Emerging culture-independent tools to enhance our understanding for soil microbial ecology

Soil bacteria, fungi, protists and archaea constitute the most diverse living communities on Earth and provide essential ecosystem services to life on this planet. However, the genetic information that they encode remained largely unexplored until recently. The main reason for this is that many soil microorganisms cannot be cultured using standard techniques (Clardy et al., 2006; Ritz, 2007) and methods that enable culture-independent exploration of their genomes have only recently become available (Jones et al., 2009; Lauber et al., 2009; Scholz et al., 2012). While these new approaches gain a lot of attention, it appears that culture-independent techniques can also be very well complemented with classical microbiological culture-dependent techniques, and in some cases impressive numbers of soil microbes have been isolated from cultures. For example, a novel high-throughput in situ cultivation platform has been developed to cultivate and isolate hitherto uncultivated microbial species from a variety of environments, including soil. In an “isolation chip” (ichip), several hundred miniature diffusion chambers can be colonised in a single environmental cell, enabling the investigation of a large and diverse array of previously inaccessible microorganisms (Kaeberlein et al., 2002; Nichols et al., 2010). In this new method, significantly more species were grown in comparison with standard media. As a one-step process, “unculturable” microorganisms inside the ichip generated pure colonies under the conditions that they had been collected from in the environment (Nichols et al., 2010). Furthermore, a recent study that simply used a variety of different cultivation media shows that up to 70% of soil microbes associated with Arabidopsis plant roots can be cultured and match the data from cultureindependent next-generation 16 ribosomal RNA (rRNA) gene amplicon sequencing(Bai et al., 2015). This chapter provides cases of emerging culture-independent techniques that will enhance our understanding of soil microbial ecology. Soil ecosystem function, biodiscovery from soil microbes and plant–microbe interactions are just some of the areas that will benefit from these new approaches.