Authors
Claire C. Winfrey (CIRES,CU Boulder, Department of Ecology and Evolutionary Biology), Caihong Vanderburgh (CIRES), A. Mobeen Zahid (CIRES,CU Boulder, Department of Ecology and Evolutionary Biology), Pankaj Trivedi (Texas Tech University), Noah Fierer (CIRES,CU Boulder, Department of Ecology and Evolutionary Biology)

Abstract

Soils support the highest diversity and biomass of bacteria of any known environment on Earth, despite highly heterogeneous conditions across space and time that can make survival challenging. One important strategy that bacterial cells employ to cope with unfavorable conditions is making spores, which, broadly defined, are resistant structures that allow cells to persist in a state of reduced metabolic activity while enduring unfavorable habitats or surviving transit to better habitats. Through culturing, we know that spore-forming bacteria occur across diverse phyla. However, only a small fraction of soil bacteria can readily be cultured, leaving the sporulation ability of most taxa simply undetermined. To test the sporulation ability of thousands of species simultaneously, we applied a culture-independent approach combining ethanol and propidium monoazide (PMA) directly to 22 soils collected from diverse environments in 10 U.S. states. Ethanol lyses cells not protected as spores, whereas PMA binds DNA from these lysed cells, effectively removing the DNA contribution of non-sporulated cells from downstream analyses. We then performed 16S rRNA gene sequencing to characterize bacteria in ethanol- and PMA-treated soils and in control soils treated with PMA alone. We identified putative spore-formers within canonical spore-forming phyla, including Bacillota, Actinomycetota, and Myxococcota, as well as among diverse taxa not previously characterized through culturing, most notably within Pseudomonadota, Planctomycetota, and Verrucomicrobiota. As hypothesized, we found that these spore-formers occurred in more locations and in more varied environmental conditions than non-spore-formers. Our work supports that a greater diversity of soil bacteria can form spore-like structures than previously recognized, with additional evidence that sporulation confers bacteria a greater ability to withstand a broad range of conditions in situ or to disperse among patches of soil habitat.