Experimental Biofilms & Synthetic Ecology

Mixed species and often highly complex microbial communities are the predominant form of biofilms in any habitat, as opposed to single species biofilm populations. To begin to unravel the intricacies involved in naturally occurring biofilms it is therefore essential to expand from the classical population biology approach and study the mechanisms of biofilm biology in communities.

Many aspects of biofilm research are severely limited by our inability to employ experimentally tractable and reproducible mixed species biofilm communities as model experimental systems. The various existing population-based models have been invaluable in uncovering much that we now know about biofilms and their functions, and are still an indispensable part of biofilm research. However, these are not very representative of biofilms in natural systems and observations of limited mixed species experimental communities to date have revealed unanticipated, emergent properties as a function of the stepwise increase in species diversity. The research challenge is to employ experimentally tractable and reproducible mixed-species biofilm communities as model systems to better understand how these communities function in their natural environments.

Defined experimental communities

SCELSE has developed experimentally tractable and reproducible experimental biofilm community models to better understand how multi-species biofilm communities function in their natural environments. Initial mixed species experimental communities have revealed unanticipated, emergent properties that are a function of the stepwise increase in species diversity.

Understanding the three-dimensional biofilm organisation, e.g. matrix structure-function, facilitates the establishment of well-functioning synthetic microbial communities and experimental biofilms. SCELSE’s research here includes: low diversity defined consortia associated with host wellbeing, e.g. for human, plant rhizosphere and coral systems; as well as high diversity experimental communities in different settings, from used water treatment flocs/granules, to environmental bioprocessing and bioremediation.

These defined communities are used for:

  • Structure-function analyses through combined ‘omics’ approaches, e.g. metatranscriptomics and metabolomics to define how mixed community biofilms form and function 
  • Developing imaging based approaches to investigate three-dimensional organization of the community and to observe in real time, key physiological gradients, e.g. oxygen and regulatory second messenger molecules, within the biofilms
  • Targeting of key physical-chemical parameters, e.g. diffusion, adhesiveness, fluidics, electroconductivity, electron shuttling mechanisms, linking community interactions and biological functions 
  • Understanding ecological traits that are important for the assembly, maintenance and function of diverse communities, including resilience, cooperation or competition effects, fitness and other traits 

Highly diverse experimental communities

With recent technological advances it is now possible to interrogate complex biofilm systems in the absence of being able to cultivate the community members or to genetically manipulate individuals. Experimental studies of highly diverse biofilm communities contribute to our understanding of biofilms in the context of environmental engineering and public health. As one example, the use of flocs and granules in water treatments is well established, but only recently have we been able to elucidate the biology behind their formation. This knowledge is integral to improving the efficiency of nutrient removal, which will offer a grand range of benefits. SCELSE is utilising engineered transformations of flocs to granules in order to:

i)    Validate empirical engineering practices 
ii)    Correlate communal metabolic activities with overall bioprocess
iii)    Show quorum sensing is a community function
iv)    Show diffusion is a function of changes in matrix properties within a granular community
v)    Establish an approach to determine the role of predator-prey interactions during community selection processes