Soil Microbiology: Past, Present and Future. Black Box to White Box to No Box at All?.

The latter half of the 20^th century saw a period of rapid growth in soil microbiology as new ideas flourished and powerful analytical techniques were adopted. Biomass determinations, enzyme assays, physiological profiling, fatty acid analysis, nitrogen cycle dynamics, etc. plus the realization that microbes function as communities and at surfaces, were all game changers. The new methods and ideas were enthusiastically adopted but, importantly, they stimulated critical thinking and fueled a desire to know more. Soon soil microbiology would become soil microbial ecology and speculations and hypotheses would become testable.

In 2015 soil microbiology is a hot topic as increasingly sophisticated molecular, microscopic, modeling and computational techniques are taking 
us closer towards untangling the three-dimensional complexity of the soil environment. We acknowledge that the communications between microbes and plants are critical to their success or failure and are beginning to decipher the many messages that are exchanged. We also appreciate that the continuous and shifting connections between above- and below-ground life are essential to our biosphere and that, in a changing climate with increasing loss of soil, microbial communities may be as much at risk as those of animals and plants.  In other words, soil microbial ecology is an integral component of macroecology.

 

At the heart of recent advances is the  ‘omics’ revolution: genomics, proteomics, transcriptomics and metabolomics.  Soil metagenomics is here to stay.  Of course, the astronomical volume of data generated demands substantial computational resources but sequencing the entire soil microbial genome is a daunting challenge. And that is even before we try to understand how each microbe works independently and collectively. Beware assuming that ‘terragenomics’ will tell us everything and (ultimately) allow us to reliably manipulate soil biology for optimal food, fiber and fuel production. There is nature and nurture in the soil microbial world and much still to be revealed concerning the regulation of activities and processes. Search for order in chaos is a human characteristic but there may not be a ‘grand theory’ to explain soil biology even if we can fully describe to contributions of cells, DNA, the genetic code and evolution.