James McDonald
Bangor University, School of Biological Sciences, Faculty Member
- Environmental microbiology, Biofilms, Bacteriology, RNA, Molecular Systematics, Geomicrobiology, and 10 moreMolecular Evolution, Microbial Ecology, Aquatic Microbial Ecology, Marine Microbial Ecology, Marine Microbiology, Metagenomics, Molecular Biology, Virology, Microbiology, and Bacteriophagesedit
- I graduated from The University of Manchester in 2004 with a degree in Microbiology with Industrial Experience. I stu... moreI graduated from The University of Manchester in 2004 with a degree in Microbiology with Industrial Experience. I studied my PhD at The University of Liverpool, entitled 'Molecular ecology of anaerobic cellulose-degrading microorganisms in landfill sites' under the supervision of Prof. Alan McCarthy and Dr. Heather Allison and graduated in December 2008.
I then continued to work at Liverpool on a DEFRA funded project concerned with the molecular ecology of Shiga-toxigenic Escherichia coli (STEC) strains and Stx bacteriophages across a farm site in Cheshire and on metagenomic/pyrosequencing projects focussed on the canine oral microbiota.
I joined the School of Biological Sciences at Bangor University in March 2010 as a Research Lecturer in Environmental Microbiology, studying the biogeochemistry of soils and sediments.edit
Faecal contamination of estuarine and coastal waters can pose a risk to human health, particularly in areas used for shellfish production or recreation. Routine microbiological water quality testing highlights areas of faecal indicator... more
Faecal contamination of estuarine and coastal waters can pose a risk to human health, particularly in areas used for shellfish production or recreation. Routine microbiological water quality testing highlights areas of faecal indicator bacteria (FIB) contamination within the water column, but fails to consider the abundance of FIB in sediments, which under certain hydrodynamic conditions can become resuspended. Sediments can enhance the survival of FIB in estuarine environments, but the influence of sediment composition on the ecology and abundance of FIB is poorly understood. To determine the relationship between sediment composition (grain size and organic matter) and the abundance of pathogen indicator bacteria (PIB), sediments were collected from four transverse transects of the Conwy estuary, UK. The abundance of culturable Escherichia coli, total coliforms, enterococci, Campylobacter, Salmonella and Vibrio spp. in sediments was determined in relation to sediment grain size, organic matter content, salinity, depth and temperature. Sediments that contained higher proportions of silt and/or clay and associated organic matter content showed significant positive correlations with the abundance of PIB. Furthermore, the abundance of each bacterial group was positively correlated with the presence of all other groups enumerated. Campylobacter spp. were not isolated from estuarine sediments. Comparisons of the number of culturable E. coli, coliform and Vibrio spp. in sediments and the water column revealed that their abundance was 281, 433 and 58-fold greater in sediments (colony forming units (CFU)/100 g) when compared with the water column (CFU/100 ml), respectively. These data provide important insights into sediment compositions that promote the abundance of PIB in estuarine environments, with important implications for the modelling and prediction of public health risk based on sediment resuspension and transport.
Research Interests:
The biodegradation of lignocellulose, the most abundant organic material in the biosphere, is a feature of many aerobic, facultatively anaerobic and obligately anaerobic bacteria and fungi. Despite widely recognized difficulties in the... more
The biodegradation of lignocellulose, the most abundant organic material in the biosphere, is a feature of many aerobic, facultatively anaerobic and obligately anaerobic bacteria and fungi. Despite widely recognized difficulties in the isolation and cultivation of individual microbial species from complex microbial populations and environments, significant progress has been made in recovering cellulolytic taxa from a range of ecological niches including the human, herbivore, and termite gut, and terrestrial, aquatic, and managed environments. Knowledge of cellulose-degrading microbial taxa is of significant importance with respect to nutrition, biodegradation, biotechnology, and the carbon-cycle, providing insights into the metabolism, physiology, and functional enzyme systems of the cellulolytic bacteria and fungi that are responsible for the largest flow of carbon in the biosphere. In this chapter, several strategies employed for the isolation and cultivation of cellulolytic microorganisms from oxic and anoxic environments are described.
Research Interests:
Most of the microorganisms responsible for nutrient cycling in the environment have yet to be cultivated, and this could include those species responsible for the degradation of cellulose. Known cellulases are well defined at the protein... more
Most of the microorganisms responsible for nutrient cycling in the environment have yet to be cultivated, and this could include those species responsible for the degradation of cellulose. Known cellulases are well defined at the protein sequence level, but gene variants are difficult to amplify from environmental DNA. The identification of novel cellulase genes independent of DNA amplification is made possible by adopting a direct metagenome sequencing approach to provide genes that can be cloned, expressed, and characterized prior to potential exploitation, all in the absence of any information on the species from which they originated. In this chapter, emerging strategies and methods that will enable the identification of novel cellulase genes and provide an unbiased perspective on gene expression in situ are presented.
Research Interests:
Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their... more
Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose ‘baits’ via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1–6% and 1–17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.
Research Interests:
The relative abundance of micromonosporas in the bacterial communities inhabiting cellulose baits, the water columns and sediments of two freshwater lakes was determined by qPCR of reverse transcribed 16S rRNA. Micromonospora spp. were... more
The relative abundance of micromonosporas in the bacterial communities inhabiting cellulose baits, the water columns and sediments of two freshwater lakes was determined by qPCR of reverse transcribed 16S rRNA. Micromonospora spp. were shown to be significant members of the active bacterial population colonising cellulosic substrates at the lake sediment, and their increased prevalence with depth was confirmed by enumeration of colony forming units.
Research Interests:
The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in... more
The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibrobacteres has been detected in the gut of wood-feeding termites, and proteomic analyses have confirmed their involvement in cellulose hydrolysis. The genome sequence of F. succinogenes rumen strain S85 has recently suggested that within this group of organisms a “third” way of attacking the most abundant form of organic carbon in the biosphere, cellulose, has evolved. This observation not only has evolutionary significance, but the superior efficiency of anaerobic cellulose hydrolysis by Fibrobacter spp., in comparison to other cellulolytic rumen bacteria that typically utilise membrane-bound enzyme complexes (cellulosomes), may be explained by this novel cellulase system. There are few bacterial phyla with potential functional importance for which there is such a paucity of phenotypic and functional data. In this review, we highlight current knowledge of the Fibrobacteres phylum, its taxonomy, phylogeny, ecology and potential as a source of novel glycosyl hydrolases of biotechnological importance.
Research Interests:
Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the... more
Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.
Research Interests:
Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured... more
Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.
Research Interests:
Research Interests:
Members of the bacterial genus Fibrobacter have long been considered important components of the anaerobic cellulolytic community in the herbivore gut, but their presence and activity in other environments is largely unknown. In this... more
Members of the bacterial genus Fibrobacter have long been considered important components of the anaerobic cellulolytic community in the herbivore gut, but their presence and activity in other environments is largely unknown. In this study, a specific polymerase chain reaction (PCR) primer set, targeting the 16S rRNA gene of Fibrobacter spp., was applied to community DNA from five landfill sites followed by temporal thermal gel electrophoresis (TTGE) analysis of cloned amplification products. Phylogenetic analysis of clone sequences indicated the presence of novel clusters closely related to the genus Fibrobacter. There are two named species, Fibrobacter succinogenes and F. intestinalis, and only two of the 58 sequenced clones were identified with them, and both were F. succinogenes. The clone sequences from landfill were recovered in five distinct clusters within the Fibrobacter lineage, and four of these were novel. Quantitative PCR (qPCR) assays of reverse-transcribed community RNA from landfill leachates and rumen fluid samples indicated that the abundance of Fibrobacter spp. relative to total bacteria varied from 0.2% to 40% in landfill, and 21% to 32% in the rumen, and these data demonstrate that fibrobacters can be a significant component of the microbial community in landfill ecosystems. This is the first evidence for Fibrobacter spp. outside the gut ecosystem, and as the only cultivated representatives of this group are actively cellulolytic, their diversity and abundance points to a possible role in cellulose hydrolysis in landfill, and perhaps other anaerobic environments also.
The microbial community composition of colonised cotton and leachate samples from landfill was quantified using Small Sub-Unit (SSU) rRNA probes (quantitative rRNA hybridisation). Relative quantification of Bacteria, Eukarya and Archaea... more
The microbial community composition of colonised cotton and leachate samples from landfill was quantified using Small Sub-Unit (SSU) rRNA probes (quantitative rRNA hybridisation). Relative quantification of Bacteria, Eukarya and Archaea revealed variations in the landfill microbial community between samples from different areas of the landfill site, and indicated the presence of potentially novel Archaea. Anaerobic fungi were quantified in rumen fluid samples, but were not sufficiently abundant for direct detection in the landfill samples.
A high-throughput 96-well plate-based method for the rapid induction of endogenous prophages from individual bacterial strains was developed. Detection of endogenous prophages was achieved by filtration of the culture liquor following... more
A high-throughput 96-well plate-based method for the rapid induction of endogenous prophages from individual bacterial strains was developed. Detection of endogenous prophages was achieved by filtration of the culture liquor following norfloxacin induction and subsequent PCR reactions targeting bacteriophage-encoded gene markers. The induction method was tested on 188 putative Shiga-toxin (Stx) producing Escherichia coli (STEC) strains and demonstrated the ability to detect both lambdoid and Stx encoding bacteriophages in strains for which plaques were not observed via plaque assay. Lambdoid bacteriophages were detected in 37% of the induced phage preparations via amplification of the Q gene, and Stx1 and Stx2 encoding phages were detected in 2% and 14% of the strains, respectively. The method therefore provided greater sensitivity for the detection of Stx and other lambdoid bacteriophage populations carried by STEC strains compared to the established method of plaque assay using bacterial indicator strains, enabling for the first time, large-scale bacteriophage population and diversity studies.
AEM Accepts, published online ahead of print on 5 February 2010
Appl. Environ. Microbiol. doi:10.1128/AEM.02923-09 2010
AEM Accepts, published online ahead of print on 5 February 2010
Appl. Environ. Microbiol. doi:10.1128/AEM.02923-09 2010
To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal... more
To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 1031 tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 × 104 to 6.5 × 106 ml−1, with one in 103 free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.
Environmental Microbiology
Published Online: Feb 9 2010 9:20PM
DOI: 10.1111/j.1462-2920.2010.02162.x
Environmental Microbiology
Published Online: Feb 9 2010 9:20PM
DOI: 10.1111/j.1462-2920.2010.02162.x