A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Song, S. J., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., Agosto Rivera, J. L., Al-Moosawi, L., Alverdy, J., Amato, K. R., Andras, J., Angenent, L. T., Antonopoulos, D. A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J. K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J. F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D. M., Braun, J., Brazelton, W., Brearley, F. Q., Campbell, A. H., Caporaso, J. G., Cardona, C., Carroll, J., Cary, S. C., Casper, B. B., Charles, T. C., Chu, H., Claar, D. C., Clark, R. G., Clayton, J. B., Clemente, J. C., Cochran, A., Coleman, M. L., Collins, G., Colwel, R. R., Contreras, M., Crary, B. B., Creer, S., Cristol, D. A., Crump, B. C., Cui, D., Daly, S. E., Davalos, L., Dawson, R. D., Defazio, J., Delsuc, F., Dionisi, H. M., Dominguez-Bello, M. G., Dowell, R., Dubinsky, E. A., Dunn, P. O., Ercolini, D., Espinoza, R. E., Ezenwa, V., Fenner, N., Findlay, H. S., Fleming, I. D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E. S., Galindo, G., Garcia, L., Garcia-Amado, M. A., Garshelis, D., Gasser, R. B., Gerdts, G., Gibson, M. K., Gifford, I., Gill, R. T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H.-P., Guyton, K., Haig, S.-J., Hale, V., Hall, R. S., Hallam, S. J., Handley, K. M., Hasan, N. A., Haydon, S. R., Hickman, J. E., Hidalgo, G., Hofmockel, K. S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J. D., Jastrow, J. D., Jex, A. R., Johnson, L. S., Johnston, E. R., Joseph, S., Jurburg, S. D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C. T. E., Kennedy, S. J., Kerkhof, L. J., King, G. M., Kling, G. W., Koehler, A. V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E. M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I. I., Liancourt, P., Liang, W., Linz, A. M., Lipson, D. A., Liu, Y., Lladser, M. E., Lozada, M., Spirito, C. M., MacCormack, W. P., MacRae-Crerar, A., Magris, M., Martín-Platero, A. M., Martín-Vivaldi, M., Martínez, L. M., Martínez-Bueno, M., Marzinelli, E. M., Mason, O. U., Mayer, G. D., McDevitt-Irwin, J. M., McDonald, J., McGuire, K. L., McMahon, K. D., McMinds, R., Medina, M., Mendelson, J. R., Metcalf, J. L., Meyer, F., Michelangeli, F., Miller, K., Mills, D. A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R. M., Munroe, P., Myrold, D., Neufeld, J. D., Ni, Y., Nicol, G. W., Nielsen, S., Nissimov, J. I., Niu, K., Nolan, M. J., Noyce, K., O’Brien, S. L., Okamoto, N., Orlando, L., Ortiz Castellano, Y., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J. M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S. B., Pollock, F. J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A. P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K. J., Rodriguezl, S. M., Rohwer, F., Roundstone, W., Safran, R. J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M. D., Scott, N. M., Seger, R. L., Seguin-Orlando, A., Seldin, L., Seyler, L. M., Shakhsheer, B., Sheets, G. M., Shen, C., Shi, Y., Shin, H., Shogan, B. D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D. P., Soler, J. J., Sperling, M., Steinberg, P. D., Stephens, B., Stevens, M. A., Taghavi, S., Tai, V., Tait, K., Tan, C. L., Tas, N., Taylor, D. L., Thomas, T., Timling, I., Turner, B. L., Urich, T., Ursell, L. K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Vega Thurber, R., Vitaglione, P., Walker, D. A., Walters, W. A., Wang, S., Wang, T., Weave, T., Webster, N. S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J. J., West, K., Whitehead, A., Whitehead, S. R., Whittingham, L. A., Willerslev, E., Williams, A. E., Wood, S. A., Woodhams, D. C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q. & Zhao, H., 23 Nov 2017, In: Nature. 551, 7681, p. 457-+

Research output: Contribution to journal › Article › peer-review

A comparison of precipitation and filtration-based SARS-CoV-2 recovery methods and the influence of temperature, turbidity, and surfactant load in urban wastewater

Kevill, J. L., Pellett, C., Farkas, K., Brown, M. R., Bassano, I., Denise, H., McDonald, J. E., Malham, S. K., Porter, J., Warren, J., Evens, N. P., Paterson, S., Singer, A. C. & Jones, D. L., 20 Feb 2022, In: Science of the Total Environment. 808, 151916.

Research output: Contribution to journal › Article › peer-review

A multiplex real‐time PCR assay enables simultaneous rapid detection and quantification of bacteria associated with acute oak decline

Crampton, B. G., Plummer, S., Kaczmarek, M., McDonald, J. & Denman, S., Sept 2020, In: Plant Pathology. 69, 7, p. 1301-1310 10 p.

Research output: Contribution to journal › Article › peer-review

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

Hassard, F., Gwyther, C. L., Farkas, K., Andrews, A., Jones, V., Cox, B., Brett, H., Jones, D., McDonald, J. & Malham, S., 1 Nov 2016, In: Frontiers in Microbiology.

Research output: Contribution to journal › Article › peer-review

Application of ecological and evolutionary theory to microbiome community dynamics across systems

McDonald, J., Marchesi, J. R. & Koskella, B., 23 Dec 2020, In: Proceedings of the Royal Society B: Biological Sciences. 287, 1941, 20202886.

Research output: Contribution to journal › Article › peer-review

Bioreduction of Sheep Carcasses Effectively Contains and Reduces Pathogen Levels under Operational and Simulated Breakdown Conditions

Golyshin, P., Gwyther, C. L., Jones, D. L., Golyshin, P. N., Edwards-Jones, G., McKillen, J., McNair, I., McDonald, J. E. & Williams, A. P., 21 May 2013, In: Environmental Science and Technology. 47, 10, p. 5267–5275

Research output: Contribution to journal › Article › peer-review

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules

McDonald, J., Larsen, N., Pennington, A., Connolly, J., Wallis, C., Rooks, D. J., Hall, N., McCarthy, A. J. & Allison, H. E., 8 Jun 2016, In: PLoS ONE. 11, 6, e0157046.

Research output: Contribution to journal › Article › peer-review

Composition of the landfill microbial community as determined by application of domian- and group-specific 16s and 18s rRNA-targeted oligonucleotide probes.

McDonald, J. E., Allison, H. E. & McCarthy, A. J., 1 Feb 2010, In: Applied and Environmental Microbiology. 76, 4, p. 1301-1306

Research output: Contribution to journal › Article › peer-review

Concentration and Quantification of SARS-CoV-2 RNA in Wastewater Using Polyethylene Glycol-Based Concentration and qRT-PCR.(vol 4, 17, 2021)

Farkas, K., Hillary, L. S., Thorpe, J., Walker, D. I., Lowther, J. A., McDonald, J. E., Malham, S. K. & Jones, D. L., 12 Nov 2021, In: Methods and Protocols. 4, 4

Research output: Contribution to journal › Article › peer-review

Concentration and quantification of SARS-CoV-2 RNA in wastewater using polyethylene glycol-based concentration and qRT-PCR

Farkas, K., Hillary, L., Thorpe, J., Walker, D., Lowther, J. A., McDonald, J., Malham, S. & Jones, D. L., 23 Feb 2021, In: Methods and Protocols. 4, 1, 10 p., 17.

Research output: Contribution to journal › Article › peer-review

Critical Evaluation of CrAssphage as a Molecular Marker for Human-Derived Wastewater Contamination in the Aquatic Environment

Farkas, K., Adriaenssens, E. M., Walker, D. I., McDonald, J., Malham, S. & Jones, D. L., 1 Jun 2019, In: Food and Environmental Virology. 11, 2, p. 113-119

Research output: Contribution to journal › Article › peer-review

Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment: A UK Perspective

Hassard, F., Sharp, J., Taft, H., Le Vay, L., Harris, J., McDonald, J., Tuson, K., Wilson, J., Jones, D. & Malham, S., Jun 2017, In: Food and Environmental Virology. 9, 2, p. 123-141

Research output: Contribution to journal › Article › peer-review

Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations

Perkins, T. L., Perrow, K. A., Rajko-Nenow, P., Jago, C. F., Jones, D. L., Malham, S. K. & McDonald, J. E., 1 Dec 2016, In: Science of the Total Environment. 572, p. 1645-1652

Research output: Contribution to journal › Article › peer-review

Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR.

McDonald, J. E., Lockhart, R. J., Cox, M. J., Allison, H. E. & McCarthy, A. J., 1 May 2008, In: Environmental Microbiology. 10, 5, p. 2360-2365

Research output: Contribution to journal › Article › peer-review

Developing Skills in Second Year Biological Science Undergraduates

Robinson, R. L. & McDonald, J. E., 1 Jul 2014, In: Bioscience Education. 22, 1, p. 42-53

Research output: Contribution to journal › Article › peer-review

Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages.

Rooks, D. J., Yan, Y., McDonald, J. E., Woodward, M. J., McCarthy, A. J. & Allison, H. E., 1 May 2010, In: Environmental Microbiology. 12, 5, p. 1194-1204

Research output: Contribution to journal › Article › peer-review

Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs

Ransom-Jones, E., Jones, D. L., Edwards, A. & McDonald, J. E., 17 Jul 2014, In: Systematic and Applied Microbiology. 37, 7, p. 502-509

Research output: Contribution to journal › Article › peer-review

Draft Genome Sequence of Clostridium sp. strain W14A isolated from a cellulose-degrading biofilm in a landfill leachate microcosm

Ransom-Jones, E. & McDonald, J., 22 Sept 2016, In: Genome Announcements. 4, 5, e0098516.

Research output: Contribution to journal › Article › peer-review

E. coli Is a Poor End-Product Criterion for Assessing the General Microbial Risk Posed From Consuming Norovirus Contaminated Shellfish

Sharp, J. H., Clements, K., Diggens, M., McDonald, J. E., Malham, S. K. & Jones, D. L., 19 Feb 2021, In: Frontiers in Microbiology. 12, p. 608888

Research output: Contribution to journal › Article › peer-review

Enhancing first year undergraduate student engagement via the School of Biological Sciences tutorials module

McDonald, J. E. & Robinson, R. L., 1 Jul 2014, In: Bioscience Education. 22, 1, p. 54-69

Research output: Contribution to journal › Article › peer-review

Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment

Farkas, K., Hassard, F., McDonald, J., Malham, S. & Jones, D., 24 Jan 2017, In: Frontiers in Microbiology. 6, p. 1-12 53.

Research output: Contribution to journal › Article › peer-review

Evaluation of Two Triplex One-Step qRT-PCR Assays for the Quantification of Human Enteric Viruses in Environmental Samples

Farkas, K., Peters, D. E., McDonald, J., de Rougemont, A., Malham, S. & Jones, D., Sept 2017, In: Food and Environmental Virology. 9, 3, p. 342-349

Research output: Contribution to journal › Article › peer-review

Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue

Broberg, M. & McDonald, J., 5 Feb 2019, In: Methods and Protocols. 2, 1, 15.

Research output: Contribution to journal › Article › peer-review

Fifty important research questions in microbial ecology

Antwis, R. E., Griffiths, S. M., Harrison, X. A., Aranega-Bou, P., Arce, A., Bettridge, A. S., Brailsford, F., de Menezes, A., Devaynes, A., Forbes, K. M., Fry, E. L., Goodhead, I., Haskell, E., Heys, C., James, C., Johnston, S. R., Lewis, G. R., Lewis, Z., Macey, M. C., McCarthy, A., McDonald, J., Mejia-Florez, N. L., O'Brien, D., Orland, C., Pautasso, M., Reid, W. D. K., Robinson, H. A., Wilson, K. & Sutherland, W. J., May 2017, In: Fems Microbiology Ecology. 93, 5, fix044.

Research output: Contribution to journal › Article › peer-review

Genomic analysis of bacteria in the Acute Oak Decline pathobiome

Doonan, J., Denman, S., Pachebat, J. A. & McDonald, J., 8 Jan 2019, In: Microbial Genomics. 5, 1, 15 p.

Research output: Contribution to journal › Article › peer-review

High-Throughput Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains

McDonald, J. E., Smith, D. L., Fogg, P. C., McCarthy, A. J. & Allison, H. E., 1 Apr 2010, In: Applied and Environmental Microbiology. 76, 7, p. 2360-2365

Research output: Contribution to journal › Article › peer-review

Host–microbiota–insect interactions drive emergent virulence in a complex tree disease

Doonan, J., Broberg, M., Denman, S. & McDonald, J., 26 Aug 2020, In: Proceedings of the Royal Society B: Biological Sciences. 287, 1933, 20200956.

Research output: Contribution to journal › Article › peer-review

Identification of Armillaria species on declined oak in Britain: implications for oak health

Denman, S., Barrett, G., Kirk, S. A., McDonald, J. & Coetzee, M. P. A., 7 Jan 2017, In: Forestry. 90, 1, p. 148-161

Research output: Contribution to journal › Article › peer-review

Impact of Sediment Concentration on the Survival of Wastewater-Derived blaCTX-M-15-Producing E. coli, and the Implications for Dispersal into Estuarine Waters

Bashawri, Y. M. A., Robins, P., Jones, D. L., McDonald, J., Cooper, D. & Williams, P., 19 Oct 2020, In: International Journal of Environmental Research and Public Health. 17, 20, 15 p., 7608.

Research output: Contribution to journal › Article › peer-review

Impact of climate change on UK estuaries: A review of past trends and potential projections

Robins, P. E., Skov, M. W., Lewis, M. J., Gimenez, L., Davies, A. G., Malham, S. K., Neill, S. P., McDonald, J. E., Whitton, T. A., Jackson, S. E. & Jago, C. F., 17 Dec 2015, In: Estuarine, Coastal and Shelf Science. 169, p. 119-135

Research output: Contribution to journal › Article › peer-review

Importance of Micromonospora spp. as colonizers of cellulose in freshwater lakes as demonstrated by quantitative reverse transcriptase PCR of 16S rRNA

de Menezes, A. B., McDonald, J. E., Allison, H. E. & McCarthy, A. J., May 2012, In: Applied and Environmental Microbiology. 78, 9, p. 3495-9 5 p.

Research output: Contribution to journal › Article › peer-review

Improving quantification of bivalve larvae in mixed plankton samples using qPCR: A case study on Mytilus edulis

Alexander, J., Malham, S., Smyth, D., Webb, J., Fidler, D., Bayford, P., McDonald, J. & Le Vay, L., 15 Feb 2021, In: Aquaculture. 532, 736003.

Research output: Contribution to journal › Article › peer-review

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

Broberg, M., Doonan, J., Mundt, F. & McDonald, J., 30 Jan 2018, In: Microbiome. 6, 21.

Research output: Contribution to journal › Article › peer-review

Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline

Denman, S., Plummer, S., Peace, A. & McDonald, J., 1 Oct 2016, In: Systematic and Applied Microbiology. 39, 7, p. 484-490

Research output: Contribution to journal › Article › peer-review

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass- Degrading Diversity Emma

Ransom-Jones, E., McCarthy, A., Haldenby, S., Doonan, J. & McDonald, J., Aug 2017, In: mSphere. 2, 4, e00300.

Research output: Contribution to journal › Article › peer-review

Metagenomic approaches to the discovery of cellulases

Rooks, D. J., McDonald, J. E. & McCarthy, A. J., 2012, In: Methods in Enzymology. 510, p. 375-94 20 p.

Research output: Contribution to journal › Article › peer-review

Methods for the isolation of cellulose-degrading microorganisms

McDonald, J. E., Rooks, D. J. & McCarthy, A. J., 2012, In: Methods in Enzymology. 510, p. 349-74 26 p.

Research output: Contribution to journal › Article › peer-review

Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline

Denman, S., Doonan, J., Ransom-Jones, E., Broberg, M., Plummer, S., Kirk, S. A., Scarlett, K., Griffiths, A., Kaczmarek, M., Foster, J., Peace, A., Golyshin, P., Hassard, F., Brown, N., Kenny, J. G. & McDonald, J., 2018, In: The ISME Journal. 12, p. 386-399

Research output: Contribution to journal › Article › peer-review

Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes.

McDonald, J. E., De Menezes, A. B., Allison, H. E. & McCarthy, A. J., 1 Aug 2009, In: Applied and Environmental Microbiology. 75, 15, p. 5148-5152

Research output: Contribution to journal › Article › peer-review

Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK

Hillary, L. S., Farkas, K., Maher, K. H., Lucaci, A., Thorpe, J., Distaso, M. A., Gaze, W. H., Paterson, S., Burke, T., Connor, T. R., McDonald, J. E., Malham, S. K. & Jones, D. L., 15 Jul 2021, In: Water Research. 200, p. 117214 1 p.

Research output: Contribution to journal › Article › peer-review

Multilocus sequence typing provides insights into the population structure and evolutionary potential of Brenneria goodwinii, associated with acute oak decline

Kaczmarek, M., Mullett, M. S., McDonald, J. & Denman, S., 1 Jun 2017, In: PLoS ONE. 12, 6, e0178390.

Research output: Contribution to journal › Article › peer-review

Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment

Hassard, F., Andrews, A., Jones, D. L., Parsons, L., Jones, V., Cox, B. A., Daldorph, P., Brett, H., McDonald, J. & Malham, S., Oct 2017, In: Frontiers in Microbiology. 8, 1996.

Research output: Contribution to journal › Article › peer-review

RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels

Hillary, L. S., Adriaenssens, E. M., Jones, D. L. & McDonald, J. E., 8 Apr 2022, In: ISME Communications. 2, 1, p. 34 34.

Research output: Contribution to journal › Article › peer-review

Seasonal and diurnal surveillance of treated and untreated wastewater for human enteric viruses

Farkas, K., Marshall, M., Cooper, D., McDonald, J. E., Malham, S. K., Peters, D. E., Maloney, J. D. & Jones, D. L., Nov 2018, In: Environmental Science and Pollution Research. 25, 33, p. 33391-33401

Research output: Contribution to journal › Article › peer-review

Seasonal and spatial dynamics of enteric viruses in wastewater and in riverine and estuarine receiving waters

Malham, S., Farkas, K., McDonald, J., Jones, D. L., Cooper, D. & de Rougemont, A., 1 Sept 2018, In: Science of the Total Environment. 634, p. 1174 1183 p.

Research output: Contribution to journal › Article › peer-review

Sediment Composition Influences Spatial Variation in the Abundance of Human Pathogen Indicator Bacteria within an Estuarine Environment

Perkins, T. L., Clements, K., Baas, J. H., Jago, C. F., Jones, D. L., Malham, S. K. & McDonald, J. E., 14 Nov 2014, In: PLoS ONE. 9, 11

Research output: Contribution to journal › Article › peer-review

Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation

George, P. B. L., Fidler, D. B., Van Nostrand, J. D., Atkinson, J. A., Mooney, S. J., Creer, S., Griffiths, R. I., McDonald, J. E., Robinson, D. A. & Jones, D. L., 14 Sept 2021, In: Frontiers in Microbiology. 12, 735022.

Research output: Contribution to journal › Article › peer-review

Soil metabolomics - current challenges and future perspectives

Brown, R., Reay, M. K., Centler, F., Chadwick, D., Bull, I. D., McDonald, J., Evershed, R. P. & Jones, D. L., 1 Jun 2024, In: Soil Biology and Biochemistry. 109382.

Research output: Contribution to journal › Article › peer-review