One more academic year (2018-2019), we have participated in the Master on Biodiversity, Function and Ecosystem Management (University of the Basque Country, Spain), coordinating a course on rehabilitation and bioremediation of contaminated soils. This year we have (1) paid special attention to microbial speciation processes and (2) discussed the concepts of top-down vs. bottom-up biology, and systems biology. We have also emphasized the need to incorporate a network perspective to studies on soil microbial communities.