Microbial ecology of the environment

To study microbes, is to study the biosphere. Carl Woese (15 July 1928–30 December 2012)

Microbes represent not only the most abundant but also exhibit the greatest diversity of any group of organisms on the planet. Through culture-dependent methods, the extraordinary physiological diversity of microbial life has long been recognised. However, with the application of molecular microbial techniques, estimates of microbial diversity have increased dramatically. In particular, the advent of low cost, next generation sequencing technologies has led to an explosion in sequence-based microbial community studies investigating taxon diversity and community structure (e.g. via rRNA gene analysis) and/or microbial function via metagenomics of the uncultivated majority of microorganisms present within the environment. Such approaches have revealed a diverse wealth of hitherto unknown microbial taxa and provided new understanding of the ecological and biological functions and adaptations of environmental microbes. What is required now is to link our understanding of microbial diversity and complexity to ecosystem function. In natural environments, microorganisms interact with both biotic and abiotic components of their ecosystems. These interactions are essential for ecosystem function with key specific functions including biogeochemical cycling, biodegradation of pollutants and the impacts of microbes upon the activity and health of plants and animals, including humans.

Defining the specific role of individual microorganisms in the environment is complex, due in part to the metabolic flexibility and diversity within individual species, and additionally by functional redundancy whereby diverse species can carry out the same biological activity. This is complicated further by the need to consider microbiology at different levels, namely:

• First, at the smallest scale, the activity of the single microbial cell;

• Second, at the population level, involving interactions and communication between members of the same species; and

• Third, at the community level where interactions occur between members of multiple microbial species, and often with plants and animals.

At each level, we also need to investigate the interrelationship of the microorganism(s) with environmental factors such as nutrient and water availability and temperature and pH and, in turn, how these affect ecological activity.

This ‘Microbial Ecology of the Environment’ Special Issue focuses on linking microbial diversity with ecosystem function. Questions to be addressed include:

• What interactions with the environment and with other organisms control microbial activity?

• How can we better understand the biotechnological potential associated with the activity and diversity of microbial communities?

• What factors influence the rate and extent of degradation of pollutants by microorganisms in the environment?

Overall, the eight ‘In Focus’ and ‘Under the Microscope’ articles offer an introduction to the importance of microbial diversity and activity to ecosystem function across diverse environments. This issue focuses on specific environments and microbial communities with an Australian focus (either of Australian environments and/or by Australian researchers) to highlight some of the key developments across the microbial ecology discipline. The first In Focus article by Justin Seymour examines our current understanding of microbial diversity and activity in the marine environment. The second In Focus article, written by Jacob Munro, Deborah Rich, Simon Dingsdag and Nick Coleman provides valuable insight into the development and use of culture-independent microbiology. In the first of the Under the Microscope articles, Eric Adetutu leads us through the microbial diversity and activity associated with caves within Australia, while Jacqueline Stroud and Mike Manefield describe the microbiology of acid sulphate soils and sulfidic sediments. The theme then focuses on applied environmental microbiology as Albert Juhasz examines the impact of bioavailability of the biodegradation of polycyclic aromatic hydrocarbons in Australian soils, while Ashley Franks and Lucie Semenec discuss the microbiology of Microbial Electrolysis Cells. Mark Osborn and Slobodanka Stojkovic continue the environmental pollution theme, with an article examining the role of microorganisms in the colonisation and degradation of plastic pollutants in marine environments. Finally, Sayali Patil, Eric Adetutu and I discuss the activity and diversity of the microbial communities in Australian contaminated groundwater.

I hope you find this Special issue both of interest and of value. I would like to thank all of the authors for their timely contributions and also the Microbiology Australia Editorial Team, led by Ian Macreadie for their guidance and assistance through the development of this issue.