Emma is an environmental microbiologist, passionate about sustainability in the mining and agriculture sectors. 

Emma completed a PhD in microbial ecology from the University of Queensland (UQ) in 2010, investigating microorganisms that could be used to reduce greenhouse gas emissions from livestock. Between 2010 and 2012 she was based at the University of Regensburg, Germany, studying microorganisms that dominate seafloor sediments. From 2013-2021 Emma undertook geomicrobiology research at UQ, aiming to understand and harness microbial processes for accelerated mine site remediation.

Her research has focused on re-forming surface crusts in iron ore areas, addressing topsoil deficits in coal mine rehabilitation and microbe-mineral interactions that are relevant for biotechnology and environmental sustainability in the mining industry. She has also provided environmental microbiology consulting for the mining and agriculture sectors. Emma is currently Lead Technical Advisor in the Better Rehabilitation Team at the Department of Environment and Science, focusing on minesite rehabilitation.


Emma's research strengths are in understanding and harnessing microbial processes for improved productivity and sustainability in the mining and agriculture sectors, and in translating research into real-world scale. A list of publications is available here: https://scholar.google.com.au/citations?user=_2HKLM0AAAAJ&hl=en


Emma's geomicrobiology research has had a strong industry focus, including a pilot-scale demonstration of microbial technology to accelerate iron ore mine remediation on site in Brazil, with Vale South America. She has also led field-scale research to address topsoil deficits during coal mine site rehabilitation in Queensland, through a partnership with BHP Mitsubishi Alliance and the Australian Coal Association Research Program. Emma has provided consulting advice to mining, agriculture and biotechnology companies looking to harness microbial processes for site remediation or improved sustainability, both in Australia and internationally.


1.    Gagen, E. J. Denman, S. E., McSweeney, C. S. (2015) ‘Acetogenesis as an alternative to methanogenesis in the rumen’. In Malik, P. K. Bhatta, R. Takahashi, J., Kohn, R. A. and Prasad C. S (eds), Livestock production and climate change. CABI, Wallingford, Oxfordshire, UK. 
2.    Malik, P. K., Bhatta, R., Gagen, E. J., Sejian, V., Soren, N. M., Prasad, C. S. (2015) ‘Alternative H2 sinks for reducing rumen methanogenesis’ In C. (eds), Climate Change Impact on Livestock: Adaptation and Mitigation, Springer, India, pp. 303-320.

1.    Paz, A., Gagen, E. J., Levett, A., Southam, G. (2021) Ferrugination of biocrusts grown on crushed ferricrete: potential for slope stabilisation. Ore Geology Reviews. Accepted May 17.
2.    Henne, A., Craw, D., Gagen, E., Southam, G. (2021) Biologically facilitated precipitation of metals in low-Fe waters at the sulphidic Mount Chalmers mine, Queensland, Australia. Ore Geology Reviews. Accepted May 16.
3.    Levett, A., Gagen, E. J., Paz, A., Vasconcelos, P., Southam, G., (2021) Strategising the bioremediation of Brazilian iron ore mines. Critical Reviews in Environmental Science and Technology. doi:10.1080/10643389.2021.1896346
4.    Vaughan, J., Tungpalan, K., Parbhakar-Fox, A., Weng, F., Gagen, E. J., Southam, G., van der Ent, A., Erskine, P., Gow, P., Valenta, R. (2021) Toward closing a loophole: recovering rare earth elements from uranium metallurgical process tailings. JOM, vol 73, 39-53. doi:10.1007/s11837-020-04451-7 
5.    Levett, A., Vasconcelos, P. M., Jones, M., Rintoul, L., Paz, A., Gagen, E. J., Southam, G. (2021) ‘Titanium mobility preserved in association with microfossils in an iron-rich duricrust’ Chemical Geology, vol 559, 119955. doi:10.1016/j.chemgeo.2020.119955
6.    Gagen, E. J., Levett, A., Paz, A., Bostelmann, H., Valadares, R. B., Bitencourt, J. A., Gastauer, M., Nunes, G. L., Oliveira, G., Vasconcelos, P. M., Tyson, G. W., Southam, G. (2020) Accelerating microbial iron cycling promotes re-cementation of surface crusts in iron ore regions. Microbial Biotechnology. doi:10.1111/1751-7915.13646
7.    Levett, A., Gagen, E. J., Zhao, Y., Vasconcelos, P. M., Southam, G., (2020) ‘Biocement stabilisation of an experimental-scale artificial slope and the reformation of iron-rich crusts. Proceedings of the National Academic of Sciences, vol 117 (31), 99 18347-18354
8.    Islam, Z. F., Welsh, C., Bayly, K., Grinter, R., Southam, G., Gagen, E. J., Greening C. (2020) ‘A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth’ ISME J, doi:10.1038/s41396-020-0713-4 
9.    Levett, A., Gagen, E. J., Rintoul, L., Guagliardio, P., Diao, H., Vasconcelos, P. M., Southam, G., (2020) ‘Characterisation of iron oxide encrusted microbial fossils’ Scientific Reports, vol 10, 9889. doi:10.1038/s41598-020-66830-z
10.    Henne, A., Craw, D., Gagen, E. J., Southam, G. (2020) ‘Experimental simulations of bacterially-mediated magnetite oxidation and observations on ferricrete formation at the Salobo IOCG mine, Brazil’ Applied Geochemistry, vol 118, 104628. doi:10.1016/j.apgeochem.2020.104628.
11.    Levett, A., Vasconcelos, P. M., Gagen, E. J., Rintoul, L., Spier, C., Guagliardo, P., Paz, A., Southam, G. (2020) ‘Microbial weathering signatures in lateritic ferruginous duricrusts’ Earth and Planetary Science Letters. Vol 538, p 116209. doi:10.1016/j.epsl.2020.116209
12.    Henne, A., Craw, D., Gagen, E. J., Southam, G. (2020) ‘Contribution of bacterially-induced oxidation of Fe-silicates in iron-rich ore to laterite formation, Salobo IOCG mine, Brazil’ Chemical Geology, vol 539, pp 119499. doi:10.1016/j.chemgeo.2020.119499 
13.    Paz, A., Gagen, E. J., Levett, A., Zhao, Y., Kopittke, P. M., Southam, G. (2020) ‘Biogeochemical cycling of iron oxides in the rhizosphere of plants grown on ferruginous duricrust (canga)’ Science of the Total Environment, vol 713 doi:10.1016/j.scitotenv.2020.136637
14.    Levett, A., Gagen, E.J., Vasconcelos, P.M., Zhao, Y., Paz, A., Southam, G. (2020) ‘Biogeochemical cycling of iron: implications for cement formation and degraded land stabilisation’ Science of the Total Environment, vol 707 doi:10.1016/j.scitotenv.2019.136128 
15.    Gagen, E.J., Zaugg, J., Tyson, G.W., Southam, G. (2019) ‘Goethite reduction by a neutrophilic member of the alphaproteobacterial genus Telmatospirillum’ Frontiers in Microbiology, doi:10.3389/fmicb.2019.02938
16.    Tait, A. W., Gagen, E. J., Wilson, S. A. Tomkins, A. G, Southam, G. (2019), ‘Eukaryotic colonisation of micrometre-scale cracks in rocks: A ‘microfluidics’ experiment using naturally weathered meteorites from the Nullarbor Plain, Australia’ Astrobiology, doi:10.1089/ast.2019.2077
17.    Levett, A., Gagen, E. J., Southam, G. (2019). ‘Small but mighty: microorganisms offer inspiration for mine remediation and waste stabilisation’ Microbiology Australia, doi: 10.1071/MA19055
18.    Henne, A, Craw, D., Gagen, E.J., Southam, G. (2019), ‘Bacterially-mediated supergene alteration and redistribution of copper in mineralised rocks at the Salobo IOCG deposit, Brazil.’ Ore Geology Reviews, doi:10.1016/j.oregeorev.2019.103210
19.    Henne, A., Craw, D., Gagen, E. J., Southam, G. (2019) ‘Bacterial influence on storage and mobilisation of metals in iron-rich mine tailings from the Salobo mine, Brazil’ Science of the Total Environment, doi:10.1016/j.scitotenv.2019.04.448
20.    Gagen, E. J., Levett, A., Paz, A., Gastauer, M., Caldeira, C. F, Valadares, R B., Bitencourt, J. A, Alves, R., Oliveira, G., Siqueira, J. O., Vasconcelos, P. M., Southam, G. (2019) ‘Biogeochemical processes in canga ecosystems: armoring of iron ore against erosion and importance in iron duricrust restoration in Brazil’ Ore Geology Reviews, doi:10.1016/j.oregeorev.2019.03.013.
21.    Gagen, E. J., Levett, A., Fortin, D., Shuster, J., Vasconcelos, P. M., Southam, G. (2018) ‘Microbial diversity in actively forming iron oxides from a highly weathered banded iron formation system’ Microbes and Environment, doi: 10.1264/jsme2.ME18019.
22.    Levett. A., Paz, A., Gagen, E. J., Diao, H., Guargliado, P., Vasconcelos, P. M., Southam, G. (2018) ‘The role of aluminium in the preservation of organic and inorganic microbial biosignatures.’ Geoscience Frontiers, doi:10.1016/j.gsf.2018.06.006.
23.    Santini, T. & Gagen, E. J. (2018) ‘Geomicrobiology of mining environments’ Microbiology Australia, doi: 10.1071/MA18010, pp 37-41.
24.    Tait, A. W., Gagen, E. J., Wilson, S. A., Tomkins, A. G., Southam, G. (2017) ‘Microbial populations of stony meteorites: Substrate controls on first colonisers’ Frontiers in Microbiology, vol 8, 1227. 
25.    Tait, A. W. Wilson, S. A. Tomkins, A. G, Gagen, E. J., Fallon, S. J. Southam, G. (2017) ‘Evaluation of meteorites as habitats for terrestrial microorganisms: Results from the Nullarbor Plain, Australia, a Mars analogue site.’ Geochimica et Cosmochimica Acta, vol 215, pp 1-16.
26.    Raudsepp, M. J., Gagen, E. J., Golding, S. D., Tyson, G. W., Southam, G. (2017) ‘The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina.’ Fuel, vol 205, pp 60-70. 
27.    Levett, A., Gagen, E. J., Shuster, J., Rintoul, L., Tobin, M., Vongsvivut, J., Bambery, K., Vasconcelos, P., Southam, G. (2016) ‘Evidence of biogeochemical processes in iron duricrust formation.’ Journal of South American Earth Sciences, vol 71, pp 131-142.
28.    Gagen, E. J., Yoshinaga, M. Y., Garcia-Prado, F., Thomm, M., Hinrichs, K-U. (2016) ‘The proteome of Thermococcus kodakarensis in the stationary phase. Implications for biosynthesis of archaeal tetraether lipids.’ Archaea, doi: 10.1155/2016/5938289. 
29.    Raudsepp, M., Gagen, E. J., Evans, P., Tyson, G., Golding, S. Southam. G. (2016) ‘The influence of hydrogeological disturbance and mining on coal seam gas microbial communities’ Geobiology, vol 14, pp163-175.
30.    Zammit, C. M., Shuster, J. P., Gagen, E. J., Southam, G. (2015) ‘The geomicrobiology of supergene metal deposits’ Elements, vol 11 (5), pp 337-342.
31.    Gagen, E. J., Padmanabha, J., Denman S. E., McSweeney, C. S. (2015) ‘Hydrogenotrophic culture enrichment reveals rumen Lachnospiraceae and Ruminococcaceae acetogens and hydrogen responsive Bacteroidetes from pasture fed cattle.’ FEMS Microbiology Letters, vol 362 (14). doi: 10.1093/femsle/fnv104.
32.    Yoshinaga, M. Y.*, Gagen, E. J.*, Wörmer, L., Broda, N. K., Meador, T. B., Wendt, J., Thomm, M & Hinrichs, K-U. (2015) ‘Methanothermobacter thermautotrophicus modulates its membrane lipids in response to hydrogen and nutrient availability’ Frontiers in Microbiology, doi: 10.3389/fmicb.2015.00005 *equal contribution.
33.    Gagen, E. J., Wang, J., Padmanabha, J., Liu, J., Carvalho de Carvalho, I. P., Liu, J., Webb, R. I., Al Jassim, R., Morrison, M. Denman, S. E., McSweeney, C. S. (2014) ‘Investigation of growth capabilities of a new acetogen isolated from an enrichment of the tammar wallaby forestomach.’ BMC Microbiology, vol 14, pp 314. 
34.    Elling, F. J., Koenneke, M., Lipp, J. S., Becker K. W., Gagen, E. J., Hinrichs, K-U. (2014) ‘Effects of growth phase on the membrane lipid composition of the thaumarchaeon Nitrosopumilus maritimus and their implications for archaeal lipid distributions in the marine environment’ Geochimica et Cosmochimica Acta, vol 141, pp 579-597. 
35.    Meador, T. B.*, Gagen, E. J.*, Loscar, M. E., Goldhammer, T., Yoshinaga, M. Y., Wendt, J., Thomm, M., Hinrichs, K-U. (2014) ‘Intact and polar lipid analysis of Thermococcus kodakarensis under control and phosphate-reduced conditions.’ Frontiers in Microbiology, doi:  10.3389/fmicb.2014.00010  *equal contribution. 
36.    Gagen, E. J., Huber, H., Meador, T., Hinrichs, K-U., Thomm, M., (2013) ‘A novel cultivation-based approach for understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from sedimentary ecosystems’ Applied and Environmental Microbiology, vol 79 (20), pp. 6400-6406. 
37.    Gagen, E. J., Mosoni, P., Denman, S. E., Al Jassim, R., McSweeney, C. S. and Forano, E. (2012) ‘Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17h after birth and raised aseptically’ Microbial Ecology, vol 64 (3), pp. 628-640. 
38.    Gagen, E. J., Denman S. E., Padmanabha, J., Al Jassim, R., McSweeney, C. S. (2010) ‘Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach’ Applied and Environmental Microbiology, vol 76 (23) pp. 7785-7795. 


LinkedIn: https://www.linkedin.com/in/emma-gagen-2a935637/
GoogleScholar: https://scholar.google.com.au/citations?user=_2HKLM0AAAAJ&hl=en
Consulting: www.environmentalmicrobiology.com.au
Twitter: @EmmaJGagen