John's reflections on teaching, research and service when he was a paid staff member

Regarding teaching, microbiology should be taught in an evolutionary context, including members of all cellular Domains and the viruses. In later years, I found that advanced students really appreciated such a deep perspective - and it's been really heartening to have former students express appreciation for your teaching long after completing the course.  In addition, perhaps only direct experience with the isolation and identification of culturable microorganisms can give us a full appreciation of microbial diversity beyond clusters on a phylogenetic tree or arrows on a metabolome plot. For me at UQ, this was most possible to apply in the Microbial Ecology and Systematics /Molecular Microbial Ecology and Identification course MY347, one very popular with both local and overseas students.   This is microbiology in the teaching tradition of Vic Skerman of course, but the high level of this course was also very appreciated by Erko Stackebrandt during his molecular evolutionary transformation of the Department of Microbiology as Head in the early 1990s.  Later we simplified the isolation tasks so that only photosynthetic bacteria and marine vibrios were assigned to student isolations (with rRNA sequencing identifications),   but during  Erko's period 'downwind' research labs'  tolerance for this course  was extended to the limit  by sulphides from sulfate-reducing Desulfovibrio isolations! 

Re teaching methods, the lecture still has a place in providing personal inspiration to students who are always searching for encouragement beyond the twittering of the endless screens of virtuality. And in laboratory teaching, the wet lab with its discard cans, Gram-stained benches and phase-contrast microscopes as well as minigels, eppendorfs and pipette tips (and bench-top 'mobile' sequencers very soon if not now) is still the place where discovery of the microbial world's wonders can occur most vividly.

Re postgraduate teaching, I thank all my past students for the great contributions they have made to the scientific progress of my lab - it has been a privilege to help them along their way, whether that has led to a scientific position exploring Zika virus at the Ministry of Health in Singapore (Dr Yi Kai Ng) or microbiome research as a University of Sydney Associate Professor (Assoc Prof Andrew Holmes), managing infection control at PA Hospital (Dr Margaret Lindsay), or  a directorship and senior scientific personnel  of UQ's and SCMB's  own Australian Centre for Ecogenomics (Prof Phil Hugenholtz and Dr Margaret Butler). One of the most memorable lab events was at my Molecular Biosciences Building lab when the havoc and broken stain reagent bottles caused by invasion by a baby possum via an aircon vent next to gum trees was a worrying  mystery to police (and myself) called near midnight by security, until solved by then PhD student Margaret Butler's detection of possum prints  on the lab floor the next morning!

My major research interests have been in the structure and biology of bacterial cells and molecular microbial evolution, especially in relation to understanding evolution of cell complexity. I stood on the pioneering shoulders of  a 'general microbiology' tradition in bacteriology for which the early Microbiology Department was known. My recent research programs have been in two areas within this field- the planctomycetes, a deep-branching distinct phylum of the Domain Bacteria with complex internal structures and important evolutionary implications, and bacterial symbionts of marine sponges. The sponge symbiont field involved productive collaboration with the School of Pharmacy and Queensland Museum on microbial biodiversity and natural product diversity among marine actinobacteria in genus Salinispora from sponges of the Great Barrier Reef. My lab studied compartmented cells of the model planctomycete Gemmata obscuriglobus as an approach to understanding origins of eukaryotes and their cells. This ARC-supported research program produced a major invited review on intracellular compartmentation in planctomycetes in the prestigious Annual Reviews of Microbiology in 2005, a major invited presentation at the prestigious Santa Fe Institute  in New Mexico USA in 2008 on “Compartmentation, Phase Separation and the Origin of Life ", New Mexico, USA,the discovery of endocytosis-like protein uptake in a bacterium in 2010 (Proceedings of the National Academy of Sciences U S A. 107(29):12883-12888), an invited review in Nature Reviews in Microbiology in 2011  (Nature Reviews Microbiology 9(6):403- 413), an invited review in Biochimica et Biophysica Acta Molecular Cell Research (BBA Molecular Cell Research Aug 2014;1843(8):1732-8. doi: 10.1016/j.bbamcr.2013.10.002.), and culminated in a major research paper in PloS ONE demonstrating nuclear pore-like structures in internal membranes of planctomycete model Gemmata obscuriglobus (PLoS One. 2017 Feb 1;12(2):e0169432. doi: 10.1371/journal.pone.0169432). It also resulted in two invitations to speak at the prestigious Les Treilles conferences (sponsored by La Fondation des Treilles) on ‘Origin and Evolution of  the Cell Nucleus’ in Tourtour, France in 2004  and on 'LUCA: ten years after’ - i.e. The Last Universal Common Ancestor: ten years after - in 2006, and presentation of a seminar in 2006 on 'Planctomycetes, verrucomicrobia and the evolution of cell organization' at Département de Microbiologie, Institut Pasteur, Paris (a highlight of my scientific life, since this is a research institute  so connected with the great Louis Pasteur himself as well as Jacques Monod, Roger Stanier and many other scientific giants that it is has special meaning for all microbiologists).  In 2013 a book on 'Planctomycetes: Cell Structure, Origins and Biology' edited by me was published by Springer, summarizing the state of 'planctomycetology'.

Regarding service, the most rewarding service outside teaching and research (including supervision of my research students) I have been able to give to UQ has been in academic advising for the Faculty of Science. The advice given to often perplexed students was I hope of value - especially to many science students completely unfamiliar with the typical career trajectory of a scientist (or the BSc as only a first step on a sometimes long road to a career-supporting position),  and those like the education student I remember who wanted to assure their relatives and themselves that mathematics/science  majors would be able to find a job teaching in a secondary school! I trust that  future foresighted STEM-oriented education budgets will always justify my affirmative answer to her.

John's activities since his retirement from working full-time with the School

I have actively published in international journals and in books published by international scientific publishing houses such as Elsevier and Academic Press since 2013 until now.  I serve on the Editorial Board  of the Antonie van Leeuwenhoek Journal of Microbiology, and was Founding Chief-Editor for MDPI journal Microorganisms from 2013 until 2016.  I am an active reviewer for international journals including in 2019 for example Nature Communications, FEMS Microbiology Letters,  PloS ONE, and Frontiers in Microbiology.

I have contributed reviewing grant applications each year since 2016 to the Faculty of Science ARC Readership scheme. I continue to the present as a grant assessor  for the ARC.

My leisure activities include playing classical clarinet in rehearsals and concerts with the Brisbane ensemble Classic Clarinets, and in concerts of classical music for solo clarinet and piano.

Researcher biography

General Research specialises in: Evolutionary microbiology, Marine microbiology; Molecular phylogenetics, genomics and bioinformatics of bacteria; Planctomycete bacteria; Bacterial cell biology and structure.

Current research projects include:

Molecular cell biology of planctomycete bacteria in relation to the origin of eukaryotes and cell compartmentalisation (ARC Large Grant).Culture, molecular phylogenetics and ultrastructure of Archaeal and Bacterial symbionts of marine sponges.