Dr Chris Rinke

Senior Lecturer

School of Chemistry and Molecular Biosciences
Faculty of Science
c.rinke@uq.edu.au
+61 7 336 54957

Overview

Chris Rinke is an ARC Future Fellow and Senior Lecturer at the Australian Centre for Ecogenomics (ACE), University of Queensland, Australia.

His research interests include the phylogeny, taxonomy and ecology of free living and symbiotic Bacteria and Archaea. He focuses on the majority of microbes which elude current culturing efforts. This so-called “Microbial Dark Matter” can only be explored with culture-independent approaches, and Chris has pioneered methods in high throughput single-cell genomics, the separation and sequencing of single bacterial and archaeal cells, and metagenomics, the direct sequencing of DNA from environmental samples.

Currently, the Rinke lab uses a range of "omics" techniques to study the phylogenetic and metabolic diversity of uncultured microbes, to investigate bacterial plastic degradation (including the gut microbiomes of polystyrene eating superworms), to describe microbial and viral communities in coastal waterways such as the Brisbane River, explore microbial compositions in shallow coastal and deep-sea subsurface sediments, characterise insect microbiomes, and to identify the main players in terrestrial hot springs. More details are available at the Rinke Lab website: http://rinkelab.org/

Chris is also a member of the Genome Taxonomy Database (GTBD; gtdb.ecogenomic.org) curation team. GTDB is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

Research Interests

  • Microbial Ecology
    - Exploring new bacterial and archaeal lineages (microbial dark matter) - Microbial plastic degradation (including the gut microbiomes of polystyrene eating superworms) - Assessing microbial and viral communities in coastal waterways such as the Brisbane River - The role of microbes in shallow coastal and deep-sea subsurface sediments - Identification of the main microbial players in terrestrial hot springs

Research Impacts

Chris has focused mainly on fundamental research projects that are essential to establishing a knowledge base for future translational applications. A recent review (Wang and Navin, 2015; https://doi.org/10.1016/j.molcel.2015.05.005) identifying single-cell genomics landmark studies across all disciplines highlighted his Microbial Dark Matter study as a milestone in single-cell sequencing. Recovering genomic blueprints of uncultured microbes via sequencing provides a rich source of novel pathways that can be explored for multiple uses including medicine, food production, and environmental remediation. By pioneering and improving upon methods for the discovery of novel Microbial Dark Matter lineages, he has considerably increased the number of microbes that can be used for novel product development.

The high-profile publications and the engaging topics of his research have resulted in frequent interest by the mainstream media. His research outputs have been picked up by several media outlets including Scientific American, Science Daily, BBC News, WIRED science, The Independent, Neue Züricher Zeitung, CBC News, and NPR.

His project focusing on taxonomy (https://doi.org/10.1038/s41564-021-00918-8) has gained considerable traction in the field of microbiology and will likely be adopted as the standard archaeal taxonomy. In addition, he recently initiated applied research projects targeting microbial plastic degradation, the microbial and viral communities of the Brisbane River and their impact on river health, and microbial communities in local aquifer bores used as drinking water source.

Currently, he focuses on bacterial plastic degradation (including the gut microbiomes of polystyrene eating superworms), microbial and viral communities in coastal waterways such as the Brisbane River, microbes in shallow coastal and deep-sea subsurface sediments, and microbial players in terrestrial hot springs in Australia.

Qualifications

  • Dr.rer.nat, The University of Vienna

Publications

View all Publications

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Available Projects

  • Natural thermal springs are produced by geothermally heated groundwater and provide opportunities for studying microbes that may represent analogues of life on ancient Earth or even other planets. In this project, we will characterise the microbial communities in a recently explored Australian hot spring ecosystem.

    • Good molecular biology skills and experience with, or a keen interest in learning more about, bioinformatics is required.
    • Suitable for PhD, Masters and Honours research projects
  • The aim of lab-on-a-chip technology is to miniaturise laboratory processes and integrate them onto a single chip. In this project, we aim to explore microbial dark matter using single-cell genomics, a culture independent method that allows us to target individual microbial cells in the environment and to amplify their genomes. By miniaturising this method on a chip using microfluidics, we aim to reinvent the single-cell genomics approach and use it to explore novel lineages from the deep biosphere to urban environments.

    • Good molecular biology skills and experience with, or a keen interest in learning more about, microfluidics is required.
    • Suitable for PhD, Masters and Honours research projects
  • The genetic code is universally conserved across all domains of life, however some exceptions exist. Most notable is the use of standard "stop" codons to encode amino acids. In this project we will investigate how widespread these “stop codon recodings” are in the archaeal and bacterial domains, investigate their evolutionary history, and infer potential metabolic advantages.

    • Basic bioinformatics skills (Unix) are required.
    • Suitable for Masters, Honours, and semester research projects

View all Available Projects

Publications

Book Chapter

  • Rinke, Christian (2018). Single-cell genomics of microbial dark matter. Microbiome analysis. (pp. 99-111) New York, United States: Humana Press. doi: 10.1007/978-1-4939-8728-3_7

Journal Article

Other Outputs

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Natural thermal springs are produced by geothermally heated groundwater and provide opportunities for studying microbes that may represent analogues of life on ancient Earth or even other planets. In this project, we will characterise the microbial communities in a recently explored Australian hot spring ecosystem.

    • Good molecular biology skills and experience with, or a keen interest in learning more about, bioinformatics is required.
    • Suitable for PhD, Masters and Honours research projects
  • The aim of lab-on-a-chip technology is to miniaturise laboratory processes and integrate them onto a single chip. In this project, we aim to explore microbial dark matter using single-cell genomics, a culture independent method that allows us to target individual microbial cells in the environment and to amplify their genomes. By miniaturising this method on a chip using microfluidics, we aim to reinvent the single-cell genomics approach and use it to explore novel lineages from the deep biosphere to urban environments.

    • Good molecular biology skills and experience with, or a keen interest in learning more about, microfluidics is required.
    • Suitable for PhD, Masters and Honours research projects
  • The genetic code is universally conserved across all domains of life, however some exceptions exist. Most notable is the use of standard "stop" codons to encode amino acids. In this project we will investigate how widespread these “stop codon recodings” are in the archaeal and bacterial domains, investigate their evolutionary history, and infer potential metabolic advantages.

    • Basic bioinformatics skills (Unix) are required.
    • Suitable for Masters, Honours, and semester research projects
  • North Stradbroke Island is a small sand island with many groundwater bodies. The microbes and viruses hidden in these aquifers have remained mostly unexplored. You will use metagenomics and viromics to explore this hidden treasure.