I'm going to guess that a lot of soil bacteria exist in complex ecological networks, aka depend on the presence of other microbes (or at least their byproducts)

I'm going to guess that a lot of soil bacteria exist in complex ecological networks, aka depend on the presence of other microbes (or at least their byproducts), which runs counter to our obsession (with good reason) with getting pure cultures when culturing them. The secondary metabolites and various factors produced by bacteria are extremely diverse, and it's a lot of work to try to try every combination. Turns out that growing infectious bacteria is a usually easier since they often grow in rich/meat broths at body temperatures. A few years ago a group at Northeastern developed a device that allows single bacteria/colonies to be isolated while still in indirect contact with the soil. https://en.wikipedia.org/wiki/Isolation_chip https://en.wikipedia.org/wiki/Isolation_chip In situ cultivation of previously uncultivable microorganisms using the ichip https://www.nature.com/articles/nprot.2017.074 https://www.nature.com/articles/nprot.2017.074 https://sci-hub.ru/10.1038/nprot.2017.074 https://sci-hub.ru/10.1038/nprot.2017.074 Looks like they patented it, not sure if others are working on similar things. To better answer your question, the inventor of the device has his own theories as to why this happens (although I like my idea better).. The phenomenon of microbial uncultivability https://www.sciencedirect.com/science/article/abs/pii/S1369527413001458 https://www.sciencedirect.com/science/article/abs/pii/S13695...