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Denesse and I are headed to a 35th annual EcoFarm Conference at Pacific Grove’s Asilomar this week. Many organic farmers were first awakened to complex life underfoot at that venue some twenty years ago when pioneering soil microbial ecologists Elaine Ingham and Vicki Bess made rousing presentations. However, as each strove to develop commercial, practical methods for characterizing the diversity and health of vast, largely invisible, living communities in farmers’ soils, animosity ensued. Bess, while admitting fewer than 5% of soil-dwelling species could be grown on artificial media, argued that a handful she cultured in petri dishes were indicative of the many. Ingham insisted on direct microscopic observation, even though she could not distinguish one bacterial species from another and fungi’s value could only be inferred from hyphal width. Acrimony so intensified that the pair refused to appear together publically. Blind leading the blind methodologies persisted until Lawrence Berkeley National Laboratory scientists’ 2008 PhyloChip invention. The credit card-sized PhyloChip rapidly sorts and quantifies bacterial populations by species from any soil sample’s easily extracted DNA “soup”. Even this awesome technological advance can’t solve the problem future Nobel Prize-winner Selman Waksman and graduate student Albert Schatz unknowingly faced in their 1943 quest to isolate what would become streptomycin, the world’s first antibiotic effective against tuberculosis, from microbes resident in a shovelful of soil outside their laboratory. What WWII-era scientists didn’t know, but today’s do, is that a single gram of plant root-intimate soil can harbor 100 billion bacteria representing over 30,000 species, only 1% of which can be isolated and grown with standard laboratory technology. The 99% thrive only in consort with vexingly complex soil communities to which they belong. Imagine the medical miracles yet locked away in that impenetrable complexity! Northeastern University microbiologist Kim Lewis imagined and his team of researchers recently did something about it, inventing a domino-sized, honeycombed iChip device, the cells of which are sandwiched between two semipermeable membranes. They load each isolated cell with a single bacterial strain, after which the whole device is reburied into the microbes’ home soil. iChip’s permeability facilitates biochemical communication by which isolated species thrive, growing into pure colonies that can be screened for novel antibiotic compounds. They’ve isolated one from backyard soil, teixobactin, which suppresses deadly MRSA, tuberculosis and hard-to-kill Enterococcus without evident resistance. Unimagined treasures await discovery in the underground, living universe we are only now learning to build spaceships to explore. –Tom Willey
National Geographic: bit.ly/1ItHZ0k Nature: bit.ly/1IO3UkZ