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Allen DM, Reyne MI, Allingham P, Levickas A, Bell SH, Lock J, Coey JD, Carson S, Lee AJ, McSparron C, Nejad BF, McKenna J, Shannon M, Li K, Curran T, Broadbent LJ, Downey DG, Power UF, Groves HE, McKinley JM, McGrath JW, Bamford CGG, Gilpin DF. Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE). J Infect Dis 2024:jiae205. [PMID: 38636496 DOI: 10.1093/infdis/jiae205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/08/2023] [Accepted: 04/16/2024] [Indexed: 04/20/2024] Open
Abstract
Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limits the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying RT-qPCR and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.
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Affiliation(s)
- Danielle M Allen
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Marina I Reyne
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Pearce Allingham
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Ashley Levickas
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Stephen H Bell
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Jonathan Lock
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Jonathon D Coey
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Stephen Carson
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Andrew J Lee
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Cormac McSparron
- Geography, Archaeology and Palaeoecology, School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, BT9 6AZ, Northern Ireland (UK)
| | - Behnam Firoozi Nejad
- Geography, Archaeology and Palaeoecology, School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, BT9 6AZ, Northern Ireland (UK)
| | - James McKenna
- Regional Virology Lab, Belfast Health and Social Care Trust (BHSCT), Royal Victoria Hospital (RVL), 274 Grosvenor Road, Belfast, BT12 6BA, Northern Ireland (UK)
| | - Mark Shannon
- Regional Virology Lab, Belfast Health and Social Care Trust (BHSCT), Royal Victoria Hospital (RVL), 274 Grosvenor Road, Belfast, BT12 6BA, Northern Ireland (UK)
| | - Kathy Li
- Regional Virology Lab, Belfast Health and Social Care Trust (BHSCT), Royal Victoria Hospital (RVL), 274 Grosvenor Road, Belfast, BT12 6BA, Northern Ireland (UK)
| | - Tanya Curran
- Regional Virology Lab, Belfast Health and Social Care Trust (BHSCT), Royal Victoria Hospital (RVL), 274 Grosvenor Road, Belfast, BT12 6BA, Northern Ireland (UK)
| | - Lindsay J Broadbent
- Section of Virology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, England (UK)
| | - Damian G Downey
- Wellcome-Wolfson Institute for Experimental Medicine (WWIEM), School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Ultan F Power
- Wellcome-Wolfson Institute for Experimental Medicine (WWIEM), School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Helen E Groves
- Wellcome-Wolfson Institute for Experimental Medicine (WWIEM), School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Jennifer M McKinley
- Geography, Archaeology and Palaeoecology, School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, BT9 6AZ, Northern Ireland (UK)
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Connor G G Bamford
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
| | - Deirdre F Gilpin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland (UK)
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2
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Bell S, Thompson TP, Marks N, Fairley D, Kettunen H, Vuorenmaa J, Orte J, Gilmore BF, McGrath JW. Rosin as a Natural Alternative for the effective disinfection of ESKAPE Pathogens and Clostridioides difficile spores. J Appl Microbiol 2024:lxae008. [PMID: 38244225 DOI: 10.1093/jambio/lxae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
AIM Hospital-acquired infections (HAIs) caused by antimicrobial-resistant ESKAPE pathogens are a significant concern for the healthcare industry, with an estimated cost of up to ${\$}$45 billion per year in the US alone. Clostridioides difficile is an additional opportunistic pathogen that also poses a serious threat to immunocompromised patients in hospitals. Infections caused by these pathogens lead to increased hospital stays and repeated readmission, resulting in a significant economic burden. Disinfectants and sporicidals are essential to reduce the risk of these pathogens in hospitals, but commercially available products can have a number of disadvantages including inefficacy, long contact times, short shelf lives, and operator health hazards. In this study we evaluated the effectiveness of Rosin (a natural substance secreted by coniferous trees as a defence mechanism against wounds in tree bark) and its commercial derivative Rosetax-21 as disinfectants and sporicidal against the six ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and spore preparations from Clostridioides difficile. METHODS AND RESULTS Both Rosin and Rosetax-21 were tested under simulated clean and dirty conditions (with BSA) against the ESKAPE pathogens, and C. difficile spore preparations. In clean conditions, Rosin (5% weight/volume: w/v) demonstrated significant efficacy against five of the ESKAPE pathogens, with A. baumannii and E. faecium being the most susceptible, and K. pneumoniae the most resistant, showing only a one-log reduction after a 5 min treatment. However, in dirty conditions, all pathogens including K. pneumoniae exhibited at least a 3-log reduction to Rosin within 5 min. Rosetax-21 (5% w/v) was found to be less effective than Rosin in clean conditions, a trend that was exacerbated in the presence of BSA. Additionally, both Rosin and Rosetax-21 at 2.5% (w/v) achieved complete eradication of C. difficile spores when combined with 0.5% glutaraldehyde, though their standalone sporicidal activity was limited. CONCLUSIONS The findings from this study highlight the potential of Rosin and Rosetax-21 as both bactericidal and sporicidal disinfectants, with their efficacy varying based on the conditions and the pathogens tested. This presents an avenue for the development of novel healthcare disinfection strategies, especially against HAIs caused by antimicrobial-resistant ESKAPE pathogens and C. difficile.
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Affiliation(s)
- Stephen Bell
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Nikki Marks
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Derek Fairley
- Regional Virology Unit, Royal Victoria Hospital, Belfast Trust, Belfast, UK
| | | | | | - Juha Orte
- Forchem Oy, Maanpääntie 3, FI-26820 Rauma
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
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3
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Marshall A, McGrath JW, Mitchell M, Fanning S, McMullan G. One size does not fit all - Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages. Microb Genom 2023; 9:001110. [PMID: 37768179 PMCID: PMC10569727 DOI: 10.1099/mgen.0.001110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Here, growth in trehalose as the sole carbon source was shown to be non-uniform across representative C. difficile strains, even though the genes for its metabolism were induced. Growth in trehalose reduced the expression of genes associated with toxin production and sporulation in the C. difficile R20291 (RT027) and M120 (RT078) strains in vitro, suggesting an inhibitory effect on virulence factors. Interestingly, the R20291 TreR transcriptional regulatory protein appeared to possess an activator function as its DNA-binding ability was increased in the presence of its effector, trehalose-6-phosphate. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.
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Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Molly Mitchell
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
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4
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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5
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Bell SH, Allen DM, Reyne MI, Lock JFW, Fitzgerald A, Levickas A, Lee AJ, Bamford CGG, Gilpin DF, McGrath JW. Improved recovery of SARS-CoV-2 from wastewater through application of RNA and DNA stabilising agents. Lett Appl Microbiol 2023:7150680. [PMID: 37133410 DOI: 10.1093/lambio/ovad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Wastewater Based Epidemiology (WBE) has become an integral part of the public health effort to track the levels of SARS-CoV-2 within communities. Detection of SARS-CoV-2 in wastewater can be challenging due to relatively low levels of virus within the sample. The wastewater matrix is also comprised of commercial and domestically derived contaminants, as well as RNases, all of which can adversely affect RT-qPCR analysis. To improve SARS-CoV-2 detection within wastewater samples we investigated both the effect of template dilution (as a means to reduce RT-qPCR inhibition) and sample stabilisation via addition of DNA/RNA Shield™ and/or RNA Later™ (to prevent RNA degradation via RNases) as a means to improve viral fragment detection. Using both methodologies a significant improvement in SARS-CoV-2 detection from wastewater samples was observed. No adverse effects of stabilising agent addition on downstream Next Generation Sequencing workflows were detected.
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Affiliation(s)
- Stephen H Bell
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Danielle M Allen
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Marina I Reyne
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Jonathan F W Lock
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Arthur Fitzgerald
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Ashley Levickas
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Andrew J Lee
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Connor G G Bamford
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - Deirdre F Gilpin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland (UK)
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6
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Mitchell M, Nguyen SV, Connor M, Fairley DJ, Donoghue O, Marshall H, Koolman L, McMullan G, Schaffer KE, McGrath JW, Fanning S. Terrisporobacter hibernicus sp. nov., isolated from bovine faeces in Northern Ireland. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748477 DOI: 10.1099/ijsem.0.005667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A new species of Terrisporobacter, a Gram-positive, spore-forming anaerobic group, proposed name Terrisporobacter hibernicus sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3T, cells of T. hibernicus sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35-40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C16 : 0 at 22.8 %. Strain MCA3T is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3T, Terrisporobacter petrolearius LAM0A37T and Terrisporobacter mayombei DSM 6539T are also included for the first time. The closed and complete genome of strain MCA3T from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of T. mayombei DSM 6539T and T. petrolearius LAM0A37T, as performed by Illumina MiSeq, provides reference genomes for these respective species of Terrisporobacter for the first time. DNA-DNA hybridization values (d4) of MCA3T to Terrisporobacter glycolicus ATCC 14880T, T. petrolearius LAM0A37T and T. mayombei DSM 6539T are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for T. hibernicus sp. nov. is MCA3T (=NCTC 14625T=LMG 32430T).
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Affiliation(s)
- Molly Mitchell
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland.,District of Columbia Department of Forensic Sciences, Public Health Laboratory, Washington, DC, USA.,Present address: Sequencing and Bioinformatics Center, American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Mairead Connor
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Department of Microbiology, Belfast Health & Social Care Trust, Belfast, Ireland
| | - Derek J Fairley
- Department of Microbiology, Belfast Health & Social Care Trust, Belfast, Ireland
| | - Orla Donoghue
- Department of Microbiology, St. Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin, Ireland
| | - Helina Marshall
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Leonard Koolman
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Geoff McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Kirsten E Schaffer
- Department of Microbiology, St. Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin, Ireland
| | - John W McGrath
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Séamus Fanning
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
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7
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Reyne MI, Allen DM, Levickas A, Allingham P, Lock J, Fitzgerald A, McSparron C, Nejad BF, McKinley J, Lee A, Bell SH, Quick J, Houldcroft CJ, Bamford CGG, Gilpin DF, McGrath JW. Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology. Sci Total Environ 2023; 857:159579. [PMID: 36270375 DOI: 10.1016/j.scitotenv.2022.159579] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/22/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
As of 8 July 2022, the World Health Organization (WHO) have reported 1010 probable cases of acute hepatitis of unknown aetiology in children worldwide, including approximately 250 cases in the United Kingdom (UK). Clinical presentations have often been severe, with liver transplantation a frequent clinical outcome. Human adenovirus F41 (HAdV-F41) has been detected in most children with acute hepatitis, but its role in the pathogenesis of this infection has yet to be established. Wastewater-based epidemiology (WBE) has become a well-established tool for monitoring the community spread of SARS-CoV-2, as well as other pathogens and chemicals. In this study, we adopted a WBE approach to monitoring levels of HAdV-F40/41 in wastewater before and during an acute hepatitis outbreak in Northern Ireland. We report increasing detection of HAdV-F40/41 in wastewater, concomitant with increasing numbers of clinical cases. Amplicon whole genome sequencing further classified the wastewater-derived HAdV as belonging to the F41 genotype which in turn was homologous to clinically derived sequences. We propose that WBE has the potential to inform community surveillance of HAdV-F41 and can further contribute to the ongoing global discussion supporting HAdV-F41 involvement in acute hepatitis cases.
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Affiliation(s)
- Marina I Reyne
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK.
| | - Danielle M Allen
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Ashley Levickas
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Pearce Allingham
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Jonathan Lock
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Arthur Fitzgerald
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Cormac McSparron
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast BT9 6AZ, Northern Ireland, UK
| | - Behnam F Nejad
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast BT9 6AZ, Northern Ireland, UK
| | - Jennifer McKinley
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast BT9 6AZ, Northern Ireland, UK
| | - Andrew Lee
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Stephen H Bell
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
| | - Joshua Quick
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Connor G G Bamford
- Wellcome-Wolfson Institute for Experimental Medicine (WWIEM), School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
| | - Deirdre F Gilpin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
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8
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Marshall A, McGrath JW, Graham R, McMullan G. Food for thought-The link between Clostridioides difficile metabolism and pathogenesis. PLoS Pathog 2023; 19:e1011034. [PMID: 36602960 PMCID: PMC9815643 DOI: 10.1371/journal.ppat.1011034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is an opportunistic pathogen that leads to antibiotic-associated diarrhoea and is a leading cause of morbidity and mortality worldwide. Antibiotic usage is the main risk factor leading to C. difficile infection (CDI), as a dysbiotic gut environment allows colonisation and eventual pathology manifested by toxin production. Although colonisation resistance is mediated by the action of secondary bile acids inhibiting vegetative outgrowth, nutrient competition also plays a role in preventing CDI as the gut microbiota compete for nutrient niches inhibiting C. difficile growth. C. difficile is able to metabolise carbon dioxide, the amino acids proline, hydroxyproline, and ornithine, the cell membrane constituent ethanolamine, and the carbohydrates trehalose, cellobiose, sorbitol, and mucin degradation products as carbon and energy sources through multiple pathways. Zinc sequestration by the host response mediates metabolic adaptation of C. difficile by perhaps signalling an inflamed gut allowing it to acquire abundant nutrients. Persistence within the gut environment is also mediated by the by-products of metabolism through the production of p-cresol, which inhibit gut commensal species growth promoting dysbiosis. This review aims to explore and describe the various metabolic pathways of C. difficile, which facilitate its survival and pathogenesis within the colonised host gut.
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Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Robert Graham
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
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9
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Lawther K, Santos FG, Oyama LB, Rubino F, Morrison S, Creevey CJ, McGrath JW, Huws SA. Resistome Analysis of Global Livestock and Soil Microbiomes. Front Microbiol 2022; 13:897905. [PMID: 35875563 PMCID: PMC9300982 DOI: 10.3389/fmicb.2022.897905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million deaths annually. Agricultural and soil environments act as antimicrobial resistance gene (ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing and dissemination of resistance genes. Due to the close interactions between humans and agricultural environments, these AMR gene reservoirs are a major risk to both human and animal health. In this study, we aimed to identify the resistance gene reservoirs present in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with those from soil. This large study brings together every poultry, swine, ruminant, and soil shotgun metagenomic sequence available on the NCBI sequence read archive for the first time. We use the ResFinder database to identify acquired antimicrobial resistance genes in over 5,800 metagenomes. ARGs were diverse and widespread within the metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance genes were the most widespread in the livestock GI microbiomes, including tet(W)_1, tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were “real” and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were shared by the four microbiomes, with 11 ARGs actively expressed in two or more microbiomes. By using all available metagenomes we were able to mine a large number of samples and describe resistomes in 37 countries. This study provides a global insight into the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes.
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Affiliation(s)
- Katie Lawther
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Fernanda Godoy Santos
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Linda Boniface Oyama
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Francesco Rubino
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Steven Morrison
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Chris J. Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Sharon Ann Huws
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
- *Correspondence: Sharon Ann Huws,
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10
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Wade MJ, Lo Jacomo A, Armenise E, Brown MR, Bunce JT, Cameron GJ, Fang Z, Farkas K, Gilpin DF, Graham DW, Grimsley JMS, Hart A, Hoffmann T, Jackson KJ, Jones DL, Lilley CJ, McGrath JW, McKinley JM, McSparron C, Nejad BF, Morvan M, Quintela-Baluja M, Roberts AMI, Singer AC, Souque C, Speight VL, Sweetapple C, Walker D, Watts G, Weightman A, Kasprzyk-Hordern B. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes. J Hazard Mater 2022; 424:127456. [PMID: 34655869 PMCID: PMC8498793 DOI: 10.1016/j.jhazmat.2021.127456] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.
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Affiliation(s)
- Matthew J Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK.
| | - Anna Lo Jacomo
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Bristol University, Department of Engineering Mathematics, Bristol BS8 1TW, UK
| | - Elena Armenise
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew R Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Joshua T Bunce
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; Department for Environment, Food and Rural Affairs, Seacole Building, 2 Marsham Street, London SW1P 4DF, UK
| | - Graeme J Cameron
- Scottish Environment Protection Agency, Strathallan House, Stirling FK9 4TZ, UK
| | - Zhou Fang
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Kata Farkas
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK
| | - Deidre F Gilpin
- Queen's University Belfast, School of Pharmacy, Lisburn Road, Belfast BT9 7BL, UK
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - Alwyn Hart
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Till Hoffmann
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Imperial College London, Department of Mathematics, London SW7 2AZ, UK
| | - Katherine J Jackson
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David L Jones
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK; The University of Western Australia, UWA School of Agriculture and Environment, Perth, WA 6009, Australia
| | - Chris J Lilley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - John W McGrath
- Queen's University Belfast, School of Biological Sciences, Chlorine Gardens, Belfast BT9 5DL, UK
| | - Jennifer M McKinley
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Cormac McSparron
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Behnam F Nejad
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Mario Morvan
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK
| | - Marcos Quintela-Baluja
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Adrian M I Roberts
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew C Singer
- UK Centre for Ecology and Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Célia Souque
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Oxford, Department of Zoology, Mansfield Road, Oxford OX1 3SZ, UK
| | - Vanessa L Speight
- University of Sheffield, Department of Civil and Structural Engineering, Mappin Street, Sheffield S1 3JD, UK
| | - Chris Sweetapple
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Exeter, Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, Exeter EX4 4QF, UK
| | - David Walker
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth DT4 8UB, UK
| | - Glenn Watts
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Andrew Weightman
- Cardiff University, Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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11
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Yang JW, Fang W, Williams PN, McGrath JW, Eismann CE, Menegário AA, Elias LP, Luo J, Xu Y. Functionalized Mesoporous Silicon Nanomaterials in Inorganic Soil Pollution Research: Opportunities for Soil Protection and Advanced Chemical Imaging. Curr Pollut Rep 2020; 6:264-280. [PMID: 32879840 PMCID: PMC7446291 DOI: 10.1007/s40726-020-00152-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
"Innovative actions towards a pollution free-planet" is a goal of the United Nations Environment Assembly (UNEA). Aided by both the Food and Agricultural Organisation (FAO) and its Global Soil Partnership under the 3rd UNEA resolution, a consensus from > 170 countries have agreed a need for accelerated action and collaboration to combat soil pollution. This initiative has been tasked to find new and improved solutions to prevent and reduce soil pollution, and it is in this context that this review provides an updated perspective on an emerging technology platform that has already provided demonstrable utility for measurement, mapping, and monitoring of toxic trace elements (TTEs) in soils, in addition to the entrapment, removal, and remediation of pollutant sources. In this article, the development and characteristics of functionalized mesoporous silica nanomaterials (FMSN) will be discussed and compared with other common metal scavenging materials. The chemistries of the common functionalizations will be reviewed, in addition to providing an outlook on some of the future directions/applications of FMSN. The use of FMSN in soil will be considered with some specific case studies focusing on Hg and As. Finally, the advantages and developments of FMSN in the widely used diffusive gradients-in-thin films (DGT) technique will be discussed, in particular, its advantages as a DGT substrate for integration with oxygen planar optodes in multilayer systems that provide 2D mapping of metal pollutant fluxes at submillimeter resolution, which can be used to measure detailed sediment-water fluxes as well as soil-root interactions, to predict plant uptake and bioavailability.
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Affiliation(s)
- Jia-Wei Yang
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland BT9 5DL UK
| | - Wen Fang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023 Jiangsu China
| | - Paul N. Williams
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland BT9 5DL UK
| | - John W. McGrath
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland BT9 5DL UK
| | - Carlos Eduardo Eismann
- Environmental Studies Center (CEA), São Paulo State University (UNESP), Avenida 24-A, 1515, Rio Claro, SP 13506-900 Brazil
| | - Amauri Antonio Menegário
- Environmental Studies Center (CEA), São Paulo State University (UNESP), Avenida 24-A, 1515, Rio Claro, SP 13506-900 Brazil
| | - Lucas Pellegrini Elias
- Environmental Studies Center (CEA), São Paulo State University (UNESP), Avenida 24-A, 1515, Rio Claro, SP 13506-900 Brazil
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023 Jiangsu China
| | - Yingjian Xu
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- GoldenKeys High-Tech Materials Co., Ltd., Building B, Innovation & Entrepreneurship Park, Guian New Area, Guian, 550025 Guizhou China
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12
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Paula FS, Chin JP, Schnürer A, Müller B, Manesiotis P, Waters N, Macintosh KA, Quinn JP, Connolly J, Abram F, McGrath JW, O'Flaherty V. The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei. Sci Rep 2019; 9:17101. [PMID: 31745137 PMCID: PMC6864096 DOI: 10.1038/s41598-019-53168-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.
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Affiliation(s)
- Fabiana S Paula
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland.
- Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Jason P Chin
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Anna Schnürer
- Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bettina Müller
- Department of Molecular Sciences, Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Panagiotis Manesiotis
- School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, UK
| | - Nicholas Waters
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
- Information and Computational Sciences, James Hutton Institute, Dundee, UK
| | - Katrina A Macintosh
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - John P Quinn
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Jasmine Connolly
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Florence Abram
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Vincent O'Flaherty
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland.
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13
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Connor MC, McGrath JW, McMullan G, Marks N, Guelbenzu M, Fairley DJ. Emergence of a non-sporulating secondary phenotype in Clostridium (Clostridioides) difficile ribotype 078 isolated from humans and animals. Sci Rep 2019; 9:13722. [PMID: 31548637 PMCID: PMC6757067 DOI: 10.1038/s41598-019-50285-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Clostridium (Clostridioides) difficile is a Gram positive, spore forming anaerobic bacterium that is a leading cause of antibiotic associated diarrhoea in the developed world. C. difficile is a genetically diverse species that can be divided into 8 phylogenetically distinct clades with clade 5 found to be genetically distant from all others. Isolates with the PCR ribotype 078 belong to clade 5, and are often associated with C. difficile infection in both humans and animals. Colonisation of animals and humans by ribotype 078 raises questions about possible zoonotic transmission, and also the diversity of reservoirs for ribotype 078 strains within the environment. One of the key factors which enables C. difficile to be a successful, highly transmissible pathogen is its ability to produce oxygen resistant spores capable of surviving harsh conditions. Here we describe the existence of a non-sporulating variant of C. difficile ribotype 078 harbouring mutations leading to premature stop codons within the master regulator, Spo0A. As sporulation is imperative to the successful transmission of C. difficile this study was undertaken to investigate phenotypic characteristics of this asporogenous phenotype with regards to growth rate, antibiotic susceptibility, toxin production and biofilm formation.
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Affiliation(s)
- M C Connor
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK.
| | - J W McGrath
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - G McMullan
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - N Marks
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - M Guelbenzu
- Veterinary Science Division, Agri-Food Biosciences Institute, Belfast, UK.,Animal Health Ireland, Carrick on Shannon, Republic of Ireland
| | - D J Fairley
- Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
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14
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Kelly SA, Magill DJ, Megaw J, Skvortsov T, Allers T, McGrath JW, Allen CCR, Moody TS, Gilmore BF. Characterisation of a solvent-tolerant haloarchaeal (R)-selective transaminase isolated from a Triassic period salt mine. Appl Microbiol Biotechnol 2019; 103:5727-5737. [PMID: 31123770 PMCID: PMC6597733 DOI: 10.1007/s00253-019-09806-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transaminase enzymes (TAms) are becoming increasingly valuable in the chemist’s toolbox as a biocatalytic route to chiral amines. Despite high profile successes, the lack of (R)-selective TAms and robustness under harsh industrial conditions continue to prove problematic. Herein, we report the isolation of the first haloarchaeal TAm (BC61-TAm) to be characterised for the purposes of pharmaceutical biocatalysis. BC61-TAm is an (R)-selective enzyme, cloned from an extremely halophilic archaeon, isolated from a Triassic period salt mine. Produced using a Haloferax volcanii–based expression model, the resulting protein displays a classic halophilic activity profile, as well as thermotolerance (optimum 50 °C) and organic solvent tolerance. Molecular modelling predicts the putative active site residues of haloarchaeal TAms, with molecular dynamics simulations providing insights on the basis of BC61-TAm’s organic solvent tolerance. These results represent an exciting advance in the study of transaminases from extremophiles, providing a possible scaffold for future discovery of biocatalytic enzymes with robust properties.
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Affiliation(s)
| | - Damian J Magill
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Julianne Megaw
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | | | - Thomas S Moody
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, UK
- Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
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15
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Macintosh KA, Chin J, Jacobs B, Cordell D, McDowell RW, Butler P, Haygarth PM, Williams P, Quinn JP, O'Flaherty V, McGrath JW. Transforming phosphorus use on the island of Ireland: A model for a sustainable system. Sci Total Environ 2019; 656:852-861. [PMID: 30530153 DOI: 10.1016/j.scitotenv.2018.11.389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 05/26/2023]
Abstract
Phosphorus is an essential part of the world food web and a non-substitutable nutrient in all biological systems. Losses of phosphorus occur along the food-supply chain and cause environmental degradation and eutrophication. A key global challenge is to meet rising worldwide food demand while protecting water and environmental quality, and seeking to manage uncertainty around potential future phosphorus price or supply shocks. This paper presents a stakeholder-generated conceptual model of potential transformative change for implementing phosphorus sustainability on the island of Ireland via an 'All-Island Phosphorus Sustainability' workshop. Key transition pathways identified by stakeholders included: incentivising phosphorus recovery, developing collaborative networks to facilitate change, developing markets and value chains for recovered products; implementing data-informed practices on-farm to prevent losses and increase efficiencies, and harmonisation of technologies with end-user needs. A comparable model was previously produced for the North American region. We describe consensus and differences around key priorities between the two regions' conceptual models, and assess how the model produced for the island of Ireland can effect system-wide change and policy moving forward. Many of the transitional pathways and future aspirations presented in both models resonate globally and are highly pertinent to other jurisdictions.
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Affiliation(s)
- Katrina A Macintosh
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, United Kingdom.
| | - Jason Chin
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, United Kingdom
| | - Brent Jacobs
- Institute for Sustainable Futures, University of Technology Sydney, Australia
| | - Dana Cordell
- Institute for Sustainable Futures, University of Technology Sydney, Australia
| | - Richard W McDowell
- AgResearch, Lincoln Science Centre, Christchurch, New Zealand; Soil and Physical Sciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Paul Butler
- Manufacturing, Engineering and Energy Commercialisation, Enterprise Ireland, Ireland
| | - Philip M Haygarth
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Paul Williams
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, United Kingdom
| | - John P Quinn
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, United Kingdom
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Ireland
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, United Kingdom
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16
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Macintosh KA, Doody DG, Withers PJA, McDowell RW, Smith DR, Johnson LT, Bruulsema TW, O'Flaherty V, McGrath JW. Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems. Sci Total Environ 2019; 649:90-98. [PMID: 30172137 DOI: 10.1016/j.scitotenv.2018.08.272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 05/20/2023]
Abstract
Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha-1 yr-1 units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.
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Affiliation(s)
- Katrina A Macintosh
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, UK.
| | | | - Paul J A Withers
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Richard W McDowell
- AgResearch, Lincoln Science Centre, Christchurch, New Zealand; Soil and Physical Sciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Douglas R Smith
- Grassland, Soil and Water Research Laboratory, USDA-ARS, TX, USA
| | - Laura T Johnson
- National Center for Water Quality Research, Heidelberg University, OH, USA
| | | | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Ireland
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast, UK
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17
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Connor MC, McGrath JW, McMullan G, Marks N, Fairley DJ. Response to methodologic variables that impact growth of Clostridium difficile in a broth culture medium without requirement for anaerobic culture conditions. Anaerobe 2019; 56:135. [PMID: 30615945 DOI: 10.1016/j.anaerobe.2018.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/28/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Mairéad C Connor
- School of Biological Sciences and the Institute for Global Food Security, Medical Biology Centre, Queens University Belfast, Northern Ireland, United Kingdom.
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, Medical Biology Centre, Queens University Belfast, Northern Ireland, United Kingdom
| | - Geoff McMullan
- School of Biological Sciences and the Institute for Global Food Security, Medical Biology Centre, Queens University Belfast, Northern Ireland, United Kingdom
| | - Nikki Marks
- School of Biological Sciences and the Institute for Global Food Security, Medical Biology Centre, Queens University Belfast, Northern Ireland, United Kingdom
| | - Derek J Fairley
- Department of Microbiology, Belfast Health & Social Care Trust, Belfast, Northern Ireland, United Kingdom
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18
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Kelly SA, Skvortsov T, Magill D, Quinn DJ, McGrath JW, Allen CCR, Moody TS, Gilmore BF. Characterization of a novel ω-transaminase from a Triassic salt mine metagenome. Biochem Biophys Res Commun 2018; 503:2936-2942. [PMID: 30119883 DOI: 10.1016/j.bbrc.2018.08.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023]
Abstract
Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the harsh conditions often demanded by industrial processes. These characteristics have, in part, driven the search for novel biocatalysts from both metagenomic sources and extreme environments. Herein, we report the isolation and characterization of an ω-TAm from a metagenome of a Triassic salt mine in Kilroot, N. Ireland, an extremely hypersaline environment formed circa 220-250 mya. The gene sequence was identified based on homology with existing bacterial TAms, synthesized within a pET28a(+) plasmid and expressed in E. coli BL21 DE3 cells. The resultant 49 kDa protein accepted (S)-methylbenzylamine (MBA) as amino donor and had a specific activity of 0.54 U/mg using α-ketoglutarate (ΑKG) as substrate. Molecular modeling and substrate docking indicated the presence of key residues, conserved in a number of other TAms. Despite the hypersaline environment from which it was isolated, the enzyme displayed low halotolerance, highlighting that not all biocatalysts will demonstrate the extreme characteristics associated with their source environment. This study does however reinforce the viability of mining metagenomic datasets as a means of discovering novel and functional biocatalysts, and adds to a currently scant list of such examples in the field of TAms.
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Affiliation(s)
- Stephen A Kelly
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Timofey Skvortsov
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Damian Magill
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Derek J Quinn
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, N. Ireland, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK
| | - Thomas S Moody
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, N. Ireland, UK; Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, N. Ireland, UK.
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Magill DJ, McGrath JW, O'Flaherty V, Quinn JP, Kulakov LA. Insights into the structural dynamics of the bacteriophage T7 DNA polymerase and its complexes. J Mol Model 2018; 24:144. [PMID: 29858666 PMCID: PMC5984650 DOI: 10.1007/s00894-018-3671-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 05/10/2018] [Indexed: 11/24/2022]
Abstract
The T7 DNA polymerase is dependent on the host protein thioredoxin (trx) for its processivity and fidelity. Using all-atom molecular dynamics, we demonstrate the specific interactions between trx and the T7 polymerase, and show that trx docking to its binding domain on the polymerase results in a significant level of stability and exposes a series of basic residues within the domain that interact with the phosphodiester backbone of the DNA template. We also characterize the nature of interactions between the T7 DNA polymerase and its DNA template. We show that the trx-binding domain acts as an intrinsic clamp, constraining the DNA via a two-step hinge motion, and characterize the interactions necessary for this to occur. Together, these insights provide a significantly improved understanding of the interactions responsible for highly processive DNA replication by T7 polymerase.
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Affiliation(s)
- Damian J Magill
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland.
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland.
| | - John W McGrath
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John P Quinn
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Leonid A Kulakov
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
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20
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Arkhipova K, Skvortsov T, Quinn JP, McGrath JW, Allen CC, Dutilh BE, McElarney Y, Kulakov LA. Temporal dynamics of uncultured viruses: a new dimension in viral diversity. ISME J 2017; 12:199-211. [PMID: 29027998 DOI: 10.1038/ismej.2017.157] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022]
Abstract
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.
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Affiliation(s)
- Ksenia Arkhipova
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Timofey Skvortsov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - John P Quinn
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
| | - John W McGrath
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Christopher Cr Allen
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - Leonid A Kulakov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
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21
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Magill DJ, Krylov VN, Shaburova OV, McGrath JW, Allen CCR, Quinn JP, Kulakov LA. Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages. PLoS One 2017; 12:e0184307. [PMID: 28877269 PMCID: PMC5587285 DOI: 10.1371/journal.pone.0184307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022] Open
Abstract
We present the analysis of two novel Pseudomonas putida phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanophage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida phage AF is likely responsible for the tropism of this phage. phiPMW represents a completely novel Pseudomonas phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group.
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Affiliation(s)
- Damian J. Magill
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Victor N. Krylov
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - Olga V. Shaburova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - John W. McGrath
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Christopher C. R. Allen
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - John P. Quinn
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Leonid A. Kulakov
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
- * E-mail:
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22
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Weerasekara AW, Jenkins S, Abbott LK, Waite I, McGrath JW, Larma I, Eroglu E, O'Donnell A, Whiteley AS. Microbial phylogenetic and functional responses within acidified wastewater communities exhibiting enhanced phosphate uptake. Bioresour Technol 2016; 220:55-61. [PMID: 27566512 DOI: 10.1016/j.biortech.2016.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5>8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics.
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Affiliation(s)
- Anjani W Weerasekara
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Sasha Jenkins
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Lynette K Abbott
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Ian Waite
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queens University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Irma Larma
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, Crawley, 35 Stirling Highway, 6009 Western Australia, Australia
| | - Ela Eroglu
- Department of Chemical Engineering, Curtin University, Perth 6845, Western Australia, Australia
| | - Anthony O'Donnell
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Andrew S Whiteley
- School of Earth and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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23
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Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
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24
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Keating C, Chin JP, Hughes D, Manesiotis P, Cysneiros D, Mahony T, Smith CJ, McGrath JW, O'Flaherty V. Biological Phosphorus Removal During High-Rate, Low-Temperature, Anaerobic Digestion of Wastewater. Front Microbiol 2016; 7:226. [PMID: 26973608 PMCID: PMC4776080 DOI: 10.3389/fmicb.2016.00226] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022] Open
Abstract
We report, for the first time, extensive biologically mediated phosphate removal from wastewater during high-rate anaerobic digestion (AD). A hybrid sludge bed/fixed-film (packed pumice stone) reactor was employed for low-temperature (12°C) anaerobic treatment of synthetic sewage wastewater. Successful phosphate removal from the wastewater (up to 78% of influent phosphate) was observed, mediated by biofilms in the reactor. Scanning electron microscopy and energy dispersive X-ray analysis revealed the accumulation of elemental phosphorus (∼2%) within the sludge bed and fixed-film biofilms. 4′, 6-diamidino-2-phenylindole (DAPI) staining indicated phosphorus accumulation was biological in nature and mediated through the formation of intracellular inorganic polyphosphate (polyP) granules within these biofilms. DAPI staining further indicated that polyP accumulation was rarely associated with free cells. Efficient and consistent chemical oxygen demand (COD) removal was recorded, throughout the 732-day trial, at applied organic loading rates between 0.4 and 1.5 kg COD m-3 d-1 and hydraulic retention times of 8–24 h, while phosphate removal efficiency ranged from 28 to 78% on average per phase. Analysis of protein hydrolysis kinetics and the methanogenic activity profiles of the biomass revealed the development, at 12°C, of active hydrolytic and methanogenic populations. Temporal microbial changes were monitored using Illumina MiSeq analysis of bacterial and archaeal 16S rRNA gene sequences. The dominant bacterial phyla present in the biomass at the conclusion of the trial were the Proteobacteria and Firmicutes and the dominant archaeal genus was Methanosaeta. Trichococcus and Flavobacterium populations, previously associated with low temperature protein degradation, developed in the reactor biomass. The presence of previously characterized polyphosphate accumulating organisms (PAOs) such as Rhodocyclus, Chromatiales, Actinobacter, and Acinetobacter was recorded at low numbers. However, it is unknown as yet if these were responsible for the luxury polyP uptake observed in this system. The possibility of efficient phosphate removal and recovery from wastewater during AD would represent a major advance in the scope for widespread application of anaerobic wastewater treatment technologies.
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Affiliation(s)
- Ciara Keating
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Jason P Chin
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast Belfast, UK
| | - Dermot Hughes
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Panagiotis Manesiotis
- School of Chemistry and Chemical Engineering, The Queen's University of Belfast Belfast, UK
| | - Denise Cysneiros
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Therese Mahony
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Cindy J Smith
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast Belfast, UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
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25
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Skvortsov T, de Leeuwe C, Quinn JP, McGrath JW, Allen CCR, McElarney Y, Watson C, Arkhipova K, Lavigne R, Kulakov LA. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. PLoS One 2016; 11:e0150361. [PMID: 26927795 PMCID: PMC4771703 DOI: 10.1371/journal.pone.0150361] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.
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Affiliation(s)
- Timofey Skvortsov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Colin de Leeuwe
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John P. Quinn
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Yvonne McElarney
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Catherine Watson
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Ksenia Arkhipova
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leonid A. Kulakov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
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26
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Casey WT, Nikodinovic-Runic J, Fonseca Garcia P, Guzik MW, McGrath JW, Quinn JP, Cagney G, Prieto MA, O'Connor KE. The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440. Environ Microbiol Rep 2013; 5:740-746. [PMID: 24115625 DOI: 10.1111/1758-2229.12076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/11/2013] [Indexed: 06/02/2023]
Abstract
The primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk), has been deleted in Pseudomonas putida KT2440. This has resulted in a threefold to sixfold reduction in polyhydroxyalkanoate (PHA) accumulation compared with the wild type under conditions of nitrogen limitation, with either temperature or oxidative (H2O2) stress, when grown on glucose. The accumulation of PHA by Δppk mutant was the same as the wild type under nitrogen-limiting growth conditions. There was no difference in polyP levels between wild-type and Δppk strains under all growth conditions tested. In the Δppk mutant proteome, polyP kinase (PPK) was undetectable, but up-regulation of the polyp-associated proteins polyP adenosine triphosphate (ATP)/nicotinamide adenine dinucleotide (NAD) kinase (PpnK), a putative polyP adenosine monophosphate (AMP) phosphotransferase (PP_1752), and exopolyphosphatase was observed. Δppk strain exhibited significantly retarded growth with glycerol as carbon and energy source (42 h of lag period compared with 24 h in wild-type strain) but similar growth to the wild-type strain with glucose. Analysis of gene transcription revealed downregulation of glycerol kinase and the glycerol facilitator respectively. Glycerol kinase protein expression was also downregulated in the Δppk mutant. The deletion of ppk did not affect motility but reduced biofilm formation. Thus, the knockout of the ppk gene has resulted in a number of phenotypic changes to the mutant without affecting polyP accumulation.
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Affiliation(s)
- William T Casey
- School of Biomedical and Biomolecular Science, University College Dublin, Belfield, Dublin, 4, Dublin, Ireland
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27
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Abstract
Organophosphonates are ancient molecules that contain the chemically stable C-P bond, which is considered a relic of the reducing atmosphere on primitive earth. Synthetic phosphonates now have a wide range of applications in the agricultural, chemical and pharmaceutical industries. However, the existence of C-P compounds as contemporary biogenic molecules was not discovered until 1959, with the identification of 2-aminoethylphosphonic acid in rumen protozoa. Here, we review advances in our understanding of the biochemistry and genetics of microbial phosphonate metabolism, and discuss the role of these compounds and of the organisms engaged in their turnover within the P cycle.
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Affiliation(s)
- John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queens University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland
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28
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Winchester MS, McGrath JW, Kaawa-Mafigiri D, Namutiibwa F, Ssendegye G, Nalwoga A, Kyarikunda E, Birungi J, Kisakye S, Ayebazibwe N, Walakira E, Rwabukwali CB. Early HIV disclosure and nondisclosure among men and women on antiretroviral treatment in Uganda. AIDS Care 2013; 25:1253-8. [PMID: 23356654 DOI: 10.1080/09540121.2013.764386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Efforts to expand access to HIV care and treatment often stress the importance of disclosure of HIV status to aid adherence, social support, and continued resource mobilization. We argue that an examination of disclosure processes early in the process of seeking testing and treatment can illuminate individual decisions and motivations, offering insight into potentially improving engagement in care and adherence. We report on baseline data of early HIV disclosure and nondisclosure, including reasons for and responses to disclosure from a cohort of men and women (n=949) currently accessing antiretroviral treatment in two regions of Uganda. We found early disclosures at the time of suspicion or testing positive for HIV by men and women to be largely for the purposes of emotional support and friendship. Responses to these selected disclosures were overwhelmingly positive and supportive, including assistance in accessing treatment. Nonetheless, some negative responses of worry, fear, or social ostracism did occur. Individuals deliberately chose to not disclose their status to partners, relatives, and others in their network, for reasons of privacy or not wanting to cause worry from the other person. These data demonstrate the strategic choices that individuals make early in the course of suspicion, testing, and treatment for HIV to mobilize resources and gain emotional or material support, and similarly their decisions and ability to maintain privacy regarding their status.
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Affiliation(s)
- M S Winchester
- a Department of Geography , The Pennsylvania State University , University Park , PA , USA
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29
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Glukhov AS, Krutilina AI, Shlyapnikov MG, Severinov K, Lavysh D, Kochetkov VV, McGrath JW, de Leeuwe C, Shaburova OV, Krylov VN, Akulenko NV, Kulakov LA. Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions. PLoS One 2012; 7:e51163. [PMID: 23236447 PMCID: PMC3517423 DOI: 10.1371/journal.pone.0051163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
The complete sequence of the 46,267 bp genome of the lytic bacteriophage tf specific to Pseudomonas putida PpG1 has been determined. The phage genome has two sets of convergently transcribed genes and 186 bp long direct terminal repeats. The overall genomic architecture of the tf phage is similar to that of the previously described Pseudomonas aeruginosa phages PaP3, LUZ24 and phiMR299-2, and 39 out of the 72 products of predicted tf open reading frames have orthologs in these phages. Accordingly, tf was classified as belonging to the LUZ24-like bacteriophage group. However, taking into account very low homology levels between tf DNA and that of the other phages, tf should be considered as an evolutionary divergent member of the group. Two distinguishing features not reported for other members of the group were found in the tf genome. Firstly, a unique end structure – a blunt right end and a 4-nucleotide 3′-protruding left end – was observed. Secondly, 14 single-chain interruptions (nicks) were found in the top strand of the tf DNA. All nicks were mapped within a consensus sequence 5′-TACT/RTGMC-3′. Two nicks were analyzed in detail and were shown to be present in more than 90% of the phage population. Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages.
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Affiliation(s)
- Anatoly S. Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | | | - Michael G. Shlyapnikov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Konstantin Severinov
- Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Daria Lavysh
- Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V. Kochetkov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - John W. McGrath
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Colin de Leeuwe
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Olga V. Shaburova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, RAMS, Moscow, Russia
| | - Victor N. Krylov
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, RAMS, Moscow, Russia
| | - Natalia V. Akulenko
- Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Leonid A. Kulakov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
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30
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Villarreal-Chiu JF, Quinn JP, McGrath JW. The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. Front Microbiol 2012; 3:19. [PMID: 22303297 PMCID: PMC3266647 DOI: 10.3389/fmicb.2012.00019] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/10/2012] [Indexed: 11/13/2022] Open
Abstract
Phosphonates are compounds that contain the chemically stable carbon–phosphorus (C–P) bond. They are widely distributed amongst more primitive life forms including many marine invertebrates and constitute a significant component of the dissolved organic phosphorus reservoir in the oceans. Virtually all biogenic C–P compounds are synthesized by a pathway in which the key step is the intramolecular rearrangement of phosphoenolpyruvate to phosphonopyruvate. However C–P bond cleavage by degradative microorganisms is catalyzed by a number of enzymes – C–P lyases, C–P hydrolases, and others of as-yet-uncharacterized mechanism. Expression of some of the pathways of phosphonate catabolism is controlled by ambient levels of inorganic P (Pi) but for others it is Pi-independent. In this report we review the enzymology of C–P bond metabolism in bacteria, and also present the results of an in silico investigation of the distribution of the genes that encode the pathways responsible, in both bacterial genomes and in marine metagenomic libraries, and their likely modes of regulation. Interrogation of currently available whole-genome bacterial sequences indicates that some 10% contain genes encoding putative pathways of phosphonate biosynthesis while ∼40% encode one or more pathways of phosphonate catabolism. Analysis of metagenomic data from the global ocean survey suggests that some 10 and 30%, respectively, of bacterial genomes across the sites sampled encode these pathways. Catabolic routes involving phosphonoacetate hydrolase, C–P lyase(s), and an uncharacterized 2-aminoethylphosphonate degradative sequence were predominant, and it is likely that both substrate-inducible and Pi-repressible mechanisms are involved in their regulation. The data we present indicate the likely importance of phosphonate-P in global biogeochemical P cycling, and by extension its role in marine productivity and in carbon and nitrogen dynamics in the oceans.
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McGrath JW, Hammerschmidt F, Kählig H, Wuggenig F, Lamprecht G, Quinn JP. Studies on the biodegradation of fosfomycin: synthesis of 13C-labeled intermediates, feeding experiments with Rhizobium huakuii PMY1, and isolation of labeled amino acids from cell mass by HPLC. Chemistry 2011; 17:13341-8. [PMID: 22012897 DOI: 10.1002/chem.201100725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 08/22/2011] [Indexed: 11/10/2022]
Abstract
Racemic (1R*,2R*)-1,2-dihydroxy-[1-(13)C(1)]propylphosphonic acid and 1-hydroxy-[1-(13)C(1)]acetone were synthesized and fed to R. huakuii PMY1. Alanine and a mixture of valine and methionine were isolated as their N-acetyl derivatives from the cell hydrolysate by reversed-phase HPLC and analyzed by NMR spectroscopy. It was found that the carbon atoms of the respective carboxyl groups were highly (13)C-labeled (up to 65 %). Hydroxyacetone is therefore considered an obligatory intermediate of the biodegradation of fosfomycin by R. huakuii PMY1.
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Affiliation(s)
- John W McGrath
- School of Biological Sciences, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland.
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Kulakova AN, Hobbs D, Smithen M, Pavlov E, Gilbert JA, Quinn JP, McGrath JW. Direct quantification of inorganic polyphosphate in microbial cells using 4'-6-diamidino-2-phenylindole (DAPI). Environ Sci Technol 2011; 45:7799-7803. [PMID: 21875055 DOI: 10.1021/es201123r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Inorganic polyphosphate (polyP) is increasingly being recognized as an important phosphorus sink within the environment, playing a central role in phosphorus exchange and phosphogenesis. Yet despite the significant advances made in polyP research there is a lack of rapid and efficient analytical approaches for the quantification of polyP accumulation in microbial cultures and environmental samples. A major drawback is the need to extract polyP from cells prior to analysis. Due to extraction inefficiencies this can lead to an underestimation of both intracellular polyP levels and its environmental pool size: we observed 23-58% loss of polyP using standard solutions and current protocols. Here we report a direct fluorescence based DAPI assay system which removes the requirement for prior polyP extraction before quantification. This increased the efficiency of polyP detection by 28-55% in microbial cultures suggesting quantitative measurement of the intracellular polyP pool. It provides a direct polyP assay which combines quantification capability with technical simplicity. This is an important step forward in our ability to explore the role of polyP in cellular biology and biogeochemical nutrient cycling.
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Affiliation(s)
- Anna N Kulakova
- School of Biological Sciences and QUESTOR Centre, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Rd., Belfast, BT9 7BL, Northern Ireland
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33
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Kulakova AN, Kulakov LA, McGrath JW, Quinn JP. The construction of a whole-cell biosensor for phosphonoacetate, based on the LysR-like transcriptional regulator PhnR from Pseudomonas fluorescens 23F. Microb Biotechnol 2011; 2:234-40. [PMID: 21261917 PMCID: PMC3815843 DOI: 10.1111/j.1751-7915.2008.00082.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The phnA gene that encodes the carbon‐phosphorus bond cleavage enzyme phosphonoacetate hydrolase is widely distributed in the environment, suggesting that its phosphonate substrate may play a significant role in biogeochemical phosphorus cycling. Surprisingly, however, no biogenic origin for phosphonoacetate has yet been established. To facilitate the search for its natural source we have constructed a whole‐cell phosphonoacetate biosensor. The gene encoding the LysR‐type transcriptional activator PhnR, which controls expression of the phosphonoacetate degradative operon in Pseudomonas fluorescens 23F, was inserted in the broad‐host‐range promoter probe vector pPROBE‐NT, together with the promoter region of the structural genes. Cells of Escherichia coli DH5α that contained the resultant construct, pPANT3, exhibited phosphonoacetate‐dependent green fluorescent protein fluorescence in response to threshold concentrations of as little as 0.5 µM phosphonoacetate, some 100 times lower than the detection limit of currently available non‐biological analytical methods; the pPANT3 biosensor construct in Pseudomonas putida KT2440 was less sensitive, although with shorter response times. From a range of other phosphonates and phosphonoacetate analogues tested, only phosphonoacetaldehyde and arsonoacetate induced green fluorescent protein fluorescence in the E. coli DH5α (pPANT3) biosensor, although at much‐reduced sensitivities (50 µM phosphonoacetaldehyde and 500 µM arsonoacetate).
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Affiliation(s)
- Anna N Kulakova
- The QUESTOR Centre and School of Biological Sciences, The Queen's University of Belfast, Belfast BT9 7BL, Northern Ireland
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34
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Cooley NA, Kulakova AN, Villarreal-Chiu JF, Gilbert JA, McGrath JW, Quinn JP. Phosphonoacetate biosynthesis: in vitro detection of a novel NADP(+)-dependent phosphonoacetaldehyde-oxidizing activity in cell-extracts of the marine Roseovarius nubinhibens ISM. Mikrobiologiia 2011; 80:329-334. [PMID: 21861368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A novel phosphonoacetaldehyde-oxidizing activity was detected in cell-extracts of the marine bacterium Roseovarius nubinhibens ISM grown on 2-aminoethylphosphonic acid (2-AEP; ciliatine). Extracts also contained 2-AEP transaminase and phosphonoacetate hydrolase activities. These findings indicate the existence of a biological route from 2-AEP via phosphonoacetaldehyde for the production of phosphonoacetate, which has not previously been shown to be a natural product. The three enzymes appear to constitute a previously-unreported pathway for the mineralization of 2-AEP which is a potentially important source of phosphorus in the nutrient-stressed marine environment.
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Affiliation(s)
- N A Cooley
- School of Biological Science, Queens University, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
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35
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Temperton B, Gilbert JA, Quinn JP, McGrath JW. Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments. PLoS One 2011; 6:e16499. [PMID: 21305044 PMCID: PMC3030594 DOI: 10.1371/journal.pone.0016499] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/20/2010] [Indexed: 11/21/2022] Open
Abstract
Polyphosphate is a ubiquitous linear homopolymer of phosphate residues linked by high-energy bonds similar to those found in ATP. It has been associated with many processes including pathogenicity, DNA uptake and multiple stress responses across all domains. Bacteria have also been shown to use polyphosphate as a way to store phosphate when transferred from phosphate-limited to phosphate-rich media--a process exploited in wastewater treatment and other environmental contaminant remediation. Despite this, there has, to date, been little research into the role of polyphosphate in the survival of marine bacterioplankton in oligotrophic environments. The three main proteins involved in polyphosphate metabolism, Ppk1, Ppk2 and Ppx are multi-domain and have differential inter-domain and inter-gene conservation, making unbiased analysis of relative abundance in metagenomic datasets difficult. This paper describes the development of a novel Isofunctional Homolog Annotation Tool (IHAT) to detect homologs of genes with a broad range of conservation without bias of traditional expect-value cutoffs. IHAT analysis of the Global Ocean Sampling (GOS) dataset revealed that genes associated with polyphosphate metabolism are more abundant in environments where available phosphate is limited, suggesting an important role for polyphosphate metabolism in marine oligotrophs.
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Affiliation(s)
- Ben Temperton
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom.
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36
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Lai MWY, Kulakova AN, Quinn JP, McGrath JW. Stimulation of phosphate uptake and polyphosphate accumulation by activated sludge microorganisms in response to sulfite addition. Water Sci Technol 2011; 63:649-653. [PMID: 21330709 DOI: 10.2166/wst.2011.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Enhanced phosphate removal from wastewaters is dependent on the synthesis and intracellular accumulation of polyphosphate by sludge microorganisms. However the role played by polyphosphate in microbial metabolism and the factors that trigger its formation remain poorly-understood. Many examples of the accumulation of the biopolymer by environmental microorganisms are documented; these include a recent report of the presence of large polyphosphate inclusions in sulfur-oxidizing marine bacteria. To investigate whether any link might exist outside the marine environment between the presence of reduced sulfur compounds and enhanced levels of microbial phosphate uptake and polyphosphate accumulation, activated sludge cultures were grown under laboratory conditions in media that contained sulfite, thiosulfate, hydrosulfite or tetrathionate. Only in the presence of sulfite was there any evidence of a stimulatory effect; in medium that contained 0.5 mM sodium sulfite some 17% more phosphate was removed by the sludge, whilst there was an almost two-fold increase in intracellular polyphosphate levels. No indications of sulfite toxicity were observed.
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Affiliation(s)
- M W-Y Lai
- School of Biological Sciences and QUESTOR Centre, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Rd., Belfast, BT9 7BL, Northern Ireland.
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37
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Bhaganna P, Volkers RJM, Bell ANW, Kluge K, Timson DJ, McGrath JW, Ruijssenaars HJ, Hallsworth JE. Hydrophobic substances induce water stress in microbial cells. Microb Biotechnol 2010; 3:701-16. [PMID: 21255365 PMCID: PMC3815343 DOI: 10.1111/j.1751-7915.2010.00203.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes – metabolites that protect against osmotic and chaotrope‐induced stresses – ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope‐induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.
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Affiliation(s)
- Prashanth Bhaganna
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
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38
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Thomas S, Burdett H, Temperton B, Wick R, Snelling D, McGrath JW, Quinn JP, Munn C, Gilbert JA. Evidence for phosphonate usage in the coral holobiont. ISME J 2009; 4:459-61. [PMID: 19956272 DOI: 10.1038/ismej.2009.129] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phosphonates are characterized by a stable carbon-phosphorus bond and commonly occur as lipid conjugates in invertebrate cell membranes. Phosphonoacetate hydrolase encoded by the phnA gene, catalyses the cleavage of phosphonoacetate to acetate and phosphate. In this study, we demonstrate the unusually high phnA diversity in coral-associated bacteria. The holobiont of eight coral species tested positive when screened for phnA using degenerate primers. In two soft coral species, Sinularia and Discosoma, sequencing of the phnA gene showed 13 distinct groups on the basis of 90% sequence identity across 100% of the sequence. A total of 16 bacterial taxa capable of using phosphonoacetate as the sole carbon and phosphorus source were isolated; 8 of which had a phnA+ genotype. This study enhances our understanding of the wide taxonomic and environmental distribution of phnA, and highlights the importance of phosphonates in marine ecosystems.
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Affiliation(s)
- S Thomas
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, Devon, UK
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39
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McGrath JW, Hammerschmidt F, Preusser W, Quinn JP, Schweifer A. Studies on the biodegradation of fosfomycin: growth of Rhizobium huakuii PMY1 on possible intermediates synthesised chemically. Org Biomol Chem 2009; 7:1944-53. [PMID: 19590792 DOI: 10.1039/b821829c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first step of the mineralisation of fosfomycin by R. huakuii PMY1 is hydrolytic ring opening with the formation of (1R,2R)-1,2-dihydroxypropylphosphonic acid. This phosphonic acid and its three stereoisomers were synthesised by chemical means and tested as their ammonium salts for mineralisation as evidenced by release of P(i). Only the (1R,2R)-isomer was degraded. A number of salts of phosphonic acids such as (+/-)-1,2-epoxybutyl-, (+/-)-1,2-dihydroxyethyl-, 2-oxopropyl-, (S)-2-hydroxypropyl-, (+/-)-1-hydroxypropyl- and (+/-)-1-hydroxy-2-oxopropylphosphonic acid were synthesised chemically, but none supported growth. In vitro C-P bond cleavage activity was however detected with the last phosphonic acid. A mechanism involving phosphite had to be discarded as it could not be used as a phosphorus source. R. huakuii PMY1 grew well on (R)- and (S)-lactic acid and hydroxyacetone, but less well on propionic acid and not on acetone or (R)- and (+/-)-1,2-propanediol. The P(i) released from (1R,2R)-1,2-dihydroxypropylphosphonic acid labelled with one oxygen-18 in the PO3H2 group did not stay long enough in the cells to allow complete exchange of 18O for 16O by enzymic turnover.
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Affiliation(s)
- John W McGrath
- School of Biology and Biochemistry, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Rd., Belfast, BT9 7BL, Northern Ireland
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40
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Kulakova AN, Kulakov LA, Villarreal-Chiu JF, Gilbert JA, McGrath JW, Quinn JP. Expression of the phosphonoalanine-degradative gene cluster from Variovorax sp. Pal2 is induced by growth on phosphonoalanine and phosphonopyruvate. FEMS Microbiol Lett 2009; 292:100-6. [PMID: 19191873 DOI: 10.1111/j.1574-6968.2008.01477.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The phosphonopyruvate hydrolase (PalA) found in Variovorax sp., Pal2, is a novel carbon-phosphorus bond cleavage enzyme, which is expressed even in the presence of high levels of phosphate, thus permitting phosphonopyruvate to be used as the sole carbon and energy source. Analysis of the regions adjacent to the palA gene revealed the presence of the five structural genes that constitute the 2-amino-3-phosphonopropionic acid (phosphonoalanine)-degradative operon. Reverse transcriptase-PCR (RT-PCR) experiments demonstrated that all five genes in the operon are transcribed as a single mRNA and that their transcription is induced by phosphonoalanine or phosphonopyruvate. Transcriptional fusions of the regulatory region of the phosphonoalanine degradative operon with the gfp gene were constructed. Expression analysis indicated that the presence of a LysR-type regulator (encoded by the palR gene) is essential for the transcription of the structural genes of the operon. Similar gene clusters were found in the sequenced genomes of six bacterial species from the Alpha-, Beta- and Gammaproteobacteria, and analysis of metagenomic libraries revealed that sequences related to palA are widely spread in the marine environment.
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Affiliation(s)
- Anna N Kulakova
- School of Biological Sciences and Questor Centre, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland
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41
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Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I. Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. Environ Microbiol 2008; 11:111-25. [PMID: 18783384 DOI: 10.1111/j.1462-2920.2008.01745.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphonates are organic compounds that contain a C-P bond and are a poorly characterized component of the marine phosphorus cycle. They may represent a potential source of bioavailable phosphorus, particularly in oligotrophic conditions. This study has investigated the distribution of the phnA gene which encodes phosphonoacetate hydrolase, the enzyme that mineralizes phosphonoacetate. Using newly designed degenerate primers targeting the phnA gene we analysed the potential for phosphonoacetate utilization in DNA and cDNA libraries constructed from a phytoplankton bloom in the Western English Channel during July 2006. Total RNA was isolated and reverse transcribed and phosphonoacetate hydrolase (phnA) transcripts were PCR amplified from the cDNA with the degenerate primers, cloned and sequenced. Phylogenetic analysis demonstrated considerable diversity with 14 sequence types yielding five unique phnA protein groups. We also identified 28 phnA homologues in a 454-pyrosequencing metagenomic and metatranscriptomic study from a coastal marine mesocosm, indicating that > 3% of marine bacteria in this study contained phnA. phnA homologues were also present in a metagenomic fosmid library from this experiment. Finally, cultures of four isolates of potential coral pathogens belonging to the Vibrionaceae contained the phnA gene. In the laboratory, these isolates were able to grow with phosphonoacetate as sole P and C source. The fact that the capacity to utilize phosphonoacetate was evident in each of the three coastal environments suggests the potential for widespread utilization of this bioavailable P source.
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Affiliation(s)
- Jack A Gilbert
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK.
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42
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Quinn JP, Kulakova AN, Cooley NA, McGrath JW. New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling. Environ Microbiol 2007. [PMID: 17803765 DOI: 10.1111/j.1462-2920.2007.01397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phosphonates are organophosphorus molecules that contain the highly stable C-P bond, rather than the more common, and more labile, C-O-P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C-P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C-P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C-P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling.
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Affiliation(s)
- John P Quinn
- School of Biological Sciences, and QUESTOR Centre, The Queen's University of Belfast, 97, Lisburn Road, Belfast BT9 7BL, UK.
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43
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Quinn JP, Kulakova AN, Cooley NA, McGrath JW. New ways to break an old bond: the bacterial carbon?phosphorus hydrolases and their role in biogeochemical phosphorus cycling. Environ Microbiol 2007; 9:2392-400. [PMID: 17803765 DOI: 10.1111/j.1462-2920.2007.01397.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Phosphonates are organophosphorus molecules that contain the highly stable C-P bond, rather than the more common, and more labile, C-O-P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C-P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C-P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C-P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling.
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Affiliation(s)
- John P Quinn
- School of Biological Sciences, and QUESTOR Centre, The Queen's University of Belfast, 97, Lisburn Road, Belfast BT9 7BL, UK.
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McNicholl BP, McGrath JW, Quinn JP. Development and application of a resazurin-based biomass activity test for activated sludge plant management. Water Res 2007; 41:127-33. [PMID: 17113621 DOI: 10.1016/j.watres.2006.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 09/28/2006] [Accepted: 10/01/2006] [Indexed: 05/12/2023]
Abstract
A rapid, robust and cost-effective method of assaying the metabolic activity of the biomass of activated sludge plants would be a valuable process control tool in the wastewater treatment industry. We have developed and optimised a simple colorimetric test protocol, based on the redox dye resazurin, in which levels of reduction of the dye are proportional to cell biomass and respiration rate in both freshly sampled municipal sludges and in a surrogate activated sludge culture, Polytox. The method has been used to assess the impact of trade wastes on the activities of two municipal activated sludge populations of differing characteristics.
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45
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Tobin KM, McGrath JW, Mullan A, Quinn JP, O'Connor KE. Polyphosphate accumulation by Pseudomonas putida CA-3 and other medium-chain-length polyhydroxyalkanoate-accumulating bacteria under aerobic growth conditions. Appl Environ Microbiol 2006; 73:1383-7. [PMID: 17158616 PMCID: PMC1828677 DOI: 10.1128/aem.02007-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida CA-3 accumulates polyphosphate (polyP) and medium-chain-length polyhydroxyalkanoate (mclPHA) concurrently under nitrogen limitation. Five other mclPHA-accumulating Pseudomonas strains are capable of simultaneous polyP and mclPHA biosynthesis. It appears that polyP is not the rate-limiting step for mclPHA accumulation in these Pseudomonas strains.
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Affiliation(s)
- Karen M Tobin
- School of Biomolecular and Biomedical Sciences, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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Moriarty TF, Mullan A, McGrath JW, Quinn JP, Elborn JS, Tunney MM. Effect of reduced pH on inorganic polyphosphate accumulation by Burkholderia cepacia complex isolates. Lett Appl Microbiol 2006; 42:617-23. [PMID: 16706902 DOI: 10.1111/j.1472-765x.2006.01930.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Burkholderia cepacia complex (Bcc) isolates causing pulmonary infection in cystic fibrosis (CF) patients grow within an acidic environment in the lung. As exposure to acid pH has been shown to increase intracellular inorganic polyphosphate (polyP) formation in some bacteria, we investigated the inter-relationship between acidic pH and polyP accumulation in Bcc isolates. METHODS AND RESULTS The formation of polyP by one Burkholderia cenocepacia clinical isolate was initially examined at a range of pH values by measuring total intracellular polyP accumulation and phosphate uptake. The pattern of polyP accumulation corresponded with the pattern of phosphate uptake with the maximum for both occurring at pH 5.5. Phosphate uptake and formation of polyP by this isolate was further determined over 48 h at pH 5.5, 6.5 and 7.5; formation of polyP was maximal at pH 5.5 at all time points studied. Sixteen of 17 additional clinical and environmental Bcc isolates examined also exhibited maximum phosphate uptake at pH 5.5. CONCLUSIONS Both clinical and environmental Bcc isolates, of five genomovars, show enhanced formation of polyP in an acidic environment. Given both the speculated role of polyP in pathogenesis, cell signalling and biofilm formation and the acidic nature of the CF lung, this may be of considerable clinical importance. SIGNIFICANCE AND IMPACT OF THE STUDY Growth of Bcc in an acidic environment, such as that found in the lungs of CF patients may be influenced in part by polyP accumulation.
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Affiliation(s)
- T F Moriarty
- Clinical and Practice Research Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland
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Mullan A, McGrath JW, Adamson T, Irwin S, Quinn JP. Pilot-scale evaluation of the application of low pH-inducible polyphosphate accumulation to the biological removal of phosphate from wastewaters. Environ Sci Technol 2006; 40:296-301. [PMID: 16433364 DOI: 10.1021/es0509782] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
To investigate the possible biotechnological application of the phenomenon of low pH-inducible phosphate uptake and polyphosphate accumulation, previously reported using pure microbial cultures and under laboratory conditions, a 2000 L activated sludge pilot plant was constructed at a municipal sewage treatment works. When operated as a single-stage reactor this removed more than 60% of influent phosphate from primary settled sewage at a pH of 6.0, as opposed to approximately 30% at the typical operational pH for the works of 7.0-7.3-yet without any deleterious effect on other treatment parameters. At these pH values the phosphorus content of the sludge was, respectively, 4.2% and 2.0%. At pH 6.0 some 33.9% of sludge microbial cells were observed to contain polyphosphate inclusions; the corresponding value at pH 7.0 was 18.7%. Such a process may serve as a prototype for the development of alternative biological and chemical options for phosphate removal from wastewaters.
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Affiliation(s)
- Alan Mullan
- School of Biology and Biochemistry and QUESTOR Centre, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
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McGrath JW, Kulakova AN, Kulakov LA, Quinn JP. In vitro detection and characterisation of a polyphosphate synthesising activity in the yeast Candida humicola G-1. Res Microbiol 2005; 156:485-91. [PMID: 15862446 DOI: 10.1016/j.resmic.2004.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 12/22/2004] [Accepted: 12/23/2004] [Indexed: 11/23/2022]
Abstract
An in vitro detectable polyphosphate-synthesising activity was characterised using two independent assay systems in extracts of the yeast Candida humicola G-1. Its properties were similar to those of a range of bacterial polyphosphate kinase enzymes. PCR amplification of C. humicola genomic DNA using universal primers for bacterial polyphosphate kinase genes yielded a product whose translated sequence showed up to 34% amino acid similarity to the bacterial enzyme.
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Affiliation(s)
- John W McGrath
- School of Biology and Biochemistry and QUESTOR Centre, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Rd., Belfast, BT9 7BL, Northern Ireland.
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McCluskey C, Quinn JP, McGrath JW. An evaluation of three new-generation tetrazolium salts for the measurement of respiratory activity in activated sludge microorganisms. Microb Ecol 2005; 49:379-87. [PMID: 16003480 DOI: 10.1007/s00248-004-0012-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Accepted: 04/05/2004] [Indexed: 05/03/2023]
Abstract
XTT (3'-[1-[(phenylamino)-carbonyl]-3,4-tetrazolium]-bis(4-methoxy-6-nitro)benzenesulfonic acid hydrate), MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt), and WST-1 (4-(3-4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio)-1,3-benzenedisulfonate) are tetrazolium salts that have become commercially available only in relatively recent years; they differ from earlier such compounds in that their reduction gives rise to a formazan product that is water soluble. We have established the sites in the prokaryotic respiratory chain at which each of the dyes is reduced to its corresponding formazan and have evaluated the suitability of each for the colorimetric estimation of electron transport system activity in populations of activated sludge microorganisms. Reduction of all three tetrazolium salts was shown to be proportional to cell biomass and oxygen uptake and to be susceptible to low levels of the reference toxicant 3,5-dichlorophenol. XTT, which was not inhibitory at concentrations of up to 2 mM and was reduced by 91% of isolates from a sample of culturable activated sludge bacteria, was chosen for further assay development. XTT-formazan production was found to be stimulated by the availability of an exogenous carbon and energy source, and by the presence of the electron-coupling agent phenazine methosulfate. Less than 3% of XTT reduction by an activated sludge sample was abiotic. An assay based on this compound could be a valuable and simple tool for the routine monitoring of the performance of wastewater treatment systems.
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Affiliation(s)
- C McCluskey
- School of Biology and Biochemistry and QUESTOR Centre, The Queen's University of Belfast, Northern Ireland
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Affiliation(s)
- John W McGrath
- School of Biology and Biochemistry, QUESTOR Center, Queen's University of Belfast, Medical Biology Centre Belfast, BT9 7BL Northern Ireland
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