Select Publications

Journal articles

Esteves AIS; Amer N; Nguyen M; Thomas T, 2016, 'Sample processing impacts the viability and cultivability of the sponge microbiome', Frontiers in Microbiology, 7, 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, 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, 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, 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

Fernandes N; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2012, 'Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra.', PLoS One, 7, pp. e50854, http://dx.doi.org/10.1371/journal.pone.0050854

Woodhouse JN; Fan L; Brown MV; Thomas T; Neilan BA, 2012, 'Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity.', Planta Medica, 78, pp. CL51, http://dx.doi.org/10.1055/s-0032-1320286

Fan L; Reynolds D; Liu M; Stark M; Kjelleberg S; Webster N; Thomas T, 2012, 'Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts', Proceedings of the National Academy of Science. USA, 109, pp. 1878 - 1887

McElroy KE; Luciani F; Thomas T, 2012, 'GemSIM: General, Error-Model based SIMulator of next-generation sequencing data', BMC Genomics, 13, pp. 1 - 9, http://dx.doi.org/10.1186/1471-2164-13-74

Brown MV; Lauro FM; Demaere MZ; Muir L; Wilkins D; Thomas T; Riddle M; Fuhrman J; Andrews-Pfannkoch C; Hoffman JM; McQuaid J; Allen A; Rintoul S; Cavicchioli R, 2012, 'Global biogeography of SAR11 marine bacteria', Molecular Systems Biology, 8, pp. 595, http://dx.doi.org/10.1038/msb.2012.28

Thomas T; Gilbert J; Meyer F, 2012, 'Metagenomics - a guide from sampling to data analysis.', BMC Microbial Informatics and Experimentation, 2, pp. 3

Fan L; Liu M; Zhong L; Kjelleberg S; Thomas T, 2012, 'Metaproteogenomic analysis of a community of sponge symbionts', ISME Journal, 6, pp. 1515 - 1525, http://dx.doi.org/10.1038/ismej.2012.1

Thole S; Kalhoefer D; Voget S; Berger M; Engelhardt T; Leisegang H; Wollherr A; Kjelleberg S; Danial R; Meinhardt S; Thomas T; Brinkhoff T, 2012, 'Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life', ISME Journal, 6, pp. 2229 - 2244, http://dx.doi.org/10.1038/ismej.2012.62

Fan L; Mcelroy KE; Thomas T, 2012, 'Reconstruction of ribosomal RNA genes from metagenomic data', PLoS ONE, 7, pp. e39948

Thomas T; Kjelleberg S; Yung PY, 2011, 'Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion', , pp. 245 - 249, http://dx.doi.org/10.1002/9781118010518.ch29

Yung PY; Kjelleberg S; Thomas T, 2011, 'A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica.', FEMS Microbiology Letters, 321, pp. 24 - 29, http://dx.doi.org/10.1111/j.1574-6968.2011.02306.x

Fan L; Kjelleberg S; Thomas T, 2011, 'Accurate Reconstruction of Microbial Community From Environmental Shotgun Sequences Avoiding Primer Bias', SHORT, pp. 58 - 58

Thomas T; Kindinger I; Yu D; Blackall L; Forehead H; Johnson CR; Manefield MJ; Esvaran M, 2011, 'An experimental model for the spatial structuring and selection of bacterial communities', Journal of Microbiological Methods, 87, pp. 165 - 168, http://dx.doi.org/10.1016/j.mimet.2011.08.010

Lauro FM; Demaere MZ; Yau S; Brown MV; Wilkins D; Ng SC; Raftery MJ; Gibson JA; Andrews-Pfannkoch C; Lewis M; Hoffman JM; Thomas T; Cavicchioli R, 2011, 'An integrative study of a meromictic lake ecosystem in Antarctica', ISME Journal, 5, pp. 879 - 895

Kumar V; Rao D; Thomas T; Kjelleberg S; Egan SG, 2011, 'Antidiatom and antibacterial activity of epiphytic bacteria isolated from Ulva lactuca in tropical waters', World Journal of Microbiology and Biotechnology, 27, pp. 1543 - 1549, http://dx.doi.org/10.1007/s11274-010-0606-1

Burke CM; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2011, 'Bacterial community assembly based on functional genes rather than species', Proceedings of the National Academy of Sciences of the United States of America, 108, pp. 14288 - 14293, http://dx.doi.org/10.1073/pnas.1101591108

McElroy K; Luciani F; Hui J; Rice S; Thomas T, 2011, 'Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification', BMC Bioinformatics, 12, pp. A2 - A2

Schleheck DF; Weiss M; Pitluck S; Bruce D; Land ML; Han S; Saunders E; Tapia R; Detter C; Brettin T; Han J; Woyke T; Goodwin L; Pennacchio L; Nolan M; Cook AM; Kjelleberg S; Thomas T, 2011, 'Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T).', Standards in Genomic Sciences, 5, pp. 298 - 310, http://dx.doi.org/10.4056/sigs.2215005


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