Blog icon

Dr David Midgley

Team Leader

https://people.csiro.au/M/D/David-Midgley

Contact details:

PO BOX 218
LINDFIELD NSW 2070 AUSTRALIA

Biography

I have a PhD in microbial ecology and work in the bioinformatics/ecology interface (primarily with Python). I have expertise in mycology, mycorrhizal biology, bioinformatics, anaerobic microbiology and microbial ecology.

I have worked with microbes in a host of environments including plant leaves and roots, biological filters, industrial holding ponds, mine sediments, animal digestive tracts, in soils, freshwater systems (rivers, creeks and lakes), marine sediments, in shallow aquifers, and in the deep subsurface.

I am currently the Team Leader of the Biogeochemistry and Microbiology Team in CSIRO Energy's Resources program. I manage an amazing group of chemists, microbiologists and geoscientists in Sydney and Perth. Below is a list of my publications.

  • 58: AG McLeish, P Greenfield, DJ Midgley, IT Paulsen (2022) Desulfuromonas sp. 'CSMB_57’, isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals. Microbial Genomics. Accepted.

  • 57: BC Campbell, P Greenfield, S Gong, EP Barnhart, DJ Midgley, IT Paulsen & SC George (2022) Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences. Environmental Microbiology. In Press.

  • 56: AG McLeish, P Greenfield, DJ Midgley, IT Paulsen (2021) Draft Genome Sequence of Desulfovibrio sp. Strain CSMB_222, Isolated from Coal Seam Formation Water. Microbiology Resource Announcements 10 (48), e00564-21

  • 55: McLeish AG, Gong S, Greenfield P, Midgley DJ & Paulsen IT (2021) Microbial community shifts on organic rocks of different maturities reveals potential catabolisers of organic matter in coal. Microbial Ecology. Accepted.

  • 54: SHW Vick, BK Fabian, CJ Dawson, C Foster, A Asher, K A Hassan, DJ Midgley, IT Paulsen & SG Tetu (2021) Delving into defence: identifying the Pseudomonas protegens Pf-5 gene suite involved in defence against secreted products of fungal, oomycete and bacterial rhizosphere competitors. Microbial Genomics. Accepted.

  • 53: Campbell BC, Gong S, Greenfield P, Midgley DJ, Paulsen IT & George SC (2021) Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 13;97(5) doi: 10.1093/femsec/fiab053.

  • 52: SHW Vick, Greenfield P, Tetu SG, Midgley DJ & Paulsen IT (2021) Draft Genome Sequence of Dietzia sp. SYD-A1 Isolated from Coal Seam Formation Water. Microbiology Resource Announcements. Accepted.

  • 51: AG McLeish, SHW Vick, M Grigore, KL Pinetown, DJ Midgley & IT Paulsen (2020) Adherent microbes in coal seam environments prefer mineral-rich and crack-associated microhabitats. International Journal of Coal Geology. Accepted.

  • 50: Vick SHW, Greenfield P, Willows RD, Tetu SG, Midgley DJ & Paulsen IT (2019) Subsurface Stappia: Success through defence, specialisation and putative pressure-dependent carbon fixation. Microbial Ecology. Accepted.

  • 49: Vick SHW, Greenfield P, Tetu SG, Midgley DJ & Paulsen IT (2019) Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams. Scientific reports 9 (1), 1-13

  • 48: Vick SHW, Gong S, Sestak S, Vergara T, Pinetown PL, Li Z, Greenfield P, Tetu S, Midgley DJ & Paulsen IT (2019) Who eats what? Unravelling microbial conversion of coal to methane. FEMS Microbiology Ecology. Accepted.

  • 47: Vick SHW, Greenfield P, Pinetown KL, Sherwood N, Gong S, Tetu SG, Midgley DJ & Paulsen IT (2019) Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams. iScience. 12. 152.

  • 46: B Sutcliffe, AJ. Harford, GC. Hose, P Greenfield, DJ. Midgley, IT. Paulsen and AA. Chariton (2019) Microbial communities are sensitive indicators for freshwater sediment copper contamination. Environmental Pollution. Accepted.

  • 45: Greenfield P, Tran-Dinh N & Midgley DJ (2018) Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets. PeerJ. Accepted.

  • 44: Midgley DJ, Sutcliffe B, Greenfield P, Tran-Dinh N (2018) Gamarada debralockiae gen. nov. sp. nov. – the genome of the most widespread Australian ericoid mycorrhizal fungus. Mycorrhiza. Accepted.

  • 43: B Sutcliffe, AA. Chariton, AJ. Harford, GC. Hose, P Greenfield, DJ. Midgley and IT. Paulsen (2018) Diverse fungal lineages in subtropical ponds are altered by sediment-bound copper. Fungal Ecology. doi.org/10.1016/j.funeco.2018.03.003

  • 42: SHW Vick, P Greenfield, N Tran-Dinh, SG Tetu, DJ Midgley, IT Paulsen (2018) The Coal Seam Microbiome (CSMB) reference set, a lingua franca for the microbial coal-to-methane community. International Journal of Coal Geology 186, 41-50.

  • 41: B Sutcliffe, AA Chariton, AJ Harford, GC Hose, S Stephenson, P Greenfield, Midgley DJ & IT Paulsen (2017) Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments Microbial Ecology, 1-15.

  • 40: Machado L,Tomkins N, Magnusson M. Midgley DJ, de Nys, R & Rosewarne CP (2017) In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis. Microbial Ecology. Accepted. doi.org/10.1007/s00248-017-1086-8

  • 39: Sutcliffe B, Chariton AA, Harford AJ, Hose GC, Greenfield P, Elbourne LDH , Oytam Y, Stephenson S, Midgley DJ and Paulsen IT (2017). Effects of uranium concentration on microbial community structure and functional potential. Environmental Microbiology. doi:10.1111/1462-2920.13839

  • 38: Midgley DJ, Greenfield P, Bissett A & Tran-Dinh N (2017). First evidence of Pezoloma ericae in Australia; using the Biomes of Australia Soil Environments (BASE) to explore the Australian phylogeography of known ericoid mycorrhizal and root-associated fungi. Mycorrhiza. doi: 10.1007/s00572-017-0769-9.

  • 37: Pitt JI, Lange L, Lacey AE, Vuong D, Midgley DJ, Greenfield P, Bradbury MI, Lacey E, Busk PK, Pilgaard B, Chooi Y and Piggott AM. (2017) Aspergillus hancockii sp. nov., A biosynthetically talented fungus endemic to southeastern Australian soils. PLOS One. doi: 10.1371/journal.pone.0170254.

  • 36: Unterweger B, Bulach D, Scoble J, Midgley DJ, Greenfield P, Lyras D, Johanesen P, and Dumsday G (2016) Characterisation of CYP101J2, CYP101J3 and CYP101J4, three 1,8-cineole-hydroxylating cytochrome P450 monooxygenases from Sphingobium yanoikuyae strain B2. Applied and Environmental Microbiology 82 (22), 6507-6517

  • 35: Vasconcellos SP, Sierra-Garcia IN, Dellagnezze BM, Vicentini R, Midgley DJ, Silva CC, Neto EVS, Volk H, Hendry P, Oliveira VM (2016) Functional and genetic characterization of EPS-producing clones from a petroleum reservoir metagenomic library. Environmental Technology. doi:10.1080/09593330.2016.1218940.

  • 34: Vick SHW, Tetu SG, Sherwood N, Pinetown P, Sestak S, Vallotton P, Elbourne LDH, Greenfield P, Johnson E, Barton D, Midgley DJ, Paulsen IT (2016) Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface. International Journal of Coal Geology. doi:10.1016/j.coal.2016.04.012

  • 33: Midgley DJ, Rosewarne CP, Greenfield P, Li D, Vockler CJ, Hitchcock CJ, Sawyer NA, Brett R, Edwards J, Pitt JI and Tran-Dinh N (2016) Genomic insights into the carbohydrate catabolism of Cairneyella variabilis gen. nov., sp. nov., the first reports from a genome of an ericoid mycorrhizal fungus from the southern hemisphere. Mycorrhiza 26(4):345-52. doi: 10.1007/s00572-016-0683-6.

  • 32: Wang H, Lin H, Rosewarne CP, Li D., Gong S., Hendry P., Greenfield P., Sherwood N and Midgley DJ (2016) Enhancing biogenic methane generation from a brown coal by combining different microbial communities. International Journal of Coal Geology. 154–155, pp. 107–110

  • 31: Deshpande V, Wang Q, Greenfield P, Charleston M, Porras-Alfaro, A, Kuske CR, Cole JR, Midgley DJ & Tran-Dinh N (2015) Fungal identification using a Bayesian Classifier and the ‘Warcup’ training set of Internal Transcribed Spacer sequences. Mycologia. doi:10.3852/14-293

  • 30: Han Wang, Hai Lin, Nai Tran-Dinh, Dongmei Li, Paul Greenfield, and David J. Midgley (2015) Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus. Genome Annoucements. Mar-Apr; 3(2): e00303-15.

  • 29: Han Wang, Hai Lin, Nai Tran-Dinh, Dongmei Li, Paul Greenfield, and David J. Midgley (2015) Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus. Genome Annoucements. Mar-Apr; 3(2): e00304-15.

  • 28: Han Wang, Hai Lin, Nai Tran-Dinh, Dongmei Li, Paul Greenfield, and David J. Midgley (2015)Draft Genome Sequence ofRuminoclostridiumsp. Ne3 from anEnrichment Culture Obtained from the Australian Subterranean Termite, Nasutitermes exitiosus. Genome Annoucements. Mar-Apr; 3(2): e00305-15.

  • 27: D Ferreira Domingos, A Fonseca de Faria, R de Souza Galaverna, M Nogueira Eberlin, P Greenfield, T Domingues Zucchi, I Soares Melo, N Tran-Dinh, DJ Midgley & VM de Oliveira (2015) Genomic and chemical insights into biosurfactant production by the mangrove-derived strain Bacillus safensis CCMA-560. Applied Microbiology and Biotechnology. DOI 10.1007/s00253-015-6377-8.

  • 26: CJ Vockler, P Greenfield, N Tran-Dinh, DJ Midgley (2014) Draft genome sequence of Bacillus pumilus Fairview, an isolate recovered from a microbial methanogenic enrichment of coal seam gas formation water from Queensland, Australia. Genome announcements 2 (2), e00279-14

  • 25: Daniela F Domingos, Bruna M Dellagnezze, Paul Greenfield, Luciana R Reyes, Itamar S Melo, David J Midgley, Valéria M Oliveira (2013) Draft genome sequence of the biosurfactant-producing bacterium Gordonia amicalis strain CCMA-559, isolated from petroleum-impacted sediment. Genome announcements 1 (6), e00894-13

  • 24: D Li, P Greenfield, CP Rosewarne, DJ Midgley (2013) Draft genome sequence of Thermoanaerobacter sp. strain A7A, reconstructed from a metagenome obtained from a high-temperature hydrocarbon reservoir in the Bass Strait, Australia. Genome announcements 1 (5), e00701-13

  • 23: Daniela F Domingos, Bruna M Dellagnezze, Paul Greenfield, Luciana R Reyes, Itamar S Melo, David J Midgley, Valéria M Oliveira (2013) Draft genome sequence of Bacillus pumilus CCMA-560, isolated from an oil-contaminated mangrove swamp. Genome announcements 1 (5), e00707-13

  • 22: B Sutcliffe, DJ Midgley, CP Rosewarne, P Greenfield, D Li (2013) Draft genome sequence of Thermotoga maritima A7A reconstructed from metagenomic sequencing analysis of a hydrocarbon reservoir in the Bass Strait, Australia. Genome announcements 1 (5), e00688-13

  • 21: Rees, DJ, Midgley DJ, Marchant A, Perkins A & Orlovich DA (2013) Morphological and molecular data for Australian Hebeloma species do not support the generic status of Anamika. Mycologia. In Press.

  • 20: Rosewarne C, Greenfield P, Li D, Tran-Dinh N, Midgley DJ and Hendry P (2012) Draft genome sequence of Methanobacterium sp. 'Maddingley', reconstructed from metagenomic sequencing of a methanogenic microbial consortium. Genome Annoucements. In Press.

  • 19: Rosewarne C, Greenfield P, Li D, Tran-Dinh N, Bradbury M, Midgley DJ and Hendry P (2012) Draft genome sequence of Clostridium sp. 'Maddingley', isolated from coal-seam gas formation water. Genome Annoucements. In Press.

  • 18: Li D, Midgley DJ, Wei X, Volk H, Daud WAW & Hendry P (2012) Addition of a palm oil analogue to oil-reservoir formation water stimulates the growth of Anaerobaculum sp. and a novel taxon from the Deferribacteraceae. J Gen Appl Micro. In press.

  • 17: Midgley DJ, Paul Greenfield P, Shaw JM, Oytam Y, Li D, Kerr CA & Hendry P (2012) Reanalysis and simulation suggest a phylogenetic microarray does not accurately profile microbial communities. PLoS One. 10.1371/journal.pone.0033875

  • 16: Bradbury MI, Greenfield P, Midgley DJ, Li D, Tran-Dinh N, Vriesekoop F & Brown J (2012) Draft genome sequence of Clostridium sporogenes PA 3679, the common non-toxigenic surrogate for proteolytic Clostridium botulinum. J Bact. 194(6):1631.

  • 15: Li D, Midgley DJ, Ross JP, Oytam Y, Abell G, Volk H, Daud WAN, Hendry P (2012) Oil field microbial ecology: insights from Malaysian oil reservoir and a systematic review of oil reservoir biodiversity worldwide. Applied and Environmental Microbiology DOI: 10.1007/s00203-012-0788-z

  • 14: Midgley DJ, McGee PA, Stewart MI & Saleeba JA (2011) Diverse assemblages of ascomycetous fungi occur in woodland, grassland and cropping soils of northern-central New South Wales, Australia. Australasian Mycologist (29) 29-36.

  • 13: Midgley D. J., Hendry P., Pinetown K. L., Fuentes D., Gong S., Mitchell D. L., Faiz M. (2010) Diverse microbial communities occur in a deep, coal seam methane reservoir in the Gippsland Basin, Australia. International Journal of Coal Geology. 82: 232-239.

  • 12: Syed N. A., Midgley D. J., Ly P. K. C., Saleeba J. A. & McGee P. A. (2009) Do plant endophytic and free-living Chaetomium species differ? Australasian Mycologist 28: 51-55.

  • 11: Daynes C. M., McGee P. A. & Midgley D. J. (2009) Utilisation of plant cell-wall polysaccharides and organic phosphorus substrates by isolates of Aspergillus and Penicillium isolated from soil. Fungal Ecology 1:94-98.

  • 10: Midgley D. J., Saleeba J. A., Stewart M. I. & McGee P. A. (2007) Novel soil lineages of Archaea are present in semi-arid soils of eastern Australia. Canadian Journal of Microbiology. 53: 129-138.

  • 9: Midgley D. J., Saleeba J. A. , Stewart M. I., Simpson A. E. & McGee P. A. (2007) Molecular diversity of soil basidiomycete communities in northern-central New South Wales, Australia. Mycological Research. 111: 370-378.

  • 8: Whiffen, L. K., Midgley, D. J. & McGee, P. A. (2007) Polyphenolic compounds interfere with quantification of protein in soil extracts using the Bradford method. Soil Biology and Biochemistry. 39: 691-694.

  • 7: Midgley, D. J., Letcher P. M. & McGee P. A. (2006) Access to organic and insoluble sources of phosphorus varies among soil Chytridiomycota. Archives of Microbiology 186: 211-217. DOI: 10.1007/s00203-006-0136-2

  • 6: Gleason, F. H., Midgley, D. J., Letcher P. M. & McGee P. A. (2006) Can soil Chytridiomycota survive and grow in different osmotic potentials? Mycological Research 110: 869-875.

  • 5: Midgley, D. J., Jordan, L. A., Saleeba, J. A. & McGee P. A. (2006) Utilisation of carbon substrates by orchid and ericoid mycorrhizal fungi from Australian dry sclerophyll forests. Mycorrhiza. 16:175-182.

  • 4: Midgley, D. J., Chambers, S. M. & Cairney, J. W. G. (2004) Utilisation of carbon substrates by multiple genotypes of ericoid mycorrhizal endophytes from Eastern Australian Ericaceae. Mycorrhiza 14: 245-251

  • 3: Midgley, D. J., Chambers, S. M. & Cairney, J. W. G. (2004) Distribution of ericoid mycorrrhizal endophytes and root-associated fungi in neighbouring Ericaceae plants in the field. Plant and Soil 259: 137-151

  • 2: Midgley, D. J., Chambers, S. M. & Cairney, J. W. G. (2004). Inorganic and organic substrates as sources of nitrogen and phosphorus for multiple genotypes of two ericoid mycorrhizal fungal taxa from Woollsia pungens Cav. (Muell.) and Leucopogon parviflorus (Andr.) Lindl. (Ericaceae) Australian Journal of Botany 52 : 559-565

  • 1: Midgley, D. J., Chambers, S. M. & Cairney, J. W. G. (2002) Spatial distribution of fungal endophyte genotypes in a Woollsia pungens (Ericaceae) root system. Australian Journal of Botany 50: 559-565.

Academic Qualifications

  • 2003

    Doctor of Philosophy (PhD), Mycorrhizal Fungal Ecology
    University of Western Sydney