Dr Rochelle Soo

BMedSc, BCA (Wellington), MSc (Honours) (Hamilton), PhD (Queensland)

UQ Amplify Researcher

School of Chemistry and Molecular Biosciences

+61 7 336 54956

r.soo@uq.edu.au

Molecular Biosciences Building (76), Room 528

View researcher profile

Primary Research Interest

Non-photosynthetic cyanobacteria and marsupial microbiomes

About Me

While studying for my undergraduate degrees at Victoria University of Wellington, NZ, I took a summer semester paper in Environmental Microbiology, which included a trip to the Institute of Geological and Nuclear Sciences to look at microbes that live in hot springs. This sparked my interest in extremophiles. I then moved to Hamilton to study at the University of Waikato under the supervision of Prof. Craig Cary at the Thermophile Research Unit, identifying the microbial diversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica. After finishing my MSc, I moved to Australia and worked at the Australian Institute of Marine Science in Townsville for 4 years as a Lab Technician for Dr. Nicole Webster, looking at microbial communities in sponges on the GBR, and Dr. Lone Hoj, in aquaculture.

I then moved to Brisbane as I was awarded an Australian Postgraduate Award to undertake a PhD at the Australian Centre for Ecogenomics (ACE), UQ, with Prof. Phil Hugenholtz and Prof. Gene Tyson. My PhD thesis was on non-photosynthetic Cyanobacteria and I completed my PhD in 2015. I stayed on at ACE as a post-doc and in 2018 I was awarded an ARC Discovery Early Career Researcher Award (DECRA), which I started in July 2019. My project aims to identify additional members from the non-photosynthetic cyanobacterial lineages and characterise their functional capabilities.

Research Focus and Collaborations

My main focus is on exploring the evolution and ecology of non-photosynthetic Cyanobacteria using metagenomics, isolation and microscopy techniques. Other projects that I’m currently working on include re-organising the phylogenetic framework for Cyanobacteria by sequencing type strains (in collaboration with over 40 scientists); surveying Australian marsupial microbiomes; and understanding how rhizosphere microbial communities change with the addition of biochar.

Funded Projects

NHMRC Ideas Grant (2022-2024): "Dual-function ribonucleases: unexpected agents of antibiotic resistance”

ARC Discovery Project (2021-2023): “Bringing Archaeal biodiversity to life from native Australian herbivores”

ARC Discovery Early Career Researcher Award (2019-2022): “Exploring the evolution and ecology of non-photosynthetic Cyanobacteria”

Publications

Journal Articles (28)

Journal Articles

Joshi, Pallav, Krco, Stefan, Davis, Samuel J., Asser, Lachlan, Brück, Thomas, Soo, Rochelle M., Bodén, Mikael, Hugenholtz, Philip, Wilson, Liam A., Schenk, Gerhard and Morris, Marc T. (2024). Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. Applied Biosciences, 3 (4), 438-449. doi: 10.3390/applbiosci3040028

Tan, Sha, Liu, Lan, Jiao, Jian-Yu, Li, Meng-Meng, Hu, Chao-Jian, Lv, Ai-Ping, Qi, Yan-Ling, Li, Yu-Xian, Rao, Yang-Zhi, Qu, Yan-Ni, Jiang, Hong-Chen, Soo, Rochelle M, Evans, Paul N, Hua, Zheng-Shuang and Li, Wen-Jun (2024). Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota. Molecular Biology and Evolution, 41 (8) ARTN msae151. doi: 10.1093/molbev/msae151

Williams, Tom A, Davin, Adrian A, Szánthó, Lénárd L, Stamatakis, Alexandros, Wahl, Noah A, Woodcroft, Ben J, Soo, Rochelle M, Eme, Laura, Sheridan, Paul O, Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip and Szöllősi, Gergely J (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18 (1) wrae129. doi: 10.1093/ismejo/wrae129

Jones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2), e0337023. doi: 10.1128/mbio.03370-23

Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2

Blyton, Michaela D. J., Pascoe, Jack, Hynes, Emily, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Frontiers in Microbiology, 14 1085090, 1-13. doi: 10.3389/fmicb.2023.1085090

Giang, Peter D., Churchman, Luke R., Stok, Jeanette E., Soo, Rochelle M. and De Voss, James J. (2022). CYP108N12 initiates p-cymene biodegradation in Rhodococcus globerulus. Archives of Biochemistry and Biophysics, 730 109410, 109410. doi: 10.1016/j.abb.2022.109410

Kochanek, Jitka, Soo, Rochelle M., Martinez, Cristina, Dakuidreketi, Aloesi and Mudge, Agnieszka M. (2022). Biochar for intensification of plant-related industries to meet productivity, sustainability and economic goals: a review. Resources, Conservation and Recycling, 179 106109, 106109. doi: 10.1016/j.resconrec.2021.106109

Blyton, Michaela D. J., Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology, 24 (9), 4209-4219. doi: 10.1111/1462-2920.15884

Blyton, Michaela D.J, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology, 24 (1), 475-493. doi: 10.1111/1462-2920.15858

Hugenholtz, Philip, Chuvochina, Maria, Oren, Aharon, Parks, Donovan H. and Soo, Rochelle M. (2021). Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME Journal, 15 (7), 1879-1892. doi: 10.1038/s41396-021-00941-x

Blyton, Michaela D. J., Soo, Rochelle M., Whisson, Desley, Marsh, Karen J., Pascoe, Jack, Le Pla, Mark, Foley, William, Hugenholtz, Philip and Moore, Ben D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Animal Microbiome, 1 (1) 6, 6. doi: 10.1186/s42523-019-0008-0

Soo, Rochelle M., Hemp, James and Hugenholtz, Philip (2019). Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radical Biology and Medicine, 140, 200-205. doi: 10.1016/j.freeradbiomed.2019.03.029

Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017). Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, 1-32. doi: 10.7717/peerj.4075

Soo, Rochelle M. , Hemp, James, Parks, Donovan H. , Fischer, Woodward W. and Hugenholtz, Philip (2017). On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 (6332), 1436-1440. doi: 10.1126/science.aal3794

Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015). Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 (5) e968, Art. No.: e968-Art. No.: e968. doi: 10.7717/peerj.968

Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073

Bourne, David G, Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013). Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 (7), 1459-1459. doi: 10.1038/ismej.2013.71

Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013). Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 (7), 1452-1458. doi: 10.1038/ismej.2012.172

Webster, N. S. , Negri, A. P. , Flores, F. , Humphrey, C. , Soo, R. , Botte, E. S. , Vogel, N. and Uthicke, S. (2013). Near‐future ocean acidification causes differences in microbial associations within diverse coral reef taxa. Environmental Microbiology Reports, 5 (2), 243-251. doi: 10.1111/1758-2229.12006

Webster, N. S., Luter, H. M., Soo, R. M., Botté, E. S., Simister, R. L., Abdo, D. and Whalan, S. (2013). Same, same but different: symbiotic bacterial associations in GBR sponges. Frontiers in Microbiology, 3 (444), 1-11. doi: 10.3389/fmicb.2012.00444

Ceh, Janja , Raina, Jean-Baptiste , Soo, Rochelle , van Keulen, Mike and Bourne, David G. (2012). Coral-bacterial communities before and after a coral mass spawning event on Ningaloo Reef. PLoS One, 7 (5) e36920, e36920. doi: 10.1371/journal.pone.0036920

Webster, Nicole S., Botte, Emmanuelle S. , Soo, Rochelle and Whalan, Steve (2011). The larval sponge holobiont exhibits high thermal tolerance. Environmental Microbiology Reports, 3 (6), 756-762. doi: 10.1111/j.1758-2229.2011.00296.x

Webster, Nicole S. , Soo, Rochelle , Cobb, Rose and Negri, Andrew P. (2011). Elevated seawater temperature causes a microbial shift on crustose coralline algae with implications for the recruitment of coral larvae. The ISME Journal, 5 (4), 759-770. doi: 10.1038/ismej.2010.152

Webster, Nicole S., Cobb, Rose E., Soo, Rochelle, Anthony, Shelley L., Battershill, Christopher N., Whalan, Steve and Evans-Illidge, Elizabeth (2011). Bacterial community dynamics in the marine sponge Rhopaloeides odorabile under in situ and ex situ cultivation. Marine Biotechnology, 13 (2), 296-304. doi: 10.1007/s10126-010-9300-4

Negri, Andrew P., Soo, Rochelle, Flores, Florita and Webster, Nicole S. (2009). Bacillus insecticides are not acutely harmful to corals and sponges. Marine Ecology - Progress Series, 381, 157-165. doi: 10.3354/meps07933

Soo, Rochelle M., Wood, Susanna A., Grzymski, Joseph J., McDonald, Ian R. and Cary, S. Craig (2009). Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica. Environmental Microbiology, 11 (3), 715-728. doi: 10.1111/j.1462-2920.2009.01859.x

Niederberger, Thomas D., McDonald, Ian R., Hacker, Amy L., Soo, Rochelle , Barrett, John E., Wall, Diana H. and Cary, S. Craig (2008). Microbial community composition in soils of Northern Victoria Land, Antarctica. Environmental Microbiology, 10 (7), 1713-1724. doi: 10.1111/j.1462-2920.2008.01593.x

Areas of research

Microbiology discipline

Molecular genetics and genomics theme