). Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Applied Microbiology and Biotechnology, 98(5), 2321-2334.
2011
Lappin-Scott HM, Burton SK (2011). Biofilms. 26th Brazilian Congress of Microbiology.
Lappin-Scott HM, Burton SK, Burton SK (2011). Biofilms working together, interactions and proteomics. 6th International Conference on Genomics.
2010
Frenzel M, Scarlett A, Rowland SJ, Galloway TS, Burton SK, Lappin-Scott HM, Booth AM (2010). Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons.
Sci Total Environ,
408(19), 4093-4101.
Abstract:
Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons.
Environmentally persistent aromatic hydrocarbons known as unresolved complex mixtures (UCMs) derived from crude oil can be accumulated by, and elicit toxicological responses in, marine organisms (e.g. mussels, Mytilus edulis). Comprehensive two-dimensional gas chromatography time-of-flight mass-spectrometry (GCxGC-ToF-MS) previously revealed that these UCMs included highly branched alkylated aromatic hydrocarbons. Here, the effects of biodegradation on the toxicity and chemical composition of an aromatic UCM hydrocarbon fraction isolated from Tia Juana Pesado (TJP) crude oil were examined. 48h exposure of mussels to the aromatic hydrocarbon fraction (F2) resulted in tissue concentrations of 900microgg(-1) (dry wt.) and approximately 45% decrease in clearance rate. Over 90% of the hydrocarbon burden corresponded to an UCM. Following a 5day recovery period, GCxGC-ToF-MS analysis of the tissues indicated depuration of most accumulated hydrocarbons and clearance rates returned to those observed in controls. To assess the potential of biodegradation to reduce UCM toxicity, TJP F2 was exposed to bacteria isolated from Whitley Bay, UK, for 46days. Mussels exposed to the undegraded TJP F2 from the abiotic control exhibited a reduction in clearance rate comparable with values for the pure crude oil TJP F2. Clearance rates of mussels exposed to biodegraded TJP F2 were statistically similar to seawater controls, suggesting biodegradation had reduced the TJP F2 toxicity. GCxGC-ToF-MS analysis revealed the same compound groups in the tissue of mussels exposed to pure TJP F2, undegraded TJP F2 and biodegraded TJP F2 samples; however >300 fewer compounds were observed in the biodegraded (954 compounds) compared to the undegraded TJP F2 (1261). The compound distributions were markedly different, possibly accounting for the decrease in toxicity. Extraction and analysis of pelleted bacterial cell material revealed that a significant proportion of the TJP F2 had adsorbed onto the cells. Thus extreme care must be taken in interpreting biodegradation data from recalcitrant UCM hydrocarbons.
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2009
Frenzel M, James P, Burton SK, Rowland SJ, Lappin-Scott HM (2009). Towards bioremediation of toxic unresolved complex mixtures of hydrocarbons: Identification of bacteria capable of rapid degradation of alkyltetralins.
Journal of Soils and Sediments,
9(2), 129-136.
Abstract:
Towards bioremediation of toxic unresolved complex mixtures of hydrocarbons: Identification of bacteria capable of rapid degradation of alkyltetralins
Background, aim and scope: Unresolved complex mixtures (UCMs) of aromatic hydrocarbons are widespread, but often overlooked, environmental contaminants. Since UCMs are generally rather resistant to bacterial degradation, bioremediation of UCM-contaminated sites by bacteria is a challenging goal. Branched chain alkyltetralins are amongst the individual classes of components of aromatic UCMs which have been identified in hydrocarbon-contaminated sediments and a number of synthetic alkyltetralins have proved toxic in laboratory studies. Thus, alkyltetralins should perhaps be amongst the targets for UCM bioremediation strategies. The slow degradation of several alkyltetralins by a microbial consortium has been reported previously; however, the bacteria involved remain unidentified and no single strain capable of alkyltetralin biodegradation has been isolated. The present project therefore aimed to enrich and identify bacterial consortia and single strains of bacteria from a naturally hydrocarbon-contaminated site (Whitley Bay, UK), which were capable of the degradation of two synthetic alkyltetralins (6-cyclohexyltetralin (CHT) and 1-(3'-methylbutyl)-7-cyclohexyltetralin (MBCHT)). Materials and methods: Bacteria were enriched from sediment collected from Whitley Bay, UK by culturing with CHT and MBCHT for a period of 4 months. Biodegradation experiments were then established and degradation of model compounds monitored by gas chromatography-mass spectrometry. Internal standards allowed the generation of quantitative data. 16S rRNA gene clone libraries were constructed from individual enrichments to allow assessment of microbial community structure. Selective media containing MBCHT were used to isolate single bacterial strains. These strains were then tested in liquid culture for their ability to degrade MBCHT. Results: the consortia obtained through enrichment culture were able to degrade 87% of CHT and 76% of MBCHT after only 46 days compared with abiotic controls. The 16S ribosomal RNA gene clone libraries of these bacteria were dominated by sequences of Rhodococcus spp. Using selective media, a strain of Rhodococcus was then isolated that was also able to biodegrade 63% of MBCHT in only 21 days. Discussion: the present report describes the isolation of a single bacterial strain able to degrade the resistant MBCHT. Although significant losses of MBCHT were observed, putative metabolites were not detectable. Rhodococcus sp. have been reported previously to be able to biodegrade a range of hydrocarbon compounds. Recommendations and perspectives: Due to their environmental persistence and toxicity, aromatic UCMs require bioremediation. The culturing and identification of such bacteria capable of rapid degradation of alkyltetralins may be an important step toward the development of bioremediation strategies for sites contaminated with toxic UCMs. © 2009 Springer-Verlag.
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2005
Burton SK, Lappin-Scott HM (2005). Geomicrobiology, the hidden depths of the biosphere.
Trends Microbiol,
13(9).
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2003
Smejkal CW, Seymour FA, Burton SK, Lappin-Scott HM (2003). Characterisation of bacterial cultures enriched on the chlorophenoxyalkanoic acid herbicides 4-(2,4-dichlorophenoxy) butyric acid and 4-(4-chloro-2-methylphenoxy) butyric acid.
J Ind Microbiol Biotechnol,
30(9), 561-567.
Abstract:
Characterisation of bacterial cultures enriched on the chlorophenoxyalkanoic acid herbicides 4-(2,4-dichlorophenoxy) butyric acid and 4-(4-chloro-2-methylphenoxy) butyric acid.
The aim of this study was to enrich and characterise bacterial consortia from soils around a herbicide production plant through their capability to degrade the herbicides 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) and 4-(4-chloro-2-methylphenoxy) butyric acid (MCPB). Partial 16S rRNA gene sequencing revealed members of the genera Stenotrophomonas, Brevundimonas, Pseudomonas, and Ochrobactrum in the 2,4-DB- and MCPB-degrading communities. The degradation of 2,4-DB and MCPB was facilitated by the combined activities of the community members. Some of the members were able to utilise other herbicides from the family of chlorophenoxyalkanoic acids. During degradation of 2,4-DB and MCPB, phenol intermediates were detected, indicating ether cleavage of the side chain as the initial step responsible for the breakdown. This was also verified using an indicator medium. Repeated attempts to amplify putatively conserved tfd genes by PCR indicated the absence of tfd genes among the consortia members. First step cleavage of the chlorophenoxybutyric acid herbicides is by ether cleavage in bacteria and is encoded by divergent or different tfd gene types. The isolation of mixed cultures capable of degrading 2,4-DB and MCPB will aid future investigations to determine both the metabolic route for dissimilation and the fate of these herbicides in natural environments.
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2001
Smejkal CW, Vallaeys T, Burton SK, Lappin-Scott HM (2001). A rapid method to screen degradation ability in chlorophenoxyalkanoic acid herbicide-degrading bacteria.
Lett Appl Microbiol,
32(4), 273-277.
Abstract:
A rapid method to screen degradation ability in chlorophenoxyalkanoic acid herbicide-degrading bacteria.
AIMS: an agar medium containing a range of related chlorophenoxyalkanoic acid herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 2-methyl-4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop and racemic 2,4-DP (2-(2,4-dichlorophenoxy) propionic acid) was developed to assess the catabolic activity of a range of degradative strains. METHODS AND RESULTS: the medium was previously developed containing 2,4-D as a carbon source to visualise degradation by the production of dark violet bacterial colonies. Strains isolated on mecoprop were able to degrade 2,4-D, MCPA, racemic mecoprop, (R)-mecoprop and racemic 2,4-DP, whereas the 2,4-D-enriched strains were limited to 2,4-D and MCPA as carbon sources. Sphingomonas sp. TFD44 solely degraded the dichlorinated compounds, 2,4-D, racemic 2,4-DP and 2,4-DB (2,4-dichlorophenoxybutyric acid). However, Sphingomonas sp. AW5, originally isolated on 2,4,5-T, was the only strain to degrade the phenoxybutyric compound MCPB (4-chloro-2-methylphenoxybutyric acid). CONCLUSION: This medium has proved to be a very effective and rapid method for screening herbicide degradation by bacterial strains. SIGNIFICANCE AND IMPACT OF THE STUDY: This method reduces the problem of assessing the biodegradability of this family of compounds to an achievable level.
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Smejkal CW, Vallaeys T, Seymour FA, Burton SK, Lappin-Scott HM (2001). Characterization of (R/S)-mecoprop [2-(2-methyl-4-chlorophenoxy) propionic acid]-degrading Alcaligenes sp.CS1 and Ralstonia sp. CS2 isolated from agricultural soils.
Environ Microbiol,
3(4), 288-293.
Abstract:
Characterization of (R/S)-mecoprop [2-(2-methyl-4-chlorophenoxy) propionic acid]-degrading Alcaligenes sp.CS1 and Ralstonia sp. CS2 isolated from agricultural soils.
The herbicide mecoprop [2-(2-methyl-4-chlorophenoxy) propionic acid] is widely applied to corn fields in order to control broad-leaved weeds. However, it is often detected in groundwater where it can be a persistent contaminant. Two mecoprop-degrading bacterial strains were isolated from agricultural soils through their capability to degrade (R/S)-mecoprop rapidly. 16S rDNA sequencing of the isolates demonstrated that one was closely related to the genera Alcaligenes sp. (designated CS1) and the other to Ralstonia sp. (designated CS2). Additionally, these isolates demonstrated ability to grow on other related herbicides, including 2,4-D (2,4-dichlorophenoxyacetic acid), MCPA [4-chloro-2-methyl phenoxy acetic acid] and (R/S)-2,4-DP [2-(2,4-dichlorophenoxy)propionic acid] as sole carbon sources. tfdABC gene-specific probes derived from the 2,4-D-degrading Variovorax paradoxus TV1 were used in hybridization analyses to establish whether tfd-like genes are present in mecoprop-degrading bacteria. Hybridization analysis demonstrated that both Alcaligenes sp. CS1 and Ralstonia sp. CS2 harboured tfdA, tfdB and tfdC genes on plasmids that have approximately > 60% sequence similarity to the tfdA, tfdB and tfdC genes of V. paradoxus. It is therefore likely that tfd-like genes may be involved in the degradation of mecoprop, and we are currently investigating this further.
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Smejkal CW, Vallaeys T, Burton SK, Lappin-Scott HM (2001). Substrate specificity of chlorophenoxyalkanoic acid-degrading bacteria is not dependent upon phylogenetically related tfdA gene types.
Biology and Fertility of Soils,
33(6), 507-513.
Abstract:
Substrate specificity of chlorophenoxyalkanoic acid-degrading bacteria is not dependent upon phylogenetically related tfdA gene types
The phenoxyalkanoic acid herbicides constitute a group of chemically related molecules that have been widely used for over 50 years. A range of bacteria have been selected from various locations for their ability to degrade these compounds. Previously reported strains able to utilise 2,4-dichlorophenoxyacetic acid (2,4-D) include, Ralstonia eutropha JMP134, Burkholderia sp. RASC and Variovorax paradoxus TV1 and Sphingomonas sp. AW5 able to utilise 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). In addition a novel set of mecoprop-degrading strains including Alcaligenes denitrificans, Alcaligenes sp. CS1 and Ralstonia sp. CS2 are here described. It has been reported recently that TfdA enzymes, initially reported to have a role in 2,4-D catabolism are also involved in the first-step cleavage of related phenoxyalkanoate herbicides. However, a diversity of tfdA gene sequences have been reported. We relate the tfdA gene type to the metabolic ability of these strains. The tfdA-like genes were investigated by polymerase chain reaction amplification using a set of specific tfdA primers. Degradation ability was observed via phenol production from a range of unsubstituted and substituted phenoxyalkanoics including, 2,4-D, 2-methyl 4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop, 2-(2,4-dichlorophenoxy) propionic acid (racemic 2,4-DP), 2,4,5-T, 2,4-dichlorophenoxybutyric acid (2,4-DB), 4-chloro-2-methylphenoxybutyric acid (MCPB) and phenoxyacetate. Mecoprop-degrading strains showed partial tfdA sequences identical to the one described for V. paradoxus TV1 (a strain isolated on 2,4-D). However, substrate specificity was not identical as V. paradoxus exhibited greatest activity towards 2,4-D and MCPA only, whereas the mecoprop-degrading strains showed intense activity towards 2,4-D, MCPA, racemic mecoprop and (R)-mecoprop as substrates. However, Sphingomonas sp. AW5 which has been shown to carry a very different tfdA-like gene was the only strain to utilise the phenoxybutyric acid MCPB as a sole carbon source. In this study, we thus demonstrate that sequence diversity is not related to substrate specificity within the tfdA-like gene family. However, phylogenetically unrelated sequences may govern substrate specific activity.
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1997
Burton SK, Van 't Ho J, Bryant JA (1997). Novel DNA-binding characteristics of a protein associated with DNA polymerase-alpha in pea.
Plant J,
12(2), 357-365.
Abstract:
Novel DNA-binding characteristics of a protein associated with DNA polymerase-alpha in pea.
DNA polymerase-alpha-primase may be isolated from pea shoot tip cells as a large (1.25 x 10(6) Da) multi-protein complex. The complex exhibits several enzyme activities and also binds to DNA. One of the DNA-binding activities has been purified as a 42 kDa polypeptide. The binding of this polypeptide to linear DNA fragments and to open circular plasmids has been studied by electron microscopy. The protein binds to restriction enzyme-generated cohesive ends of linear fragments and also exhibits some interstitial binding. Binding at the ends of linear molecules is very markedly reduced if the molecules are previously treated with S1 nuclease. The protein also binds to open circular plasmids; the number of binding sites is increased by exposing the plasmids to gamma-irradiation prior to the DNA-protein interaction. In these experiments, the number of protein units bound is directly related to the radiation dose. With both linear and open circular molecules, binding of the protein to the DNA leads to an apparent shortening of the DNA molecule. These observations, taken with the finding that the protein does not bind to completely single-stranded DNA, lead to the suggestion that the protein binds to double-stranded-single-stranded (ds-ss) junctions in DNA and that binding causes the DNA to wrap round the protein.
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