Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes

• Published in: Applied and environmental microbiology 2023-02, Vol.89 (2), p.e0172722-e0172722
• Main Authors: Prüß, Birgit M, Horne, Shelley M, Bauer, Erika Shay, Pirner, Collin, Schwartz, Madelyn, Petersen, Morgan L, Bergholz, Peter W
• Format: Article
• Language: English
• Subjects: Animals; Base Composition; Biofilms; Cell migration; Chemotaxis; E coli; Environmental Microbiology; Escherichia coli; Escherichia coli Proteins - genetics; Evolution; Flagella; Flagellin; Genes; Genetic diversity; Genetic variance; Genome-wide association studies; Genome-Wide Association Study; Genomes; Humans; Malic acid; Metabolism; Mutation; Phenotypes; Phylogeny; Plates; Putrescine; River basins; RNA, Ribosomal, 16S; Semisolids; Sequence Analysis, DNA; Soil; Soil environment; Soil isolates; Soils
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.01727-22

This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS elements in the flagellin-encoding gene . A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants ( - and - ) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.