Lecturer (Academic Level B)

Ben Woodcroft Group
Centre for Microbiome Research

Queensland University of Technology

2025 - current

• Promoted November 2025 (Senior Postdoctoral Researcher).
• Maintainer of Bin Chicken, CoverM, Galah and Aviary; contributor to SingleM.
• Associate supervisor of one PhD student; informal guidance to eight other PhD students and six postdoctoral researchers.

Postdoctoral Research Fellow

Ben Woodcroft Group
Centre for Microbiome Research

Queensland University of Technology

2021 - 2025

• Primary postdoctoral researcher for the QUT team of the NSF-funded EMERGE project, leading microbial genome recovery and downstream analyses of Arctic permafrost wetland metagenomes (>7,000 species recovered).
• Developed Bin Chicken for targeted recovery of low-abundance metagenome-assembled genomes through intelligent coassembly; scaled up with NCMAS allocations on NCI and Pawsey to recover >140,000 novel species.
• First author of CoverM; contributor to SingleM/Sandpiper; maintainer of Aviary and Galah.

Rhizobial Motility Researcher

Philip Poole Laboratory
Department of Plant Sciences

University of Oxford

2017 - 2021

• Determining the role of flagellar-based motility and chemotaxis in the symbiosis of Rhizobium leguminosarum with Pisum sativum (pea plant).
• Characterising the influence of the metabolic potential of the environment, especially through the phosphor-transferase system, on the swimming ability of Rhizobium leguminosarum.

Software Development Intern

The Zooniverse
Department of Physics (Astrophysics)

University of Oxford

2019

• Software development for The Zooniverse, a community science website established by the Department for Astrophysics.
• Developed a GraphQL based statistical database of users and visitors to the website in Ruby, Bash and Python.

Synthetic Biology Researcher

Philip Poole Laboratory
Department of Plant Sciences

University of Oxford

2017

• Characterising nitrogen-fixation ability of Pseudomonas stutzeri and genetically modified Pseudomonas fluorescens Pf-5 and SBW25.

Plant Biochemistry Researcher

Andrew Smith Laboratory
Department of Plant Sciences

University of Oxford

2017

• Sequencing Portulaca oleracea with Oxford Nanopore MinION technology. This plant performs both CAM and C4 photosynthesis.
• Extracted and analysed the activity of various phosphoenolpyruvate carboxylases from C3 and CAM photosynthetic plants.

Metagenomics Researcher

Australian Centre for Ecogenomics

University of Queensland

2015 - 2016

• Used the newly developed in-situ chemotaxis assay (ISCA) device to capture bacteria that display chemotaxis towards environmentally relevant compounds, including poly(ethylene terephthalate) degradation products and pesticides (diuron and atrazine).
• Then analysed the captured microbes using culture-independent methods (e.g. 16S rRNA gene amplicon and metagenomics) to provide the microbial population attracted by each individual chemoattractant and their metabolic potential.

Graduate Research Assistant

Australian Centre for Ecogenomics

University of Queensland

2016

• Compared small sea water samples before and after homogenisation to provide metagenomic data of the microheterogeneity of microbial life at such volumes.

Undergraduate Researcher

Advanced Study Program in Science (ASPinS)
Centre for Advanced Imaging

University of Queensland

2015

• Wrote code in R to estimate individual false-discovery rates across NMR metabolomics data split into columns along the ppm.
• This allowed the amelioration of the multiple testings problem, without relying on a uniform FDR assumption.

Research Assistant

Queensland Alliance for Agriculture and Food Innovation

University of Queensland

2014

• Compared the glycogen extracted through the traditional sucrose-gradient method to that extracted from formalin fixed samples.

Undergraduate Researcher

Advanced Study Program in Science (ASPinS)
Queensland Alliance for Agriculture and Food Innovation

University of Queensland

2013

• Testing the amount and structure of glycogen in mouse livers at different times after eating through an assay, size-exclusion chromatography and transmission electron microscopy of extracted glycogen.

Methanotrophic potential of a northern fen

Frontiers in Environmental Science (2026) 14

N/A

2026

• Rachel M. Wilson, Jared B. Ellenbogen, Shuai Yang, …, Samuel T. N. Aroney, et al.

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Nature Microbiology (2026) 11:1800–1814

N/A

2026

• Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, et al.

Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes

Nature Methods (2025) 22:2516–2524

N/A

2025

• Samuel T. N. Aroney, Rhys J. P. Newell, Gene W. Tyson, et al.
• Role: first

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper

Nature Biotechnology (2025) 44:948–953

N/A

2025

• Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, et al.

CoverM: read alignment statistics for metagenomics

Bioinformatics (2025) 41

N/A

2025

• Samuel T N Aroney, Rhys J P Newell, Jakob N Nissen, et al.
• Role: first

The Microflora Danica atlas of Danish environmental microbiomes

Nature (2025) 649:971–981

N/A

2025

• C. M. Singleton, T. B. N. Jensen, F. Delogu, …, S. T. N. Aroney, et al.

Stable states in an unstable landscape: microbial resistance at the front line of climate change

openRxiv (2025) [preprint]

N/A

2025

• Dylan R. Cronin, Hannah Holland-Moritz, Derek A. Smith, Samuel T. N. Aroney, et al.
• Role: co-first

GlobDB: a comprehensive species-dereplicated microbial genome resource

Bioinformatics Advances (2024) 5

N/A

2024

• Daan R Speth, Nick Pullen, Samuel T N Aroney, et al.

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient

Nature Microbiology (2024) 9:2892–2908

N/A

2024

• Viviana Freire-Zapata, Hannah Holland-Moritz, Dylan R. Cronin, Sam Aroney, et al.

The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTSNtr regulation

Environmental Microbiology (2024) 26

N/A

2024

• Samuel T. N. Aroney, Francesco Pini, Celia Kessler, et al.
• Role: first

Rhizobium determinants of rhizosphere persistence and root colonization

The ISME Journal (2024) 18

N/A

2024

• Hayley E Knights, Vinoy K Ramachandran, Beatriz Jorrin, …, Samuel T N Aroney, et al.

Aviary: hybrid assembly and genome recovery from metagenomes with Aviary

Software (2024)

N/A

2024

• Rhys J. P. Newell, Samuel T. N. Aroney, Julian Zaugg, et al.
• Role: maintainer

Galah: more scalable dereplication for metagenome assembled genomes

Software (2024)

N/A

2024

• Samuel T. N. Aroney, Antonio Pedro Camargo, Gene W. Tyson, et al.
• Role: maintainer

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

Microbial Genomics (2022) 8

N/A

2022

• Jiarui Sun, Apoorva Prabhu, Samuel T. N. Aroney, et al.

Rhizobial Chemotaxis and Motility Systems at Work in the Soil

Frontiers in Plant Science (2021) 12

N/A

2021

• Samuel T. N. Aroney, Philip S. Poole, Carmen Sánchez-Cañizares
• Role: first

Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

Proceedings of the National Academy of Sciences (2020) 117:23823–23834

N/A

2020

• Rachel M. Wheatley, Brandon L. Ford, Li Li, Samuel T. N. Aroney, et al.

A rapid extraction method for glycogen from formalin-fixed liver

Carbohydrate Polymers (2015) 118:9–15

N/A

2015

• Mitchell A. Sullivan, Shihan Li, Samuel T.N. Aroney, et al.

Changes in Glycogen Structure over Feeding Cycle Sheds New Light on Blood-Glucose Control

Biomacromolecules (2014) 15:660–665

N/A

2014

• Mitchell A. Sullivan, Samuel T. N. Aroney, Shihan Li, et al.

DPhil, Microbiology

Department of Plant Sciences
Supervisor: Prof Philip Poole

University of Oxford

2016 - 2021

• Role and regulation of chemotaxis and motility in Rhizobium leguminosarum
• Interdisciplinary Bioscience Doctoral Training Partnership (BBSRC)

B.S., Honours (First Class)

Australian Centre for Ecogenomics
Supervisor: Prof Gene Tyson

University of Queensland

2015 - 2016

• Investigating bacterial chemotaxis towards marine pollutants

B.S., Biochemistry and Molecular Biology

School of Chemistry and Molecular Biology

University of Queensland

2012 - 2015

HDR Engagement Committee

School of Biomedical Sciences

Queensland University of Technology

2024 - current

• Member of the QUT School of Biomedical Sciences HDR engagement committee: event organisation, student registration and engagement.
• Organised six career and wellbeing events across 2024-25; attendance rose from 8 to 40.

Reviewing

N/A

N/A

2023 - current

• Reviewed nine manuscripts for journals including Nature Communications, The ISME Journal, ISME Communications and Polar Science.
• Member of the ISME Early Career Scientist Reviewer Pool (three-year appointment).

HPC Administration Team

Centre for Microbiome Research

Queensland University of Technology

current

• Maintain infrastructure code and contribute to workshops and planning for the Centre’s HPC.
• Led an optimisation of storage usage and file counts that improved filesystem performance.

MVIF Pacific Organising Committee

Microbiome Virtual International Forum

N/A

2025 - current

• Assign applicants to presentation types, plan keynotes and run the webinar backend for four events in 2025 (2,500 unique attendees).

Chair, School of Biomedical Sciences HDR Symposium (2026)

School of Biomedical Sciences

Queensland University of Technology

2026

• Chaired the symposium again: 56 HDR students (23 talks), with $5,000 in sponsorship raised.

Chair, School of Biomedical Sciences HDR Symposium (2024)

School of Biomedical Sciences

Queensland University of Technology

2024

• Oversaw scheduling, keynotes, registration, abstract scoring and presentation selection for 67 HDR students (53 talks, 37 posters).
• Raised $20,000 in industry sponsorship and organised two keynote speakers.

Certificate course in Developing Learning and Teaching

Staff and Educational Development Association

University of Oxford

2020

• The award is aligned to the UK Professional Standards Framework (UKPSF) for Teaching and Supporting Learning in Higher Education, at Descriptor 1.

Graduate Safety Representative

Department of Plant Sciences

University of Oxford

2019 - 2020

• Departmental graduate safety representative for safety committee meetings and graduate student contact.
• This has involved managing the Department’s response to the COVID-19 crisis and determining the safest way to return to work.

Environmental Metagenomics (week-long online course)

Centre for Microbiome Research

Queensland University of Technology

N/A

• Developed and delivered a course covering read processing, assembly and binning, and functional characterisation.

In vitro enzyme kinetics

Department of Plant Sciences

University of Oxford

2019 - 2020

• Demonstrating for In vitro enzyme kinetics practical, focussing on the kinetics of alcohol dehydrogenase.

Statistics and Data Management

Doctoral Training Centre

University of Oxford

2020

• Demonstrating for Statistics and Data Management intermediate course, a broad overview of scientific statistics focussing on statistical modeling.

Programming for Life Scientists

Doctoral Training Centre

University of Oxford

2017 - 2019

• Demonstrating for the programming module using the languages Python and C.

Plants and People

Department of Plant Sciences

University of Oxford

2019

• Tutorials about the role of motility and chemotaxis in the soil and in the rhizobium-legume symbiosis.

Analysis of Scientific Data

Faculty of Science

University of Queensland

2015 - 2016

• Demonstrating for Analysis of Scientific Data (STAT1201), focussing on experimental design, data modelling and statistics.

Inorganic, physical and organic chemistry

School of Chemistry and Molecular Biology

University of Queensland

2014 - 2015

• 1st Year inorganic, physical and organic chemistry peer-assisted study sessions (CHEM1090/CHEM1100).

Chemistry and Statistics tutoring

Faculty of Science

University of Queensland

2014 - 2015

• Drop-in tutoring at the Science Learning Centre for 1st Year Chemistry and Statistics.

130,000 new species from across the globe enrich the tree of life

ISME20

Auckland, New Zealand

2026

• Poster.

130,000 new species from across the globe enrich the tree of life

JAMS Symposium

Brisbane, Australia

2026

130,000 new microbial species hidden in public DNA data

QUT ECR symposium

Queensland University of Technology

2026

• Poster; awarded first place.

Discovering 24,000 new microbial species with Bin Chicken

School of Biomedical Sciences

Queensland University of Technology

2026

Directed coassembly recovers many novel microbial genomes

19th International Symposium on Microbial Ecology (ISME19)

Cape Town, South Africa

2024

• Poster.

Targeted coassembly recovers 24,000 novel species

Australian Microbial Ecology Conference (AusME)

Sydney, Australia

2024

• Talk.

A fork in the metabolic road: microbial communities impacting emission dynamics of thawing permafrost

Australian Microbial Ecology Conference (AusME)

Melbourne, Australia

2022

• Poster.

Strategically navigating through the soil: the integrated sensory systems of the legume symbiont Rhizobium leguminosarum

Sensory Transduction in Microorganisms Conference

Ventura, CA

2020

• Presentation and Poster for the Gordon Research Conference on Sensory Transduction in Microorganisms.

Role and regulation of chemotaxis and motility in the Rhizobium-legume symbiosis

Department of Plant Sciences

University of Oxford

2018

• DPhil Transfer of Status presentation at the Department of Plant Sciences.

Investigating bacterial chemotaxis towards marine pollutants

School of Chemistry and Molecular Biology

University of Queensland

2016

• Honours seminar presentation at the School of Chemistry and Molecular Biology.

ECR Paper of the Year

School of Biomedical Sciences

Queensland University of Technology

2026

First place poster

QUT ECR symposium

Queensland University of Technology

2026

NCMAS computational allocation

National Computational Merit Allocation Scheme

N/A

2026 - 2026

NCMAS computational allocation (NCI and Pawsey)

National Computational Merit Allocation Scheme

N/A

2025 - 2025

• Awarded for large-scale Bin Chicken genome recovery.

Brasenose Oxford-Australia Clarendon Scholarship

University of Oxford

N/A

2016 - 2020

• A highly prestigous scholarship selectively offered for graduate study at the University of Oxford.

Brasenose Studentship Fund

University of Oxford

N/A

2020

• Provided funding to travel to California to present my research at the Sensory Transduction in Microorganisms Conference.

Vice-Chancellor’s Education Award

University of Oxford

N/A

2020

• Award received for demonstrations given in the Programming for Life Scientists course.
• The course offers high level training in computer programming to a highly diverse cohort of graduate students at Oxford University.

UQ Honours Scholarship

University of Queensland

N/A

2015 - 2016

• A competitive scholarship to support students undertaking the Honours program at the Unversity.

UQ Excellence Scholarship

University of Queensland

N/A

2012 - 2015

• A highly competitive full scholarship for top-ranked students entering the University.

UQ Summer Research Scholarship

University of Queensland

N/A

2013 - 2014

• A competitive scholarship to support undergraduate student participation in the University’s Summer Research Program.

UQ Summer Research Scholarship

University of Queensland

N/A

2012 - 2013

• A competitive scholarship to support undergraduate student participation in the University’s Summer Research Program.

Perspectives: Electronic Learning Resource

Oxford University Press

Oxford, United Kingdom

2020

• Interviewed about the underwater agricultural research centre, Nemo’s Garden, for a series of videos made available through the Perspectives electronic learning resource.

Science short: Bacterial World

Museum of Natural History

Oxford, United Kingdom

2019

• Interactive presentation about the bacterial symbiosis in root nodules aimed at non-expert adults.

Super Science Saturday: People and Planet

Museum of Natural History

Oxford, United Kingdom

2018

• Organizing and running a ‘Root-nodules’ stall for families, to help them understand the fixation of nitrogen by bacteria in pea plants.

Inside Cells Day

Museum of Natural History

Oxford, United Kingdom

2017

• Presentation about ‘Fertilizers and the Environment’ to A-level High School Students.