By Professor Torsten Thomas

Journal articles

Thompson LR; Sanders JG; McDonald D; Amir A; Ladau J; Locey KJ; Prill RJ; Tripathi A; Gibbons SM; Ackermann G; Navas-Molina JA; Janssen S; Kopylova E; Vázquez-Baeza Y; González A; Morton JT; Mirarab S; Zech Xu Z; Jiang L; Haroon MF; Kanbar J; Zhu Q; Jin Song S; Kosciolek T; Bokulich NA; Lefler J; Brislawn CJ; Humphrey G; Owens SM; Hampton-Marcell J; Berg-Lyons D; McKenzie V; Fierer N; Fuhrman JA; Clauset A; Stevens RL; Shade A; Pollard KS; Goodwin KD; Jansson JK; Gilbert JA; Knight R; Thomas T; Marzinelli E; Nielsen S; Steinberg P; Campbell A; Moitinho e Silva L; Munroe P, 2017, 'A communal catalogue reveals Earth’s multiscale microbial diversity', Nature, 551, pp. 457 - 463, http://dx.doi.org/10.1038/nature24621

Moitinho-Silva L; Nielsen S; Amir A; Gonzalez A; Ackermann GL; Cerrano C; Astudillo-Garcia C; Easson C; Sipkema D; Liu F; Steinert G; Kotoulas G; McCormack GP; Feng G; Bell JJ; Vicente J; Bjork JR; Montoya JM; Olson JB; Reveillaud J; Steindler L; Pineda M-C; Marra MV; Ilan M; Taylor MW; Polymenakou P; Erwin PM; Schupp PJ; Simister RL; Knight R; Thacker RW; Costa R; Hill RT; Lopez-Legentil S; Dailianis T; Ravasi T; Hentschel U; Li Z; Webster NS; Thomas T, 2017, 'The sponge microbiome project', GIGASCIENCE, 6, http://dx.doi.org/10.1093/gigascience/gix077

Zozaya-Valdés E; Roth-Schulze AJ; Egan S; Thomas T, 2017, 'Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra', Environmental Microbiology, 19, pp. 3012 - 3024, http://dx.doi.org/10.1111/1462-2920.13758

Moitinho-Silva L; Díez-Vives C; Batani G; Esteves AIS; Jahn MT; Thomas T, 2017, 'Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics', Isme Journal, 11, pp. 1651 - 1666, http://dx.doi.org/10.1038/ismej.2017.25

Song WZ; Thomas T, 2017, 'Binning-refiner: Improving genome bins through the combination of different binning programs', Bioinformatics, 33, pp. 1873 - 1875, http://dx.doi.org/10.1093/bioinformatics/btx086

Moitinho-Silva L; Steinert G; Nielsen S; Hardoim CCP; Wu YC; McCormack GP; López-Legentil S; Marchant R; Webster N; Thomas T; Hentschel U, 2017, 'Predicting the HMA-LMA status in marine sponges by machine learning', Frontiers in Microbiology, 8, pp. 752, http://dx.doi.org/10.3389/fmicb.2017.00752

Ye J; Joseph SD; Ji M; Nielsen S; Mitchell DRG; Donne S; Horvat J; Wang J; Munroe P; Thomas T, 2017, 'Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars', Isme Journal, 11, pp. 1087 - 1101, http://dx.doi.org/10.1038/ismej.2016.187

Esteves AIS; Cullen A; Thomas T, 2017, 'Competitive interactions between sponge-associated bacteria', FEMS Microbiology Ecology, 93, http://dx.doi.org/10.1093/femsec/fix008

Díez-Vives C; Moitinho-Silva L; Nielsen S; Reynolds D; Thomas T, 2017, 'Expression of eukaryotic-like protein in the microbiome of sponges', Molecular Ecology, 26, pp. 1432 - 1451, http://dx.doi.org/10.1111/mec.14003

Song W; Steensen K; Thomas T, 2017, 'HgtSIM: A simulator for horizontal gene transfer (HGT) in microbial communities', Peerj, 2017, pp. e4015, http://dx.doi.org/10.7717/peerj.4015

Nielsen S; Walburn JW; Vergés A; Thomas T; Egan S, 2017, 'Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens', Peerj, 2017, pp. e3317, http://dx.doi.org/10.7717/peerj.3317

Roth-Schulze AJ; Zozaya-Valdés E; Steinberg PD; Thomas T, 2016, 'Partitioning of functional and taxonomic diversity in surface-associated microbial communities', Environmental Microbiology, 18, pp. 4391 - 4402, http://dx.doi.org/10.1111/1462-2920.13325

Kumar V; Zozaya-Valdes E; Kjelleberg S; Thomas T; Egan S, 2016, 'Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra', Environmental Microbiology, 18, pp. 3962 - 3975, http://dx.doi.org/10.1111/1462-2920.13403

Reynolds D; Thomas T, 2016, 'Evolution and function of eukaryotic-like proteins from sponge symbionts', Molecular Ecology, 25, pp. 5242 - 5253, http://dx.doi.org/10.1111/mec.13812

Thomas T; Moitinho-Silva L; Lurgi M; Björk JR; Easson C; Astudillo-García C; Olson JB; Erwin PM; López-Legentil S; Luter H; Chaves-Fonnegra A; Costa R; Schupp PJ; Steindler L; Erpenbeck D; Gilbert J; Knight R; Ackermann G; Victor Lopez J; Taylor MW; Thacker RW; Montoya JM; Hentschel U; Webster NS, 2016, 'Diversity, structure and convergent evolution of the global sponge microbiome', Nature Communications, 7, http://dx.doi.org/10.1038/ncomms11870

Nielsen S; Needham B; Leach ST; Day AS; Jaffe A; Thomas T; Ooi CY, 2016, 'Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis', Scientific Reports, 6, pp. 24857, http://dx.doi.org/10.1038/srep24857

Lutz C; Thomas T; Steinberg P; Kjelleberg S; Egan S, 2016, 'Effect of interspecific competition on trait variation in Phaeobacter inhibens biofilms', Environmental Microbiology, 18, pp. 1635 - 1645, http://dx.doi.org/10.1111/1462-2920.13253

Webster NS; Thomas T, 2016, 'The sponge hologenome', Mbio, 7, pp. 10.1128/mbio.00135 - 10.1128/mbio.00116, http://dx.doi.org/10.1128/mBio.00135-16

Esteves AIS; Amer N; Nguyen M; Thomas T, 2016, 'Sample processing impacts the viability and cultivability of the sponge microbiome', Frontiers in Microbiology, 7, pp. 499, http://dx.doi.org/10.3389/fmicb.2016.00499

Ye J; Zhang R; Nielsen S; Joseph SD; Huang D; Thomas T, 2016, 'A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00372

Zozaya-Valdés E; Roth-Schulze AJ; Thomas T, 2016, 'Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00161

Lachnit T; Thomas T; Steinberg P, 2016, 'Expanding our understanding of the seaweed holobiont: RNA Viruses of the Red Alga Delisea pulchra', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.01489

Aslam F; Yasmin A; Thomas T, 2016, 'Genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an effective bioremediator', Genome Announcements, 4, pp. e01068 - e01016, http://dx.doi.org/10.1128/genomeA.01068-16

Marzinelli EM; Campbell AH; Zozaya Valdes E; Vergés A; Nielsen S; Wernberg T; de Bettignies T; Bennett S; Caporaso JG; Thomas T; Steinberg PD, 2015, 'Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography', Environmental Microbiology, 17, pp. 4078 - 4088, http://dx.doi.org/10.1111/1462-2920.12972

Joseph S; Husson O; Graber ER; Van Zwieten L; Taherymoosavi S; Thomas T; Nielsen S; Ye J; Pan G; Chia C; Munroe P; Allen J; Lin Y; Fan X; Donne S, 2015, 'The electrochemical properties of biochars and how they affect soil redox properties and processes', Agronomy, 5, pp. 322 - 340, http://dx.doi.org/10.3390/agronomy5030322

Ye J; Nielsen S; Joseph S; Thomas T, 2015, 'High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy', Plos One, 10, http://dx.doi.org/10.1371/journal.pone.0126404

Gardiner M; Thomas T; Egan S, 2015, 'A glutathione peroxidase (GpoA) plays a role in the pathogenicity of Nautella italica strain R11 towards the red alga Delisea pulchra', FEMS Microbiology Ecology, 91, http://dx.doi.org/10.1093/femsec/fiv021

Luter HM; Widder S; Botté ES; Wahab MA; Whalan S; Moitinho-Silva L; Thomas T; Webster NS, 2015, 'Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens', Peerj, 2015, http://dx.doi.org/10.7717/peerj.1435

Gutierrez-Zamora ML; Lee M; Manefield M; Thomas T, 2015, 'Biotransformation of coal linked to nitrification', International Journal of Coal Geology, 137, pp. 136 - 141, http://dx.doi.org/10.1016/j.coal.2014.12.001

Egan S; Thomas T, 2015, 'Editorial for: Microbial symbiosis of marine sessile hosts- diversity and function', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.00585

Gardiner M; Fernandes ND; Nowakowski D; Raftery M; Kjelleberg S; Zhong L; Thomas T; Egan S, 2015, 'VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.01130

YAO C; JOSEPH S; Lianqing LI; PAN G; LIN Y; MUNROE P; PACE B; TAHERYMOOSAVI S; ZWIETEN LV; THOMAS T; NIELSEN S; Jun YE; DONNE S, 2015, 'Developing More Effective Enhanced Biochar Fertilisers for Improvement of Pepper Yield and Quality', Pedosphere, 25, pp. 703 - 712, http://dx.doi.org/10.1016/S1002-0160(15)30051-5

JOSEPH S; POW D; DAWSON K; MITCHELL DRG; RAWAL A; HOOK J; TAHERYMOOSAVI S; ZWIETEN LV; RUST J; DONNE S; MUNROE P; PACE B; GRABER E; THOMAS T; NIELSEN S; Jun YE; LIN Y; PAN G; Lianqing LI; SOLAIMAN ZM, 2015, 'Feeding Biochar to Cows: An Innovative Solution for Improving Soil Fertility and Farm Productivity', Pedosphere, 25, pp. 666 - 679, http://dx.doi.org/10.1016/S1002-0160(15)30047-3

Thomas JM; Thomas T; Stuetz RM; Ashbolt NJ, 2014, 'Your garden hose: A potential health risk due to Legionella spp. growth facilitated by free-living amoebae', Environmental Science and Technology, 48, pp. 10456 - 10464, http://dx.doi.org/10.1021/es502652n

Nielsen S; Minchin T; Kimber S; van Zwieten L; Gilbert J; Munroe P; Joseph S; Thomas T, 2014, 'Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilisers', Agriculture Ecosystems and Environment, 191, pp. 73 - 82, http://dx.doi.org/10.1016/j.agee.2014.04.006

Gunawan C; Limbri H; Thomas T; Smith A; Scott J; Rosche B, 2014, 'Coal-Packed Methane Biofilter for Mitigation of Green House Gas Emissions from Coal Mine Ventilation Air', PLoS One, 9, pp. e94641, http://dx.doi.org/10.1371/journal.pone.0094641

McElroy K; Thomas T; Luciani F, 2014, 'Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions.', Microb Inform Exp, 4, pp. 1, http://dx.doi.org/10.1186/2042-5783-4-1

Egan S; Fernandes ND; Kumar V; Gardiner M; Thomas T, 2014, 'Bacterial pathogens, virulence mechanism and host defence in marine macroalgae', Environmental Microbiology, 16, pp. 925 - 938, http://dx.doi.org/10.1111/1462-2920.12288

McElroy KE; Hui JGK; Woo JKK; Luk AWS; Webb JS; Kjelleberg S; Rice SA; Thomas T, 2014, 'Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation', Proceedings of the National Academy of Sciences of the United States of America, 111, pp. E1419 - E1427, http://dx.doi.org/10.1073/pnas.1314340111

Zozaya-Valdes E; Egan S; Thomas T, 2014, 'A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens.', Frontiers in microbiology, 6, pp. 146 - 146

Nguyen MTHD; Liu M; Thomas T, 2013, 'Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis', Molecular ecology

Woodhouse JN; Fan L; Brown MV; Thomas T; Neilan BA, 2013, 'Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges', The ISME journal

Woo JKK; McElroy K; Rice SA; Kirov SM; Thomas T; Kjelleberg S, 2013, 'Draft genome sequence of the chronic, nonclonal cystic fibrosis isolate Pseudomonas aeruginosa strain 18A', Genome announcements, 1

Bougouffa S; Yang JK; Le OO; Wang Y; Batang Z; Al-Suwailem A; Egan S; Harder T; Burke C; Steinberg P; others , 2013, 'Further Readings in Geomicrobiology', Geomicrobiology Journal, 30, pp. 768 - 768, http://dx.doi.org/10.1080/01490451.2013.809976

Burke CM; Liu M; Britton WJ; Triccas J; Thomas T; Smith A; Allen S; Salomon R; Harry E, 2013, 'Harnessing Single Cell Sorting to Identify Cell Division Genes and Regulators in Bacteria', PLoS ONE, 8, pp. e60964, http://dx.doi.org/10.1371/journal.pone.0060964

Fan L; Liu ; Simister RL; Webster N; Thomas T, 2013, 'Marine microbial symbiosis heats up: The phylogenetic and functional response of a sponge holobiont to thermal stress', ISME Journal, 7, pp. 991 - 1002, http://dx.doi.org/10.1038/ismej.2012.165

Weiss M; Kesbert AI; Labutti KM; Weiss ; Weiss ; Hauser L; Copealand AC; Woyke T; Lowry SR; Lucas S; Land M; Goodwin L; Kjelleberg SA; Cook AM; Buhmann MT; Thomas T; Schleheck DF, 2013, 'Permanent draft genome sequence of Comamonas testosteroni KF-1', Standards in Genomic Sciences, 8, pp. 239 - 254, http://dx.doi.org/10.4056/sigs.3847890

Joseph S; Graber ER; Chia C; Munroe PR; Donne SW; Thomas T; Marjo CE; Rutlidge HT; Pan G; Li L; Taylor P; Rawal A; Hook JM; Nielsen S, 2013, 'Shifting paradigms: Development of high-efficiency biochar fertilizers based on nano-structures and soluble components', Carbon Management, 4, pp. 323 - 343, http://dx.doi.org/10.4155/cmt.13.23

Egan SG; Harder T; Burke CM; Steinberg PD; Kjelleberg S; Thomas T, 2013, 'The seaweed holobiont: understanding seaweed–bacteria interactions.', FEMS Microbiology Reviews, 37, pp. 462 - 476, http://dx.doi.org/10.1111/1574-6976.12011

Penesyan A; Ballestriero F; Daim M; Kjelleberg S; Thomas T; Egan SG, 2012, 'Assessing the effectiveness of functional genetic screens for the identification of bioactive metabolites', Marine Drugs, 11, pp. 40 - 49, http://www.mdpi.com/1660-3397/11/1/40

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