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Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis

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Abstract

One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.

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Data availability

The names of the repositories/repositories and accession number(s) can be found in the Supplementary Material for this manuscript. The genomes were submitted to the National Center for Biotechnology Information (NCBI) GenBank under the bioproject number PRJNA950099.

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Acknowledgements

The authors expressed their gratitude to the technical support team of the Cluster at Universidade Federal de Viçosa.

Funding

This work was financially supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq (Process APQ-02381-21), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/Programa de Excelência Acadêmica-Finance Code 001 (CAPES ProEx grant 23038.019105/2016-86) and Fundação de Amparo à Pesquisa do Estado de Minas Gerais—FAPEMIG (Process 402644/2021-2).

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  1. Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil

    Osiel Silva Gonçalves & Mateus Ferreira Santana

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  1. Osiel Silva Gonçalves
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OSG.: investigation, visualization, writing—original draft, and writing—review and editing; MFS.: conceptualization, funding acquisition, resources, supervision, validation, writing—review and editing.

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Correspondence to Mateus Ferreira Santana.

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Gonçalves, O.S., Santana, M.F. Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis. Microb Ecol 86, 2687–2702 (2023). https://doi.org/10.1007/s00248-023-02275-x

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