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Greening Lab research

CollaborationsStudent research projects | Publications

About Associate Professor Chris Greening

Associate Professor Chris Greening leads the One Health Microbiology group and the Antimicrobial Resistance Testing & Surveillance Facility at Monash University’s Biomedicine Discovery Institute. Following a first-class degree in Molecular and Cellular Biochemistry at the University of Oxford (2010), he undertook a doctorate at the University of Otago (2013) investigating the physiological roles of the hydrogenases in mycobacteria. He then gained postdoctoral and lecturing experience at the University of Otago, CSIRO, and Australian National University. In 2016, he was appointed as a group leader in Monash University’s School of Biological Sciences and completed an environmentally-focused ARC DECRA Fellowship. In 2021, he moved to Monash’s Department of Microbiology to take up a medically-focused NHMRC EL2 Fellowship. Trained in the fields of biochemistry and microbiology, Chris also has experience in genetics, microbial ecology, and molecular evolution, and thrives working across disciplines. In 2019, he was awarded the Australian Society of Microbiology's Jim Pittard Award for Outstanding Early Career Researcher.


Our research

Current projects

Visit Associate Professor Chris Greening’s  Monash research profile to see a full listing of current projects.

Research overview

Bacteria can persist in almost all environments due to their unprecedented ability to survive nutrient deprivation and resist antimicrobial treatment. To achieve this, environmental and pathogenic bacteria alike enter stress-resistant dormant states. We use an interdisciplinary approach to investigate the causes and consequences of bacterial persistence.

We investigate the metabolic processes that allow bacteria to stay energised and resist stresses in their dormant states. For example, we have shown that a wide range of bacteria switch from growing on organic sources to surviving on atmospheric trace gases such as hydrogen and carbon monoxide. In other words, they can live on air! Moreover, we have provided evidence that fermentation is a widespread mechanism of energy conservation, and revealed critical roles for cofactor F420 in mycobacterial persistence and drug resistance.

Understanding the metabolism of microorganisms in their dormant state has broad implications. For example, bacteria that ‘live on air’ simultaneously control levels of climate-relevant atmospheric gases and enhance the resilience and productivity of soil ecosystems worldwide. Among pathogens, we are targeting the processes that enable Mycobacterium tuberculosis to survive in host tissues and informing interventions to prevent diarrhoeal pathogens from persisting in the environment. Our research falls into four broad themes:

1. Global biodiversity: How does life exist in extreme environments?

Our world is inhabited by a tremendous abundance and diversity of microorganisms. Even extreme environments, from Yellowstone to Antarctica, harbour rich microbial communities. This reflects that microbes are highly metabolically versatile: they can thrive even in environments deprived of the organic carbon and oxygen required for animal life. What’s more, microbes are capable of resisting environmental stresses and reducing energy expenditure by entering dormant states analogous to seeds. We explore how microbes make energy and carbon in ecosystems worldwide. These insights enable us to address fundamental questions about community assembly, primary production, evolution, and astrobiology. Along the way, this research has taken us to plenty of interesting places: Antarctic soils, volcanic craters, and deep-sea seeps to name a few.

Major projects:

We have previously shown metabolic flexibility enables microorganisms to survive in deprived or variable environments. Our seminal finding is that most soil bacteria are capable of ‘living on air’, i.e. they use atmospheric hydrogen and carbon monoxide as energy sources. This trait extends to phyla as diverse as Actinobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, and Proteobacteria. Such atmospheric energy sources support primary production in oligotrophic ecosystems, providing an alternative basis for ecosystem function to solar or geological energy. Our work has also uncovered how interactions of fermentative and respiratory bacteria underlie the function of diverse sediments and the process of eukaryogenesis. We have also contributed to the development of ecological metrics and theory.

This figure shows the microbial community structure of three desert soils from Eastern Antarctica. We showed these diverse communities have a low capacity for photosynthesis and are instead primarily supported by atmospheric trace gases as energy and carbon sources. Adapted from Ji & Greening et al., Nature 2017.

2. Infectious disease: Targeting energetics to kill tuberculosis

Tuberculosis caused more deaths in 2019 than any other infectious disease (~1.3 million) and latently infects a third of the world’s population, predominantly in the developing world. A major barrier to the disease’s treatment is the capacity of its causative agent to persist in host tissues. This contributes to the difficulty in clearing infections and the development of antibiotic resistance due to fractional killing. Improved treatment depends on understanding and targeting the mechanisms that facilitate persistence and resistance. To achieve this, we study the metabolic basis of mycobacterial persistence. We investigate the physiological roles and biochemical mechanisms of multiple redox enzymes implicated in persistence. The end goal is to validate novel targets for pharmaceutical development.

Major projects:

Our work has revealed the unusual redox cofactor F420 is critical for redox homeostasis and drug metabolism in mycobacteria. We have resolved its biosynthesis pathway and solved crystal structures of its enzymes as a basis for drug development. Understanding this pathway is also critical to pre-empt resistance to clinical prodrugs pretomanid and delamanid, which are both activated by F420. We have also shown that mycobacteria are more energetically flexible than previously thought. For example, they adapt to energy starvation by consuming alternative energy sources such as carbon monoxide gas and survive hypoxia by rewiring their redox metabolism. This flexibility offers both opportunities and challenges for the development of metabolism as a target space for tuberculosis treatment.

The figure shows crystal structures of the mycobacterial enzyme FbiA. After resolving the enigmatic biosynthesis pathway of F420, we solved substrate- and product-bound structures of the key enzyme FbiA, revealing formation of the novel intermediate dehydro-F420-0. Adapted from Grinter et al., mSystems 2020.

3. Global change: How do bacteria control the atmosphere?

Microorganisms regulate atmospheric composition by consuming and producing various climate-relevant trace gases. For example, soil bacteria consume over 300 million tonnes of hydrogen and carbon monoxide from the atmosphere each year — they scavenge these gases using high-affinity metalloenzymes and use them as alternative energy sources for persistence. Other microorganisms regulate methane and carbon dioxide levels. We have collected evidence that scavenging of atmospheric trace gases is widespread among microorganisms. We are now performing interdisciplinary studies to better understand the biochemical basis, physiological role, and ecological significance of trace gas scavenging and other gas-cycling processes. The knowledge is being used to help predict and mitigate greenhouse gas emissions.

Major projects:

By pairing biogeochemical and microbiological analysis, we have previously uncovered the mediators and dynamics of atmospheric methane cycling across diverse ecosystems, spanning ruminants, wetlands, oil seeps, termite mounds, and even trees. Moreover, we have identified another phylum capable of mitigating methane emissions and revealed that methane-oxidising bacteria are a highly metabolically versatile group. More broadly, we are at forefront of resolving the mediators of the hydrogen and carbon monoxide cycles. We have shown that dormant soil microorganisms consume atmospheric hydrogen and carbon monoxide as dependable energy sources and resolved the enzymatic pathways involved.

This figure shows results of a genomic survey of metabolic genes present in isolates from ruminants. Shown are the diverse pathways and organisms that control H2 cycling in ruminants and in turn influence substrate availability for methane-producing archaea.

4. Public health: Informing interventions to reduce pathogens and AMR

Pathogen and antimicrobial resistance (AMR) levels are devastatingly high in regions with inadequate water, sanitation, and hygiene (WASH). Approximately 1.7 billion cases and 1.6 million deaths of diarrhoeal disease occur each year, with a disproportionate burden in children under five. A ‘one health’ approach is urgently needed to address this tragedy; through studying the relationships between environmental and human health, it is possible to develop scalable built interventions to reduce pathogen and AMR transmission. We are working closely with Asia-Pacific communities within transdisciplinary research teams to deploy unified monitoring approaches, resolve transmission pathways, and develop scalable interventions to improve environmental conditions and human health.

Major projects:

Through RISE in Fiji and the Centre to Impact AMR in Melbourne, we have developed unified molecular approaches to monitor multiple pathogens and AMR genes across host and environmental reservoirs. For example, we have shown TaqMan array cards can quantify broad panels of diarrhoeal pathogens (bacteria, viruses, protists, helminths) across different samples (stool, animal scats, waters, soils, sewage). In turn, this technology allows tracing of transmission pathways and assessing interventions. In other work, we have shown that colonic hydrogen metabolism is a surprisingly widespread process among both commensal and pathogenic bacteria. This has laid the foundations for multiple other projects in this space to understand hydrogen homeostasis in gastrointestinal health, disease, and disorders.

The above figure shows the levels of enteric pathogens in 130 samples. Enteric pathogen abundance (top) and prevalence (bottom) was monitored using TaqMan array cards, revealing a high pathogen load in child stool and environmental waters from informal settlements in Fiji. Adapted from Lappan et al., Lancet Planetary Health 2021.

Techniques/expertise

We take an interdisciplinary approach to understand biological processes at all levels of organisation: from enzymatic mechanisms to ecosystem importance. To achieve this, we employ a versatile suite of bacteriology, molecular biology, microbial ecology, protein biochemistry, structural biology, systems biology, genomics, and biogeochemical approaches. The benefits of an integrative microbiology approach are reflected by our work demonstrating the ubiquity of microbial H2 metabolism and multifaceted importance of mycobacterial F420 metabolism. We synergise the diverse expertise within the team and also collaborate with world experts in areas where we are non-experts.


Collaborations

We collaborate with many scientists and research organisations around the world. Some of our more significant national and international collaborators are listed below. Click on the map to see the details for each of these collaborators (dive into specific publications and outputs by clicking on the dots).

We are chief investigators on three major applied programs that tackle key challenges in human health and sustainability. In each of these programs, we work with different researchers (e.g. clinicians, engineers, ecologists, social scientists) and stakeholders (e.g. communities, industry, government, hospitals) to facilitate translation of fundamental research into applied practice. Within the Centre to Impact AMR, we also run a facility for antimicrobial resistance surveillance and antimicrobial compound / device testing.

Major collaborations include with:

Professor Steven Chown, School of Biological Sciences, Monash University
Professor Gregory Cook, University of Otago
Professor Perran Cook, School of Chemistry, Monash University
Professor Holger Daims, University of Vienna
Dr Xiyang Dong, Sun Yat Sen University
Dr Rhys Grinter, Department of Microbiology, Monash University
Professor Philip Hugenholtz, Australian National University
Professor Karin Leder, School of Public Health and Preventive Medicine, Monash University
Professor Trevor Lithgow, Department of Microbiology, Monash University
Professor Damien Maher, Southern Cross University
Professor Melodie McGeoch, La Trobe University
Dr Sergio Morales, University of Otago
Professor Colin Jackson, Australian National University
Dr Anja Spang, Netherlands Institute of Marine Research
Associate Professor Matthew Stott, University of Canterbury
Professor Dena Lyras, Department of Microbiology, Monash University
Dr Samuel Forster, Hudson Institute for Medical Research


Student research projects

The Greening Lab offers a variety of Honours, Masters and PhD projects for students interested in joining our group. There are also a number of short term research opportunities available.

Projects in this lab are formulated based on student aspirations and expectations. Please send a short project proposal to chris.greening@monash.edu explaining your desire for research training. If your ambition can be accommodated, we will discuss this with you.

Scholarship support is available to new PhD students. PhD postgraduate scholarships are available for Australian citizens or permanent residents with a H1 Honours degree. We have positions for international students: applicants are advised to check the Graduate studies web pages for information on entry requirements, tuition fee, and scholarships prior to application.

Postdocs opportunities are also available and you are encouraged to contact Associate Professor Chris Greening regarding potential projects that align with the presented research themes.