List of scientific publications utilising the data generated through the Australian Microbiome initiative (including the BASE and Marine Microbes initiatives)

Papers – Initiative introductions
  • Bissett, A., Fitzgerald, A., Meintjes, T., Mele, P., Reith, F., & Dennis, P. et al. (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience5(1)
  • Brown, M. V., Van De Kamp, J., Ostrowski, M., Seymour, J. R., Ingleton, T., Messer, L. F., & Nelson, T. M. et al. (2018). Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative. Scientific data, 5: 180130.  
Papers and Proceedings – Consortium’s research activities


  • Ramoneda, J., et al. (2023) Building a genome-based understanding of bacterial pH preferences. Sci. Adv. 9, eadf8998.


  • O’Brien, J., McParland, E.L., Bramucci, A.R. et al. (2022) Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton. ISME Commun. 2, 16.
  • Liddicoat C., S.L. Krauss, A. Bissett, R. J. Borrett, L. C. Ducki, S. D. Peddle, P. Bullock, M. P. Dobrowolski, A Grigg, M Tibbett, M F. Breed (2022). Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets. J Env Management, 310, 114748.
  • Sow, S.L.S., Brown, M.V., Clarke, L.J., Bissett, A., van de Kamp, J., Trull, T.W., Raes, E.J., Seymour, J.R., Bramucci, A.R., Ostrowski, M., Boyd, P.W., Deagle, B.E., Pardo, P.C., Sloyan, B.M., Bodrossy, L., (2022). Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors. Env. Microbiology .
  • Lem, A.J., Liddicoat, C., Bissett, A., Cando-Dumancela, C., Gardner, M.G., Peddle, S.D., Watson, C.D. and Breed, M.F. (2022). Does revegetation cause soil microbiota recovery? Evidence from revisiting a revegetation chronosequence six years after initial sampling. Restor Ecol. Accepted Author Manuscript e13635. 
  • Doane, M.P., Ostrowski, M., Brown, M., Bramucci, A., Bodrossy, L., Kamp, J. van de, Bissett, A., Steinberg, P., Doblin, M.A., and Seymour, J. (2022). Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions. BioRxiv, 2022.05.02.490371.
  • Hallstrøm, S., Raina, J.-B., Ostrowski, M., Parks, D. H., Tyson, G. W., Hugenholtz, P., Stocker, R., Seymour, J. R., & Riemann, L. (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal 2022, 1–10.
  • Mills, J. G. (2022). Restoring Urban and Human Microbiotas.
  • O’Brien, J., McParland, E. L., Bramucci, A. R., Ostrowski, M., Siboni, N., Ingleton, T., Brown, M. V., Levine, N. M., Laverock, B., Petrou, K., & Seymour, J. (2022). The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters. Frontiers in Microbiology, 13.
  • Peddle, S. D., Bissett, A., Borrett, R. J., Bullock, P., Gardner, M. G., Liddicoat, C., Tibbett, M., Breed, M. F., & Krauss, S. L. (2022). Soil DNA chronosequence analysis shows bacterial community re-assembly following post-mining forest rehabilitation. Restoration Ecology, e13706.
  • Reun, N. Le, Bramucci, A., O’brien, J., Ostrowski, M., Brown, M. V., Van de Kamp, J., Bodrossy, L., Raina, J. B., Ajani, P., & Seymour, J. (2022). Diatom Biogeography, Temporal Dynamics, and Links to Bacterioplankton across Seven Oceanographic Time-Series Sites Spanning the Australian Continent. Microorganisms, 10(2), 338.
  • Song, W., Zhang, S., & Thomas, T. (2022). MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads. Bioinformatics, 38(15), 3684–3688.
  • Taylor, J. A., Díez-Vives, C., Nielsen, S., Wemheuer, B., & Thomas, T. (2022). Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environmental Microbiology, 24(5), 2299–2314.
  • Viscarra Rossel, R. A., Yang, Y., Bissett, A., Behrens, T., Dixon, K., Nevil, P., & Li, S. (2022). Environmental controls of soil fungal abundance and diversity in Australia’s diverse ecosystems. Soil Biology and Biochemistry, 170, 108694.
  • Waymouth, V., Miller, R. E., Kasel, S., Ede, F., Bissett, A., & Aponte, C. (2022). Riparian fungal communities respond to land-use mediated changes in soil properties and vegetation structure. Plant and Soil, 475(1), 491–513.
  • Yang, Y., Shen, Z., Bissett, A., & Viscarra Rossel, R. A. (2022). Estimating soil fungal abundance and diversity at a macroecological scale with deep learning spectrotransfer functions. SOIL, 8(1), 223–235.
  • Nilsson RH, Andersson AF, Bissett A, Finstad AG, Fossøy F, Grosjean M, Hope M, Jeppesen TS, Kõljalg U, Lundin D, Prager M, Suominen S, Svenningsen CS, Schigel D (2022) Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms. Metabarcoding and Metagenomics 6: e84960.
  • Raes, E. J., Hörstmann, C., Landry, M. R., Beckley, L. E., Marin, M., Thompson, P., Antoine, D., Focardi, A., O’Brien, J., Ostrowski, M., & Waite, A. M. (2022). Dynamic change in an ocean desert: Microbial diversity and trophic transfer along the 110 °E meridional in the Indian Ocean. Deep Sea Research Part II: Topical Studies in Oceanography, 201, 105097.
  • Raina, JB., Lambert, B.S., Parks, D.H. et al. (2022) Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature 605, 132–138.
  • Ray, A.E., Zaugg, J., Benaud, N. et al. (2022) Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. ISME J.


  • Samuel, R.M., Meyer, R., Buttigieg, P.L., Davies, N., Jeffery, N.W., Meyer, C., Pavloudi, C., Pitz, K.J., Sweetlove, M., Theroux, S., van de Kamp, J. and Watts, A. (2021). Toward a global public repository of community protocols to encourage best practices in biomolecular ocean observing and research. Front. Mar. Sci. 8:758694.
  • Waymouth, V., Miller, R. E., Kasel, S., Ede, F., Bissett, A., & Aponte, C. (2021). Soil bacterial community responds to land-use change in riparian ecosystems. Forests, 12(2), 157.
  • Taylor, J.A., Palladino, G., Wemheuer, B. et al. (2021). Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME J 15, 503–519
  • Song, W., Wemheuer, B., Steinberg, P.D. et al. (2021). Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. ISME J 15, 807–817
  • McLennan K., Ruvindy R., Ostrowski M., Murray S. (2021). Assessing the use of molecular barcoding and qPCR for investigating the ecology of Prorocentrum minimum (Dinophyceae), a harmful algal species Microorganisms, 9(3), 510
  • Phelps, C.M., Mcmahon, K., Bissett, A., Bernasconi, R., Steinberg, P.D., Thomas, T., Marzinelli, E.M., & Huggett, M.J. (2021). Supplementary Table 11: Regional zOTU table (data as relative abundances). Edith Cowan University.
  • Ji, M., Williams, T. J., Montgomery, K., Wong, H. L., Zaugg, J., Berengut, J. F., Bissett, A., Chuvochina, M., Hugenholtz, P., & Ferrari, B. C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. ISME Journal, 1–16.
  • Record, N. R., Countway, P. D., Kanwit, K., & Fernández-Robledo, J. A. (2021). Rise of the rare biosphere. Elementa: Science of the Anthropocene, 9(1).
  • Raes, E. (2021). Like the ocean’s ‘gut flora’: we sailed from Antarctica to the equator to learn how bacteria affect ocean health. The Conversation.
  • Phelps, C. M., McMahon, K., Bissett, A., Bernasconi, R., Steinberg, P. D., Thomas, T., Marzinelli, E. M., & Huggett, M. J. (2021). The surface bacterial community of an Australian kelp shows cross-continental variation and relative stability within regions. FEMS Microbiology Ecology, 97(7).
  • Freestone, M. W., Swarts, N. D., Reiter, N., Tomlinson, S., Sussmilch, F. C., Wright, M. M., Holmes, G. D., Phillips, R. D., & Linde, C. C. (2021). Continental scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia. Annals of Botany.
  • Bowd, E. J., Banks, S. C., Bissett, A., May, T. W., & Lindenmayer, D. B. (2021). Direct and indirect disturbance impacts in forests. In Ecology Letters (Vol. 24, Issue 6, pp. 1225–1236). Blackwell Publishing Ltd.
  • Montgomery, K., Williams, T. J., Brettle, M., Berengut, J. F., Zhang, E., Zaugg, J., Hugenholtz, P., & Ferrari, B. C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology.
  • Raes, E. J., Karsh, K., Sow, S. L. S., Ostrowski, M., Brown, M. V., van de Kamp, J., Franco-Santos, R. M., Bodrossy, L., & Waite, A. M. (2021). Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. Nature Communications, 12(1), 1–12.
  • Bowd, E. J., Banks, S. C., Bissett, A., May, T. W., & Lindenmayer, D. B. (2021). Disturbance alters the forest soil microbiome. Molecular Ecology.
  • Glasl, B., Haskell, J. B., Aires, T., Serrão, E. A., Bourne, D. G., Webster, N. S., & Frade, P. R. (2021). Microbial Surface Biofilm Responds to the Growth-Reproduction-Senescence Cycle of the Dominant Coral Reef Macroalgae Sargassum spp. Life 2021, 11(11), 1199.
  • Clarke, L. J., Suter, L., King, R., Bissett, A., Bestley, S., & Deagle, B. E. (2021). Bacterial epibiont communities of panmictic Antarctic krill are spatially structured. Molecular Ecology, 30(4), 1042–1052.


  • Davoodian, N., Jackson, C. J., Holmes, G. D., and Lebel, T. (2020). Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria. Applications in Plant Sciences 8( 9): e11392.
  • Marchioro GM, Glasl B, Engelen AH, Serrão EA, Bourne DG, Webster NS, Frade PR. (2020). Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters. PeerJ 8:e9644
  • Oliverio, A.M., A Bissett, K McGuire, K Saltonstall, B L. Turner, N Fierer (2020). The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities. mBio, 11 (5) e01718-20
  • Ray A E., Zhang E, Terauds A, Ji M, Kong W, Ferrari B C. (2020). Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation. Frontiers in Microbiology, 11:1936
  • Wemheuer, F., Taylor, J. A., Daniel, R., Johnston, E., Meinicke, P., Thomas, T., & Wemheuer, B. (2020). Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environmental Microbiome, 15(1), 11.
  • Glasl B, Robbins S, Frade PR, Marangon E, Laffy PW, Bourne DG, Webster NS. (2020) Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME Journal, 1–16.
  • Yan, D., Gellie, N. J., Mills, J. G., Connell, G., Bissett, A., Lowe, A. J., & Breed, M. F. (2020) A soil archaeal community responds to a decade of ecological restoration. Restoration Ecology, 28(1), 63-72.
  • Finn, D., Yu, J., & Penton, C. R. (2020) Soil quality shapes the composition of microbial community stress response and core cell metabolism functional genes. Applied Soil Ecology, 148, 103483.
  • Li, J., Nie, M., & Pendall, E. (2020) Soil physico-chemical properties are more important than microbial diversity and enzyme activity in controlling carbon and nitrogen stocks near Sydney, Australia. Geoderma, 366, 114201.
  • Uetake, J., Hill, T. C. J., Moore, K. A., DeMott, P. J., Protat, A., & Kreidenweis, S. M. (2020). Airborne bacteria confirm the pristine nature of the Southern Ocean boundary layer. Proceedings of the National Academy of Sciences, 117(24), 13275 – 13282.
  • Větrovský, T., Morais, D., Kohout, P., Lepinay, C., Gallardo, C. A., Hollá, S. A., Bahnmann, B. D., Bílohnědá, K., Brabcová, V., D’Alò, F., Human, Z. R., Jomura, M., Kolařík, M., Kvasničková, J., Lladó, S., López-Mondéjar, R., Martinović, T., Mašínová, T., Meszárošová, L., et al & Baldrian, P. (2020). GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies. BioRxiv, 2020.04.24.060384.
  • Waymouth, V., Miller, R. E., Ede, F., Bissett, A., & Aponte, C. (2020). Variation in soil microbial communities: elucidating relationships with vegetation and soil properties, and testing sampling effectiveness. Plant Ecology, 221(9), 1–15.
  • Mills, J. G., Bissett, A., Gellie, N. J. C., Lowe, A. J., Selway, C. A., Thomas, T., Weinstein, P., Weyrich, L. S., & Breed, M. F. (2020). Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design. Restoration Ecology, rec.13175.
  • Quigley, K. M., Alvarez Roa, C., Torda, G., Bourne, D. G., & Willis, B. L. (2020). Co‐dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. MicrobiologyOpen, 9(2).
  • Focardi, A., Ostrowski, M., Goossen, K., Brown, M. V., & Paulsen, I. (2020). Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System. Viruses, 12(3), 317.
  • Raes, E. J., van de Kamp, J., Bodrossy, L., Fong, A. A., Riekenberg, J., Holmes, B. H., Erler, D. V., Eyre, B. D., Weil, S.-S., & Waite, A. M. (2020). N2 Fixation and New Insights Into Nitrification From the Ice-Edge to the Equator in the South Pacific Ocean. Frontiers in Marine Science, 7, 389.
  • Zhang, E., Thibaut, L. M., Terauds, A., Raven, M., Tanaka, M. M., Van Dorst, J., Wong, S. Y., Crane, S., & Ferrari, B. C. (2020). Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: A tale of two oases. Microbiome, 8(1), 37.
  • Ostrowski, M., Seymour, J., Messer, L., Varkey, D., Goosen, K., Smith, M., Bissett, A., Van De Kamp, J., Bodrossy, L., & Brown, M. (2020). Status of Australian marine microbial assemblages State and Trends of Australia’s Oceans Report Key Data Streams National Reference Stations 2.7 State and Trends of Australia’s Ocean Report Time-Series published.
  • Araujo, R., Gupta, V. V. S. R., Reith, F., Bissett, A., Mele, P., & Franco, C. M. M. (2020). Biogeography and emerging significance of Actinobacteria in Australia and Northern Antarctica soils. Soil Biology and Biochemistry, 146, 107805.
  • Messer, L. F., Ostrowski, M., Doblin, M. A., Petrou, K., Baird, M. E., Ingleton, T., Bissett, A., Van de Kamp, J., Nelson, T., Paulsen, I., Bodrossy, L., Fuhrman, J. A., Seymour, J. R., & Brown, M. V. (2020). Microbial tropicalization driven by a strengthening western ocean boundary current. Global Change Biology, 26(10), 5613-5629.
  • Li, J., Nie, M., Powell, J. R., Bissett, A., & Pendall, E. (2020). Soil physico-chemical properties are critical for predicting carbon storage and nutrient availability across Australia. Environmental Research Letters, 15(9), 094088.
  • Sow, S. L. S. S., Trull, T. W., & Bodrossy, L. (2020). Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Frontiers in Microbiology, 11, 1847.
  • Hurtado-McCormick, V., [Justin Seymour, Peter Ralph] (2020). The Zostera muelleri seagrass microbiome. PhD Thesis.
  • Frade, P. R., Glasl, B., Matthews, S. A., Mellin, C., Serrão, E. A., Wolfe, K., Mumby, P. J., Webster, N. S., & Bourne, D. G. (2020). Spatial patterns of microbial communities across surface waters of the Great Barrier Reef. Communications Biology, 3(1), 442.


  • Liddicoat C., Weinstein P., Bissett A., Gellie N., Mills J., Waycott M. and M.F. Breed (2019) Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health? Environment International, 129: 105-117.
  • Yang, Y., Viscarra Rossel, R. A., Li, S., Bissett, A., Lee, J., Shi, Z., Behrens, T., & Court, L. (2019) Soil bacterial abundance and diversity better explained and predicted with spectro-transfer functions. Soil Biology and Biochemistry, 129: 29-38.
  • Glasl, B., Bourne, D. G., Frade, P. R., Thomas, T., Schaffelke, B., & Webster, N. S. (2019). Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome, 7(1), 94.
  • Egidi E., Wood J., Celestina C., May T., Mele P., Edwards J., Powell J., Bissett A., Franks A. (2019) Delving into the dark ecology: A continent-wide assessment of patterns of composition in soil fungal communities from Australian tussock grasslands. Fungal Ecology, 39: 356-370.
  • Větrovský, T., Kohout, P., Kopecký, M., Machac, A., Man, M., Bahnmann, B. D., Brabcová, V., Choi, J., Meszárošová, L., Human, Z. R., Lepinay, C., Lladó, S., López-Mondéjar, R., Martinović, T., Mašínová, T., Morais, D., Navrátilová, D., Odriozola, I., Štursová, M., et al & Baldrian, P. (2019). A meta-analysis of global fungal distribution reveals climate-driven patterns. Nature Communications, 10(1), 5142.
  • Benaud, N., Zhang, E., van Dorst, J., Brown, M. V, Kalaitzis, J. A., Neilan, B. A., & Ferrari, B. C. (2019). Harnessing long-read amplicon sequencing to uncover NRPS and Type I PKS gene sequence diversity in polar desert soils. FEMS Microbiology Ecology, 95(4).
  • Zhang, E., Thibaut, L. M., Terauds, A., Wong, S., Dorst, J. van, Tanaka, M. M., & Ferrari, B. C. (2019). Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica. BioRxiv, 559666.
  • Wong, S. Y., Charlesworth, J. C., Benaud, N., Burns, B. P., & Ferrari, B. C. (2019). Novel Quorum Sensing Activity in East Antarctic Soil Bacteria. BioRxiv, 749861.
  • Badis, Y., Klochkova, T. A., Brakel, J., Arce, P., Ostrowski, M., Tringe, S. G., Kim, G. H., & Gachon, C. M. M. (2019). Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide. European Journal of Phycology, 1–10.
  • Clarke, L. J., Suter, L., King, R., Bissett, A., & Deagle, B. E. (2019). Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities. Frontiers in Microbiology, 9.
  • Scully, R. P. (2019). Mapping every microbe. New Scientist, 242(3234), 10.
  • Wong SY, Charlesworth JC, Benaud N, Burns BP, Ferrari BC. (2019) Communication within East Antarctic soil bacteria. Appl Environ Microbiol 86(1):e01968-19.


  • Liddicoat, C., Bi, P., Waycott, M., Glover, J., Breed, M., & Weinstein, P. (2018). Ambient soil cation exchange capacity inversely associates with infectious and parasitic disease risk in regional Australia. Science Of The Total Environment, 626: 117-125
  • Delgado-Baquerizo, M., Reith, F., Dennis, P., Hamonts, K.,Powell, J., & Young, A. et al. (2018). Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology, 99(3), 583–596.
  • Raes, E. J., Bodrossy, L., van de Kamp, J., Bissett, A.,Ostrowski, M., Brown, M. V., & Waite, A. M. et al. (2018). Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean. Proceedings of the National Academy of Sciences, 201719335.
  • Bissett, A. and Brown, M.V. (2018) Alpha-diversity is strongly influenced by the composition of other samples when using multiplexed sequencing approaches, Soil Biology and Biochemistry, 127: 79-81
  • Eldridge, D. J., Maestre, F. T., Koen, T. B., & Delgado-Baquerizo, M. (2018). Australian dryland soils are acidic and nutrient-depleted, and have unique microbial communities compared with other drylands. Journal of Biogeography, 45(12), 2803–2814.
  • Lee, J., Garland, G. M., Viscarra Rossel, R. A., Rossel, R. A. V., & Viscarra Rossel, R. A. (2018). Continental soil drivers of ammonium and nitrate in Australia. Soil, 4(3), 213–224.
  • Lee, J., Garland, G. M., & Rossel, R. A. V. (2018). Corrigendum to: Continental soil drivers of ammonium and nitrate in Australia. Soil, 4, 213–224.
  • Delgado-Baquerizo, M., Eldridge, D. J., Travers, S. K., Val, J., Oliver, I., & Bissett, A. (2018). Effects of climate legacies on above- and belowground community assembly. Global Change Biology, 24(9), 4330–4339.
  • Glasl, B., Bourne, D. G., Frade, P. R., & Webster, N. S. (2018). Establishing microbial baselines to identify indicators of coral reef health. Microbiology Australia.
  • Lebel, T., Pennycook, S., & Baarrett, M. (2018). Two new species of Pisolithus (Sclerodermataceae) from Australasia, and an assessment of the confused nomenclature of P. tinctorius. Phytotaxa, 348(3), 163.
  • C M Phelps, R Bernasconi, M Danks, J M Gasol, A J M Hopkins, J Jones, C R J Kavazos, B C Martin, F Tarquinio, M. J. H. (2018). Microbiomes of Western Australian marine environments. Journal of the Royal Society of Western Australia, 101, 17–43.


  • Yan, D., Mills, J., Gellie, N., Bissett, A., Lowe, A., and Breed, M. (2017). High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration. Biological Conservation, 217: 113-120
  • Noronha, M., Lacerda Júnior, G., Gilbert, J., and de Oliveira, V. (2017). Taxonomic and functional patterns across soil microbial communities of global biomes. Science Of The Total Environment, 609: 1064-1074
  • Delgado-Baquerizo, M., Bissett, A., Eldridge, D., Maestre, F., He, J., and Wang, J. et al. (2017). Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities. Nature Ecology & Evolution, 1(9): 1339-1347
  • Delgado-Baquerizo, M., Powell, J., Hamonts, K., Reith, F., Mele, P., & Brown, M. et al. (2017). Circular linkages between soil biodiversity, fertility and plant productivity are limited to top soil at the continental scale. New Phytologist, 215(3): 1186-1196
  • Midgley, D., Greenfield, P., Bissett, A., and 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, 27(6): 587-594
  • Gellie, N., Mills, J., Breed, M., and Lowe, A. (2017). Revegetation rewilds the soil bacterial microbiome of an old field. Molecular Ecology, 26(11): 2895-2904
  • Glasl, B., Webster, N.S. and Bourne, D.G. (2017) Microbial indicators as a diagnostic tool for assessing water quality and climate stress in coral reef ecosystems. Marine Biology, 164: 91
  • Pirotta, V., Smith, A., Ostrowski, M., Russell, D., Jonsen, I.D., Grech, A.& Harcourt, R. (2017) An Economical Custom-Built Drone for Assessing Whale Health. Frontiers in Marine Science, 4: 425
  • Yeoh, Y.K., Dennis, P.G., Paungfoo-Lonhienne, C., Weber, L., Brackin, R., Ragan, M.A., Schmidt, S. and Hugenholtz, P. (2017) Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature communications, 8(1): 215.
  • Ji, M., Greening, C., Vanwonterghem, I., Carere, C. R., Bay, S. K., Steen, J. A., Montgomery, K., Lines, T., Beardall, J., van Dorst, J., Snape, I., Stott, M. B., Hugenholtz, P., & Ferrari, B. C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552(7685), 400–403.
  • Bissett, A., Fitzgerald, A., Court, L., Meintjes, T., Mele, P. M., Reith, F., Dennis, P. G., Breed, M. F., Brown, B., Brown, M. V., Brugger, J., Byrne, M., Caddy-Retalic, S., Carmody, B., Coates, D. J., Correa, C., Ferrari, B. C., Gupta, V. V. S. R., Hamonts, K., … Young, A. (2017). Erratum to: Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. GigaScience, 6(5).


  • Yeoh, Y. K., Paungfoo‐Lonhienne, C., Dennis, P. G., Robinson, N., Ragan, M. A., Schmidt, S., and Hugenholtz, P. (2016) The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application. Environmental microbiology, 18(5): 1338-1351.
  • Karan, M., Liddell, M., Prober, S. M., Arndt, S., Beringer, J., Boer, M., Cleverly, J., Eamus, D., Grace, P., Van Gorsel, E., Hero, J.-M., Hutley, L., Macfarlane, C., Metcalfe, D., Meyer, W., Pendall, E., Sebastian, A., & Wardlaw, T. (2016). The Australian SuperSite Network: A continental, long-term terrestrial ecosystem observatory. Science of The Total Environment, 568, 1263–1274.


  • Paungfoo-Lonhienne, C., Yeoh, Y. K., Kasinadhuni, N. R. P., Lonhienne, T. G. A., Robinson, N., Hugenholtz, P., Ragan, M. A., & Schmidt, S. (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Scientific Reports, 5(1), 8678.
  • Gillings, M. R., Gaze, W. H., Pruden, A., Smalla, K., Tiedje, J. M., & Zhu, Y.-G. (2015). Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. The ISME Journal, 9(6), 1269–1279.

Understanding the Impacts of Subsurface Drip Irrigation on Soil Microbial Communities in the Context of Processing Tomato Production. Michelle Quach, Masters of Agricultural Science Student, University of Melbourne, R. P. S. B. A. P. M. and P. J. H. A Preliminary Report. Australian Processing Tomato Grower, Sept. 2017

GBRMPA ELibrary: Monitoring additional values within the Reef 2050 Integrated Monitoring and Reporting Program: final report of the microbes expert group. (2021).

Presentations – Posters and Talks