Climate change and the recent financial crisis clearly show that humans have entered the anthropocene, an unprecedented era of fast and possibly dangerous changes. Unprecedented changes call for unprecedented thinking. Indeed, agriculture research has been too long driven solely by the need for higher yields using classical agrosciences, whatever adverse ecological effects. Agricultural research needs the input of other sciences such as ecological, economic, social and political sciences. Those uncommon sciences emerge in agricultural research since few decades, but there is actually no precise trends and data on the speed of emergence of specific topics. Therefore, here we report: 1) an analysis of the emergence of topics in the journal Agronomy for Sustainable Development, and 2) a review of selected articles published in 2009. First, to analyse topic emergence we studied three data sets: most-cited articles from 1999 to 2009, topic hits in article text from 1999 to 2009, and most downloaded articles in 2009. We found the following major points. Most-cited articles show that transgenic plants and biofuels are clearly emerging topics since 2007 whereas soil carbon and climate change are the major mainstream topics of the last 10 years. Topic hits analysis allows to rank topics by mean emergence date, e.g. 2008.3 for 'genetically modified' and 2005.3 for 'irrigation'. Accordingly the 10 most emerging topics over 1999-2009 are biofuels, genetically modified, conservation agriculture, urban agriculture, sociology, organic farming, carbon sequestration, phytoremediation, mulch, and biodiversity. Analysis of most downloaded articles in 2009 show the predominance of topics such as carbon, climate, biodiversity, biofuels, pollutants, beneficial microbes, transgenic plants, and organic farming. Second, we reviewed selected articles published in 2009 with emphasis on emerging topics. We find that sociology is clearly bringing novel and unexpected findings to design sustainable agriculture. Transgenic crops are highly innovative but show many unknowns that needs to be carefully studied using various disciplines. Climate change has many scientifically proven effects on terrestrial ecosystems and agriculture. Here, soil carbon loss should be of particular attention because it rules the long-term fate of many factors such as atmospheric CO2, erosion, and water and nutrient supply. Biodiversity loss due to industrial monocropping is leading scientists to disclose alternative, more diverse cropping systems that optimize biodiversity, pest control and yield.