Publications

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

2021

  • 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 Microorganisms9(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. Samuel RM, Meyer R, Buttigieg PL, Davies N, Jeffery NW, Meyer C, Pavloudi C, Pitz KJ, 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. doi: 10.3389/fmars.2021.758694
  • 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 Microorganisms9(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.

2020

  • 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
  • A M. Oliverio, 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, 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.
  • 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.
  • 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 www.imosoceanreport.org.au 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.
  • Wong SY, Charlesworth JC, Benaud N, Burns BP, Ferrari BC. 2020. Communication within East Antarctic soil bacteria. Appl Environ Microbiol 86:e01968-19.

2019

  • 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., Thomas, T., Schaffelke, B., and Webster, N. (2019) Microbial predictors of environmental perturbations in coral reef ecosystems. BioRxiv, 524173.
  • 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.

2018

  • 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.
  • Wemheuer, F., Taylor, J. A., Daniel, R., Johnston, E., Meinicke, P., Thomas, T., & Wemheuer, B. (2018). Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences. BioRxiv, 490037.
  • 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.

2017

  • 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.
  • 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).

2016

  • 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.

2015

  • 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.
Presentations – Talks
Presentations – Posters